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Sample records for conformational transition intermediates

  1. HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations.

    Science.gov (United States)

    Ma, Xiaochu; Lu, Maolin; Gorman, Jason; Terry, Daniel S; Hong, Xinyu; Zhou, Zhou; Zhao, Hong; Altman, Roger B; Arthos, James; Blanchard, Scott C; Kwong, Peter D; Munro, James B; Mothes, Walther

    2018-03-21

    HIV-1 entry into cells requires binding of the viral envelope glycoprotein (Env) to receptor CD4 and coreceptor. Imaging of individual Env molecules on native virions shows Env trimers to be dynamic, spontaneously transitioning between three distinct well-populated conformational states: a pre-triggered Env (State 1), a default intermediate (State 2) and a three-CD4-bound conformation (State 3), which can be stabilized by binding of CD4 and coreceptor-surrogate antibody 17b. Here, using single-molecule Fluorescence Resonance Energy Transfer (smFRET), we show the default intermediate configuration to be asymmetric, with individual protomers adopting distinct conformations. During entry, this asymmetric intermediate forms when a single CD4 molecule engages the trimer. The trimer can then transition to State 3 by binding additional CD4 molecules and coreceptor.

  2. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

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    Barry J Grant

    2009-03-01

    Full Text Available Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75 intermediate between GTP and GDP states, or distinct loop3 (46-49, loop7 (105-110, and alpha5 C-terminus (159-166 conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74 with alpha3-loop7 (93-110, loop2 (26-37 with loop10 (145-151, and loop3 (46-49 with alpha5 (152-167. The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD simulations, is a low-frequency motion intrinsic to the structure.

  3. Characterization of monomeric intermediates during VSV glycoprotein structural transition.

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    Aurélie A Albertini

    2012-02-01

    Full Text Available Entry of enveloped viruses requires fusion of viral and cellular membranes, driven by conformational changes of viral glycoproteins. Crystal structures provide static pictures of pre- and post-fusion conformations of these proteins but the transition pathway remains elusive. Here, using several biophysical techniques, including analytical ultracentrifugation, circular dichroïsm, electron microscopy and small angle X-ray scattering, we have characterized the low-pH-induced fusogenic structural transition of a soluble form of vesicular stomatitis virus (VSV glycoprotein G ectodomain (G(th, aa residues 1-422, the fragment that was previously crystallized. While the post-fusion trimer is the major species detected at low pH, the pre-fusion trimer is not detected in solution. Rather, at high pH, G(th is a flexible monomer that explores a large conformational space. The monomeric population exhibits a marked pH-dependence and adopts more elongated conformations when pH decreases. Furthermore, large relative movements of domains are detected in absence of significant secondary structure modification. Solution studies are complemented by electron micrographs of negatively stained viral particles in which monomeric ectodomains of G are observed at the viral surface at both pH 7.5 and pH 6.7. We propose that the monomers are intermediates during the conformational change and thus that VSV G trimers dissociate at the viral surface during the structural transition.

  4. Excited state conformational dynamics in carotenoids: dark intermediates and excitation energy transfer.

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    Beck, Warren F; Bishop, Michael M; Roscioli, Jerome D; Ghosh, Soumen; Frank, Harry A

    2015-04-15

    A consideration of the excited state potential energy surfaces of carotenoids develops a new hypothesis for the nature of the conformational motions that follow optical preparation of the S2 (1(1)Bu(+)) state. After an initial displacement from the Franck-Condon geometry along bond length alternation coordinates, it is suggested that carotenoids pass over a transition-state barrier leading to twisted conformations. This hypothesis leads to assignments for several dark intermediate states encountered in femtosecond spectroscopic studies. The Sx state is assigned to the structure reached upon the onset of torsional motions near the transition state barrier that divides planar and twisted structures on the S2 state potential energy surface. The X state, detected recently in two-dimensional electronic spectra, corresponds to a twisted structure well past the barrier and approaching the S2 state torsional minimum. Lastly, the S(∗) state is assigned to a low lying S1 state structure with intramolecular charge transfer character (ICT) and a pyramidal conformation. It follows that the bent and twisted structures of carotenoids that are found in photosynthetic light-harvesting proteins yield excited-state structures that favor the development of an ICT character and optimized energy transfer yields to (bacterio)chlorophyll acceptors. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Unconventional actin conformations localize on intermediate filaments in mitosis

    International Nuclear Information System (INIS)

    Hubert, Thomas; Vandekerckhove, Joel; Gettemans, Jan

    2011-01-01

    Research highlights: → Unconventional actin conformations colocalize with vimentin on a cage-like structure in metaphase HEK 293T cells. → These conformations are detected with the anti-actin antibodies 1C7 ('lower dimer') and 2G2 ('nuclear actin'), but not C4 (monomeric actin). → Mitotic unconventional actin cables are independent of filamentous actin or microtubules. → Unconventional actin colocalizes with vimentin on a nocodazole-induced perinuclear dense mass of cables. -- Abstract: Different structural conformations of actin have been identified in cells and shown to reside in distinct subcellular locations of cells. In this report, we describe the localization of actin on a cage-like structure in metaphase HEK 293T cells. Actin was detected with the anti-actin antibodies 1C7 and 2G2, but not with the anti-actin antibody C4. Actin contained in this structure is independent of microtubules and actin filaments, and colocalizes with vimentin. Taking advantage of intermediate filament collapse into a perinuclear dense mass of cables when microtubules are depolymerized, we were able to relocalize actin to such structures. We hypothesize that phosphorylation of intermediate filaments at mitosis entry triggers the recruitment of different actin conformations to mitotic intermediate filaments. Storage and partition of the nuclear actin and antiparallel 'lower dimer' actin conformations between daughter cells possibly contribute to gene transcription and transient actin filament dynamics at G1 entry.

  6. Intermediate conformation between native β-sheet and non-native α-helix is a precursor of trifluoroethanol-induced aggregation of Human Carbonic Anhydrase-II

    International Nuclear Information System (INIS)

    Gupta, Preeti; Deep, Shashank

    2014-01-01

    Highlights: • HCAII forms amyloid-like aggregates at moderate concentration of trifluoroethanol. • Protein adopts a state between β-sheet and α-helix at moderate % of TFE. • Hydrophobic surface(s) of partially structured conformation forms amyloid. • High % of TFE induces stable α-helical state preventing aggregation. - Abstract: In the present work, we examined the correlation between 2,2,2-trifluoroethanol (TFE)-induced conformational transitions of human carbonic anhydrase II (HCAII) and its aggregation propensity. Circular dichroism data indicates that protein undergoes a transition from β-sheet to α-helix on addition of TFE. The protein was found to aggregate maximally at moderate concentration of TFE at which it exists somewhere between β-sheet and α-helix, probably in extended non-native β-sheet conformation. Thioflavin-T (ThT) and Congo-Red (CR) assays along with fluorescence microscopy and transmission electron microscopy (TEM) data suggest that the protein aggregates induced by TFE possess amyloid-like features. Anilino-8-naphthalene sulfonate (ANS) binding studies reveal that the exposure of hydrophobic surface(s) was maximum in intermediate conformation. Our study suggests that the exposed hydrophobic surface and/or the disruption of the structural features protecting a β-sheet protein might be the major reason(s) for the high aggregation propensity of non-native intermediate conformation of HCAII

  7. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

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    Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

    2011-01-01

    The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

  8. Identification of key residues for protein conformational transition using elastic network model.

    Science.gov (United States)

    Su, Ji Guo; Xu, Xian Jin; Li, Chun Hua; Chen, Wei Zu; Wang, Cun Xin

    2011-11-07

    Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

  9. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan

    2014-10-07

    Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain.

  10. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan; Uyaver, Sahin; Sun, Shuyu

    2014-01-01

    Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain.

  11. Visualizing multistep elevator-like transitions of a nucleoside transporter.

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    Hirschi, Marscha; Johnson, Zachary Lee; Lee, Seok-Yong

    2017-05-04

    Membrane transporters move substrates across the membrane by alternating access of their binding sites between the opposite sides of the membrane. An emerging model of this process is the elevator mechanism, in which a substrate-binding transport domain moves a large distance across the membrane. This mechanism has been characterized by a transition between two states, but the conformational path that leads to the transition is not yet known, largely because the available structural information has been limited to the two end states. Here we present crystal structures of the inward-facing, intermediate, and outward-facing states of a concentrative nucleoside transporter from Neisseria wadsworthii. Notably, we determined the structures of multiple intermediate conformations, in which the transport domain is captured halfway through its elevator motion. Our structures present a trajectory of the conformational transition in the elevator model, revealing multiple intermediate steps and state-dependent conformational changes within the transport domain that are associated with the elevator-like motion.

  12. H/L transition time estimation in JET using conformal predictors

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, S., E-mail: sergio.gonzalez@ciemat.es [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Vega, J. [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Murari, A. [Consorzio RFX, Associazione EURATOM/ENEA per la Fusione, Padova 4-25127 (Italy); Pereira, A. [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Dormido-Canto, S.; Ramirez, J.M. [Departamento de Informatica y Automatica, UNED, Madrid 28040 (Spain)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer H/L transitions have been predicted using H/L and L/H models. Black-Right-Pointing-Pointer Models have been built using conformal predictors to hedge the prediction with confidence and credibility measures. Black-Right-Pointing-Pointer Models have been trained using linear and radial basis function kernels. Black-Right-Pointing-Pointer Conformal measures have proven their usefulness to validate data-driven models. - Abstract: Recent advances in data mining allow the automatic recognition of physical phenomena in the databases of fusion devices without human intervention. This is important to create large databases of physical events (thereby increasing the statistical relevance) in an unattended manner. Important examples are the L/H and H/L transitions. In this contribution, a novel technique is introduced to automatically locate H/L transitions in JET by using conformal predictors. The focus is on H/L transitions because typically there is not a clear signature in the time series of the most widely available signals to recognize the change of confinement. Conformal predictors hedge their prediction by means of two parameters: confidence and credibility. The technique has been based on binary supervised classifiers to separate the samples of the respective confinement modes. Results with several underlying classifiers are presented.

  13. Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

    Science.gov (United States)

    Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

    2014-03-01

    A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.

  14. Evidence for an intermediate conformational state of LacY.

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    Jiang, Xiaoxu; Guan, Lan; Zhou, Yonggang; Hong, Wen-Xu; Zhang, Qinghai; Kaback, H Ronald

    2012-03-20

    LacY mutant Cys154 → Gly exhibits a periplasmic-closed crystal structure identical to the WT, but is periplasmic-open in the membrane. The mutant hardly catalyzes transport, but binds galactosides from either side of the membrane with the same affinity and is resistant to site-directed proteolysis relative to the pseudo-WT. Site-directed alkylation was also applied to 11 single-Cys mutants in Cys154 → Gly LacY in right-side-out membrane vesicles or after solubilization and purification in dodecyl-β-D-maltopyranoside (DDM). Unlike the pseudo-WT, Cys replacements on the periplasmic side of the Cys154 → Gly mutant label rapidly in the membrane without sugar, but labeling decreases markedly after the mutant proteins are purified. Thus, Cys154 → Gly LacY likely favors a higher-energy intermediate periplasmic-open conformation in situ, but collapses to a lower-energy periplasmic-closed conformation in DDM after purification. Notably, branched-chain or neopentyl glycol maltoside detergents stabilize Cys154 → Gly LacY in the membrane-embedded form.

  15. Conformal invariance at a deconfinement phase transition in (2+1) dimensions

    International Nuclear Information System (INIS)

    Christensen, J.; Damgaard, P.H.

    1990-08-01

    The conformal dimension of the Polyakov line at the deconfinement phase transition of (2+1)-dimensional SU(2) lattice gauge theory is determined numerically using two-dimensional finite size conformal field theory. Excellent agreement with two-dimensional Ising model values is found for both the renormalized coupling on a spatially toroidal geometry and the conformal dimensions on a finite-width strip geometry. (orig.)

  16. Phase Transitions, Geometrothermodynamics, and Critical Exponents of Black Holes with Conformal Anomaly

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    Jie-Xiong Mo

    2014-01-01

    Full Text Available We investigate the phase transitions of black holes with conformal anomaly in canonical ensemble. Some interesting and novel phase transition phenomena have been discovered. It is shown that there are striking differences in both Hawking temperature and phase structure between black holes with conformal anomaly and those without it. Moreover, we probe in detail the dependence of phase transitions on the choice of parameters. The results show that black holes with conformal anomaly have much richer phase structure than those without it. There would be two, only one, or no phase transition points depending on the parameters. The corresponding parameter regions are derived both numerically and graphically. Geometrothermodynamics are built up to examine the phase structure we have discovered. It is shown that Legendre invariant thermodynamic scalar curvature diverges exactly where the specific heat diverges. Furthermore, critical behaviors are investigated by calculating the relevant critical exponents. And we prove that these critical exponents satisfy the thermodynamic scaling laws.

  17. Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases.

    Science.gov (United States)

    Wong, Chung F

    2016-01-01

    This short article examines the usefulness of fast simulations of conformational transition paths in elucidating enzymatic mechanisms and guiding drug discovery for protein kinases. It applies the transition path method in the MOIL software package to simulate the paths of conformational transitions between six pairs of structures from the Protein Data Bank. The structures along the transition paths were found to resemble experimental structures that mimic transient structures believed to form during enzymatic catalysis or conformational transitions, or structures that have drug candidates bound. These findings suggest that such simulations could provide quick initial insights into the enzymatic mechanisms or pathways of conformational transitions of proteins kinases, or could provide structures useful for aiding structure-based drug design. © 2015 The Protein Society.

  18. Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

    Science.gov (United States)

    Onuk, Emre; Badger, John; Wang, Yu Jing; Bardhan, Jaydeep; Chishti, Yasmin; Akcakaya, Murat; Brooks, Dana H; Erdogmus, Deniz; Minh, David D L; Makowski, Lee

    2017-08-29

    Crystal structures of adenylate kinase (AdK) from Escherichia coli capture two states: an "open" conformation (apo) obtained in the absence of ligands and a "closed" conformation in which ligands are bound. Other AdK crystal structures suggest intermediate conformations that may lie on the transition pathway between these two states. To characterize the transition from open to closed states in solution, X-ray solution scattering data were collected from AdK in the apo form and with progressively increasing concentrations of five different ligands. Scattering data from apo AdK are consistent with scattering predicted from the crystal structure of AdK in the open conformation. In contrast, data from AdK samples saturated with Ap5A do not agree with that calculated from AdK in the closed conformation. Using cluster analysis of available structures, we selected representative structures in five conformational states: open, partially open, intermediate, partially closed, and closed. We used these structures to estimate the relative abundances of these states for each experimental condition. X-ray solution scattering data obtained from AdK with AMP are dominated by scattering from AdK in the open conformation. For AdK in the presence of high concentrations of ATP and ADP, the conformational ensemble shifts to a mixture of partially open and closed states. Even when AdK is saturated with Ap5A, a significant proportion of AdK remains in a partially open conformation. These results are consistent with an induced-fit model in which the transition of AdK from an open state to a closed state is initiated by ATP binding.

  19. Phase transition and gravitational wave phenomenology of scalar conformal extensions of the Standard Model

    Energy Technology Data Exchange (ETDEWEB)

    Marzola, Luca; Racioppi, Antonio; Vaskonen, Ville [National Institute of Chemical Physics and Biophysics, Tallinn (Estonia)

    2017-07-15

    Thermal corrections in classically conformal models typically induce a strong first-order electroweak phase transition, thereby resulting in a stochastic gravitational background that could be detectable at gravitational wave observatories. After reviewing the basics of classically conformal scenarios, in this paper we investigate the phase transition dynamics in a thermal environment and the related gravitational wave phenomenology within the framework of scalar conformal extensions of the Standard Model. We find that minimal extensions involving only one additional scalar field struggle to reproduce the correct phase transition dynamics once thermal corrections are accounted for. Next-to-minimal models, instead, yield the desired electroweak symmetry breaking and typically result in a very strong gravitational wave signal. (orig.)

  20. Targeted Molecular Dynamics to determine Focal Adhesion Targeting Domain Folding Intermediates

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    Pallavi Mohanty

    2017-10-01

    Full Text Available The Focal adhesion kinase (FAT domain of Focal Adhesion Kinase is a four helical bundle known for conformational plasticity. FAT adopts two distinctly different conformations i.e., close (cFAT and arm-exchanged (aeFAT states under native conditions [1]. The slow transition from cFAT to aeFAT is likely to proceed through an open intermediate state that allows YENV motif to attain β-turn conformation and phosphorylation of Y925 by Src kinases [2]. The two end states of FAT are known to interact with Paxillin and are responsible for maintaining steady state in Heart while intermediate conformation interacts with Grb2-SH2 leading to Pathological Cardiac Hypertrophy (PAH [2]. 10ns Targeted Molecular Dynamics (TMD was done between c- and aeFAT in order to explore the conformational transition and to capture pathologically relevant oFAT. Cluster and dynamic cross correlation analysis (DCCA of TMD generated trajectory was done and the selected FAT intermediate was docked with Grb2-SH2 using HADDOCK v2.2 docking followed by molecular dynamics. Conservation analysis of FAT-Grb2 binding site was done using CONSURF [3]. A Pharmacophore FAT-Grb2 complex was generated using SPARKv1.2 and submitted for Virtual screening using BLAZE v4. Drug likeliness and ADMET properties were calculated using MOLINSPIRATION tool. TMD reveals six clusters and DCCA showed positively and negatively correlated region along the transition pathway. Intermediates with competence for Grb2 interaction were docked with Grb2 and best binding complex was further refined. MMPBSA binding energy calculations revealed the best binding pose where the phosphorylated YENV motif of Human FAT interacted with a charged and hydrophobic pocket of Grb2. The conservation analysis showed that the charged pocket was more conserved in comparison with the hydrophobic pocket, hence providing useful insights on binding and specificity determining residues in Grb2. Virtual screening using the pharmacophore

  1. The Role of Conserved Waters in Conformational Transitions of Q61H K-ras

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    Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Gorfe, Alemayehu A.

    2012-01-01

    To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 µs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the Cα atoms of G60 at switch 2 and G10 at the P-loop and the N-Cα-C-O dihedral (ξ) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/ξ plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition. PMID:22359497

  2. Structural basis and kinetics of force-induced conformational changes of an αA domain-containing integrin.

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    Xue Xiang

    Full Text Available Integrin α(Lβ₂ (lymphocyte function-associated antigen, LFA-1 bears force upon binding to its ligand intercellular adhesion molecule 1 (ICAM-1 when a leukocyte adheres to vascular endothelium or an antigen presenting cell (APC during immune responses. The ligand binding propensity of LFA-1 is related to its conformations, which can be regulated by force. Three conformations of the LFA-1 αA domain, determined by the position of its α₇-helix, have been suggested to correspond to three different affinity states for ligand binding.The kinetics of the force-driven transitions between these conformations has not been defined and dynamically coupled to the force-dependent dissociation from ligand. Here we show, by steered molecular dynamics (SMD simulations, that the αA domain was successively transitioned through three distinct conformations upon pulling the C-terminus of its α₇-helix. Based on these sequential transitions, we have constructed a mathematical model to describe the coupling between the αA domain conformational changes of LFA-1 and its dissociation from ICAM-1 under force. Using this model to analyze the published data on the force-induced dissociation of single LFA-1/ICAM-1 bonds, we estimated the force-dependent kinetic rates of interstate transition from the short-lived to intermediate-lived and from intermediate-lived to long-lived states. Interestingly, force increased these transition rates; hence activation of LFA-1 was accelerated by pulling it via an engaged ICAM-1.Our study defines the structural basis for mechanical regulation of the kinetics of LFA-1 αA domain conformational changes and relates these simulation results to experimental data of force-induced dissociation of single LFA-1/ICAM-1 bonds by a new mathematical model, thus provided detailed structural and kinetic characterizations for force-stabilization of LFA-1/ICAM-1 interaction.

  3. Partially folded intermediates during trypsinogen denaturation

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    Martins N.F.

    1999-01-01

    Full Text Available The equilibrium unfolding of bovine trypsinogen was studied by circular dichroism, differential spectra and size exclusion HPLC. The change in free energy of denaturation was = 6.99 ± 1.40 kcal/mol for guanidine hydrochloride and = 6.37 ± 0.57 kcal/mol for urea. Satisfactory fits of equilibrium unfolding transitions required a three-state model involving an intermediate in addition to the native and unfolded forms. Size exclusion HPLC allowed the detection of an intermediate population of trypsinogen whose Stokes radii varied from 24.1 ± 0.4 Å to 26.0 ± 0.3 Å for 1.5 M and 2.5 M guanidine hydrochloride, respectively. During urea denaturation, the range of Stokes radii varied from 23.9 ± 0.3 Å to 25.7 ± 0.6 Å for 4.0 M and 6.0 M urea, respectively. Maximal intrinsic fluorescence was observed at about 3.8 M urea with 8-aniline-1-naphthalene sulfonate (ANS binding. These experimental data indicate that the unfolding of bovine trypsinogen is not a simple transition and suggest that the equilibrium intermediate population comprises one intermediate that may be characterized as a molten globule. To obtain further insight by studying intermediates representing different stages of unfolding, we hope to gain a better understanding of the complex interrelations between protein conformation and energetics.

  4. Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π-Cation Interaction.

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    Halder, Ritaban; Manna, Rabindra Nath; Chakraborty, Sandipan; Jana, Biman

    2017-06-15

    Large-scale conformational transition from open to closed state of adenylate kinase (ADK) is essential for its catalytic cycle. Apo-ADK undergoes conformational transition in a way that closely resembles an open-to-closed conformational transition. Here, equilibrium simulations, free-energy simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations in combination with several bioinformatics approaches have been used to explore the molecular origin of this conformational transition in apo-ADK. In addition to its conventional open state, Escherichia coli apo-ADK adopts conformations that resemble a closed-like intermediate, the "half-open-half-closed" (HOHC) state, and a π-cation interaction can account for the stability of this HOHC state. Energetics and the electronic properties of this π-cation interaction have been explored using QM/MM calculations. Upon rescinding the π-cation interaction, the conformational landscape of the apo-ADK changes completely. The apo-ADK population is shifted completely toward the open state. This π-cation interaction is highly conserved in bacterial ADK; the cationic guanidinium moiety of a conserved ARG interacts with the delocalized π-electron cloud of either PHE or TYR. Interestingly, this study demonstrates the modulation of a principal protein dynamics by a conserved specific π-cation interaction across different organisms.

  5. Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.

    Science.gov (United States)

    Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

    2017-09-19

    The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding.

  6. First Order Electroweak Phase Transition from (Non)Conformal Extensions of the Standard Model

    DEFF Research Database (Denmark)

    Sannino, Francesco; Virkajärvi, Jussi

    2015-01-01

    We analyse and compare the finite-temperature electroweak phase transition properties of classically (non)conformal extensions of the Standard Model. In the classically conformal scenarios the breaking of the electroweak symmetry is generated radiatively. The models feature new scalars coupled co...... the associated models are testable at the upcoming Large Hadron Collider run two experiments....

  7. pH-Driven Ordering Transitions in Liquid Crystal Induced by Conformational Changes of Cardiolipin.

    Science.gov (United States)

    Sidiq, Sumyra; Verma, Indu; Pal, Santanu Kumar

    2015-04-28

    We report an investigation of interfacial phenomena occurring at aqueous-liquid crystal (LC) interfaces that triggers an orientational ordering transition of the LC in the presence of cardiolipin (CL) by varying pH, salt concentration and valence. In particular, the effects of three different conformational isomeric forms of the CL are observed to cause the response of the LC ordering to vary significantly from one to another at those interfaces. An ordering transition of the LC was observed when the CL is mostly in undissociated (at pH 2) and/or in bicyclic (at pH 4) conformation in which LC shows changes in the optical appearance from bright to dark. By contrast, no change in the optical appearance of the LC was observed when the pH of the system increases to 8 or higher in which the CL mostly exists in the open conformation. Fluorescence microscopy measurements further suggest that pH-dependent conformational forms of the CL have different ability to self-assemble (thus different packing efficiency) at aqueous-LC interfaces leading to dissimilar orientational behavior of the LC. Specifically, we found that change in headgroup-headgroup repulsion of the central phosphatidyl groups of the CL plays a key role in tuning the lipid packing efficiency and thus responses to interfacial phenomena. Orientational ordering transition of the LC was also observed as a function of increasing the ionic strength (buffer capacity) and strongly influenced in the presence of mono and divalent cations. Langmuir-Blodgett (LB) and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) measurements provide further insight in modulation of the lipid packing efficiency and alkyl chain conformation of the CL at different pH and ionic conditions. Overall, the results presented in this paper establish that LCs offer a promising approach to differentiate different conformations (label free detection) of the CL through ordering transition of the LC at aqueous

  8. Frustration-guided motion planning reveals conformational transitions in proteins.

    Science.gov (United States)

    Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid; van den Bedem, Henry

    2017-10-01

    Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics-inspired motion planning procedure called dCC-RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25 Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/. © 2017 Wiley Periodicals, Inc.

  9. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    Energy Technology Data Exchange (ETDEWEB)

    Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao [Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Huang, Xuhui, E-mail: xuhuihuang@ust.hk [Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); The HKUST Shenzhen Research Institute, Shenzhen (China)

    2016-04-21

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  10. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    Science.gov (United States)

    Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

    2016-04-01

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  11. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    International Nuclear Information System (INIS)

    Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

    2016-01-01

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  12. Line broadening in multiphoton processes with a resonant intermediate transition

    International Nuclear Information System (INIS)

    Wang, C.C.; James, J.V.; Xia, J.

    1983-01-01

    The linewidth of the excitation spectrum for multiphoton ionization is found to be broadened much more severely than the cascade fluorescence originating from the resonant intermediate level. These results are due to the mutual effects of the ionizing and resonating transitions, which are not properly accounted for in perturbative treatments

  13. Laser induced popcornlike conformational transition of nanodiamond as a nanoknife

    International Nuclear Information System (INIS)

    Chang, C.-C.; Chen, P.-H.; Chu, H.-L.; Lee, T.-C.; Chou, C.-C.; Chao, J.-I; Su, C.-Y.; Chen, J.S.; Tsai, J.-S.; Tsai, C.-M.; Ho, Y.-P.; Sun, K.W.; Cheng, C.-L.; Chen, F.-R.

    2008-01-01

    Nanodiamond (ND) is surrounded by layers of graphite on its surface. This unique structure feature creates unusual fluorescence spectra, which can be used as an indicator to monitor its surface modification. Meanwhile, the impurity, nitroso (C-N=O) inside the ND can be photolyzed by two-photon absorption, releasing NO to facilitate the formation of a sp 3 diamond structure in the core of ND and transforming it into a sp 2 graphite structure. Such a conformational transition enlarges the size of ND from 8 to 90 nm, resulting in a popcornlike structure. This transition reaction may be useful as nanoknives in biomedical application

  14. In silico Exploration of the Conformational Universe of GPCRs.

    Science.gov (United States)

    Rodríguez-Espigares, Ismael; Kaczor, Agnieszka A; Selent, Jana

    2016-07-01

    The structural plasticity of G protein coupled receptors (GPCRs) leads to a conformational universe going from inactive to active receptor states with several intermediate states. Many of them have not been captured yet and their role for GPCR activation is not well understood. The study of this conformational space and the transition dynamics between different receptor populations is a major challenge in molecular biophysics. The rational design of effector molecules that target such receptor populations allows fine-tuning receptor signalling with higher specificity to produce drugs with safer therapeutic profiles. In this minireview, we outline highly conserved receptor regions which are considered determinant for the establishment of distinct receptor states. We then discuss in-silico approaches such as dimensionality reduction methods and Markov State Models to explore the GPCR conformational universe and exploit the obtained conformations through structure-based drug design. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

    Science.gov (United States)

    Palenik, Mark C; Rodriguez, Jorge H

    2014-07-07

    Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

  16. Thermodynamic Analysis of the Conformational Transition in Aqueous Solutions of Isotactic and Atactic Poly(Methacrylic Acid and the Hydrophobic Effect

    Directory of Open Access Journals (Sweden)

    Ksenija Kogej

    2016-04-01

    Full Text Available The affinity of amphiphilic compounds for water is important in various processes, e.g., in conformational transitions of biopolymers, protein folding/unfolding, partitioning of drugs in the living systems, and many others. Herein, we study the conformational transition of two isomer forms of poly(methacrylic acid (PMA, isotactic (iPMA and atactic (aPMA, in water. These isomers are chemically equivalent and differ only in the arrangement of functional groups along the chain. A complete thermodynamic analysis of the transition of the PMA chains from the compact to the extended form (comprising the conformational transition in water in the presence of three alkali chlorides is conducted by determining the free energy, enthalpy, and entropy changes of the process as a function of temperature, and therefrom also the heat capacity change. The heat capacity change of the transition is positive (+20 J/K mol for aPMA and negative (−50 J/K mol for iPMA. This result suggests a different affinity of PMA isomers for water. The conformational transition of iPMA is parallel to the transfer of polar solutes into water, whereas that of aPMA agrees with the transfer of nonpolar solutes into water.

  17. Conformational transition of κ-casein in micellar environment: Insight from the tryptophan fluorescence

    Science.gov (United States)

    Mishra, Smruti; Meher, Geetanjali; Chakraborty, Hirak

    2017-11-01

    Intrinsically disordered proteins (IDPs) are under intense analysis due to their structural flexibility and importance in biological functions. Minuscule modulation in the microenvironment induces significant conformational changes in IDPs, and these non-native conformations of the IDPs often induce aggregation and cause cell death. Changes in the membrane composition often change the microenvironment, which promote conformational change and aggregation of IDPs. κ-Casein, an important milk protein, belongs to the class of IDPs containing net negative charges. In this present work, we have studied the interaction of κ-casein with cetyltrimethyl ammonium bromide (CTAB), a positively charged surfactant, utilizing various steady state fluorescence, time-resolved fluorescence and circular dichroism spectroscopy. Our results clearly indicate that κ-casein undergoes at least two conformational transitions in presence of various concentrations of CTAB. The intrinsically disordered κ-casein assumes a partially folded conformation at lower concentration of CTAB, which adopts an unstructured conformation at higher concentration of CTAB. The partially folded conformation of κ-casein at a lower CTAB concentration might be induced by the favorable electrostatic interaction between the positively charged surfactant headgroup and net negative charges of the protein, whereas surfactant nature of CTAB is being pronounced at higher concentration of CTAB.

  18. Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB

    Directory of Open Access Journals (Sweden)

    Beibei eWang

    2015-04-01

    Full Text Available The tripartite efflux pump assembly AcrAB-TolC is the major multidrug resistance transporter in E. coli. The inner membrane transporter AcrB is a homotrimer, energized by the proton movement down the transmembrane electrochemical gradient. The asymmetric crystal structures of AcrB with three monomers in distinct conformational states (access (A, binding (B and extrusion (E support a functional rotating mechanism, in which each monomer of AcrB cycles among the three states in a concerted way. However, the relationship between the conformational changes during functional rotation and drug translocation has not been totally understood. Here, we explored the conformational changes of the AcrB homotrimer during the ABE→BEA transition in different substrate-binding states using targeted MD simulations. It was found that the dissociation of substrate from the distal binding pocket of B monomer is closely related to the concerted conformational changes in the translocation pathway, especially the side chain reorientation of Phe628 and Tyr327. A second substrate binding at the proximal binding pocket of A monomer evidently accelerates the conformational transitions as well as substrate dissociation in B monomer. The acceleration effect of the multi-substrate binding mode provides a molecular explanation for the positive cooperativity observed in the kinetic studies of substrate efflux and deepens our understanding of the functional rotating mechanism of AcrB.

  19. Intermediate state trapping of a voltage sensor

    DEFF Research Database (Denmark)

    Lacroix, Jérôme J; Pless, Stephan Alexander; Maragliano, Luca

    2012-01-01

    Voltage sensor domains (VSDs) regulate ion channels and enzymes by undergoing conformational changes depending on membrane electrical signals. The molecular mechanisms underlying the VSD transitions are not fully understood. Here, we show that some mutations of I241 in the S1 segment of the Shaker...... Kv channel positively shift the voltage dependence of the VSD movement and alter the functional coupling between VSD and pore domains. Among the I241 mutants, I241W immobilized the VSD movement during activation and deactivation, approximately halfway between the resting and active states......, and drastically shifted the voltage activation of the ionic conductance. This phenotype, which is consistent with a stabilization of an intermediate VSD conformation by the I241W mutation, was diminished by the charge-conserving R2K mutation but not by the charge-neutralizing R2Q mutation. Interestingly, most...

  20. Transitions of tethered chain molecules under tension.

    Science.gov (United States)

    Luettmer-Strathmann, Jutta; Binder, Kurt

    2014-09-21

    An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. To investigate these effects theoretically, we study tethered chains under tension with Wang-Landau simulations of a bond-fluctuation lattice model. Applying our model to pulling experiments on biological molecules we obtain a good description of experimental data in the intermediate force range, where universal features dominate and finite size effects are small. For tethered chains in poor solvent, we observe the predicted two-phase coexistence at transitions from the globule to stretched conformations and also discover direct transitions from crystalline to stretched conformations. A phase portrait for finite chains constructed by evaluating the density of states for a broad range of solvent conditions and tensions shows how increasing tension leads to a disappearance of the globular phase. For chains in good solvents tethered to hard and attractive surfaces we find the predicted scaling with the chain length in the low-force regime and show that our results are well described by an analytical, independent-bond approximation for the bond-fluctuation model for the highest tensions. Finally, for a hard or slightly attractive surface the stretching of a tethered chain is a conformational change that does not correspond to a phase transition. However, when the surface attraction is sufficient to adsorb a chain it will undergo a desorption transition at a critical value of the applied force. Our results for force-induced desorption show the transition to be discontinuous with partially desorbed conformations in the coexistence region.

  1. Analysis of an ATP-induced conformational transition of ABC transporter MsbA using a coarse-grained model.

    Science.gov (United States)

    Arai, Naoki; Furuta, Tadaomi; Sakurai, Minoru

    2017-01-01

    Upon the binding of ATP molecules to nucleotide binding domains (NBDs), ATP-binding cassette (ABC) exporters undergo a conformational transition from an inward-facing (IF) to an outward-facing (OF) state. This molecular event is a typical example of chemo-mechanical coupling. However, the underlying mechanism remains unclear. In this study, we analyzed the IF→OF transition of a representative ABC exporter, MsbA, by solving the equation of motion under an elastic network model (ENM). ATP was represented as a single node in ENM or replaced by external forces. When two ATP nodes were added to the ENM of the IF state protein, the two NBDs dimerized; subsequently, the two transmembrane domains opened toward the extracellular side, resulting in the formation of the OF structure. Such a conformational transition was also reproduced by applying external forces, which caused the rotational motion of the NBDs instead of the addition of ATP nodes. The process of the conformational transition was analyzed in detail using cross-correlation maps for node-node interactions. More importantly, it was revealed that the ATP binding energy is converted into distortion energy of several transmembrane helices. These results are useful for understanding the chemo-mechanical coupling in ABC transporters.

  2. Distribution, transition and thermodynamic stability of protein conformations in the denaturant-induced unfolding of proteins.

    Science.gov (United States)

    Bian, Liujiao; Ji, Xu

    2014-01-01

    Extensive and intensive studies on the unfolding of proteins require appropriate theoretical model and parameter to clearly illustrate the feature and characteristic of the unfolding system. Over the past several decades, four approaches have been proposed to describe the interaction between proteins and denaturants, but some ambiguity and deviations usually occur in the explanation of the experimental data. In this work, a theoretical model was presented to show the dependency of the residual activity ratio of the proteins on the molar denaturant concentration. Through the characteristic unfolding parameters ki and Δmi in this model, the distribution, transition and thermodynamic stability of protein conformations during the unfolding process can be quantitatively described. This model was tested with the two-state unfolding of bovine heart cytochrome c and the three-state unfolding of hen egg white lysozyme induced by both guanidine hydrochloride and urea, the four-state unfolding of bovine carbonic anhydrase b induced by guanidine hydrochloride and the unfolding of some other proteins induced by denaturants. The results illustrated that this model could be used accurately to reveal the distribution and transition of protein conformations in the presence of different concentrations of denaturants and to evaluate the unfolding tendency and thermodynamic stability of different conformations. In most denaturant-induced unfolding of proteins, the unfolding became increasingly hard in next transition step and the proteins became more unstable as they attained next successive stable conformation. This work presents a useful method for people to study the unfolding of proteins and may be used to describe the unfolding and refolding of other biopolymers induced by denaturants, inducers, etc.

  3. Conformal symmetry in two-dimensional space: recursion representation of conformal block

    International Nuclear Information System (INIS)

    Zamolodchikov, A.B.

    1988-01-01

    The four-point conformal block plays an important part in the analysis of the conformally invariant operator algebra in two-dimensional space. The behavior of the conformal block is calculated in the present paper in the limit in which the dimension Δ of the intermediate operator tends to infinity. This makes it possible to construct a recursion relation for this function that connects the conformal block at arbitrary Δ to the blocks corresponding to the dimensions of the zero vectors in the degenerate representations of the Virasoro algebra. The relation is convenient for calculating the expansion of the conformal block in powers of the uniformizing parameters q = i π tau

  4. Transitional Disks Associated with Intermediate-Mass Stars: Results of the SEEDS YSO Survey

    Science.gov (United States)

    Grady, C.; Fukagawa, M.; Maruta, Y.; Ohta, Y.; Wisniewski, J.; Hashimoto, J.; Okamoto, Y.; Momose, M.; Currie, T.; McElwain, M.; hide

    2014-01-01

    Protoplanetary disks are where planets form, grow, and migrate to produce the diversity of exoplanet systems we observe in mature systems. Disks where this process has advanced to the stage of gap opening, and in some cases central cavity formation, have been termed pre-transitional and transitional disks in the hope that they represent intermediate steps toward planetary system formation. Recent reviews have focussed on disks where the star is of solar or sub-solar mass. In contrast to the sub-millimeter where cleared central cavities predominate, at H-band some T Tauri star transitional disks resemble primordial disks in having no indication of clearing, some show a break in the radial surface brightness profile at the inner edge of the outer disk, while others have partially to fully cleared gaps or central cavities. Recently, the Meeus Group I Herbig stars, intermediate-mass PMS stars with IR spectral energy distributions often interpreted as flared disks, have been proposed to have transitional and pre-transitional disks similar to those associated with solar-mass PMS stars, based on thermal-IR imaging, and sub-millimeter interferometry. We have investigated their appearance in scattered light as part of the Strategic Exploration of Exoplanets and Disks with Subaru (SEEDS), obtaining H-band polarimetric imagery of 10 intermediate-mass stars with Meeus Group I disks. Augmented by other disks with imagery in the literature, the sample is now sufficiently large to explore how these disks are similar to and differ from T Tauri star disks. The disk morphologies seen in the Tauri disks are also found for the intermediate-mass star disks, but additional phenomena are found; a hallmark of these disks is remarkable individuality and diversity which does not simply correlate with disk mass or stellar properties, including age, including spiral arms in remnant envelopes, arms in the disk, asymmetrically and potentially variably shadowed outer disks, gaps, and one disk

  5. Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates

    International Nuclear Information System (INIS)

    Hardin, C.C.; Watson, T.; Henderson, E.; Prosser, J.K.

    1991-01-01

    Telomeric DNA consists of G- and C-rich strands that are always polarized such that the G-rich strand extends past the 3' end of the duplex to form a 12-16-base overhang. These overhanging strands can self-associate in vitro to form intramolecular structures that have several unusual physical properties and at least one common feature, the presence of non-Watson-Crick G·G base pairs. The term G-DNA was coined for this class of structures. On the basis of gel electrophoresis, imino proton NMR, and circular dichroism (CD) results, the authors find that changing the counterions from sodium to potassium specifically induces conformational transitions in the G-rich telomeric DNA from Tetrahymena, d(T 2 G 4 ) 4 (TET4), which results in a change from the intramolecular species to an apparent multistranded structure, accompanied by an increase in the melting temperature of the base pairs of >25 degree, as monitored by loss of the imino proton NMR signals. They infer that the multistranded structure is a quadruplex. The results indicate that specific differences in ionic interactions can result in a switch in telomeric DNAs between intramolecular hairpin-like or quadruplex-containing species and intermolecular quadruplex structures, all of which involve G·G base pairing interaction. They propose a model in which duplex or hairpin forms of G-DNA are folding intermediates in the formation of either 1-, 2-, or 4-stranded quadruplex structures

  6. An intracellular interaction network regulates conformational transitions in the dopamine transporter

    DEFF Research Database (Denmark)

    Kniazeff, Julie; Shi, Lei; Løland, Claus Juul

    2008-01-01

    Neurotransmitter:sodium symporters (NSS)(1) mediate sodium-dependent reuptake of neurotransmitters from the synaptic cleft and are targets for many psychoactive drugs. The crystal structure of the prokaryotic NSS protein, LeuT, was recently solved at high resolution; however, the mechanistic...... and the intracellular milieu. The mechanism that emerges from these findings may be unique to the NSS family, where the local disruption of ionic interactions modulates the transition of the transporter between the outward- and inward-facing conformations....

  7. The Building Game: From Enumerative Combinatorics to Conformational Diffusion

    Science.gov (United States)

    Johnson-Chyzhykov, Daniel; Menon, Govind

    2016-08-01

    We study a discrete attachment model for the self-assembly of polyhedra called the building game. We investigate two distinct aspects of the model: (i) enumerative combinatorics of the intermediate states and (ii) a notion of Brownian motion for the polyhedral linkage defined by each intermediate that we term conformational diffusion. The combinatorial configuration space of the model is computed for the Platonic, Archimedean, and Catalan solids of up to 30 faces, and several novel enumerative results are generated. These represent the most exhaustive computations of this nature to date. We further extend the building game to include geometric information. The combinatorial structure of each intermediate yields a systems of constraints specifying a polyhedral linkage and its moduli space. We use a random walk to simulate a reflected Brownian motion in each moduli space. Empirical statistics of the random walk may be used to define the rates of transition for a Markov process modeling the process of self-assembly.

  8. Reduced-Amide Inhibitor of Pin1 Binds in a Conformation Resembling a Twisted-Amide Transition State†

    Science.gov (United States)

    Xu, Guoyan G.; Zhang, Yan; Mercedes-Camacho, Ana Y.; Etzkorn, Felicia A.

    2011-01-01

    The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R–pSer–Ψ[CH2N]–Pro–2-(indol-3-yl)-ethylamine, 1 (R = fluorenylmethoxycarbonyl, Fmoc), and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC50 value of 6.3 μM, which is 4.5-fold better inhibition for Pin1 than our comparable ground state analogue, a cis-amide alkene isostere containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination, and resulted in an IC50 value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser, and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1. PMID:21980916

  9. Conformality lost

    International Nuclear Information System (INIS)

    Kaplan, David B.; Lee, Jong-Wan; Son, Dam T.; Stephanov, Mikhail A.

    2009-01-01

    We consider zero-temperature transitions from conformal to nonconformal phases in quantum theories. We argue that there are three generic mechanisms for the loss of conformality in any number of dimensions: (i) fixed point goes to zero coupling, (ii) fixed point runs off to infinite coupling, or (iii) an IR fixed point annihilates with a UV fixed point and they both disappear into the complex plane. We give both relativistic and nonrelativistic examples of the last case in various dimensions and show that the critical behavior of the mass gap behaves similarly to the correlation length in the finite temperature Berezinskii-Kosterlitz-Thouless (BKT) phase transition in two dimensions, ξ∼exp(c/|T-T c | 1/2 ). We speculate that the chiral phase transition in QCD at large number of fermion flavors belongs to this universality class, and attempt to identify the UV fixed point that annihilates with the Banks-Zaks fixed point at the lower end of the conformal window.

  10. An alternative conformation of the gp41 heptad repeat 1 region coiled coil exists in the human immunodeficiency virus (HIV-1) envelope glycoprotein precursor

    International Nuclear Information System (INIS)

    Mische, Claudia C.; Yuan Wen; Strack, Bettina; Craig, Stewart; Farzan, Michael; Sodroski, Joseph

    2005-01-01

    The human immunodeficiency virus (HIV-1) transmembrane envelope glycoprotein, gp41, which mediates virus-cell fusion, exists in at least three different conformations within the trimeric envelope glycoprotein complex. The structures of the prefusogenic and intermediate states are unknown; structures representing the postfusion state have been solved. In the postfusion conformation, three helical heptad repeat 2 (HR2) regions pack in an antiparallel fashion into the hydrophobic grooves on the surface of a triple-helical coiled coil formed by the heptad repeat 1 (HR1) regions. We studied the prefusogenic conformation of gp41 by mutagenic alteration of membrane-anchored and soluble forms of the HIV-1 envelope glycoproteins. Our results indicate that, in the HIV-1 envelope glycoprotein precursor, the gp41 HR1 region is in a conformation distinct from that of a trimeric coiled coil. Thus, the central gp41 coiled coil is formed during the transition of the HIV-1 envelope glycoproteins from the precursor state to the receptor-bound intermediate

  11. Global conformational dynamics of a Y-family DNA polymerase during catalysis.

    Directory of Open Access Journals (Sweden)

    Cuiling Xu

    2009-10-01

    Full Text Available Replicative DNA polymerases are stalled by damaged DNA while the newly discovered Y-family DNA polymerases are recruited to rescue these stalled replication forks, thereby enhancing cell survival. The Y-family DNA polymerases, characterized by low fidelity and processivity, are able to bypass different classes of DNA lesions. A variety of kinetic and structural studies have established a minimal reaction pathway common to all DNA polymerases, although the conformational intermediates are not well defined. Furthermore, the identification of the rate-limiting step of nucleotide incorporation catalyzed by any DNA polymerase has been a matter of long debate. By monitoring time-dependent fluorescence resonance energy transfer (FRET signal changes at multiple sites in each domain and DNA during catalysis, we present here a real-time picture of the global conformational transitions of a model Y-family enzyme: DNA polymerase IV (Dpo4 from Sulfolobus solfataricus. Our results provide evidence for a hypothetical DNA translocation event followed by a rapid protein conformational change prior to catalysis and a subsequent slow, post-chemistry protein conformational change. Surprisingly, the DNA translocation step was induced by the binding of a correct nucleotide. Moreover, we have determined the directions, rates, and activation energy barriers of the protein conformational transitions, which indicated that the four domains of Dpo4 moved in a synchronized manner. These results showed conclusively that a pre-chemistry conformational change associated with domain movements was too fast to be the rate-limiting step. Rather, the rearrangement of active site residues limited the rate of correct nucleotide incorporation. Collectively, the conformational dynamics of Dpo4 offer insights into how the inter-domain movements are related to enzymatic function and their concerted interactions with other proteins at the replication fork.

  12. A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state.

    Science.gov (United States)

    Xu, Guoyan G; Zhang, Yan; Mercedes-Camacho, Ana Y; Etzkorn, Felicia A

    2011-11-08

    The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.

  13. Solid-to-hybrid transitioning armature railgun with non-conforming-to-prejudice bore profile

    Science.gov (United States)

    Solberg, Jerome Michael

    2012-12-04

    An improved railgun, railgun barrel, railgun projectile, and railgun system for accelerating a solid-to-hybrid transitioning armature projectile using a barrel having a bore that does not conform to a cross-sectional profile of the projectile, to contact and guide the projectile only by the rails in a low pressure bore volume so as to minimize damage, failure, and/or underperformance caused by plasma armatures, insulator ablation, and/or restrikes.

  14. Reversible conformational transition gives rise to 'zig-zag' temperature dependence of the rate constant of irreversible thermoinactivation of enzymes.

    Science.gov (United States)

    Levitsky VYu; Melik-Nubarov, N S; Siksnis, V A; Grinberg VYa; Burova, T V; Levashov, A V; Mozhaev, V V

    1994-01-15

    We have obtained unusual 'zig-zag' temperature dependencies of the rate constant of irreversible thermoinactivation (k(in)) of enzymes (alpha-chymotrypsin, covalently modified alpha-chymotrypsin, and ribonuclease) in a plot of log k(in) versus reciprocal temperature (Arrhenius plot). These dependencies are characterized by the presence of both ascending and descending linear portions which have positive and negative values of the effective activation energy (Ea), respectively. A kinetic scheme has been suggested that fits best for a description of these zig-zag dependencies. A key element of this scheme is the temperature-dependent reversible conformational transition of enzyme from the 'low-temperature' native state to a 'high-temperature' denatured form; the latter form is significantly more stable against irreversible thermoinactivation than the native enzyme. A possible explanation for a difference in thermal stabilities is that low-temperature and high-temperature forms are inactivated according to different mechanisms. Existence of the suggested conformational transition was proved by the methods of fluorescence spectroscopy and differential scanning calorimetry. The values of delta H and delta S for this transition, determined from calorimetric experiments, are highly positive; this fact underlies a conclusion that this heat-induced transition is caused by an unfolding of the protein molecule. Surprisingly, in the unfolded high-temperature conformation, alpha-chymotrypsin has a pronounced proteolytic activity, although this activity is much smaller than that of the native enzyme.

  15. Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.

    Science.gov (United States)

    Chakraborty, Debayan; Wales, David J

    2018-01-04

    The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.

  16. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    Science.gov (United States)

    Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet

    2013-12-01

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  17. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    International Nuclear Information System (INIS)

    Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet; Peter, Christine

    2013-01-01

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties

  18. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    Energy Technology Data Exchange (ETDEWEB)

    Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet, E-mail: msayar@ku.edu.tr [College of Engineering, Koç University, 34450 Istanbul (Turkey); Peter, Christine [Max Planck Institute for Polymer Research, 55128 Mainz (Germany); Department of Chemistry, University of Konstanz, 78547 Konstanz (Germany)

    2013-12-21

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  19. Conformational changes in glycine tri- and hexapeptide

    DEFF Research Database (Denmark)

    Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2006-01-01

    conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods...... also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids....

  20. Conformational intermediate of the amyloidogenic protein beta 2-microglobulin at neutral pH

    DEFF Research Database (Denmark)

    Heegaard, N H; Sen, J W; Kaarsholm, N C

    2001-01-01

    electrophoresis that two conformers spontaneously exist in aqueous buffers at neutral pH. Upon treatment of wild-type beta(2)-microglobulin with acetonitrile or trifluoroethanol, two conformations were also observed. These conformations were in equilibrium dependent on the sample temperature and the percentage...

  1. Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain.

    Science.gov (United States)

    Li, Qufei; Wanderling, Sherry; Sompornpisut, Pornthep; Perozo, Eduardo

    2014-02-01

    Voltage-gated ion channels respond to transmembrane electric fields through reorientations of the positively charged S4 helix within the voltage-sensing domain (VSD). Despite a wealth of structural and functional data, the details of this conformational change remain controversial. Recent electrophysiological evidence showed that equilibrium between the resting ('down') and activated ('up') conformations of the KvAP VSD from Aeropyrum pernix can be biased through reconstitution in lipids with or without phosphate groups. We investigated the structural transition between these functional states, using site-directed spin-labeling and EPR spectroscopic methods. Solvent accessibility and interhelical distance determinations suggest that KvAP gates through S4 movements involving an ∼3-Å upward tilt and simultaneous ∼2-Å axial shift. This motion leads to large accessibly changes in the intracellular water-filled crevice and supports a new model of gating that combines structural rearrangements and electric-field remodeling.

  2. Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

    Directory of Open Access Journals (Sweden)

    Qing Wang

    2016-05-01

    Full Text Available Free energy calculations of the potential of mean force (PMF based on the combination of targeted molecular dynamics (TMD simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35. The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes.

  3. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn; Zhu, Weiliang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); Shi, Jiye, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [UCB Pharma, 216 Bath Road, Slough SL1 4EN (United Kingdom)

    2015-03-28

    The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much less computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.

  4. Detection of Intermediate-Period Transiting Planets with a Network of Small Telescopes: transitsearch.org

    Science.gov (United States)

    Seagroves, Scott; Harker, Justin; Laughlin, Gregory; Lacy, Justin; Castellano, Tim

    2003-12-01

    We describe a project (transitsearch.org) currently attempting to discover transiting intermediate-period planets orbiting bright parent stars, and we simulate that project's performance. The discovery of such a transit would be an important astronomical advance, bridging the critical gap in understanding between HD 209458b and Jupiter. However, the task is made difficult by intrinsically low transit probabilities and small transit duty cycles. This project's efficient and economical strategy is to photometrically monitor stars that are known (from radial velocity surveys) to bear planets, using a network of widely spaced observers with small telescopes. These observers, each individually capable of precision (1%) differential photometry, monitor candidates during the time windows in which the radial velocity solution predicts a transit if the orbital inclination is close to 90°. We use Monte Carlo techniques to simulate the performance of this network, performing simulations with different configurations of observers in order to optimize coordination of an actual campaign. Our results indicate that transitsearch.org can reliably rule out or detect planetary transits within the current catalog of known planet-bearing stars. A distributed network of skilled amateur astronomers and small college observatories is a cost-effective method for discovering the small number of transiting planets with periods in the range 10 days

  5. Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites.

    Science.gov (United States)

    Wise, John G

    2012-06-26

    Multidrug resistance proteins that belong to the ATP-binding cassette family like the human P-glycoprotein (ABCB1 or Pgp) are responsible for many failed cancer and antiviral chemotherapies because these membrane transporters remove the chemotherapeutics from the targeted cells. Understanding the details of the catalytic mechanism of Pgp is therefore critical to the development of inhibitors that might overcome these resistances. In this work, targeted molecular dynamics techniques were used to elucidate catalytically relevant structures of Pgp. Crystal structures of homologues in four different conformations were used as intermediate targets in the dynamics simulations. Transitions from conformations that were wide open to the cytoplasm to transition state conformations that were wide open to the extracellular space were studied. Twenty-six nonredundant transitional protein structures were identified from these targeted molecular dynamics simulations using evolutionary structure analyses. Coupled movement of nucleotide binding domains (NBDs) and transmembrane domains (TMDs) that form the drug binding cavities were observed. Pronounced twisting of the NBDs as they approached each other as well as the quantification of a dramatic opening of the TMDs to the extracellular space as the ATP hydrolysis transition state was reached were observed. Docking interactions of 21 known transport ligands or inhibitors were analyzed with each of the 26 transitional structures. Many of the docking results obtained here were validated by previously published biochemical determinations. As the ATP hydrolysis transition state was approached, drug docking in the extracellular half of the transmembrane domains seemed to be destabilized as transport ligand exit gates opened to the extracellular space.

  6. Conformational Analysis of DNA Repair Intermediates by Time-Resolved Fluorescence Spectroscopy

    OpenAIRE

    Lin, Su; Horning, David P.; Szostak, Jack W.; Chaput, John C.

    2009-01-01

    DNA repair enzymes are essential for maintaining the integrity of the DNA sequence. Unfortunately, very little is known about how these enzymes recognize damaged regions along the helix. Structural analysis of cellular repair enzymes bound to DNA reveals that these enzymes are able to recognize DNA in a variety of conformations. However, the prevalence of these deformations in the absence of enzymes remains unclear, as small populations of DNA conformations are often difficult to detect by NM...

  7. Reversible switching of fluorophore property based on intrinsic conformational transition of adenylate kinase during its catalytic cycle.

    Science.gov (United States)

    Fujii, Akira; Hirota, Shun; Matsuo, Takashi

    2013-07-17

    Adenylate kinase shows a conformational transition (OPEN and CLOSED forms) during substrate binding and product release to mediate the phosphoryl transfer between ADP and ATP/AMP. The protein motional characteristics will be useful to construct switching systems of fluorophore properties caused by the catalytic cycle of the enzyme. This paper demonstrates in situ reversible switching of a fluorophore property driven by the conformational transition of the enzyme. The pyrene-conjugated mutant adenylate kinase is able to switch the monomer/excimer emission property of pyrene on addition of ADP or P(1)P(5)-di(adenosine-5')pentaphosphate (Ap5A, a transition state analog). The observation under the dilute condition (~0.1 μM) indicates that the emission spectral change was caused by the motion of a protein molecule and not led by protein-protein interactions through π-π stacking of pyrene rings. The switching can be reversibly conducted by using hexokinase-coupling reaction. The fashion of the changes in emission intensities at various ligand concentrations is different between ADP, Mg(2+)-bound ADP, and Mg(2+)-bound Ap5A. The emission property switching is repeatable by a sequential addition of a substrate in a one-pot process. It is proposed that the property of a synthetic molecule on the enzyme surface is switchable in response to the catalytic cycle of adenylate kinase.

  8. Transition from 2-D radiotherapy to 3-D conformal and intensity modulated radiotherapy

    International Nuclear Information System (INIS)

    2008-05-01

    Cancer is one of the leading causes of death globally and radiotherapy is currently an essential component in the management of cancer patients, either alone or in combination with surgery or chemotherapy, both for cure or palliation. It is now recognized that safe and effective radiotherapy service needs not only substantial capital investment in radiotherapy equipment and specially designed facilities but also continuous investment in maintenance and upgrading of the equipment to comply with the technical progress, but also in training the staff. The recent IAEA-TECDOC publication 'Setting up a Radiotherapy Programme: Clinical, Medical Physics, Radiation Protection and Safety Aspects' provides general guidelines for designing and implementing radiotherapy services in Member States. Advances in computer technology have enabled the possibility of transitioning from basic 2- dimensional treatment planning and delivery (2-D radiotherapy) to a more sophisticated approach with 3-dimensional conformal radiotherapy (3-D CRT). Whereas 2-D radiotherapy can be applied with simple equipment, infrastructure and training, transfer to 3-D conformal treatments requires more resources in technology, equipment, staff and training. A novel radiation treatment approach using Intensity Modulated Radiation Therapy (IMRT) that optimizes the delivery of radiation to irregularly shaped tumour volumes demands even more sophisticated equipment and seamless teamwork, and consequentially more resources, advanced training and more time for treatment planning and verification of dose delivery than 3-D CRT. Whereas 3-D CRT can be considered as a standard, IMRT is still evolving. Due to the increased interest of Member States to the modern application of radiotherapy the IAEA has received a number of requests for guidance coming from radiotherapy departments that wish to upgrade their facilities to 3-D CRT and IMRT through Technical Cooperation programme. These requests are expected to increase

  9. Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft

    Directory of Open Access Journals (Sweden)

    MacKerell Alexander D

    2007-03-01

    Full Text Available Abstract Background The N-terminal SH2 domain (N-SH2 of the non-receptor tyrosine phosphatase SHP-2 is involved both in localization of SHP-2 by recognition of phosphotyrosine (pY peptides and self-inhibition of SHP-2 phosphatase activity through the formation of a protein – protein interface with the phosphatase domain. Mutations that disrupt this interface break the coupling between pY-peptide binding cleft conformation and self-inhibition, thereby increasing both SHP-2 phosphatase activity and pY-peptide binding affinity, and are associated with the congenital condition Noonan syndrome and various pediatric leukemias. To better characterize the molecular process involved in N-SH2 pY-dependent binding, we have applied explicit-solvent molecular dynamics simulations to study the closed-to-open transition of the N-SH2 pY-peptide binding cleft. Results The existence of stable conformations in the left-handed helical and the extended regions of Tyr66 φ/ψ space prevent rapid interconversion of the backbone and create a conformational switch such that Tyr66 in a left-handed helical backbone conformation results in an open cleft and in an extended backbone conformation results in a closed cleft. The stable conformations arise from deep, well-localized free-energy minima in the left-handed helical and extended regions of the Tyr66 φ/ψ map. Changing the Tyr66 backbone conformation from extended to left-handed helical induces a closed-to-open transition in the cleft, and the reverse change in backbone conformation induces the reverse, open-to-closed transition. In the open-cleft state, weak solvent-exposed interactions involving the sidechains of Tyr66, Asp40, Lys55, and Gln57 serve to anchor the Tyr66 sidechain to the surface of the protein and away from the binding cleft entrance, thereby facilitating pY-peptide access to the binding cleft. Conclusion The simulations point to a regulatory role for Tyr66 and surrounding residues in SHP-2 function

  10. [Artificial Cysteine Bridges on the Surface of Green Fluorescent Protein Affect Hydration of Its Transition and Intermediate States].

    Science.gov (United States)

    Melnik, T N; Nagibina, G S; Surin, A K; Glukhova, K A; Melnik, B S

    2018-01-01

    Studying the effect of cysteine bridges on different energy levels of multistage folding proteins will enable a better understanding of the process of folding and functioning of globular proteins. In particular, it will create prospects for directed change in the stability and rate of protein folding. In this work, using the method of differential scanning microcalorimetry, we have studied the effect of three cysteine bridges introduced in different structural elements of the green fluorescent protein on the denaturation enthalpies, activation energies, and heat-capacity increments when this protein passes from native to intermediate and transition states. The studies have allowed us to confirm that, with this protein denaturation, the process hardly damages the structure initially, but then changes occur in the protein structure in the region of 4-6 beta sheets. The cysteine bridge introduced in this region decreases the hydration of the second transition state and increases the hydration of the second intermediate state during the thermal denaturation of the green fluorescent protein.

  11. Conformal invariance and two-dimensional physics

    International Nuclear Information System (INIS)

    Zuber, J.B.

    1993-01-01

    Actually, physicists and mathematicians are very interested in conformal invariance: geometric transformations which keep angles. This symmetry is very important for two-dimensional systems as phase transitions, string theory or node mathematics. In this article, the author presents the conformal invariance and explains its usefulness

  12. Normal mode-guided transition pathway generation in proteins.

    Directory of Open Access Journals (Sweden)

    Byung Ho Lee

    Full Text Available The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this.

  13. Computer-Based Junior High/Intermediate School Program of Transitional Bilingual Education, Community School District 3, Manhattan. Final Evaluation Report, 1992-93. OREA Report.

    Science.gov (United States)

    Duque, Diana L.

    The Computer-Based Junior High/Intermediate School Program of Transitional Bilingual Education was a federally funded program in its third year of operation in one intermediate school and two junior high schools in Manhattan (New York) in 1992-93. During this period, it served 244 native Spanish-speaking, limited-English-proficient (LEP) students…

  14. Src kinase conformational activation: thermodynamics, pathways, and mechanisms.

    Directory of Open Access Journals (Sweden)

    Sichun Yang

    2008-03-01

    Full Text Available Tyrosine kinases of the Src-family are large allosteric enzymes that play a key role in cellular signaling. Conversion of the kinase from an inactive to an active state is accompanied by substantial structural changes. Here, we construct a coarse-grained model of the catalytic domain incorporating experimental structures for the two stable states, and simulate the dynamics of conformational transitions in kinase activation. We explore the transition energy landscapes by constructing a structural network among clusters of conformations from the simulations. From the structural network, two major ensembles of pathways for the activation are identified. In the first transition pathway, we find a coordinated switching mechanism of interactions among the alphaC helix, the activation-loop, and the beta strands in the N-lobe of the catalytic domain. In a second pathway, the conformational change is coupled to a partial unfolding of the N-lobe region of the catalytic domain. We also characterize the switching mechanism for the alphaC helix and the activation-loop in detail. Finally, we test the performance of a Markov model and its ability to account for the structural kinetics in the context of Src conformational changes. Taken together, these results provide a broad framework for understanding the main features of the conformational transition taking place upon Src activation.

  15. The Fusion Loops of the Initial Prefusion Conformation of Herpes Simplex Virus 1 Fusion Protein Point Toward the Membrane

    Directory of Open Access Journals (Sweden)

    Juan Fontana

    2017-08-01

    Full Text Available All enveloped viruses, including herpesviruses, must fuse their envelope with the host membrane to deliver their genomes into target cells, making this essential step subject to interference by antibodies and drugs. Viral fusion is mediated by a viral surface protein that transits from an initial prefusion conformation to a final postfusion conformation. Strikingly, the prefusion conformation of the herpesvirus fusion protein, gB, is poorly understood. Herpes simplex virus (HSV, a model system for herpesviruses, causes diseases ranging from mild skin lesions to serious encephalitis and neonatal infections. Using cryo-electron tomography and subtomogram averaging, we have characterized the structure of the prefusion conformation and fusion intermediates of HSV-1 gB. To this end, we have set up a system that generates microvesicles displaying full-length gB on their envelope. We confirmed proper folding of gB by nondenaturing electrophoresis-Western blotting with a panel of monoclonal antibodies (MAbs covering all gB domains. To elucidate the arrangement of gB domains, we labeled them by using (i mutagenesis to insert fluorescent proteins at specific positions, (ii coexpression of gB with Fabs for a neutralizing MAb with known binding sites, and (iii incubation of gB with an antibody directed against the fusion loops. Our results show that gB starts in a compact prefusion conformation with the fusion loops pointing toward the viral membrane and suggest, for the first time, a model for gB’s conformational rearrangements during fusion. These experiments further illustrate how neutralizing antibodies can interfere with the essential gB structural transitions that mediate viral entry and therefore infectivity.

  16. Kinetic intermediates en route to the final serpin-protease complex: studies of complexes of α1-protease inhibitor with trypsin.

    Science.gov (United States)

    Maddur, Ashoka A; Swanson, Richard; Izaguirre, Gonzalo; Gettins, Peter G W; Olson, Steven T

    2013-11-01

    Serpin protein protease inhibitors inactivate their target proteases through a unique mechanism in which a major serpin conformational change, resulting in a 70-Å translocation of the protease from its initial reactive center loop docking site to the opposite pole of the serpin, kinetically traps the acyl-intermediate complex. Although the initial Michaelis and final trapped acyl-intermediate complexes have been well characterized structurally, the intermediate stages involved in this remarkable transformation are not well understood. To better characterize such intermediate steps, we undertook rapid kinetic studies of the FRET and fluorescence perturbation changes of site-specific fluorophore-labeled derivatives of the serpin, α1-protease inhibitor (α1PI), which report the serpin and protease conformational changes involved in transforming the Michaelis complex to the trapped acyl-intermediate complex in reactions with trypsin. Two kinetically resolvable conformational changes were observed in the reactions, ascribable to (i) serpin reactive center loop insertion into sheet A with full protease translocation but incomplete protease distortion followed by, (ii) full conformational distortion and movement of the protease and coupled serpin conformational changes involving the F helix-sheet A interface. Kinetic studies of calcium effects on the labeled α1PI-trypsin reactions demonstrated both inactive and low activity states of the distorted protease in the final complex that were distinct from the intermediate distorted state. These studies provide new insights into the nature of the serpin and protease conformational changes involved in trapping the acyl-intermediate complex in serpin-protease reactions and support a previously proposed role for helix F in the trapping mechanism.

  17. New open conformation of SMYD3 implicates conformational selection and allostery

    Directory of Open Access Journals (Sweden)

    Nicholas Spellmon

    2016-12-01

    Full Text Available SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly “closed” substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an “open” conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD. The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation.

  18. Glutamate Induced Thermal Equilibrium Intermediate and Counteracting Effect on Chemical Denaturation of Proteins.

    Science.gov (United States)

    Anumalla, Bramhini; Prabhu, N Prakash

    2018-01-25

    When organisms are subjected to stress conditions, one of their adaptive responses is accumulation of small organic molecules called osmolytes. These osmolytes affect the structure and stability of the biological macromolecules including proteins. The present study examines the effect of a negatively charged amino acid osmolyte, glutamate (Glu), on two model proteins, ribonuclease A (RNase A) and α-lactalbumin (α-LA), which have positive and negative surface charges at pH 7, respectively. These proteins follow two-state unfolding transitions during both heat and chemical induced denaturation processes. The addition of Glu stabilizes the proteins against temperature and induces an early equilibrium intermediate during unfolding. The stability is found to be enthalpy-driven, and the free energy of stabilization is more for α-LA compared to RNase A. The decrease in the partial molar volume and compressibility of both of the proteins in the presence of Glu suggests that the proteins attain a more compact state through surface hydration which could provide a more stable conformation. This is also supported by molecule dynamic simulation studies which demonstrate that the water density around the proteins is increased upon the addition of Glu. Further, the intermediates could be completely destabilized by lower concentrations (∼0.5 M) of guanidinium chloride and salt. However, urea subverts the Glu-induced intermediate formed by α-LA, whereas it only slightly destabilizes in the case of RNase A which has a positive surface charge and could possess charge-charge interactions with Glu. This suggests that, apart from hydration, columbic interactions might also contribute to the stability of the intermediate. Gdm-induced denaturation of RNase A and α-LA in the absence and the presence of Glu at different temperatures was carried out. These results also show the Glu-induced stabilization of both of the proteins; however, all of the unfolding transitions followed two

  19. Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates.

    Science.gov (United States)

    Nemecek, Daniel; Cheng, Naiqian; Qiao, Jian; Mindich, Leonard; Steven, Alasdair C; Heymann, J Bernard

    2011-11-25

    The initial assembly product of bacteriophage ϕ6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The procapsid, a compact icosahedrally symmetric particle with deeply recessed vertices, expands to the spherical mature capsid, increasing the volume available to accommodate the genome by 2.5-fold. It has been proposed that expansion and packaging are linked, with each stage in expansion presenting a binding site for a particular RNA segment. To investigate procapsid transformability, we induced expansion by acidification, heating, and elevated salt concentration. Cryo-electron microscopy reconstructions after all three treatments yielded the same partially expanded particle. Analysis by cryo-electron tomography showed that all vertices of a given capsid were either in a compact or an expanded state, indicating a highly cooperative transition. To benchmark the mature capsid, we analyzed filled (in vivo packaged) capsids. When these particles were induced to release their RNA, they reverted to the same intermediate state as expanded procapsids (intermediate 1) or to a second, further expanded state (intermediate 2). This partial reversibility of expansion suggests that the mature spherical capsid conformation is obtained only when sufficient outward pressure is exerted by packaged RNA. The observation of two intermediates is consistent with the proposed three-step packaging process. The model is further supported by the observation that a mutant capable of packaging the second RNA segment without previously packaging the first segment has enhanced susceptibility for switching spontaneously from the procapsid to the first intermediate state. Published by Elsevier Ltd.

  20. Cryo-EM structures of two bovine adenovirus type 3 intermediates

    International Nuclear Information System (INIS)

    Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin; Xiong, Wei; Sun, Wei; Yang, Chongwen; Zhang, Kai; Wang, Ying; Liu, Hongrong; Huang, Xiaojun; Ji, Gang; Sun, Fei; Zheng, Congyi; Zhu, Ping

    2014-01-01

    Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure represents a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process

  1. Cryo-EM structures of two bovine adenovirus type 3 intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xiong, Wei [State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Luo-jia-shan, Wuhan, Hubei 430072 (China); Sun, Wei; Yang, Chongwen; Zhang, Kai; Wang, Ying [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Liu, Hongrong [College of Physics and Information Science, Hunan Normal University, Changsha, Hunan 410081 (China); Huang, Xiaojun; Ji, Gang; Sun, Fei [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Zheng, Congyi, E-mail: cctcc202@whu.edu.cn [State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Luo-jia-shan, Wuhan, Hubei 430072 (China); Zhu, Ping, E-mail: zhup@ibp.ac.cn [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-02-15

    Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure represents a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process.

  2. Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain.

    Science.gov (United States)

    Li, Jing; Rodnin, Mykola V; Ladokhin, Alexey S; Gross, Michael L

    2014-11-04

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.

  3. Hydrogen–Deuterium Exchange and Mass Spectrometry Reveal the pH-Dependent Conformational Changes of Diphtheria Toxin T Domain

    Science.gov (United States)

    2015-01-01

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our “standard condition” (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W+-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8–9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8–9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain. PMID:25290210

  4. Ab-initio vibrational properties of transition metal chalcopyrite alloys determined as high-efficiency intermediate-band photovoltaic materials

    International Nuclear Information System (INIS)

    Palacios, P.; Aguilera, I.; Wahnon, P.

    2008-01-01

    In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS 2 chalcopyrite and transition metal substituted (CuGaS 2 )M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloys showing a narrow transition metal band isolated in the semiconductor band gap. The substitutes used in the present work are the 3d metal elements, Titanium and Chromium. For the theoretical calculations we use standard density functional theory at local density and generalized gradient approximation levels. We found that the optical phonon branches of the transition metal chalcopyrite, are very sensitive to the specific bonding geometry and small changes in the transition metal environment

  5. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations.

    Science.gov (United States)

    Zhitnikova, M Y; Shestopalova, A V

    2017-11-01

    The structural adjustments of the sugar-phosphate DNA backbone (switching of the γ angle (O5'-C5'-C4'-C3') from canonical to alternative conformations and/or C2'-endo → C3'-endo transition of deoxyribose) lead to the sequence-specific changes in accessible surface area of both polar and non-polar atoms of the grooves and the polar/hydrophobic profile of the latter ones. The distribution of the minor groove electrostatic potential is likely to be changing as a result of such conformational rearrangements in sugar-phosphate DNA backbone. Our analysis of the crystal structures of the short free DNA fragments and calculation of their electrostatic potentials allowed us to determine: (1) the number of classical and alternative γ angle conformations in the free B-DNA; (2) changes in the minor groove electrostatic potential, depending on the conformation of the sugar-phosphate DNA backbone; (3) the effect of the DNA sequence on the minor groove electrostatic potential. We have demonstrated that the structural adjustments of the DNA double helix (the conformations of the sugar-phosphate backbone and the minor groove dimensions) induce changes in the distribution of the minor groove electrostatic potential and are sequence-specific. Therefore, these features of the minor groove sizes and distribution of minor groove electrostatic potential can be used as a signal for recognition of the target DNA sequence by protein in the implementation of the indirect readout mechanism.

  6. Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy.

    Science.gov (United States)

    Collauto, Alberto; DeBerg, Hannah A; Kaufmann, Royi; Zagotta, William N; Stoll, Stefan; Goldfarb, Daniella

    2017-06-14

    Ligand binding can induce significant conformational changes in proteins. The mechanism of this process couples equilibria associated with the ligand binding event and the conformational change. Here we show that by combining the application of W-band double electron-electron resonance (DEER) spectroscopy with microfluidic rapid freeze quench (μRFQ) it is possible to resolve these processes and obtain both equilibrium constants and reaction rates. We studied the conformational transition of the nitroxide labeled, isolated carboxy-terminal cyclic-nucleotide binding domain (CNBD) of the HCN2 ion channel upon binding of the ligand 3',5'-cyclic adenosine monophosphate (cAMP). Using model-based global analysis, the time-resolved data of the μRFQ DEER experiments directly provide fractional populations of the open and closed conformations as a function of time. We modeled the ligand-induced conformational change in the protein using a four-state model: apo/open (AO), apo/closed (AC), bound/open (BO), bound/closed (BC). These species interconvert according to AC + L ⇌ AO + L ⇌ BO ⇌ BC. By analyzing the concentration dependence of the relative contributions of the closed and open conformations at equilibrium, we estimated the equilibrium constants for the two conformational equilibria and the open-state ligand dissociation constant. Analysis of the time-resolved μRFQ DEER data gave estimates for the intrinsic rates of ligand binding and unbinding as well as the rates of the conformational change. This demonstrates that DEER can quantitatively resolve both the thermodynamics and the kinetics of ligand binding and the associated conformational change.

  7. Atomic cranks and levers control sugar ring conformations

    International Nuclear Information System (INIS)

    Zhang Qingmin; Lee, Gwangrog; Marszalek, Piotr E

    2005-01-01

    In this paper we review the conformational analysis of sugar rings placed under tension during mechanical manipulations of single polysaccharide molecules with the atomic force microscope and during steered molecular dynamics simulations. We examine the role of various chemical bonds and linkages between sugar rings in inhibiting or promoting their conformational transitions by means of external forces. Small differences in the orientation of one chemical bond on the sugar ring can produce significantly different mechanical properties at the polymer level as exemplified by two polysaccharides: cellulose, composed of β-1→4-linked D-glucose, and amylose, composed of α-1→4-linked D-glucose. In contrast to β-glucose rings, which are mechanically stable and produce simple entropic elasticity of the chain, α-glucose rings flip under tension from their chair to a boat-like structure and these transitions produce deviations of amylose elasticity from the freely jointed chain model. We also examine the deformation of two mechanically complementary 1→6-linked polysaccharides: pustulan, a β-1→6-linked glucan, and dextran, a α-1→6-linked glucan. Forced rotations about the C 5 -C 6 bonds govern the elasticity of pustulan, and complex conformational transitions that involve simultaneous C 5 -C 6 rotations and chair-boat transitions govern the elasticity of dextran. Finally, we discuss the likelihood of various conformational transitions in sugar rings in biological settings and speculate on their significance

  8. Low temperature characterization of the photocurrent produced by two-photon transitions in a quantum dot intermediate band solar cell

    International Nuclear Information System (INIS)

    Antolin, E.; Marti, A.; Stanley, C.R.; Farmer, C.D.; Canovas, E.; Lopez, N.; Linares, P.G.; Luque, A.

    2008-01-01

    Conceived to exceed the conversion efficiency of conventional photovoltaic devices, the intermediate band solar cell bases its operation on exploiting, besides the usual band-to-band optical transitions, the absorption of two sub-bandgap photons. For the present, the only technology used to implement an intermediate band in real devices has been the growth of an InAs/GaAs quantum dot superlattice. In practice, the obtained material shows two limitations: the narrow energy gap between conduction and intermediate band and the appearance of growth defects due to the lattice stress. The consequences are the presence of non-radiative recombination mechanisms and the thermal escape of electrons from the intermediate to the conduction band, hindering the splitting of the quasi-Fermi levels associated with the intermediate and conduction bands and the observation of photocurrent associated with the two-photon absorption. By reducing the temperature at which the devices are characterised we have suppressed the parasitic thermal mechanisms and have succeeded in measuring the photocurrent caused by the absorption of two below bandgap photons. In this work, the characterization of this photocurrent at low temperature is presented and discussed

  9. Conditions for the test emplacement of intermediate-level radioactive wastes in chamber 8a of the 511 m level of the Asse Salt Mine

    International Nuclear Information System (INIS)

    1984-01-01

    The Gesellschaft fuer Strahlen- und Umweltforschung mbH (GSF) emplaces intermediate-level radioactive wastes which accumulate in an activity involving the use of radioactive materials that is licensed or reported in the Federal Republic of Germany or which are stored on an interim basis by the appropriate licensing or inspection agencies in chamber 8a of the 511 m level of the Asse Salt Mine in Remlingen near Wolfenbuettel in conjunction with an engineering test program. The type and form of the intermediate-level wastes must conform to certain conditions so that there are no hazards to personnel and the repository during transfer and subsequent storage. It is therefore necessary for the radioactive wastes to be treated and packaged before delivery in such a way that they satisfy the conditions presented in this document. The GSF shall inform the companies and organizations delivering wastes about its experiences with emplacement operations. The Conditions for the Test Emplacement of Intermediate-Level Radioactive Wastes in Chamber 8a of the 511 m Level of the Asse Salt Mine must be adapted to conform to the latest state of science and the art. The GSF must therefore reserve the right to modify the conditions, allowing for an appropriate transition period

  10. Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate.

    Science.gov (United States)

    Chen, Yaozong; Jiang, Yiping; Guo, Zhihong

    2016-12-06

    o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation. By comparison to the ATP-bound preadenylation conformation, structural changes are identified in both the reactants and the active site to allow inference about how these changes accommodate and facilitate the adenylation reaction and to directly support an in-line backside attack nucleophilic substitution mechanism for the first half-reaction. Mutational analysis suggests that the conserved His196 plays an important role in desolvation of the active site rather than stabilizing the transition state of the adenylation reaction. In addition, comparison of the new structure with a previously determined OSB-AMP-bound structure of the same enzyme allows us to propose a release mechanism of the C domain in its alteration to form the thioesterification conformation. These findings allow us to better understand the domain alternation catalytic mechanism of MenE as well as many other adenylating enzymes.

  11. Characterization of a structural intermediate of flavivirus membrane fusion.

    Directory of Open Access Journals (Sweden)

    Karin Stiasny

    2007-02-01

    Full Text Available Viral membrane fusion proceeds through a sequence of steps that are driven by triggered conformational changes of viral envelope glycoproteins, so-called fusion proteins. Although high-resolution structural snapshots of viral fusion proteins in their prefusion and postfusion conformations are available, it has been difficult to define intermediate structures of the fusion pathway because of their transient nature. Flaviviruses possess a class II viral fusion protein (E mediating fusion at acidic pH that is converted from a dimer to a trimer with a hairpin-like structure during the fusion process. Here we show for tick-borne encephalitis virus that exposure of virions to alkaline instead of acidic pH traps the particles in an intermediate conformation in which the E dimers dissociate and interact with target membranes via the fusion peptide without proceeding to the merger of the membranes. Further treatment to low pH, however, leads to fusion, suggesting that these monomers correspond to an as-yet-elusive intermediate required to convert the prefusion dimer into the postfusion trimer. Thus, the use of nonphysiological conditions allows a dissection of the flavivirus fusion process and the identification of two separate steps, in which membrane insertion of multiple copies of E monomers precedes the formation of hairpin-like trimers. This sequence of events provides important new insights for understanding the dynamic process of viral membrane fusion.

  12. Thermodynamics of single polyethylene and polybutylene glycols with hydrogen-bonding ends: A transition from looped to open conformations

    Science.gov (United States)

    Lee, Eunsang; Paul, Wolfgang

    2018-02-01

    A variety of linear polymer precursors with hydrogen bonding motifs at both ends enable us to design supramolecular polymer systems with tailored macroscopic properties including self-healing. In this study, we investigate thermodynamic properties of single polyethylene and polybutylene glycols with hydrogen bonding motifs. In this context, we first build a coarse-grained model of building blocks of the supramolecular polymer system based on all-atom molecular structures. The density of states of the single precursor is obtained using the stochastic approximation Monte Carlo method. Constructing canonical partition functions from the density of states, we find the transition from looped to open conformations at transition temperatures which are non-monotonously changing with an increasing degree of polymerization due to the competition between chain stiffness and loop-forming entropy penalty. In the complete range of chain length under investigation, a coexistence of the looped and open morphologies at the transition temperature is shown regardless of whether the transition is first-order-like or continuous. Polyethylene and polybutylene glycols show similar behavior in all the thermodynamic properties but the transition temperature of the more flexible polybutylene glycol is shown to change more gradually.

  13. Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule.

    Science.gov (United States)

    Rosen, Laura E; Connell, Katelyn B; Marqusee, Susan

    2014-10-14

    The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates.

  14. Structure and phase transitions of monolayers of intermediate-length n-alkanes on graphite studied by neutron diffraction and molecular dynamics simulation

    Science.gov (United States)

    Diama, A.; Matthies, B.; Herwig, K. W.; Hansen, F. Y.; Criswell, L.; Mo, H.; Bai, M.; Taub, H.

    2009-08-01

    We present evidence from neutron diffraction measurements and molecular dynamics (MD) simulations of three different monolayer phases of the intermediate-length alkanes tetracosane (n-C24H50 denoted as C24) and dotriacontane (n-C32H66 denoted as C32) adsorbed on a graphite basal-plane surface. Our measurements indicate that the two monolayer films differ principally in the transition temperatures between phases. At the lowest temperatures, both C24 and C32 form a crystalline monolayer phase with a rectangular-centered (RC) structure. The two sublattices of the RC structure each consists of parallel rows of molecules in their all-trans conformation aligned with their long axis parallel to the surface and forming so-called lamellas of width approximately equal to the all-trans length of the molecule. The RC structure is uniaxially commensurate with the graphite surface in its [110] direction such that the distance between molecular rows in a lamella is 4.26 Å=√3 ag, where ag=2.46 Å is the lattice constant of the graphite basal plane. Molecules in adjacent rows of a lamella alternate in orientation between the carbon skeletal plane being parallel and perpendicular to the graphite surface. Upon heating, the crystalline monolayers transform to a "smectic" phase in which the inter-row spacing within a lamella expands by ˜10% and the molecules are predominantly oriented with the carbon skeletal plane parallel to the graphite surface. In the smectic phase, the MD simulations show evidence of broadening of the lamella boundaries as a result of molecules diffusing parallel to their long axis. At still higher temperatures, they indicate that the introduction of gauche defects into the alkane chains drives a melting transition to a monolayer fluid phase as reported previously.

  15. Conformational kinetics of aliphatic tails

    Science.gov (United States)

    Ferrarini, Alberta; Moro, Giorgio; Nordio, Pier Luigi

    The master equation describing the random walk between sites identified with the stable conformers of a chain molecule, represents the extension to the time domain of the Rotational Isomeric State model. The asymptotic analysis of the multidimensional diffusion equation in the continuous torsional variables subjected to the configurational potential, provides a rigorous justification for the discrete models, and it supplies, without resorting to phenomenological parameters, molecular definitions of the kinetic rates for the conformational transitions occurring at each segment of the chain. The coupling between the torsional variables is fully taken into account, giving rise to cooperative effects. A complete calculation of the specific correlation functions which describe the time evolution of the angular functions probed by N.M.R. and dielectric relaxation measurements, has been performed for alkyl chains attached to a massive core. The resulting behaviour has been compared with the decay of trans and gauche populations of specific bonds, expressed in terms of suitable correlation functions whose time integrals lead quite naturally to the definition of effective kinetic constants for the conformational transitions.

  16. Conformational changes in hemoglobin triggered by changing the iron charge

    International Nuclear Information System (INIS)

    Croci, S.; Achterhold, K.; Ortalli, I.; Parak, F. G.

    2008-01-01

    In this work the hemoglobin conformational changes induced by changing the iron charge have been studied and compared with Myoglobin. Moessbauer spectroscopy was used to follow the change of the iron conformation. In order to compare the conformational relaxation of hemoglobin and myoglobin, and to study a possible influence of the quaternary structure, an intermediate metastable state of hemoglobin has been created by low temperature X-ray irradiation of methemoglobin. The irradiation reduces the Fe(III) of the heme groups to Fe(II) Low Spin, where the water is still bound on the sixth coordination. Heating cycles performed at temperatures from 140 K to 200 K allow the molecules to overcome an activation energy barrier and to relax into a stable conformation such as deoxy-hemoglobin or carboxy-hemoglobin, if CO is present. Slightly different structures (conformational substates) reveal themselves as a distribution of energy barriers (ΔG). The distribution of the activation energy, for the decay of the Fe(II) Low Spin intermediate, has been fitted with a Gaussian. For comparison, published myoglobin data were re-analysed in the same way. The average energy value at characteristic temperature is very similar in case of myoglobin and hemoglobin. The larger Gaussian energy distribution for myoglobin with respect to hemoglobin shows that more conformational substates are available. This may be caused by a larger area exposed to water. In hemoglobin, part of the surface of the chains is not water accessible due to the quaternary structure.

  17. α-helix to β-hairpin transition of human amylin monomer

    Science.gov (United States)

    Singh, Sadanand; Chiu, Chi-cheng; Reddy, Allam S.; de Pablo, Juan J.

    2013-04-01

    The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a β-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the β-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the β-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a β-hairpin is an activated process and could constitute the nucleation event for fibril growth.

  18. Regularities of intermediate adsorption complex relaxation

    International Nuclear Information System (INIS)

    Manukova, L.A.

    1982-01-01

    The experimental data, characterizing the regularities of intermediate adsorption complex relaxation in the polycrystalline Mo-N 2 system at 77 K are given. The method of molecular beam has been used in the investigation. The analytical expressions of change regularity in the relaxation process of full and specific rates - of transition from intermediate state into ''non-reversible'', of desorption into the gas phase and accumUlation of the particles in the intermediate state are obtained

  19. High-pressure behavior of intermediate scapolite: compressibility, structure deformation and phase transition

    Science.gov (United States)

    Lotti, Paolo; Comboni, Davide; Merlini, Marco; Hanfland, Michael

    2018-05-01

    Scapolites are common volatile-bearing minerals in metamorphic rocks. In this study, the high-pressure behavior of an intermediate member of the scapolite solid solution series (Me47), chemical formula (Na1.86Ca1.86K0.23Fe0.01)(Al4.36Si7.64)O24[Cl0.48(CO3)0.48(SO4)0.01], has been investigated up to 17.79 GPa, by means of in situ single-crystal synchrotron X-ray diffraction. The isothermal elastic behavior of the studied scapolite has been described by a III-order Birch-Murnaghan equation of state, which provided the following refined parameters: V 0 = 1110.6(7) Å3, {K_{{V_0}}} = 70(2) GPa ({β _{{V_0}}} = 0.0143(4) GPa-1) and {K_{{V}}^' = 4.8(7). The refined bulk modulus is intermediate between those previously reported for Me17 and Me68 scapolite samples, confirming that the bulk compressibility among the solid solution increases with the Na content. A discussion on the P-induced structure deformation mechanisms of tetragonal scapolite at the atomic scale is provided, along with the implications of the reported results for the modeling of scapolite stability. In addition, a single-crystal to single-crystal phase transition, which is displacive in character, has been observed toward a triclinic polymorph at 9.87 GPa. The high-pressure triclinic polymorph was found to be stable up to the highest pressure investigated.

  20. Matrix elements of intraband transitions in quantum dot intermediate band solar cells: the influence of quantum dot presence on the extended-state electron wave-functions

    International Nuclear Information System (INIS)

    Nozawa, Tomohiro; Arakawa, Yasuhiko

    2014-01-01

    The intraband transitions which are essential for quantum dot intermediate band solar cells (QD IBSCs) are theoretically investigated by estimating the matrix elements from a ground bound state, which is often regarded as an intermediate band (IB), to conduction band (CB) states for a structure with a quantum dot (QD) embedded in a matrix (a QD/matrix structure). We have found that the QD pushes away the electron envelope functions (probability densities) from the QD region in almost all quantum states above the matrix CB minimum. As a result, the matrix elements of the intraband transitions in the QD/matrix structure are largely reduced, compared to those calculated assuming the envelope functions of free electrons (i.e., plane-wave envelope functions) in a matrix structure as the final states of the intraband transitions. The result indicates the strong influence of the QD itself on the intraband transitions from the IB to the CB states in QD IBSC devices. This work will help in better understanding the problem of the intraband transitions and give new insight, that is, engineering of quantum states is indispensable for the realization of QD IBSCs with high solar energy conversion efficiencies. (paper)

  1. Monitoring conformational dynamics with solid-state R1ρ experiments

    International Nuclear Information System (INIS)

    Quinn, Caitlin M.; McDermott, Ann E.

    2009-01-01

    A new application of solid-state rotating frame (R 1ρ ) relaxation experiments to observe conformational dynamics is presented. Studies on a model compound, dimethyl sulfone (DMS), show that R 1ρ relaxation due to reorientation of a chemical shift anisotropy (CSA) tensor undergoing chemical exchange can be used to monitor slow-to-intermediate timescale conformational exchange processes. Control experiments used d 6 -DMS and alanine to confirm that the technique is monitoring reorientation of the CSA tensor rather than dipolar interactions or methyl group rotation. The application of this method to proteins could represent a new site-specific probe of conformational dynamics

  2. From global to heavy-light: 5-point conformal blocks

    International Nuclear Information System (INIS)

    Alkalaev, Konstantin; Belavin, Vladimir

    2016-01-01

    We consider Virasoro conformal blocks in the large central charge limit. There are different regimes depending on the behavior of the conformal dimensions. The most simple regime is reduced to the global sl(2,ℂ) conformal blocks while the most complicated one is known as the classical conformal blocks. Recently, Fitzpatrick, Kaplan, and Walters showed that the two regimes are related through the intermediate stage of the so-called heavy-light semiclassical limit. We study this idea in the particular case of the 5-point conformal block. To find the 5-point global block we use the projector technique and the Casimir operator approach. Furthermore, we discuss the relation between the global and the heavy-light limits and construct the heavy-light block from the global block. In this way we reproduce our previous results for the 5-point perturbative classical block obtained by means of the monodromy method.

  3. Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Zeynab Mohammad Hosseini Naveh

    Full Text Available Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP, a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD and Temperature Accelerated Molecular Dynamics (TAMD simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.

  4. Dry molten globule intermediates and the mechanism of protein unfolding.

    Science.gov (United States)

    Baldwin, Robert L; Frieden, Carl; Rose, George D

    2010-10-01

    New experimental results show that either gain or loss of close packing can be observed as a discrete step in protein folding or unfolding reactions. This finding poses a significant challenge to the conventional two-state model of protein folding. Results of interest involve dry molten globule (DMG) intermediates, an expanded form of the protein that lacks appreciable solvent. When an unfolding protein expands to the DMG state, side chains unlock and gain conformational entropy, while liquid-like van der Waals interactions persist. Four unrelated proteins are now known to form DMGs as the first step of unfolding, suggesting that such an intermediate may well be commonplace in both folding and unfolding. Data from the literature show that peptide amide protons are protected in the DMG, indicating that backbone structure is intact despite loss of side-chain close packing. Other complementary evidence shows that secondary structure formation provides a major source of compaction during folding. In our model, the major free-energy barrier separating unfolded from native states usually occurs during the transition between the unfolded state and the DMG. The absence of close packing at this barrier provides an explanation for why phi-values, derived from a Brønsted-Leffler plot, depend primarily on structure at the mutational site and not on specific side-chain interactions. The conventional two-state folding model breaks down when there are DMG intermediates, a realization that has major implications for future experimental work on the mechanism of protein folding. 2010 Wiley-Liss, Inc.

  5. Essential role of conformational selection in ligand binding.

    Science.gov (United States)

    Vogt, Austin D; Pozzi, Nicola; Chen, Zhiwei; Di Cera, Enrico

    2014-02-01

    Two competing and mutually exclusive mechanisms of ligand recognition - conformational selection and induced fit - have dominated our interpretation of ligand binding in biological macromolecules for almost six decades. Conformational selection posits the pre-existence of multiple conformations of the macromolecule from which the ligand selects the optimal one. Induced fit, on the other hand, postulates the existence of conformational rearrangements of the original conformation into an optimal one that are induced by binding of the ligand. In the former case, conformational transitions precede the binding event; in the latter, conformational changes follow the binding step. Kineticists have used a facile criterion to distinguish between the two mechanisms based on the dependence of the rate of relaxation to equilibrium, kobs, on the ligand concentration, [L]. A value of kobs decreasing hyperbolically with [L] has been seen as diagnostic of conformational selection, while a value of kobs increasing hyperbolically with [L] has been considered diagnostic of induced fit. However, this simple conclusion is only valid under the rather unrealistic assumption of conformational transitions being much slower than binding and dissociation events. In general, induced fit only produces values of kobs that increase with [L] but conformational selection is more versatile and is associated with values of kobs that increase with, decrease with or are independent of [L]. The richer repertoire of kinetic properties of conformational selection applies to kinetic mechanisms with single or multiple saturable relaxations and explains the behavior of nearly all experimental systems reported in the literature thus far. Conformational selection is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism. On the other hand, induced fit is never necessary and

  6. Enhanced conformational sampling using enveloping distribution sampling.

    Science.gov (United States)

    Lin, Zhixiong; van Gunsteren, Wilfred F

    2013-10-14

    To lessen the problem of insufficient conformational sampling in biomolecular simulations is still a major challenge in computational biochemistry. In this article, an application of the method of enveloping distribution sampling (EDS) is proposed that addresses this challenge and its sampling efficiency is demonstrated in simulations of a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, i.e., a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix, separated by a high energy barrier. Standard MD simulations of this peptide using the GROMOS 53A6 force field did not reach convergence of the free enthalpy difference between the two helices even after 500 ns of simulation time. The use of soft-core non-bonded interactions in the centre of the peptide did enhance the number of transitions between the helices, but at the same time led to neglect of relevant helical configurations. In the simulations of a two-state EDS reference Hamiltonian that envelops both the physical peptide and the soft-core peptide, sampling of the conformational space of the physical peptide ensures that physically relevant conformations can be visited, and sampling of the conformational space of the soft-core peptide helps to enhance the transitions between the two helices. The EDS simulations sampled many more transitions between the two helices and showed much faster convergence of the relative free enthalpy of the two helices compared with the standard MD simulations with only a slightly larger computational effort to determine optimized EDS parameters. Combined with various methods to smoothen the potential energy surface, the proposed EDS application will be a powerful technique to enhance the sampling efficiency in biomolecular simulations.

  7. Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

    Directory of Open Access Journals (Sweden)

    Joseph L Baker

    2013-04-01

    Full Text Available Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon

  8. Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

    Science.gov (United States)

    Baker, Joseph L; Biais, Nicolas; Tama, Florence

    2013-04-01

    Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P) from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD) simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon stretching.

  9. Enzymatic Detoxication, Conformational Selection, and the Role of Molten Globule Active Sites*

    Science.gov (United States)

    Honaker, Matthew T.; Acchione, Mauro; Zhang, Wei; Mannervik, Bengt; Atkins, William M.

    2013-01-01

    The role of conformational ensembles in enzymatic reactions remains unclear. Discussion concerning “induced fit” versus “conformational selection” has, however, ignored detoxication enzymes, which exhibit catalytic promiscuity. These enzymes dominate drug metabolism and determine drug-drug interactions. The detoxication enzyme glutathione transferase A1–1 (GSTA1–1), exploits a molten globule-like active site to achieve remarkable catalytic promiscuity wherein the substrate-free conformational ensemble is broad with barrierless transitions between states. A quantitative index of catalytic promiscuity is used to compare engineered variants of GSTA1–1 and the catalytic promiscuity correlates strongly with characteristics of the thermodynamic partition function, for the substrate-free enzymes. Access to chemically disparate transition states is encoded by the substrate-free conformational ensemble. Pre-steady state catalytic data confirm an extension of the conformational selection model, wherein different substrates select different starting conformations. The kinetic liability of the conformational breadth is minimized by a smooth landscape. We propose that “local” molten globule behavior optimizes detoxication enzymes. PMID:23649628

  10. Towards an Approximate Conformance Relation for Hybrid I/O Automata

    Directory of Open Access Journals (Sweden)

    Morteza Mohaqeqi

    2016-12-01

    Full Text Available Several notions of conformance have been proposed for checking the behavior of cyber-physical systems against their hybrid systems models. In this paper, we explore the initial idea of a notion of approximate conformance that allows for comparison of both observable discrete actions and (sampled continuous trajectories. As such, this notion will consolidate two earlier notions, namely the notion of Hybrid Input-Output Conformance (HIOCO by M. van Osch and the notion of Hybrid Conformance by H. Abbas and G.E. Fainekos. We prove that our proposed notion of conformance satisfies a semi-transitivity property, which makes it suitable for a step-wise proof of conformance or refinement.

  11. The effect of conformational transition of gelatin-polysaccharide polyelectrolyte complex on its functional properties

    Directory of Open Access Journals (Sweden)

    Tomáš Valenta

    2017-01-01

    Full Text Available The blends of gelatin and shear-thinning hydrocolloids (guar gum, kappa-carrageenan and xanthan gum were examined to determine the effect of the conformational change on the functional properties of the solutions. The polyelectrolyte complexes of 0.5% gelatin/0.5% polysaccharide in 70 mM KCl or 70 mM NaCl were investigated by the laboratory rheometer and conductivity meter in the temperature range 25 - 45 °C. The rheological data were fitted by the power-law and Herschel-Bulkley model to obtain the flow parameters. The functional properties of the samples were substantially affected by the conformational change of the polysaccharide, as well as by the type of the hydrocolloid and salt solution. There was an evident change of viscosity and conductivity of the solutions upon heating, corresponding to the helix-coil transition of the polysaccharide at temperature about 35 °C. The type of the salt solvent had an effect on the gelation properties of the samples. Gelatin/kappa-carrageenan blend in NaCl provided a gel of high consistency at ambient temperature (20 - 25 °C, whereas the blend in KCl did not gel in the studied temperature range. The potential stability of the blends was determined by zeta-potential analysis. The low values of ζ-potential indicate that the gelatin/polysaccharide blends are electrically unstable systems which tend to coagulate. The mixtures of gelatin/polysaccharide electrostatic complexes may have a great potential in many food applications.

  12. Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Kai Wang

    Full Text Available Hierarchical organization of free energy landscape (FEL for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL, and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF. Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100 ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs.

  13. General Information for Transportation and Conformity

    Science.gov (United States)

    Transportation conformity is required by the Clean Air Act section 176(c) (42 U.S.C. 7506(c)) to ensure that federal funding and approval are given to highway and transit projects that are consistent with SIP.

  14. Conformal invariance an introduction to loops, interfaces and stochastic Loewner evolution

    CERN Document Server

    Karevski, Dragi

    2012-01-01

    Conformal invariance has been a spectacularly successful tool in advancing our understanding of the two-dimensional phase transitions found in classical systems at equilibrium. This volume sharpens our picture of the applications of conformal invariance, introducing non-local observables such as loops and interfaces before explaining how they arise in specific physical contexts. It then shows how to use conformal invariance to determine their properties. Moving on to cover key conceptual developments in conformal invariance, the book devotes much of its space to stochastic Loewner evolution (SLE), detailing SLE’s conceptual foundations as well as extensive numerical tests. The chapters then elucidate SLE’s use in geometric phase transitions such as percolation or polymer systems, paying particular attention to surface effects. As clear and accessible as it is authoritative, this publication is as suitable for non-specialist readers and graduate students alike.

  15. Optical properties of chalcopyrite-type intermediate transition metal band materials from first principles

    International Nuclear Information System (INIS)

    Aguilera, I.; Palacios, P.; Wahnon, P.

    2008-01-01

    The optical properties of a novel potential high-efficiency photovoltaic material have been studied. This material is based on a chalcopyrite-type semiconductor (CuGaS 2 ) with some Ga atom substituted by Ti and is characterized by the formation of an isolated transition-metal band between the valence band and the conduction band. We present a study in which ab-initio density functional theory calculations within the generalized gradient approximation are carried out to determine the optical reflectivity and absorption coefficient of the materials of interest. Calculations for the host semiconductor are in good agreement with experimental results within the limitations of the approach. We find, as desired, that because of the intermediate band, the new Ti-substituted material would be able to absorb photons of energy lower than the band-gap of the host chalcopyrite. We also analyze the partial contributions to the main peaks of its spectrum

  16. Control of the conformations of ion Coulomb crystals in a Penning trap

    Science.gov (United States)

    Mavadia, Sandeep; Goodwin, Joseph F.; Stutter, Graham; Bharadia, Shailen; Crick, Daniel R.; Segal, Daniel M.; Thompson, Richard C.

    2013-01-01

    Laser-cooled atomic ions form ordered structures in radiofrequency ion traps and in Penning traps. Here we demonstrate in a Penning trap the creation and manipulation of a wide variety of ion Coulomb crystals formed from small numbers of ions. The configuration can be changed from a linear string, through intermediate geometries, to a planar structure. The transition from a linear string to a zigzag geometry is observed for the first time in a Penning trap. The conformations of the crystals are set by the applied trap potential and the laser parameters, and agree with simulations. These simulations indicate that the rotation frequency of a small crystal is mainly determined by the laser parameters, independent of the number of ions and the axial confinement strength. This system has potential applications for quantum simulation, quantum information processing and tests of fundamental physics models from quantum field theory to cosmology. PMID:24096901

  17. Effects of macromolecular crowding on protein conformational changes.

    Directory of Open Access Journals (Sweden)

    Hao Dong

    2010-07-01

    Full Text Available Many protein functions can be directly linked to conformational changes. Inside cells, the equilibria and transition rates between different conformations may be affected by macromolecular crowding. We have recently developed a new approach for modeling crowding effects, which enables an atomistic representation of "test" proteins. Here this approach is applied to study how crowding affects the equilibria and transition rates between open and closed conformations of seven proteins: yeast protein disulfide isomerase (yPDI, adenylate kinase (AdK, orotidine phosphate decarboxylase (ODCase, Trp repressor (TrpR, hemoglobin, DNA beta-glucosyltransferase, and Ap(4A hydrolase. For each protein, molecular dynamics simulations of the open and closed states are separately run. Representative open and closed conformations are then used to calculate the crowding-induced changes in chemical potential for the two states. The difference in chemical-potential change between the two states finally predicts the effects of crowding on the population ratio of the two states. Crowding is found to reduce the open population to various extents. In the presence of crowders with a 15 A radius and occupying 35% of volume, the open-to-closed population ratios of yPDI, AdK, ODCase and TrpR are reduced by 79%, 78%, 62% and 55%, respectively. The reductions for the remaining three proteins are 20-44%. As expected, the four proteins experiencing the stronger crowding effects are those with larger conformational changes between open and closed states (e.g., as measured by the change in radius of gyration. Larger proteins also tend to experience stronger crowding effects than smaller ones [e.g., comparing yPDI (480 residues and TrpR (98 residues]. The potentials of mean force along the open-closed reaction coordinate of apo and ligand-bound ODCase are altered by crowding, suggesting that transition rates are also affected. These quantitative results and qualitative trends will

  18. Conformational analysis and circular dichroism of bilirubin, the yellow pigment of jaundice

    Science.gov (United States)

    Lightner, David A.; Person, Richard; Peterson, Blake; Puzicha, Gisbert; Pu, Yu-Ming; Bojadziev, Stefan

    1991-06-01

    Conformational analysis of (4Z, 15Z)-bilirubin-IX(alpha) by molecular mechanics computations reveals a global energy minimum folded conformation. Powerful added stabilization is achieved through intramolecular hydrogen bonding. Theoretical treatment of bilirubin as a molecular exciton predicts an intense bisignate circular dichroism spectrum for the folded conformation: (Delta) (epsilon) is congruent to 270 L (DOT) mole-1 (DOT) cm-1 for the $OM450 nm electronic transition(s). Synthesis of bilirubin analogs with propionic acid groups methylated at the (alpha) or (beta) position introduces an allosteric effect that allows for an optical resolution of the pigments, with enantiomers exhibiting the theoretically predicted circular dichroism.

  19. An Expression of Periodic Phenomena of Fashion on Sexual Selection Model with Conformity Genes and Memes

    Science.gov (United States)

    Mutoh, Atsuko; Tokuhara, Shinya; Kanoh, Masayoshi; Oboshi, Tamon; Kato, Shohei; Itoh, Hidenori

    It is generally thought that living things have trends in their preferences. The mechanism of occurrence of another trends in successive periods is concerned in their conformity. According to social impact theory, the minority is always exists in the group. There is a possibility that the minority make the transition to the majority by conforming agents. Because of agent's promotion of their conform actions, the majority can make the transition. We proposed an evolutionary model with both genes and memes, and elucidated the interaction between genes and memes on sexual selection. In this paper, we propose an agent model for sexual selection imported the concept of conformity. Using this model we try an environment where male agents and female agents are existed, we find that periodic phenomena of fashion are expressed. And we report the influence of conformity and differentiation on the transition of their preferences.

  20. Intermediate coupling collision strengths from LS coupled R-matrix elements

    International Nuclear Information System (INIS)

    Clark, R.E.H.

    1978-01-01

    Fine structure collision strength for transitions between two groups of states in intermediate coupling and with inclusion of configuration mixing are obtained from LS coupled reactance matrix elements (R-matrix elements) and a set of mixing coefficients. The LS coupled R-matrix elements are transformed to pair coupling using Wigner 6-j coefficients. From these pair coupled R-matrix elements together with a set of mixing coefficients, R-matrix elements are obtained which include the intermediate coupling and configuration mixing effects. Finally, from the latter R-matrix elements, collision strengths for fine structure transitions are computed (with inclusion of both intermediate coupling and configuration mixing). (Auth.)

  1. Compact conformations of human protein disulfide isomerase.

    Directory of Open Access Journals (Sweden)

    Shang Yang

    Full Text Available Protein disulfide isomerase (PDI composed of four thioredoxin-like domains a, b, b', and a', is a key enzyme catalyzing oxidative protein folding in the endoplasmic reticulum. Large scale molecular dynamics simulations starting from the crystal structures of human PDI (hPDI in the oxidized and reduced states were performed. The results indicate that hPDI adopts more compact conformations in solution than in the crystal structures, which are stabilized primarily by inter-domain interactions, including the salt bridges between domains a and b' observed for the first time. A prominent feature of the compact conformations is that the two catalytic domains a and a' can locate close enough for intra-molecular electron transfer, which was confirmed by the characterization of an intermediate with a disulfide between the two domains. Mutations, which disrupt the inter-domain interactions, lead to decreased reductase activity of hPDI. Our molecular dynamics simulations and biochemical experiments reveal the intrinsic conformational dynamics of hPDI and its biological impact.

  2. Cooperative structural transitions in amyloid-like aggregation

    Science.gov (United States)

    Steckmann, Timothy; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

    2017-04-01

    Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's, and others. Although proteins that undergo aggregation vary widely in their primary structure, they all produce a cross-β motif with the proteins in β-strand conformations perpendicular to the fibril axis. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. To better understand the molecular basis of the protein structural transitions and aggregation, we report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain H-bonds during aggregation into amyloid fibrils. For our MD simulations, we found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. This temperature dependence allows us to investigate the dynamics on a molecular level. We report on the thermodynamics and cooperativity of the transformations. The structural transitions that occurred in a specific temperature window for ccβ in our investigations may also occur in other amyloid forming proteins but with biochemical parameters controlling the dynamics rather than temperature.

  3. A surprising role for conformational entropy in protein function

    Science.gov (United States)

    Wand, A. Joshua; Moorman, Veronica R.; Harpole, Kyle W.

    2014-01-01

    Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a grand challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to experimentally access is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned and what the future may hold for this emerging view of protein function. PMID:23478875

  4. Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

    Science.gov (United States)

    Kim, Do-Nyun; Altschuler, Josiah; Strong, Campbell; McGill, Gaël; Bathe, Mark

    2011-01-01

    The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function.

  5. Molecular dynamics studies of the conformation of sorbitol

    Science.gov (United States)

    Lerbret, A.; Mason, P.E.; Venable, R.M.; Cesàro, A.; Saboungi, M.-L.; Pastor, R.W.; Brady, J.W.

    2009-01-01

    Molecular dynamics simulations of a 3 m aqueous solution of D-sorbitol (also called D-glucitol) have been performed at 300 K, as well as at two elevated temperatures to promote conformational transitions. In principle, sorbitol is more flexible than glucose since it does not contain a constraining ring. However, a conformational analysis revealed that the sorbitol chain remains extended in solution, in contrast to the bent conformation found experimentally in the crystalline form. While there are 243 staggered conformations of the backbone possible for this open-chain polyol, only a very limited number were found to be stable in the simulations. Although many conformers were briefly sampled, only eight were significantly populated in the simulation. The carbon backbones of all but two of these eight conformers were completely extended, unlike the bent crystal conformation. These extended conformers were stabilized by a quite persistent intramolecular hydrogen bond between the hydroxyl groups of carbon C-2 and C-4. The conformational populations were found to be in good agreement with the limited available NMR data except for the C-2–C-3 torsion (spanned by the O-2–O-4 hydrogen bond), where the NMR data supports a more bent structure. PMID:19744646

  6. Conformational effects in photoelectron circular dichroism

    Science.gov (United States)

    Turchini, S.

    2017-12-01

    Photoelectron circular dichroism (PECD) is a novel type of spectroscopy, which presents surprising sensitivity to conformational effects in chiral systems. While classical photoelectron spectroscopy mainly responds to conformational effects in terms of energy level shifts, PECD provides a rich and detailed response to tiny changes in electronic and structural properties by means of the intensity dispersion of the circular dichroism as a function of photoelectron kinetic energy. In this work, the basics of PECD will be outlined, emphasizing the role of interference from the l,l+/- 1 outgoing partial wave of the photoelectron in the PECD transition matrix element, which is responsible for the extreme sensitivity to conformational effects. Examples using molecular systems and interfaces will shed light on the powerful application of PECD to classical conformational effects such as group substitution, isomerism, conformer population and clustering. Moreover, the PECD results will be reported in challenging new fields where conformations play a key role, such as vibrational effects, transient chirality and time- resolved experiments. To date, PECD has mostly been based on synchrotron radiation facilities, but it also has a future as a table-top lab experiment by means of multiphoton ionization. An important application of PECD as an analytical tool will be reported. The aim of this review is to illustrate that in PECD, the presence of conformational effects is essential for understanding a wide range of effects from a new perspective, making it different from classical spectroscopy.

  7. Conformal Nets II: Conformal Blocks

    Science.gov (United States)

    Bartels, Arthur; Douglas, Christopher L.; Henriques, André

    2017-08-01

    Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

  8. Molecular dynamics simulations of conformation changes of HIV-1 regulatory protein on graphene

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Daohui; Li, Libo; He, Daohang; Zhou, Jian, E-mail: jianzhou@scut.edu.cn

    2016-07-30

    Graphical abstract: Preferential adsorption of Vpr13-33 on graphene accompanied by early conformational change from α-helix to β-sheet structures was observed by molecular simulations. This work presents the molecular mechanism of graphene-induced peptide conformational alteration and sheds light on developing graphene-based materials to inhibit HIV. - Highlights: • Graphene induced early structural transition of Vpr13-33 is studied by MD simulations. • Both π-π stacking and hydrophobic interactions orchestrate the peptide adsorption. • Vpr has an increased propensity of β-sheet content on graphene surface. • To develop graphene-based materials to inhibit HIV is possible. - Abstract: The fragment of viral protein R (Vpr), Vpr13-33, plays an important role in regulating nuclear importing of HIV genes through channel formation in which it adopts a leucine-zipper-like alpha-helical conformation. A recent experimental study reported that helical Vpr13-33 would transform to β-sheet or random coil structures and aggregate on the surface of graphene or graphene oxide through hydrophobic interactions. Due to experimental limitations, however, there is still a considerable lack of understanding on the adsorption dynamics at the early stage of the conformational transition at water-graphene interface and the underlying driving force at molecular level. In this study, atomistic molecular dynamics simulations were used to explore the conformation transition phenomena. Vpr13-33 kept α-helical structure in solution, but changed to β-sheet structure when strongly adsorbed onto graphene. Preferential adsorption of Vpr13-33 on graphene is dominated by hydrophobic interactions. The cluster analysis identified the most significant populated conformation and the early stage of structure conversion from α-helical to β-sheet was found, but the full β-sheet propagation was not observed. Free energy landscape analysis further complemented the transformation analysis of

  9. Molecular dynamics simulations of conformation changes of HIV-1 regulatory protein on graphene

    International Nuclear Information System (INIS)

    Zhao, Daohui; Li, Libo; He, Daohang; Zhou, Jian

    2016-01-01

    Graphical abstract: Preferential adsorption of Vpr13-33 on graphene accompanied by early conformational change from α-helix to β-sheet structures was observed by molecular simulations. This work presents the molecular mechanism of graphene-induced peptide conformational alteration and sheds light on developing graphene-based materials to inhibit HIV. - Highlights: • Graphene induced early structural transition of Vpr13-33 is studied by MD simulations. • Both π-π stacking and hydrophobic interactions orchestrate the peptide adsorption. • Vpr has an increased propensity of β-sheet content on graphene surface. • To develop graphene-based materials to inhibit HIV is possible. - Abstract: The fragment of viral protein R (Vpr), Vpr13-33, plays an important role in regulating nuclear importing of HIV genes through channel formation in which it adopts a leucine-zipper-like alpha-helical conformation. A recent experimental study reported that helical Vpr13-33 would transform to β-sheet or random coil structures and aggregate on the surface of graphene or graphene oxide through hydrophobic interactions. Due to experimental limitations, however, there is still a considerable lack of understanding on the adsorption dynamics at the early stage of the conformational transition at water-graphene interface and the underlying driving force at molecular level. In this study, atomistic molecular dynamics simulations were used to explore the conformation transition phenomena. Vpr13-33 kept α-helical structure in solution, but changed to β-sheet structure when strongly adsorbed onto graphene. Preferential adsorption of Vpr13-33 on graphene is dominated by hydrophobic interactions. The cluster analysis identified the most significant populated conformation and the early stage of structure conversion from α-helical to β-sheet was found, but the full β-sheet propagation was not observed. Free energy landscape analysis further complemented the transformation analysis of

  10. ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

    Science.gov (United States)

    Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

    2018-05-08

    Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  11. Can Morphing Methods Predict Intermediate Structures?

    Science.gov (United States)

    Weiss, Dahlia R.; Levitt, Michael

    2009-01-01

    Movement is crucial to the biological function of many proteins, yet crystallographic structures of proteins can give us only a static snapshot. The protein dynamics that are important to biological function often happen on a timescale that is unattainable through detailed simulation methods such as molecular dynamics as they often involve crossing high-energy barriers. To address this coarse-grained motion, several methods have been implemented as web servers in which a set of coordinates is usually linearly interpolated from an initial crystallographic structure to a final crystallographic structure. We present a new morphing method that does not extrapolate linearly and can therefore go around high-energy barriers and which can produce different trajectories between the same two starting points. In this work, we evaluate our method and other established coarse-grained methods according to an objective measure: how close a coarse-grained dynamics method comes to a crystallographically determined intermediate structure when calculating a trajectory between the initial and final crystal protein structure. We test this with a set of five proteins with at least three crystallographically determined on-pathway high-resolution intermediate structures from the Protein Data Bank. For simple hinging motions involving a small conformational change, segmentation of the protein into two rigid sections outperforms other more computationally involved methods. However, large-scale conformational change is best addressed using a nonlinear approach and we suggest that there is merit in further developing such methods. PMID:18996395

  12. Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser-Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations.

    Science.gov (United States)

    Najbauer, Eszter E; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

    2015-08-20

    The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, six conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-life of (3.7 ± 0.5) × 10(3) s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser-induced conversions revealed that the excitation of the stretching overtone of both the side chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations.

  13. Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis

    Science.gov (United States)

    Suo, Zucai

    2014-01-01

    Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme commonly used for DNA amplification in PCR. However, little has been done to characterize the motions of other structural domains of Taq Pol or any other DNA polymerase during catalysis. Here, we used stopped-flow Förster resonance energy transfer (FRET) to investigate the conformational dynamics of all five structural domains of the full-length Taq Pol relative to the DNA substrate during nucleotide binding and incorporation. Our study provides evidence for a rapid conformational change step induced by dNTP binding and a subsequent global conformational transition involving all domains of Taq Pol during catalysis. Additionally, our study shows that the rate of the global transition was greatly increased with the truncated form of Taq Pol lacking the N-terminal domain. Finally, we utilized a mutant of Taq Pol containing a de novo disulfide bond to demonstrate that limiting protein conformational flexibility greatly reduced the polymerization activity of Taq Pol. PMID:24931550

  14. Perturbation formalism for the complex poles and widths of the transition matrix with an application to intermediate structure phenomena

    International Nuclear Information System (INIS)

    Perez, R.B.; de Saussure, G.; Olsen, D.K.; Difilippo, F.C.

    1978-01-01

    The complex poles and widths of the transition T matrix are determined by the trajectory equations which consist of a set of first order nonlinear differential equations. A hierarchy of approximate solutions to the trajectory equations is developed by iterative methods. The results of this formalism are compared with exact solutions for the case of some strongly interacting pairs of resonances in two iron isotopes. In the presence of intermediate structure the average neutron reaction cross section is interpreted in terms of a resonant strength function which exhibits peaks at neutron energies corresponding to ''doorways'' levels

  15. Conformational Stability of the NH2-Terminal Propeptide of the Precursor of Pulmonary Surfactant Protein SP-B.

    Directory of Open Access Journals (Sweden)

    Ángeles Bañares-Hidalgo

    Full Text Available Assembly of pulmonary surfactant lipid-protein complexes depends on conformational changes coupled with proteolytic maturation of proSP-B, the precursor of pulmonary surfactant protein B (SP-B, along the surfactant biogenesis pathway in pneumocytes. Conformational destabilization of the N-terminal propeptide of proSP-B (SP-BN triggers exposure of the mature SP-B domain for insertion into surfactant lipids. We have studied the conformational stability during GdmCl- or urea-promoted unfolding of SP-BN with trp fluorescence and circular dichroism spectroscopies. Binding of the intermediate states to bis-ANS suggests their molten globule-like character. ΔG0H2O was ~ 12.7 kJ·mol-1 either with urea or GdmCl. None of the thermal transitions of SP-BN detected by CD correspond to protein unfolding. Differential scanning calorimetry of SP-BN evidenced two endothermic peaks involved in oligomer dissociation as confirmed with 2 M urea. Ionic strength was relevant since at 150 mM NaCl, the process originating the endotherm at the highest temperature was irreversible (Tm2 = 108.5°C with an activation energy of 703.8 kJ·mol-1. At 500 mM NaCl the process became reversible (Tm2 = 114.4°C and data were fitted to the Non-two States model with two subpeaks. No free thiols in the propeptide could be titrated by DTNB with or without 5.7 M GdmCl, indicating disulfide bonds establishment.

  16. Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations

    Science.gov (United States)

    Najbauer, Eszter E.; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

    2018-01-01

    The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, 6 conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-live of (3.7±0.5)·103 s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser induced conversions revealed that the excitation of the stretching overtone of both the side-chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations. PMID:26201050

  17. Conformational Diffusion and Helix Formation Kinetics

    International Nuclear Information System (INIS)

    Hummer, Gerhard; Garcia, Angel E.; Garde, Shekhar

    2000-01-01

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society

  18. Conformational Diffusion and Helix Formation Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, Gerhard [Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States); Garcia, Angel E. [Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Garde, Shekhar [Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180 (United States)

    2000-09-18

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society.

  19. Quantum-chemical calculation of energies and spectral characteristics of conformers in derivatives of phenylphosphine

    International Nuclear Information System (INIS)

    Chuvashev, D.D.; Ratovskii, G.V.; Zakzhevskii, V.G.

    1987-01-01

    The phenylphosphines PhPX 2 calculated by the MNDO method are characterized by two potential minima corresponding to the bisector and gonal conformations. For X = Cl, F, and C=N the bisector conformer predominates considerably, but for X = H and CH 3 the populations of the conformers are approximately the same. The characteristics of the electron transitions of the conformers found, determined by the CNDO/S method, differ substantially, which makes it possible to analyze the conformational compositions of arylphosphines by means of UV spectroscopy. In excited ππ* states the gonal conformation is characterized by a substantial donor effect of the PX 2 group, whereas the bisector conformation gives a certain acceptor effect

  20. MicroRNA Cluster miR-17-92 Regulates Neural Stem Cell Expansion and Transition to Intermediate Progenitors in the Developing Mouse Neocortex

    Directory of Open Access Journals (Sweden)

    Shan Bian

    2013-05-01

    Full Text Available During development of the embryonic neocortex, tightly regulated expansion of neural stem cells (NSCs and their transition to intermediate progenitors (IPs are critical for normal cortical formation and function. Molecular mechanisms that regulate NSC expansion and transition remain unclear. Here, we demonstrate that the microRNA (miRNA miR-17-92 cluster is required for maintaining proper populations of cortical radial glial cells (RGCs and IPs through repression of Pten and Tbr2 protein. Knockout of miR-17-92 and its paralogs specifically in the developing neocortex restricts NSC proliferation, suppresses RGC expansion, and promotes transition of RGCs to IPs. Moreover, Pten and Tbr2 protectors specifically block silencing activities of endogenous miR-17-92 and control proper numbers of RGCs and IPs in vivo. Our results demonstrate a critical role for miRNAs in promoting NSC proliferation and modulating the cell-fate decision of generating distinct neural progenitors in the developing neocortex.

  1. Investigation of light-induced conformation changes in spiropyran-modified succinylated poly(L-lysine).

    Science.gov (United States)

    Cooper, T M; Stone, M O; Natarajan, L V; Crane, R L

    1995-08-01

    To determine the maximum range of coupling between side-chain photochromism and polypeptide conformation change, we modified the carboxylate side chains of succinylated poly(L-lysine) with a spiropyran to form polypeptide I. The extent of modification was determined to be 35.5%. The spacer group length between the polypeptide alpha-carbon and the dye was 12 atoms, providing minimum polypeptide-dye interaction. Conformation changes were monitored by circular dichroism as a function of light adaptation and solvent composition (hexafluoroisopropanol [HFIP] vs trifluoroethanol [TFE]). Under all solvent compositions, the dark-adapted dye was in the merocyanine form. Light adaptation by visible light converted the dye to the spiropyran form. When dissolved in TFE, I adopted a helical conformation insensitive to light adaptation. With increasing percentage HFIP, a solvent-induced helix-to-coil transition was observed around 80% (vol/vol) HFIP. At 100% HFIP, both light- and dark-adapted forms of I were in the coil state. Near the midpoint of the solvent-induced helix-to-coil transition, light adaptation caused conformation changes. Applying helix-to-coil transition theory, we measured a statistically significant difference in coil segment-HFIP binding constant for light- vs dark-adapted solutions (6.38 +/- 0.03 M-1 vs 6.56 +/- 0.03 M-1), but not for the nucleation parameter sigma (1.2 +/- 0.4 10(-3) vs 1.3 +/- 0.3 x 10(-3). The small binding constant difference translated to a light-induced binding energy difference of 17 cal/mol/monomer. Near the midpoint of the helix-to-coil transition, collective interactions between monomer units made possible the translation of a small energy difference (less than RT) into large macromolecular conformation changes.(ABSTRACT TRUNCATED AT 250 WORDS)

  2. Comments on intermediate-scale models

    International Nuclear Information System (INIS)

    Ellis, J.; Enqvist, K.; Nanopoulos, D.V.; Olive, K.

    1987-01-01

    Some superstring-inspired models employ intermediate scales m I of gauge symmetry breaking. Such scales should exceed 10 16 GeV in order to avoid prima facie problems with baryon decay through heavy particles and non-perturbative behaviour of the gauge couplings above m I . However, the intermediate-scale phase transition does not occur until the temperature of the Universe falls below O(m W ), after which an enormous excess of entropy is generated. Moreover, gauge symmetry breaking by renormalization group-improved radiative corrections is inapplicable because the symmetry-breaking field has not renormalizable interactions at scales below m I . We also comment on the danger of baryon and lepton number violation in the effective low-energy theory. (orig.)

  3. Escherichia coli Phosphoenolpyruvate Dependent Phosphotransferase System. NMR Studies of the Conformation of HPr and P-HPr and the Mechanism of Energy Coupling

    NARCIS (Netherlands)

    Dooijewaard, G.; Roossien, F.F.; Robillard, G.T.

    1979-01-01

    1H and 31P nuclear magnetic resonance investigations of the phosphoprotein intermediate P-HPr and the parent molecule HPr of the E. coli phosphoenolpyruvate dependent phosphotransferase system (PTS) show that HPr can exist in two conformations. These conformations influence the protonation state of

  4. On the stability of rotational discontinuities and intermediate shocks

    International Nuclear Information System (INIS)

    Lee, L.C.; Huang, L.; Chao, J.K.

    1989-01-01

    The stability of rotational discontinuities and intermediate shocks is studied based on a hybrid simulation code. The simulation results show that rotational discontinuities are stable and intermediate shocks are not stationary. Intermediate shocks tend to evolve to rotational discontinuities and waves. The authors employ several different initial profiles for the magnetic field in the transition region and find that the final structure of the discontinuities or shocks is not sensitive to the initial magnetic field profile. The present results are different from those obtained from the resistive MHD simulations. Furthermore, their study indicates that the kinetic effect of particles plays an important role in the structure and stability of rotational discontinuities and intermediate shocks

  5. Low temperature intermediate band metallic behavior in Ti implanted Si

    Energy Technology Data Exchange (ETDEWEB)

    Olea, Javier, E-mail: oleaariza@fis.ucm.es; Pastor, David; Garcia-Hemme, Eric; Garcia-Hernansanz, Rodrigo; Prado, Alvaro del; Martil, Ignacio; Gonzalez-Diaz, German

    2012-08-31

    Si samples implanted with very high Ti doses and subjected to Pulsed-Laser Melting (PLM) have been electrically analyzed in the scope of a two-layer model previously reported based on the Intermediate Band (IB) theory. Conductivity and Hall effect measurements using the van der Pauw technique suggest that the insulator-metal transition takes place for implantation doses in the 10{sup 14}-10{sup 16} cm{sup -2} range. Results of the sample implanted with the 10{sup 16} cm{sup -2} dose show a metallic behavior at low temperature that is explained by the formation of a p-type IB out of the Ti deep levels. This suggests that the IB would be semi-filled, which is essential for IB photovoltaic devices. - Highlights: Black-Right-Pointing-Pointer We fabricated high dose Ti implanted Si samples for intermediate band research. Black-Right-Pointing-Pointer We measured the electronic transport properties in the 7-300 K range. Black-Right-Pointing-Pointer We show an insulator to metallic transition when the intermediate band is formed. Black-Right-Pointing-Pointer The intermediate band is semi-filled and populated by holes. Black-Right-Pointing-Pointer We satisfactorily explain the electrical behavior by an intermediate band model.

  6. Poly (3, 4-ethylendioxithiophene) (PEDOT) oxidation: activation energy and conformational energy

    International Nuclear Information System (INIS)

    Otero, T F; Romero, M C

    2008-01-01

    The oxidation kinetics of films of the conducting polymer PEDOT-C1O4 after electrochemical reduction by polarization at increasing cathodic potential was studied by potential steps. The response i/t presents a maximum at intermediate oxidation times. At the maximum the reaction occurs under chemical kinetic control following the expected current variations from the Chemical and Electrochemical Kinetics, when reactant concentrations or temperatures are changed. The obtained activation energy of the oxidation present two ranges as a function of the cathodic potential of prepolarization: constant values after prepolarization at low cathodic potentials and a lineal variation after prepolarization at increasing high cathodic potentials. According with the conformational relaxation model during electrochemical reduction the polymer shrinks, closes and packs the conformational structure. The activation energy for the subsequent oxidation includes two terms: the constant chemical activation energy and the conformational energy required to relax the packed polymeric structure. The conformational energy only appears after prepolarization at more cathodic potentials than the closing potential where more packed conformations were obtained. The conformational activation energy accounts the energetic requirements to relax and unfold the polymeric chains generating the required free volume to lodge balancing counterions; meanwhile the chemical activation energy accounts the energetic requirements for the electrochemical reaction to occur.

  7. Carrier behavior in special multilayer device composed of different transition metal oxide-based intermediate connectors

    International Nuclear Information System (INIS)

    Deng, Yan-Hong; Chen, Xiang-Yu; Ou, Qing-Dong; Wang, Qian-Kun; Jiang, Xiao-Cheng; Zhang, Dan-Dan; Li, Yan-Qing

    2014-01-01

    The impact of illumination on the connection part of the tandem organic light-emitting diodes was studied by using a special organic multilayer sample consisted of two organic active layers coupled with different transition metal oxide (TMO)-based intermediate connectors (ICs). Through measuring the current density-voltage characteristic, interfacial electronic structures, and capacitance-voltage characteristic, we observe an unsymmetrical phenomenon in current density-voltage and capacitance-voltage curves of Mg:Alq 3 /MoO 3 and MoO 3 composed devices, which was induced by the charge spouting zone near the ICs region and the recombination state in the MoO 3 layer. Moreover, Mg:Alq 3 /MoO 3 composed device displays a photovoltaic effect and the V oc shifts to forward bias under illumination. Our results demonstrate that the TMO-based IC structure coupled with photovoltaic effect can be a good approach for the study of photodetector, light sensor, and so on.

  8. Future possibilities with intermediate-energy neutron beams

    International Nuclear Information System (INIS)

    Brady, F.P.

    1987-01-01

    Future possibilities for using neutrons of intermediate energies (50 - 200 MeV) as a probe of the nucleus are discussed. Some of the recent thinking concerning a systematic approach for studying elastic and inelastic scattering of electrons and hadrons and the important role of medium- and intermediate-energy neutrons in such a programme is reviewed. The advantages of neutrons in this energy range over neutrons with lower energies and over intermediate-energy pions for determining nuclear-transition and ground state densities, and for distinguishing proton from neutron density (isovector sensitivity), are noted. The important role of (n,p) charge exchange reactions in nuclear excitation studies is also reviewed. Experimental methods for utilizing neutrons as probes in elastic, inelastic, and charge exchange studies at these energies are discussed

  9. Phase Transitions for Flat Anti - de Sitter Black Holes

    International Nuclear Information System (INIS)

    Surya, Sumati; Schleich, Kristin; Witt, Donald M.

    2001-01-01

    We reexamine the thermodynamics of anti - de Sitter (adS) black holes with Ricci flat horizons using the adS soliton as the thermal background. We find that there is a phase transition which is dependent not only on the temperature but also on the black hole area, which is an independent parameter. As in the spherical adS black hole, this phase transition is related via the adS/conformal-field-theory correspondence to a confinement-deconfinement transition in the large-N gauge theory on the conformal boundary at infinity

  10. Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations.

    Science.gov (United States)

    Brás, Natércia F; Fernandes, Pedro A; Ramos, Maria J; Schwartz, Steven D

    2018-02-06

    Human α-phosphoglucomutase 1 (α-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) through two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in the gluconeogenesis raises the glucose output levels, α-PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human α-PGM. We performed transition-path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties. Our calculations revealed that both steps proceed through a concerted S N 2-like mechanism, with a loose metaphosphate-like TS. Even though experimental data suggests that the two steps are identical, we observed noticeable differences: 1) the transition state ensemble has a well-defined TS region and a late TS for the second step, and 2) larger coordinated protein motions are required to reach the TS of the second step. We have identified key residues (Arg23, Ser117, His118, Lys389), and the Mg 2+ ion that contribute in different ways to the reaction coordinate. Accelerated molecular dynamics simulations suggest that the G16P intermediate may reorient without leaving the enzymatic binding pocket, through significant conformational rearrangements of the G16P and of specific loop regions of the human α-PGM. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Perspective: Spectroscopy and kinetics of small gaseous Criegee intermediates

    International Nuclear Information System (INIS)

    Lee, Yuan-Pern

    2015-01-01

    The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH 2 OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O 2 , with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH 2 OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH 2 I + O 2 , which is critical to laboratory studies of CH 2 OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO 2 , SO 2 , water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH 3 CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research

  12. Comments on intermediate-scale models

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, J.; Enqvist, K.; Nanopoulos, D.V.; Olive, K.

    1987-04-23

    Some superstring-inspired models employ intermediate scales m/sub I/ of gauge symmetry breaking. Such scales should exceed 10/sup 16/ GeV in order to avoid prima facie problems with baryon decay through heavy particles and non-perturbative behaviour of the gauge couplings above m/sub I/. However, the intermediate-scale phase transition does not occur until the temperature of the Universe falls below O(m/sub W/), after which an enormous excess of entropy is generated. Moreover, gauge symmetry breaking by renormalization group-improved radiative corrections is inapplicable because the symmetry-breaking field has not renormalizable interactions at scales below m/sub I/. We also comment on the danger of baryon and lepton number violation in the effective low-energy theory.

  13. Comparison of static conformal field with multiple noncoplanar arc techniques for stereotactic radiosurgery or stereotactic radiotherapy

    International Nuclear Information System (INIS)

    Hamilton, Russell J.; Kuchnir, Franca T.; Sweeney, Patrick; Rubin, Steven J.; Dujovny, Manuel; Pelizzari, Charles A.; Chen, George T. Y.

    1995-01-01

    Purpose: Compare the use of static conformal fields with the use of multiple noncoplanar arcs for stereotactic radiosurgery or stereotactic radiotherapy treatment of intracranial lesions. Evaluate the efficacy of these treatment techniques to deliver dose distributions comparable to those considered acceptable in current radiotherapy practice. Methods and Materials: A previously treated radiosurgery case of a patient presenting with an irregularly shaped intracranial lesion was selected. Using a three-dimensional (3D) treatment-planning system, treatment plans using a single isocenter multiple noncoplanar arc technique and multiple noncoplanar conformal static fields were generated. Isodose distributions and dose volume histograms (DVHs) were computed for each treatment plan. We required that the 80% (of maximum dose) isodose surface enclose the target volume for all treatment plans. The prescription isodose was set equal to the minimum target isodose. The DVHs were analyzed to evaluate and compare the different treatment plans. Results: The dose distribution in the target volume becomes more uniform as the number of conformal fields increases. The volume of normal tissue receiving low doses (> 10% of prescription isodose) increases as the number of static fields increases. The single isocenter multiple arc plan treats the greatest volume of normal tissue to low doses, approximately 1.6 times more volume than that treated by four static fields. The volume of normal tissue receiving high (> 90% of prescription isodose) and intermediate (> 50% of prescription isodose) doses decreases by 29 and 22%, respectively, as the number of static fields is increased from four to eight. Increasing the number of static fields to 12 only further reduces the high and intermediate dose volumes by 10 and 6%, respectively. The volume receiving the prescription dose is more than 3.5 times larger than the target volume for all treatment plans. Conclusions: Use of a multiple noncoplanar

  14. Holographic multiverse and conformal invariance

    Energy Technology Data Exchange (ETDEWEB)

    Garriga, Jaume [Departament de Física Fonamental i Institut de Ciències del Cosmos, Universitat de Barcelona, Martí i Franquès 1, 08193 Barcelona (Spain); Vilenkin, Alexander, E-mail: jaume.garriga@ub.edu, E-mail: vilenkin@cosmos.phy.tufts.edu [Institute of Cosmology, Department of Physics and Astronomy, Tufts University, 212 College Ave., Medford, MA 02155 (United States)

    2009-11-01

    We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV.

  15. Holographic multiverse and conformal invariance

    International Nuclear Information System (INIS)

    Garriga, Jaume; Vilenkin, Alexander

    2009-01-01

    We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV

  16. A new fundamental type of conformational isomerism

    Science.gov (United States)

    Canfield, Peter J.; Blake, Iain M.; Cai, Zheng-Li; Luck, Ian J.; Krausz, Elmars; Kobayashi, Rika; Reimers, Jeffrey R.; Crossley, Maxwell J.

    2018-06-01

    Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term `akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

  17. Conformal field theory in conformal space

    International Nuclear Information System (INIS)

    Preitschopf, C.R.; Vasiliev, M.A.

    1999-01-01

    We present a new framework for a Lagrangian description of conformal field theories in various dimensions based on a local version of d + 2-dimensional conformal space. The results include a true gauge theory of conformal gravity in d = (1, 3) and any standard matter coupled to it. An important feature is the automatic derivation of the conformal gravity constraints, which are necessary for the analysis of the matter systems

  18. Conformational transitions and interactions underlying the function of membrane embedded receptor protein kinases.

    Science.gov (United States)

    Bocharov, Eduard V; Sharonov, Georgy V; Bocharova, Olga V; Pavlov, Konstantin V

    2017-09-01

    Among membrane receptors, the single-span receptor protein kinases occupy a broad but specific functional niche determined by distinctive features of the underlying transmembrane signaling mechanisms that are briefly overviewed on the basis of some of the most representative examples, followed by a more detailed discussion of several hierarchical levels of organization and interactions involved. All these levels, including single-molecule interactions (e.g., dimerization, liganding, chemical modifications), local processes (e.g. lipid membrane perturbations, cytoskeletal interactions), and larger scale phenomena (e.g., effects of membrane surface shape or electrochemical potential gradients) appear to be closely integrated to achieve the observed diversity of the receptor functioning. Different species of receptor protein kinases meet their specific functional demands through different structural features defining their responses to stimulation, but certain common patterns exist. Signaling by receptor protein kinases is typically associated with the receptor dimerization and clustering, ligand-induced rearrangements of receptor domains through allosteric conformational transitions with involvement of lipids, release of the sequestered lipids, restriction of receptor diffusion, cytoskeleton and membrane shape remodeling. Understanding of complexity and continuity of the signaling processes can help identifying currently neglected opportunities for influencing the receptor signaling with potential therapeutic implications. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Low-Mode Conformational Search Method with Semiempirical Quantum Mechanical Calculations: Application to Enantioselective Organocatalysis.

    Science.gov (United States)

    Kamachi, Takashi; Yoshizawa, Kazunari

    2016-02-22

    A conformational search program for finding low-energy conformations of large noncovalent complexes has been developed. A quantitatively reliable semiempirical quantum mechanical PM6-DH+ method, which is able to accurately describe noncovalent interactions at a low computational cost, was employed in contrast to conventional conformational search programs in which molecular mechanical methods are usually adopted. Our approach is based on the low-mode method whereby an initial structure is perturbed along one of its low-mode eigenvectors to generate new conformations. This method was applied to determine the most stable conformation of transition state for enantioselective alkylation by the Maruoka and cinchona alkaloid catalysts and Hantzsch ester hydrogenation of imines by chiral phosphoric acid. Besides successfully reproducing the previously reported most stable DFT conformations, the conformational search with the semiempirical quantum mechanical calculations newly discovered a more stable conformation at a low computational cost.

  20. Tribological Behavior of Oil-Lubricated Laser Textured Steel Surfaces in Conformal Flat and Non-Conformal Contacts

    Energy Technology Data Exchange (ETDEWEB)

    Kovalchenko, A. M. [Inst. for Problems of Materials Science, Dept. 7, 3 Krzhizhanovsky Street, Kyiv 03142, UA (Corresponding author), e-mail: andrii.kovalchenko@gatech.edu; Erdemir, A. [Argonne National Lab., Energy Systems Division, 9700 South Cass Avenue, Argonne, IL 60439 US; Ajayi, O. O. [Argonne National Lab., Energy Systems Division, 9700 South Cass Avenue, Argonne, IL 60439 US; Etsion, I. [Technion-Israel Inst. of Technology, Dept. of Mechanical Engineering, Haifa 32000, IL

    2017-01-30

    Changing the surface texture of sliding surfaces is an effective way to manipulate friction and wear of lubricated surfaces. Having realized its potential, we have done very extensive studies on the effects of laser surface texturing (LST, which involves the creation of an array of microdimples on a surface) on friction and wear behavior of oil-lubricated steel surfaces in the early 2000s. In this paper, we reviewed some of our research accomplishments and assessed future directions of the laser texturing field in many diverse industrial applications. Our studies specifically addressed the impact of laser texturing on friction and wear of both the flat conformal and initial non-conformal point contact configurations using a pin-on-disk test rig under fully-flooded synthetic oil lubricants with different viscosities. Electrical resistance measurement between pin and LST disks was also used to determine the operating lubrication regimes in relation to friction. In conformal contact, we confirmed that LST could significantly expand the operating conditions for hydrodynamic lubrication to significantly much higher loads and slower speeds. In particular, with LST and higher viscosity oils, the low-friction full hydrodynamic regime was shifted to the far left in the Stribeck diagram. Overall, the beneficial effects of laser surface texturing were more pronounced at higher speeds and loads and with higher viscosity oil. LST was also observed to reduce the magnitude of friction coefficients in the boundary regime. For the non-conformal contact configuration, we determined that LST would produce more abrasive wear on the rubbing counterface compared to the untreated surfaces due to a reduction in lubricant fluid film thickness, as well as the highly uneven and rough nature of the textured surfaces. However, this higher initial wear rate has led to faster generation of a conformal contact, and thus transition from the high-friction boundary to lower friction mixed

  1. Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices

    Science.gov (United States)

    Galak, Jeff; Gray, Kurt; Elbert, Igor; Strohminger, Nina

    2016-01-01

    How much do our choices represent stable inner preferences versus social conformity? We examine conformity and consistency in sartorial choices surrounding a common life event of new norm exposure: relocation. A large-scale dataset of individual purchases of women’s shoes (16,236 transactions) across five years and 2,007 women reveals a balance of conformity and consistency, moderated by changes in location socioeconomic status. Women conform to new local norms (i.e., average heel size) when moving to relatively higher status locations, but mostly ignore new local norms when moving to relatively lower status locations. In short, at periods of transition, it is the fashion norms of the rich that trickle down to consumers. These analyses provide the first naturalistic large-scale demonstration of the tension between psychological conformity and consistency, with real decisions in a highly visible context. PMID:27144595

  2. Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices.

    Directory of Open Access Journals (Sweden)

    Jeff Galak

    Full Text Available How much do our choices represent stable inner preferences versus social conformity? We examine conformity and consistency in sartorial choices surrounding a common life event of new norm exposure: relocation. A large-scale dataset of individual purchases of women's shoes (16,236 transactions across five years and 2,007 women reveals a balance of conformity and consistency, moderated by changes in location socioeconomic status. Women conform to new local norms (i.e., average heel size when moving to relatively higher status locations, but mostly ignore new local norms when moving to relatively lower status locations. In short, at periods of transition, it is the fashion norms of the rich that trickle down to consumers. These analyses provide the first naturalistic large-scale demonstration of the tension between psychological conformity and consistency, with real decisions in a highly visible context.

  3. Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices.

    Science.gov (United States)

    Galak, Jeff; Gray, Kurt; Elbert, Igor; Strohminger, Nina

    2016-01-01

    How much do our choices represent stable inner preferences versus social conformity? We examine conformity and consistency in sartorial choices surrounding a common life event of new norm exposure: relocation. A large-scale dataset of individual purchases of women's shoes (16,236 transactions) across five years and 2,007 women reveals a balance of conformity and consistency, moderated by changes in location socioeconomic status. Women conform to new local norms (i.e., average heel size) when moving to relatively higher status locations, but mostly ignore new local norms when moving to relatively lower status locations. In short, at periods of transition, it is the fashion norms of the rich that trickle down to consumers. These analyses provide the first naturalistic large-scale demonstration of the tension between psychological conformity and consistency, with real decisions in a highly visible context.

  4. Polarization control of intermediate state absorption in resonance-mediated multi-photon absorption process

    International Nuclear Information System (INIS)

    Xu, Shuwu; Yao, Yunhua; Jia, Tianqing; Ding, Jingxin; Zhang, Shian; Sun, Zhenrong; Huang, Yunxia

    2015-01-01

    We theoretically and experimentally demonstrate the control of the intermediate state absorption in an (n + m) resonance-mediated multi-photon absorption process by the polarization-modulated femtosecond laser pulse. An analytical solution of the intermediate state absorption in a resonance-mediated multi-photon absorption process is obtained based on the time-dependent perturbation theory. Our theoretical results show that the control efficiency of the intermediate state absorption by the polarization modulation is independent of the laser intensity when the transition from the intermediate state to the final state is coupled by the single-photon absorption, but will be affected by the laser intensity when this transition is coupled by the non-resonant multi-photon absorption. These theoretical results are experimentally confirmed via a two-photon fluorescence control in (2 + 1) resonance-mediated three-photon absorption of Coumarin 480 dye and a single-photon fluorescence control in (1 + 2) resonance-mediated three-photon absorption of IR 125 dye. (paper)

  5. Prediction of the transition energies of atomic No and Lr by the intermediate Hamiltonian coupled cluster method

    International Nuclear Information System (INIS)

    Borschevsky, A.; Eliav, E.; Kaldor, U.; Vilkas, M.J.; Ishikawa, Y.

    2007-01-01

    Complete text of publication follows: Measurements of the spectroscopic properties of the superheavy elements present a serious challenge to the experimentalist. Their short lifetimes and the low quantities of their production necessitate reliable prediction of transition energies to avoid the need for broad wavelength scans and to assist in identifying the lines. Thus, reliable high-accuracy calculations are necessary prior and parallel to experimental research. Nobelium and Lawrencium are at present the two most likely candidates for spectroscopic measurements, with the first experiments planned at GSI, Darmstadt. The intermediate Hamiltonian (IH) coupled cluster method is applied to the ionization potentials, electron affinities, and excitation energies of atomic nobelium and lawrencium. Large basis sets are used (37s31p26d21f16g11h6i). All levels of a particular atom are obtained simultaneously by diagonalizing the IH matrix. The matrix elements correspond to all excitations from correlated occupied orbitals to virtual orbitals in a large P space, and are 'dressed' by folding in excitations to higher virtual orbitals (Q space) at the coupled cluster singles-and-doubles level. Lamb-shift corrections are included. The same approach was applied to the lighter homologues of Lr and No, lutetium and ytterbium, for which many transition energies are experimentally known, in order to assess the accuracy of the calculation. The average absolute error of 20 excitation energies of Lu is 423 cm -1 , and the error limits for Lr are therefore put at 700 cm -1 . Predicted Lr excitations with large transition moments in the prime range for the planned experiment, 20,000-30,000 cm -1 , are 7p → 8s at 20,100 cm -1 and 7p →p 7d at 28,100 cm -1 . In case of Yb, the calculated ionization potential was within 20 cm -1 of the experiment, and the average error of the 20 lowest calculated excitations was about 300 cm -1 . Hence, the error limits of nobelium are set to 800 cm -1

  6. Millimeter and Submillimeter Wave Spectroscopy of Higher Energy Conformers of 1,2-PROPANEDIOL

    Science.gov (United States)

    Zakharenko, Olena; Bossa, Jean-Baptiste; Lewen, Frank; Schlemmer, Stephan; Müller, Holger S. P.

    2017-06-01

    We have performed a study of the millimeter/submillimeter wave spectrum of four higher energy conformers of 1,2-propanediol (continuation of the previous study on the three lowest energy conformers. The present analysis of rotational transitions carried out in the frequency range 38 - 400 GHz represents a significant extension of previous microwave work. The new data were combined with previously-measured microwave transitions and fitted using a Watson's S-reduced Hamiltonian. The final fits were within experimental accuracy, and included spectroscopic parameters up to sixth order of angular momentum, for the ground states of the four higher energy conformers following previously studied ones: g'Ga, gG'g', aGg' and g'Gg. The present analysis provides reliable frequency predictions for astrophysical detection of 1,2-propanediol by radio telescope arrays at millimeter wavelengths. J.-B. Bossa, M.H. Ordu, H.S.P. Müller, F. Lewen, S. Schlemmer, A&A 570 (2014) A12)

  7. Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.

    Directory of Open Access Journals (Sweden)

    Vasyl V Mykuliak

    2018-04-01

    Full Text Available Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

  8. Conformational changes in DNA gyrase revealed by limited proteolysis

    DEFF Research Database (Denmark)

    Kampranis, S C; Maxwell, A

    1998-01-01

    We have used limited proteolysis to identify conformational changes in DNA gyrase. Gyrase exhibits a proteolytic fingerprint dominated by two fragments, one of approximately 62 kDa, deriving from the A protein, and another of approximately 25 kDa from the B protein. Quinolone binding to the enzyme......-DNA intermediate by calcium ions does not reveal any protection, suggesting that the quinolone-induced conformational change is different from an "open-gate" state of the enzyme. A quinolone-resistant mutant of gyrase fails to give the characteristic quinolone-associated proteolytic signature. The ATP...... does not prevent dimerization since incubation of the enzyme-DNA complex with both ADPNP and quinolones gives rise to a complex whose proteolytic pattern retains the characteristic signature of dimerization but has lost the quinolone-induced protection. As a result, the quinolone-gyrase complex can...

  9. Structure of a low-population intermediate state in the release of an enzyme product.

    Science.gov (United States)

    De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

    2015-01-09

    Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

  10. Toward TeV Conformality

    International Nuclear Information System (INIS)

    Appelquist, T.; Fleming, G. T.; Neil, E. T.; Avakian, A.; Babich, R.; Brower, R. C.; Cohen, S. D.; Rebbi, C.; Schaich, D.; Cheng, M.; Vranas, P.; Clark, M. A.; Kiskis, J.; Osborn, J. C.

    2010-01-01

    We study the chiral properties of an SU(3) gauge theory with N f massless Dirac fermions in the fundamental representation when N f is increased from 2 to 6. For N f =2, our lattice simulations lead to a value of /F 3 , where F is the Nambu-Goldstone-boson decay constant and is the chiral condensate, which agrees with the measured QCD value. For N f =6, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as N f increases further, toward the critical value for transition from confinement to infrared conformality.

  11. Engineering polyelectrolyte multilayer structure at the nanometer length scale by tuning polymer solution conformation.

    Science.gov (United States)

    Boddohi, Soheil; Killingsworth, Christopher; Kipper, Matt

    2008-03-01

    Chitosan (a weak polycation) and heparin (a strong polyanion) are used to make polyelectrolyte multilayers (PEM). PEM thickness and composition are determined as a function of solution pH (4.6 to 5.8) and ionic strength (0.1 to 0.5 M). Over this range, increasing pH increases the PEM thickness; however, the sensitivity to changes in pH is a strong function of ionic strength. The PEM thickness data are correlated to the polymer conformation in solution. Polyelectrolyte conformation in solution is characterized by gel permeation chromatography (GPC). The highest sensitivity of PEM structure to pH is obtained at intermediate ionic strength. Different interactions govern the conformation and adsorption phenomena at low and high ionic strength, leading to reduced sensitivity to solution pH at extreme ionic strengths. The correspondence between PEM thickness and polymer solution conformation offers opportunities to tune polymer thin film structure at the nanometer length scale by controlling simple, reproducible processing conditions.

  12. Synthesis of Α-azido-oximes from chiral cyclo-hexanones. Conformation monitoring by NMR

    International Nuclear Information System (INIS)

    Alves, R.J.; Fontes Prado, M.A.; Oliveira, A.B. de; Souza Filho, J.D. de; GArcia, J.I.; Olesker, A.; Lukacs, G.

    1993-01-01

    Carbon hydrates are the greatest source of chirality due to a large number of functional groups. Such compounds present preferential conformations, which result in reactions which high level of stereo-selectivity. This work is concerned to the preparation of intermediates to several other synthesis of biological interest and how the above mentioned properties influence these synthesis

  13. Quantum Chemical Investigation of the Transition States and Intermediates for the Reaction of the Nitrosonium Ion with the Pentaammineazidocobalt(III) Ion.

    Science.gov (United States)

    Rotzinger, François P

    2016-12-19

    The water exchange reaction on Co(NH 3 ) 5 OH 2 3+ was investigated with various density functionals and basis sets. A Gibbs activation energy (ΔG ⧧ ) agreeing with experiment was obtained with the long-range-corrected functionals ωB97X-D3 and LC-BOP-LRD, SMD hydration, and modified Karlsruhe def2-TZVP basis sets. This computational technique was then applied to the reaction of NO + with Co(NH 3 ) 5 N 3 2+ . All of the possible pathways were investigated, NO + attack at the terminal N of Co(NH 3 ) 5 N 3 2+ via the E and the Z isomers of the transition states, and NO + attack at the bound N of azide, also via both isomers. The most favorable pathway proceeds via the attack at the bound N via the Z isomer. This leads to the intermediate with an oxatetrazole ligand bound to Co(III) at the N in the 3-position, Co(NH 3 ) 5 (cycl-N 4 O) 3+ , which undergoes N 2 elimination to yield the Co(NH 3 ) 5 N 2 O 3+ intermediate. The subsequent substitution of N 2 O by water follows the I d mechanism with retention of the configuration. No evidence for the existence of the square-pyramidal pentacoordinated intermediate Co(NH 3 ) 5 3+ was found. All of the investigated intermediates, Co(NH 3 ) 5 N 2 3+ , Co(NH 3 ) 5 [E-N(N 2 )(NO)] 3+ , Co(NH 3 ) 5 (E-ON 4 ) 3+ , Co(NH 3 ) 5 ON 2 3+ , Co(NH 3 ) 5 (cycl-N 4 O) 3+ , and Co(NH 3 ) 5 N 2 O 3+ , exhibit short lifetimes of less than ∼60 μs and react via the I d mechanism.

  14. Conformational elasticity can facilitate TALE-DNA recognition.

    Science.gov (United States)

    Lei, Hongxing; Sun, Jiya; Baldwin, Enoch P; Segal, David J; Duan, Yong

    2014-01-01

    Sequence-programmable transcription activator-like effector (TALE) proteins have emerged as a highly efficient tool for genome engineering. Recent crystal structures depict a transition between an open unbound solenoid and more compact DNA-bound solenoid formed by the 34 amino acid repeats. How TALEs switch conformation between these two forms without substantial energetic compensation, and how the repeat-variable di-residues (RVDs) discriminate between the cognate base and other bases still remain unclear. Computational analysis on these two aspects of TALE-DNA interaction mechanism has been conducted in order to achieve a better understanding of the energetics. High elasticity was observed in the molecular dynamics simulations of DNA-free TALE structure that started from the bound conformation where it sampled a wide range of conformations including the experimentally determined apo and bound conformations. This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding. To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson-Boltzmann surface area (PBSA) and other approaches. The PBSA calculations indicated that the native RVD-base structures had lower binding free energy than mismatched structures for most of the RVDs examined. Our theoretical analyses provided new insight on the dynamics and energetics of TALE-DNA binding mechanism. © 2014 Elsevier Inc. All rights reserved.

  15. Probing Protein Multidimensional Conformational Fluctuations by Single-Molecule Multiparameter Photon Stamping Spectroscopy

    Science.gov (United States)

    2015-01-01

    Conformational motions of proteins are highly dynamic and intrinsically complex. To capture the temporal and spatial complexity of conformational motions and further to understand their roles in protein functions, an attempt is made to probe multidimensional conformational dynamics of proteins besides the typical one-dimensional FRET coordinate or the projected conformational motions on the one-dimensional FRET coordinate. T4 lysozyme hinge-bending motions between two domains along α-helix have been probed by single-molecule FRET. Nevertheless, the domain motions of T4 lysozyme are rather complex involving multiple coupled nuclear coordinates and most likely contain motions besides hinge-bending. It is highly likely that the multiple dimensional protein conformational motions beyond the typical enzymatic hinged-bending motions have profound impact on overall enzymatic functions. In this report, we have developed a single-molecule multiparameter photon stamping spectroscopy integrating fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic approach enables simultaneous observations of both FRET-related site-to-site conformational dynamics and molecular rotational (or orientational) motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have further observed wide-distributed rotational flexibility along orientation coordinates by recording fluorescence anisotropy and simultaneously identified multiple intermediate conformational states along FRET coordinate by monitoring time-dependent donor lifetime, presenting a whole picture of multidimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending enzymatic turnover motions under enzymatic reaction conditions. By analyzing the autocorrelation functions of both lifetime and anisotropy trajectories, we have also observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional conformational fluctuation dynamics, providing a fundamental

  16. Conformational inversion-topomerization mechanism of ethylcyclohexyl isomers and its role in combustion kinetics

    KAUST Repository

    Bian, Huiting

    2016-07-26

    With the "strain-free" cyclic structure, cyclohexane and alkyl cyclohexanes (and their radicals) have various conformers (e.g. chair, boat, and twist etc.) by pseudorotation of the alkyl ring. Noting that different conformers will undergo different types of H-migration reactions, the mechanism of conformational change may impact the distribution of cyclohexyl and the branched cyclohexyl radical isomers during cyclohexane and alkyl cyclohexanes combustion. Consequently, it will influence the formation of subsequent decomposition products. In this work, the conformational inversion-topomerization mechanism and H-migration reactions for six ethylcyclohexyl radical isomers were systematically studied by ab initio calculations and the transition state theory. The updated sub-mechanism of these conformational changes is incorporated into an ethylcyclohexane pyrolysis model. By comparing the simulated results of the "complete" model including the sub-mechanism of conformational changes and the simplified model ignoring these processes, the effect of inversion-topomerization mechanism on the relative concentrations of various ethylcyclohexyl radicals and the formation of subsequent decomposition products were revealed. © 2016.

  17. Glycine Perturbs Local and Global Conformational Flexibility of a Transmembrane Helix

    DEFF Research Database (Denmark)

    Högel, Philipp; Götz, Alexander; Kuhne, Felix

    2018-01-01

    Flexible transmembrane helices frequently support the conformational transitions between different functional states of membrane proteins. While proline is well known to distort and destabilize transmembrane helices, the role of glycine is still debated. Here, we systematically investigated the e...

  18. Dynamical Symmetries and Causality in Non-Equilibrium Phase Transitions

    Directory of Open Access Journals (Sweden)

    Malte Henkel

    2015-11-01

    Full Text Available Dynamical symmetries are of considerable importance in elucidating the complex behaviour of strongly interacting systems with many degrees of freedom. Paradigmatic examples are cooperative phenomena as they arise in phase transitions, where conformal invariance has led to enormous progress in equilibrium phase transitions, especially in two dimensions. Non-equilibrium phase transitions can arise in much larger portions of the parameter space than equilibrium phase transitions. The state of the art of recent attempts to generalise conformal invariance to a new generic symmetry, taking into account the different scaling behaviour of space and time, will be reviewed. Particular attention will be given to the causality properties as they follow for co-variant n-point functions. These are important for the physical identification of n-point functions as responses or correlators.

  19. Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

    International Nuclear Information System (INIS)

    Ovchinnikov, Victor; Karplus, Martin

    2014-01-01

    A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes

  20. Restricted conformal invariance in QCD and its predictive power for virtual two-photon processes

    CERN Document Server

    Müller, D

    1998-01-01

    The conformal algebra provides powerful constraints, which guarantee that renormalized conformally covariant operators exist in the hypothetical conformal limit of the theory, where the $\\beta$-function vanishes. Thus, in this limit also the conformally covariant operator product expansion on the light cone holds true. This operator product expansion has predictive power for two-photon processes in the generalized Bjorken region. Only the Wilson coefficients and the anomalous dimensions that are known from deep inelastic scattering are required for the prediction of all other two-photon processes in terms of the process-dependent off-diagonal expectation values of conformal operators. It is checked that the next-to-leading order calculations for the flavour non-singlet meson transition form factors are consistent with the corrections to the corresponding Wilson coefficients in deep inelasitic scattering.

  1. Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

    Science.gov (United States)

    Sullivan, David C; Lim, Carmay

    2006-08-24

    Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.

  2. About the structure of quantum intermediate state of superconductors

    International Nuclear Information System (INIS)

    Ledenev, O.P.

    2008-01-01

    The calculation of spatial structure of a quantum intermediate state in Type I superconductors is completed. Theoretical model of thermodynamics of considered state was proposed by Andreev. It is shown, that in a quantum case, the period of structure appears significantly smaller and has different dependence on both the magnetic field and temperature than in the classical intermediate Landau state. The decrease of thickness of normal layers results in increase of characteristic distance between the quantum Andreev levels of electronic excitations, and the transition to the quantum intermediate from classical state is realized at higher temperatures ∼1 K, than it was supposed in previous works. The comparison of calculation data with experimental results, for example using the sample of mono-crystal gallium, is conducted

  3. Direct observation of unimolecular decay of CH{sub 3}CH{sub 2}CHOO Criegee intermediates to OH radical products

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Yi; Liu, Fang; Lester, Marsha I., E-mail: milester@sas.upenn.edu [Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 (United States); Klippenstein, Stephen J. [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2016-07-28

    The unimolecular decay of carbonyl oxide intermediates, known as Criegee intermediates, produced in alkene ozonolysis is a significant source of OH radicals in the troposphere. Here, the rate of appearance of OH radical products is examined directly in the time-domain for a prototypical alkyl-substituted Criegee intermediate, CH{sub 3}CH{sub 2}CHOO, following vibrational activation under collision-free conditions. Complementary statistical Rice–Ramsperger–Kassel–Marcus calculations of the microcanonical unimolecular decay rate for CH{sub 3}CH{sub 2}CHOO are also carried out at energies in the vicinity of the barrier for 1,4 hydrogen atom transfer that leads to OH products. Tunneling through the barrier, derived from high level electronic structure calculations, contributes significantly to the decay rate. Infrared transitions of CH{sub 3}CH{sub 2}CHOO are identified in the CH stretch overtone region, which are detected by ultraviolet laser-induced fluorescence of the resultant OH products. The features observed are attributed to CH vibrational excitations and conformational forms utilizing insights from theory. Both experiment and theory yield unimolecular decay rates for CH{sub 3}CH{sub 2}CHOO of ca. 10{sup 7} s{sup −1}, which are slower than those obtained for syn-CH{sub 3}CHOO or (CH{sub 3}){sub 2}COO reported previously [Fang et al., J. Chem. Phys. 144, 061102 (2016)] at similar energies. Master equation modeling is also utilized to predict the thermal decay rate of CH{sub 3}CH{sub 2}CHOO under atmospheric conditions, giving a rate of 279 s{sup −1} at 298 K.

  4. Single Molecule Cluster Analysis Identifies Signature Dynamic Conformations along the Splicing Pathway

    Science.gov (United States)

    Blanco, Mario R.; Martin, Joshua S.; Kahlscheuer, Matthew L.; Krishnan, Ramya; Abelson, John; Laederach, Alain; Walter, Nils G.

    2016-01-01

    The spliceosome is the dynamic RNA-protein machine responsible for faithfully splicing introns from precursor messenger RNAs (pre-mRNAs). Many of the dynamic processes required for the proper assembly, catalytic activation, and disassembly of the spliceosome as it acts on its pre-mRNA substrate remain poorly understood, a challenge that persists for many biomolecular machines. Here, we developed a fluorescence-based Single Molecule Cluster Analysis (SiMCAn) tool to dissect the manifold conformational dynamics of a pre-mRNA through the splicing cycle. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified a conformation adopted late in splicing by a 3′ splice site mutant, invoking a mechanism for substrate proofreading. SiMCAn presents a novel framework for interpreting complex single molecule behaviors that should prove widely useful for the comprehensive analysis of a plethora of dynamic cellular machines. PMID:26414013

  5. Solution conformation of 2-aminopurine dinucleotide determined by ultraviolet two-dimensional fluorescence spectroscopy

    International Nuclear Information System (INIS)

    Widom, Julia R; Marcus, Andrew H; Johnson, Neil P; Von Hippel, Peter H

    2013-01-01

    We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analogue of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS)—a fluorescence-detected variation of 2D electronic spectroscopy—to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point–dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R 12 = 3.5 ± 0.5 Å , twist angle θ 12 = 5° ± 5° ), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV–2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein–nucleic acid complexes. (paper)

  6. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    International Nuclear Information System (INIS)

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

    2015-01-01

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH 2 OO and anti/syn-CH 3 C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH 2 OO and anti-CH 3 C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH 3 C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH 3 C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH 3 group by the terminal O atom producing CH 2 C(H)O–OH. At 298 K, the intramolecular insertion process in CH 2 OO was found to be 600 times faster than the commonly assumed ring-closing reaction

  7. Conformational dependence of a protein kinase phosphate transfer reaction

    Science.gov (United States)

    Labute, Montiago; Henkelman, Graeme; Tung, Chang-Shung; Fenimore, Paul; McMahon, Ben

    2007-03-01

    Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase have been calculated using plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. Our results demonstrate that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site [1]. [1] G.H. Henkelman, M.X. LaBute, C.-S. Tung, P.W. Fenimore, B.H. McMahon, Proc. Natl. Acad. Sci. USA vol. 102, no. 43:15347-15351 (2005).

  8. Theoretical Kinetic Study of the Formic Acid Catalyzed Criegee Intermediate Isomerization: Multistructural Anharmonicity and Atmospheric Implications

    KAUST Repository

    Monge Palacios, Manuel

    2018-01-29

    We performed a theoretical study on the double hydrogen shift isomerization reaction of a six carbon atom Criegee intermediate (C6-CI), catalyzed by formic acid (HCOOH), to produce vinylhydroperoxide (VHP), C6-CI+HCOOH→VHP+HCOOH. This Criegee intermediate can serve as a surrogate for larger CIs derived from important volatile organic compounds like monoterpenes, whose reactivity is not well understood and are difficult to handle computationally. The reactant HCOOH exerts a pronounced catalytic effect on the studied reaction by lowering the barrier height, but the kinetic enhancement is hindered by the multistructural anharmonicity. First, the rigid ring-structure adopted by the saddle point to facilitate simultaneous transfer of two atoms does not allow formation of as many conformers as those formed by the reactant C6-CI. And second, the flexible carbon chain of C6-CI facilitates the formation of stabilizing intramolecular C–H···O hydrogen bonds; this stabilizing effect is less pronounced in the saddle point structure due to its tightness and steric effects. Thus, the contribution of the reactant C6-CI conformers to the multistructural partition function is larger than that of the saddle point conformers. The resulting low multistructural anharmonicity factor partially cancels out the catalytic effect of the carboxylic acid, yielding in a moderately large rate coefficient, k(298 K) = 4.9·10-13 cm3 molecule-1 s-1. We show that carboxylic acids may promote the conversion of stabilized Criegee intermediates into vinylhydroperoxides in the atmosphere, which generates OH radicals and leads to secondary organic aerosol, thereby affecting the oxidative capacity of the atmosphere and ultimately the climate.

  9. MORPH-PRO: a novel algorithm and web server for protein morphing.

    Science.gov (United States)

    Castellana, Natalie E; Lushnikov, Andrey; Rotkiewicz, Piotr; Sefcovic, Natasha; Pevzner, Pavel A; Godzik, Adam; Vyatkina, Kira

    2013-07-11

    Proteins are known to be dynamic in nature, changing from one conformation to another while performing vital cellular tasks. It is important to understand these movements in order to better understand protein function. At the same time, experimental techniques provide us with only single snapshots of the whole ensemble of available conformations. Computational protein morphing provides a visualization of a protein structure transitioning from one conformation to another by producing a series of intermediate conformations. We present a novel, efficient morphing algorithm, Morph-Pro based on linear interpolation. We also show that apart from visualization, morphing can be used to provide plausible intermediate structures. We test this by using the intermediate structures of a c-Jun N-terminal kinase (JNK1) conformational change in a virtual docking experiment. The structures are shown to dock with higher score to known JNK1-binding ligands than structures solved using X-Ray crystallography. This experiment demonstrates the potential applications of the intermediate structures in modeling or virtual screening efforts. Visualization of protein conformational changes is important for characterization of protein function. Furthermore, the intermediate structures produced by our algorithm are good approximations to true structures. We believe there is great potential for these computationally predicted structures in protein-ligand docking experiments and virtual screening. The Morph-Pro web server can be accessed at http://morph-pro.bioinf.spbau.ru.

  10. Conformational stability analyses of alpha subunit I domain of LFA-1 and Mac-1.

    Directory of Open Access Journals (Sweden)

    Debin Mao

    Full Text Available β₂ integrin of lymphocyte function-associated antigen-1 (LFA-1 or macrophage-1 antigen (Mac-1 binds to their common ligand of intercellular adhesion molecule-1 (ICAM-1 and mediates leukocyte-endothelial cell (EC adhesions in inflammation cascade. Although the two integrins are known to have distinct functions, the corresponding micro-structural bases remain unclear. Here (steered-molecular dynamics simulations were employed to elucidate the conformational stability of α subunit I domains of LFA-1 and Mac-1 in different affinity states and relevant I domain-ICAM-1 interaction features. Compared with low affinity (LA Mac-1, the LA LFA-1 I domain was unstable in the presence or absence of ICAM-1 ligand, stemming from diverse orientations of its α₇-helix with different motifs of zipper-like hydrophobic junction between α₁- and α₇-helices. Meanwhile, spontaneous transition of LFA-1 I domain from LA state to intermediate affinity (IA state was first visualized. All the LA, IA, and high affinity (HA states of LFA-1 I domain and HA Mac-1 I domain were able to bind to ICAM-1 ligand effectively, while LA Mac-1 I domain was unfavorable for binding ligand presumably due to the specific orientation of S144 side-chain that capped the MIDAS ion. These results furthered our understanding in correlating the structural bases with their functions of LFA-1 and Mac-1 integrins from the viewpoint of I domain conformational stability and of the characteristics of I domain-ICAM-1 interactions.

  11. Workers’ Conformism

    Directory of Open Access Journals (Sweden)

    Nikolay Ivantchev

    2013-10-01

    Full Text Available Conformism was studied among 46 workers with different kinds of occupations by means of two modified scales measuring conformity by Santor, Messervey, and Kusumakar (2000 – scale for perceived peer pressure and scale for conformism in antisocial situations. The hypothesis of the study that workers’ conformism is expressed in a medium degree was confirmed partly. More than a half of the workers conform in a medium degree for taking risk, and for the use of alcohol and drugs, and for sexual relationships. More than a half of the respondents conform in a small degree for anti-social activities (like a theft. The workers were more inclined to conform for risk taking (10.9%, then – for the use of alcohol, drugs and for sexual relationships (8.7%, and in the lowest degree – for anti-social activities (6.5%. The workers who were inclined for the use of alcohol and drugs tended also to conform for anti-social activities.

  12. Conformational explosion: Understanding the complexity of short chain para-dialkylbenzene potential energy surfaces

    Science.gov (United States)

    Mishra, Piyush; Hewett, Daniel M.; Zwier, Timothy S.

    2018-05-01

    The single-conformation ultraviolet and infrared spectroscopy of three short-chain para-dialkylbenzenes (para-diethylbenzene, para-dipropylbenzene, and para-dibutylbenzene) is reported for the jet-cooled, isolated molecules. The present study builds off previous work on single-chain n-alkylbenzenes, where an anharmonic local mode Hamiltonian method was developed to account for stretch-bend Fermi resonance in the alkyl CH stretch region [D. P. Tabor et al., J. Chem. Phys. 144, 224310 (2016)]. The jet-cooled molecules are interrogated using laser-induced fluorescence (LIF) excitation, fluorescence dip infrared spectroscopy, and dispersed fluorescence. The LIF spectra in the S1 ← S0 origin region show a dramatic increase in the number of resolved transitions with increasing length of the alkyl chains, reflecting an explosion in the number of unique low-energy conformations formed when two independent alkyl chains are present. Since the barriers to isomerization of the alkyl chain are similar in size, this results in an "egg carton" shaped potential energy surface. A combination of electronic frequency shift and alkyl CH stretch infrared spectra is used to generate a consistent set of conformational assignments. Using these experimental techniques in conjunction with computational methods, subsets of origin transitions in the LIF excitation spectrum can be classified into different conformational families. Two conformations are resolved in para-diethylbenzene, seven in para-dipropylbenzene, and about nineteen in para-dibutylbenzene. These chains are largely independent of each other as there are no new single-chain conformations induced by the presence of a second chain. A cursory LIF excitation scan of para-dioctylbenzene shows a broad congested spectrum at frequencies consistent with interactions of alkyl chains with the phenyl π cloud.

  13. Conformations of cationized linear oligosaccharides revealed by FTMS combined with in-ESI H/D exchange.

    Science.gov (United States)

    Kostyukevich, Yury; Kononikhin, Alexey; Popov, Igor; Nikolaev, Eugene

    2015-10-01

    Previously (Kostyukevich et al. Anal Chem 2014, 86, 2595), we have reported that oligosaccharides anions are produced in the electrospray in two different conformations, which differ by the rate of gas phase hydrogen/deuterium (H/D) exchange reaction. In the present paper, we apply the in-electrospray ionization (ESI) source H/D exchange approach for the investigation of the oligosaccharides cations formed by attaching of metal ions (Na, K) to the molecule. It was observed that the formation of different conformers can be manipulated by varying the temperature of the desolvating capillary of the ESI interphase. Separation of the conformers was performed using gas phase H/D approach. Because the conformers have different rates of the H/D exchange reaction, the deuterium distribution spectrum becomes bimodal. It was found that the conformation corresponding to the slow H/D exchange rate dominates in the spectrum when the capillary temperature is low (~200 °C), and the conformation corresponding to the fast H/D exchange rate dominates at high (~400 °C) temperatures. In the intermediate temperature region, two conformers are present simultaneously. It was also observed that large oligosaccharide requires higher temperature for the formation of another conformer. It was found that the presence of the conformers considerably depends on the solvent used for ESI and the pH. We have compared these results with the previously performed in-ESI source H/D exchange experiments with peptides and proteins. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Single molecule insights on conformational selection and induced fit mechanism

    DEFF Research Database (Denmark)

    Hatzakis, Nikos

    2014-01-01

    . To describe the molecular basis of this behavior, two main mechanisms have been advanced: 'induced fit' and 'conformational selection'. Our understanding of these models relies primarily on NMR, computational studies and kinetic measurements. These techniques report the average behavior of a large ensemble...... of unsynchronized molecules, often masking intrinsic dynamic behavior of proteins and biologically significant transient intermediates. Single molecule measurements are emerging as a powerful tool for characterizing protein function. They offer the direct observation and quantification of the activity, abundance...

  15. Conformational inversion-topomerization mechanism of ethylcyclohexyl isomers and its role in combustion kinetics

    KAUST Repository

    Bian, Huiting; Wang, Zhandong; Sun, Jinhua; Zhang, Feng

    2016-01-01

    the formation of subsequent decomposition products. In this work, the conformational inversion-topomerization mechanism and H-migration reactions for six ethylcyclohexyl radical isomers were systematically studied by ab initio calculations and the transition

  16. Conformation radiotherapy and conformal radiotherapy

    International Nuclear Information System (INIS)

    Morita, Kozo

    1999-01-01

    In order to coincide the high dose region to the target volume, the 'Conformation Radiotherapy Technique' using the multileaf collimator and the device for 'hollow-out technique' was developed by Prof. S. Takahashi in 1960. This technique can be classified a type of 2D-dynamic conformal RT techniques. By the clinical application of this technique, the late complications of the lens, the intestine and the urinary bladder after radiotherapy for the maxillary cancer and the cervical cancer decreased. Since 1980's the exact position and shape of the tumor and the surrounding normal tissues can be easily obtained by the tremendous development of the CT/MRI imaging technique. As a result, various kinds of new conformal techniques such as the 3D-CRT, the dose intensity modulation, the tomotherapy have been developed since the beginning of 1990'. Several 'dose escalation study with 2D-/3D conformal RT' is now under way to improve the treatment results. (author)

  17. Water Evaporation and Conformational Changes from Partially Solvated Ubiquitin

    Directory of Open Access Journals (Sweden)

    Saravana Prakash Thirumuruganandham

    2010-01-01

    Full Text Available Using molecular dynamics simulation, we study the evaporation of water molecules off partially solvated ubiquitin. The evaporation and cooling rates are determined for a molecule at the initial temperature of 300 K. The cooling rate is found to be around 3 K/ns, and decreases with water temperature in the course of the evaporation. The conformation changes are monitored by studying a variety of intermediate partially solvated ubiquitin structures. We find that ubiquitin shrinks with decreasing hydration shell and exposes more of its hydrophilic surface area to the surrounding.

  18. Conformational transformations induced by the charge-curvature interaction at finite temperature

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Gorria, Carlos; Christiansen, Peter Leth

    2008-01-01

    The role of thermal fluctuations on the conformational dynamics of a single closed filament is studied. It is shown that, due to the interaction between charges and bending degrees of freedom, initially circular aggregates may undergo transformation to polygonal shape. The transition occurs both...

  19. Killing tensors and conformal Killing tensors from conformal Killing vectors

    International Nuclear Information System (INIS)

    Rani, Raffaele; Edgar, S Brian; Barnes, Alan

    2003-01-01

    Koutras has proposed some methods to construct reducible proper conformal Killing tensors and Killing tensors (which are, in general, irreducible) when a pair of orthogonal conformal Killing vectors exist in a given space. We give the completely general result demonstrating that this severe restriction of orthogonality is unnecessary. In addition, we correct and extend some results concerning Killing tensors constructed from a single conformal Killing vector. A number of examples demonstrate that it is possible to construct a much larger class of reducible proper conformal Killing tensors and Killing tensors than permitted by the Koutras algorithms. In particular, by showing that all conformal Killing tensors are reducible in conformally flat spaces, we have a method of constructing all conformal Killing tensors, and hence all the Killing tensors (which will in general be irreducible) of conformally flat spaces using their conformal Killing vectors

  20. Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II.

    Science.gov (United States)

    Nemtseva, Elena V; Lashchuk, Olesya O; Gerasimova, Marina A; Melnik, Tatiana N; Nagibina, Galina S; Melnik, Bogdan S

    2017-12-21

    In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

  1. Pressure-induced phase transition of 1-butyl-3-methylimidazolium hexafluorophosphate [bmim][PF6

    Science.gov (United States)

    Takekiyo, Takahiro; Hatano, Naohiro; Imai, Yusuke; Abe, Hiroshi; Yoshimura, Yukihiro

    2011-03-01

    We have investigated the pressure-induced Raman spectral change of 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) using Raman spectroscopy. The relative Raman intensity at 590 cm-1 of the CH2 rocking band assigned to the gauche conformer of the NCCC dihedral angle of the butyl group in the [bmim]+ cation increases when the pressure-induced liquid-crystalline phase transition occurs, while that at 610 cm-1 assigned to the trans conformer decreases. Our results show that the high-pressure phase transition of [bmim][PF6] causes the increase of the gauche conformer of the [bmim]+ cation.

  2. Molecular insight into conformational transmission of human P-glycoprotein

    International Nuclear Information System (INIS)

    Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

    2013-01-01

    P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through α-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp

  3. Workshop on hadron structure from photo-reactions at intermediate energies: Proceedings

    International Nuclear Information System (INIS)

    Nathan, A.M.; Sandorfi, A.M.

    1992-01-01

    This report contains papers on the following topics: The proton compton effect: Recent measurements of the electric and magnetic polorizabilities of the proton; experiments on the electric polarizability of the neutron; chiral symmetry and nucleon polarizabilities; chiral model predictions for electromagnetic polarizabilities of the nucleon, a consumer report; the polarizabilities of bound nucleons; nucleon polarizability in free space and in nuclear matter; mechanisms of photon scattering on nucleons at intermediate energies; pion polarizabilities in chiral perturbation theory; pion polarizabilities and the shielding of σ(700)-meson exchange in γγ→ππ processes; pion and kaon polarizabilities in the quark confinement model; radiative pion photoproduction and pion polarizabilities; pion and sigma polarizabilities and radiative transitions; the quadrupole amplitude in the γΝ-Δ transition; pion photoproduction and the γΝ-Δ amplitudes; effective- lagrangians, Watson's theorem, and the E2/M1 mixing ratio in the excitation of the delta resonance; new measurements of the p(rvec γ, π o ) reaction; multipole analyses and photo-decay couplings at intermediate energies; compton scattering off the proton; connections between compton scattering and pion photoproduction in the delta region; single-pion electroproduction and the transverse one-half and scalar helicity transition form factors; relativistic effects, QCD mixing angles, and Ν → Νγ and Δ → γΝ transition form factors; electroproduction studies of the Ν → Δ transition at bates and CEBAF

  4. Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation.

    Science.gov (United States)

    Wasserman, Michael R; Alejo, Jose L; Altman, Roger B; Blanchard, Scott C

    2016-04-01

    Directional translocation of the ribosome through the mRNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of tRNA and mRNA substrates with respect to the large and small ribosomal subunits. Using pre-steady state, single-molecule fluorescence resonance energy transfer imaging, we tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations revealed direct evidence of structurally and kinetically distinct late intermediates during substrate movement, whose resolution determines the rate of translocation. These steps involve intramolecular events within the EF-G-GDP-bound ribosome, including exaggerated, reversible fluctuations of the small-subunit head domain, which ultimately facilitate peptidyl-tRNA's movement into its final post-translocation position.

  5. Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method.

    Science.gov (United States)

    Lu, Chao; Li, Xubin; Wu, Dongsheng; Zheng, Lianqing; Yang, Wei

    2016-01-12

    In aqueous solution, solute conformational transitions are governed by intimate interplays of the fluctuations of solute-solute, solute-water, and water-water interactions. To promote molecular fluctuations to enhance sampling of essential conformational changes, a common strategy is to construct an expanded Hamiltonian through a series of Hamiltonian perturbations and thereby broaden the distribution of certain interactions of focus. Due to a lack of active sampling of configuration response to Hamiltonian transitions, it is challenging for common expanded Hamiltonian methods to robustly explore solvent mediated rare conformational events. The orthogonal space sampling (OSS) scheme, as exemplified by the orthogonal space random walk and orthogonal space tempering methods, provides a general framework for synchronous acceleration of slow configuration responses. To more effectively sample conformational transitions in aqueous solution, in this work, we devised a generalized orthogonal space tempering (gOST) algorithm. Specifically, in the Hamiltonian perturbation part, a solvent-accessible-surface-area-dependent term is introduced to implicitly perturb near-solute water-water fluctuations; more importantly in the orthogonal space response part, the generalized force order parameter is generalized as a two-dimension order parameter set, in which essential solute-solvent and solute-solute components are separately treated. The gOST algorithm is evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine (Ala10) peptide. On the basis of a fully automated sampling protocol, the gOST simulation enabled repetitive folding and unfolding of the solvated peptide within a single continuous trajectory and allowed for detailed constructions of Ala10 folding/unfolding free energy surfaces. The gOST result reveals that solvent cooperative fluctuations play a pivotal role in Ala10 folding/unfolding transitions. In addition, our assessment

  6. Fast, clash-free RNA conformational morphing using molecular junctions.

    Science.gov (United States)

    Héliou, Amélie; Budday, Dominik; Fonseca, Rasmus; van den Bedem, Henry

    2017-07-15

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation. The source code, binaries and data are available at https://simtk.org/home/kgs . amelie.heliou@polytechnique.edu or vdbedem@stanford.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  7. Replacement between conformity and counter-conformity in consumption decisions.

    Science.gov (United States)

    Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

    2013-02-01

    This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future.

  8. HIV-1 gp41 Fusion Intermediate: A Target for HIV Therapeutics

    Directory of Open Access Journals (Sweden)

    Chungen Pan

    2010-02-01

    Full Text Available Human immunodeficiency virus (HIV-1 infection is initiated by the binding of gp120 envelope glyco-protein to its cell receptor (CD4 and a coreceptor (CXCR4 or CCR5, followed by a series of conformational changes in the gp41 transmembrane subunit. These changes include insertion of fusion peptide into the target cell membrane and association of C-heptad repeat (CHR peptide with the N-heptad repeat (NHR trimer, a pre-hairpin fusion intermediate. A stable six-helix bundle core is then formed, bringing the viral envelope and target cell membrane into close proximity for fusion. Peptides derived from the CHR region, such as T20 and C34, inhibit HIV-1 fusion by interacting with the gp41 fusion intermediate. A number of anti-HIV-1 peptides and small molecule compounds targeting the gp41 NHR-trimer have been identified. By combining HIV fusion/entry inhibitors targeting different sites in the gp41 fusion intermediate, a potent synergistic effect takes place, resulting in a potential new therapeutic strategy for the HIV infection/AIDS. Here, we present an overview of the current development of anti-HIV drugs, particularly those targeting the gp41 fusion intermediate.

  9. Relation between anchorings of liquid crystals and conformation changes in aligning agents by the Langmuir-Blodgett film technique investigation

    International Nuclear Information System (INIS)

    Zhu, Y.; Lu, Z.; Wei, Y.

    1995-01-01

    The anchoring direction of liquid crystals on a solid substrate surface depends upon many parameters characterizing the liquid-crystal--substrate interface, a variation of which may change this anchoring direction leading to the so-called anchoring transition. Here, based on the Langmuir-Blodgett film technique, we present two model systems to study the relation between anchoring directions and the conformation changes in aligning agents. A double-armed crown ether liquid crystal and a side chain polymer liquid crystal at an air-water interface both show phase transitions, accompanied by conformation changes. However, when the monolayers in different phases were transferred onto solid substrates to orient liquid crystals, we found that for the crown ether material the conformation change can alter the anchoring of liquid crystals between homeotropic and homogeneous alignments, while for the polymer liquid crystal, despite the conformation changes, the liquid crystals can only be aligned homeotropically. The involved mechanisms were briefly discussed in terms of the Landau-type phenomenological theory

  10. Twelve massless flavors and three colors below the conformal window

    International Nuclear Information System (INIS)

    Fodor, Zoltan; Holland, Kieran; Kuti, Julius; Nogradi, Daniel; Schroeder, Chris

    2011-01-01

    We report new results for a frequently discussed gauge theory with twelve fermion flavors in the fundamental representation of the SU(3) color gauge group. The model, controversial with respect to its conformality, is important in non-perturbative studies searching for a viable composite Higgs mechanism beyond the Standard Model (BSM). In comparison with earlier work, our new simulations apply larger volumes and probe deeper in fermion and pion masses toward the chiral limit. Investigating the controversy, we subject the model to opposite hypotheses with respect to the conformal window. In the first hypothesis, below the conformal window, we test chiral symmetry breaking (χSB) with its Goldstone spectrum, F π , the χSB condensate, and several composite hadron states as analytic functions of the fermion mass when varied in a limited range with our best effort to control finite volume effects. In the second test, for the alternate hypothesis inside the conformal window, we probe conformal behavior driven by a single anomalous mass dimension under the assumption of unbroken chiral symmetry at vanishing fermion mass. Our results at fixed gauge coupling, based on the assumptions of the two hypotheses we define, show low level of confidence in the conformal scenario with leading order scaling analysis. Relaxing the important assumption of leading mass-deformed conformality with its conformal finite size scaling would require added theoretical understanding of the scaling violation terms in the conformal analysis and a comprehensive test of its effects on the confidence level of the fits. Results for the running coupling, based on the force between static sources, and preliminary indications for the finite temperature transition are also presented. Staggered lattice fermions with stout-suppressed taste breaking are used throughout the simulations.

  11. Milestoning with transition memory

    Science.gov (United States)

    Hawk, Alexander T.; Makarov, Dmitrii E.

    2011-12-01

    Milestoning is a method used to calculate the kinetics and thermodynamics of molecular processes occurring on time scales that are not accessible to brute force molecular dynamics (MD). In milestoning, the conformation space of the system is sectioned by hypersurfaces (milestones), an ensemble of trajectories is initialized on each milestone, and MD simulations are performed to calculate transitions between milestones. The transition probabilities and transition time distributions are then used to model the dynamics of the system with a Markov renewal process, wherein a long trajectory of the system is approximated as a succession of independent transitions between milestones. This approximation is justified if the transition probabilities and transition times are statistically independent. In practice, this amounts to a requirement that milestones are spaced such that trajectories lose position and velocity memory between subsequent transitions. Unfortunately, limiting the number of milestones limits both the resolution at which a system's properties can be analyzed, and the computational speedup achieved by the method. We propose a generalized milestoning procedure, milestoning with transition memory (MTM), which accounts for memory of previous transitions made by the system. When a reaction coordinate is used to define the milestones, the MTM procedure can be carried out at no significant additional expense as compared to conventional milestoning. To test MTM, we have applied its version that allows for the memory of the previous step to the toy model of a polymer chain undergoing Langevin dynamics in solution. We have computed the mean first passage time for the chain to attain a cyclic conformation and found that the number of milestones that can be used, without incurring significant errors in the first passage time is at least 8 times that permitted by conventional milestoning. We further demonstrate that, unlike conventional milestoning, MTM permits

  12. Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

    Science.gov (United States)

    Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran; Zhang, Nan; Buck, Martin; Zhang, Xiaodong

    2017-07-06

    Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  13. Three-dimensional conformal pancreas treatment: comparison of four- to six-field techniques

    International Nuclear Information System (INIS)

    Higgins, Patrick D.; Sohn, Jason W.; Fine, Robert M.; Schell, Michael C.

    1995-01-01

    Purpose: We compare practical conformal treatment approaches to pancreatic cancer using 6 and 18 MV photons and contrast those approaches against standard techniques. Methods and Materials: A four-field conformal technique for treating pancreas cancer has been developed using nonopposed 18 MV photons. This approach has been extended to 6 MV photon application by the addition of one to two fields. These techniques have been optimized to increase sparing of normal liver and bowel, compared with opposed-field methods, to improve patient tolerance of high doses. In this study we compare these techniques in a simulated tumor model in a cylindrical phantom. Dose-volume analysis is used to quantify differences between the conformal, nonopposed techniques with conformal, opposed field methods. This model is also used to evaluate the effect of 1-2 cm setup errors on dose-volume coverage. Results: Dose-volume analysis demonstrates that five-to-six field conformal treatments using 6 MV photons provides similar or better dose coverage and normal tissue sparing characteristics as an optimized 18 MV, four-field approach when 1-2 cm margins are included for setup uncertainty. All approaches using nonopposed beam geometry provide significant reduction in the volume of tissue encompassed by the 30-50% isodose surfaces, as compared with four-field box techniques. Conclusions: Three-dimensional (3D) conformal treatments can be designed that significantly improve dose-volume characteristics over conventional treatment designs without costing unacceptable amounts of machine time. Further, deep intraabdominal sites can be adequately accessed and treated on intermediate energy machines with a relatively moderate increase in machine time

  14. Multifragmentation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Jacak, B.V.; Britt, H.C.; Claesson, G.

    1986-01-01

    There has been considerable recent interest in the production of intermediate mass fragments (A > 4) in intermediate and high energy nucleus-nucleus collisions. The mechanism for production of these fragments is not well understood and has been described by models employing a variety of assumptions. Some examples are: disassembly of a system in thermal equilibrium into nucleons and nuclear fragments, liquid-vapor phase transitions in nuclear matter, final state coalescence of nucleons and dynamical correlations between nucleons at breakup. Previous studies of fragment production, with one exception, have been single particle inclusive measurements; the observed fragment mass (or charge) distributions can be described by all of the models above. To gain insight into the fragment production mechanism, the authors used the GSI/LBL Plastic Ball detector system to get full azimuthal coverage for intermediate mass fragments in the forward hemisphere in the center of mass system while measuring all the light particles in each event. The authors studied the systems 200 MeV/nucleon Au + Au and Au + Fe

  15. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Trong-Nghia [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Department of Physical Chemistry, Hanoi University of Science and Technology, Hanoi (Viet Nam); Putikam, Raghunath; Lin, M. C., E-mail: chemmcl@emory.edu [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China)

    2015-03-28

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} group by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

  16. Conformal house

    DEFF Research Database (Denmark)

    Ryttov, Thomas Aaby; Sannino, Francesco

    2010-01-01

    fixed point. As a consistency check we recover the previously investigated bounds of the conformal windows when restricting to a single matter representation. The earlier conformal windows can be imagined to be part now of the new conformal house. We predict the nonperturbative anomalous dimensions...... at the infrared fixed points. We further investigate the effects of adding mass terms to the condensates on the conformal house chiral dynamics and construct the simplest instanton induced effective Lagrangian terms...

  17. Steered molecular dynamics simulations of a bacterial type IV pilus reveal characteristics of an experimentally-observed, force-induced conformational transition

    Science.gov (United States)

    Baker, Joseph; Biais, Nicolas; Tama, Florence

    2011-10-01

    Type IV pili (T4P) are long, filamentous structures that emanate from the cellular surface of many infectious bacteria. They are built from a 158 amino acid long subunit called pilin. T4P can grow to many micrometers in length, and can withstand large tension forces. During the infection process, pili attach themselves to host cells, and therefore naturally find themselves under tension. We investigated the response of a T4 pilus to a pulling force using the method of steered molecular dynamics (SMD) simulation. Our simulations expose to the external environment an amino acid sequence initially hidden in the native filament, in agreement with experimental data. Therefore, our simulations might be probing the initial stage of the transition to a force-induced conformation of the T4 pilus. Additional exposed amino acid sequences that might be useful targets for drugs designed to mitigate bacterial infection were also predicted.

  18. Experimental study of the polyamorphism of water. II. The isobaric transitions between HDA and VHDA at intermediate and high pressures

    Science.gov (United States)

    Handle, Philip H.; Loerting, Thomas

    2018-03-01

    Since the first report of very-high density amorphous ice (VHDA) in 2001 [T. Loerting et al., Phys. Chem. Chem. Phys. 3, 5355-5357 (2001)], the status of VHDA as a distinct amorphous ice has been debated. We here study VHDA and its relation to expanded high density amorphous ice (eHDA) on the basis of isobaric heating experiments. VHDA was heated at 0.1 ≤ p ≤ 0.7 GPa, and eHDA was heated at 1.1 ≤ p ≤ 1.6 GPa to achieve interconversion. The behavior upon heating is monitored using in situ volumetry as well as ex situ X-ray diffraction and differential scanning calorimetry. We do not observe a sharp transition for any of the isobaric experiments. Instead, a continuous expansion (VHDA) or densification (eHDA) marks the interconversion. This suggests that a continuum of states exists between VHDA and HDA, at least in the temperature range studied here. This further suggests that VHDA is the most relaxed amorphous ice at high pressures and eHDA is the most relaxed amorphous ice at intermediate pressures. It remains unclear whether or not HDA and VHDA experience a sharp transition upon isothermal compression/decompression at low temperature.

  19. Ligand induced change of β2 adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis.

    Science.gov (United States)

    Bai, Qifeng; Pérez-Sánchez, Horacio; Zhang, Yang; Shao, Yonghua; Shi, Danfeng; Liu, Huanxiang; Yao, Xiaojun

    2014-08-14

    The reported crystal structures of β2 adrenergic receptor (β2AR) reveal that the open and closed states of the water channel are correlated with the inactive and active conformations of β2AR. However, more details about the process by which the water channel states are affected by the active to inactive conformational change of β2AR remain illusive. In this work, molecular dynamics simulations are performed to study the dynamical inactive and active conformational change of β2AR induced by inverse agonist ICI 118,551. Markov state model analysis and free energy calculation are employed to explore the open and close states of the water channel. The simulation results show that inverse agonist ICI 118,551 can induce water channel opening during the conformational transition of β2AR. Markov state model (MSM) analysis proves that the energy contour can be divided into seven states. States S1, S2 and S5, which represent the active conformation of β2AR, show that the water channel is in the closed state, while states S4 and S6, which correspond to the intermediate state conformation of β2AR, indicate the water channel opens gradually. State S7, which represents the inactive structure of β2AR, corresponds to the full open state of the water channel. The opening mechanism of the water channel is involved in the ligand-induced conformational change of β2AR. These results can provide useful information for understanding the opening mechanism of the water channel and will be useful for the rational design of potent inverse agonists of β2AR.

  20. Boundary and interface CFTs from the conformal bootstrap

    Energy Technology Data Exchange (ETDEWEB)

    Gliozzi, Ferdinando [Dipartimento di Fisica, Università di Torino,Via P. Giuria 1 I-10125 Torino (Italy); Istituto Nazionale di Fisica Nucleare - sezione di Torino,Via P. Giuria 1 I-10125 Torino (Italy); Liendo, Pedro [IMIP, Humboldt-Universität zu Berlin, IRIS Adelershof,Zum Großen Windkanal 6, 12489 Berlin (Germany); Meineri, Marco [Scuola Normale Superiore,Piazza dei Cavalieri 7 I-56126 Pisa (Italy); Istituto Nazionale di Fisica Nucleare - sezione di Pisa,Largo B. Pontecorvo, 3, 56127 Pisa (Italy); Rago, Antonio [Centre for Mathematical Sciences, Plymouth University,Drake Circus, Plymouth, PL4 8AA (United Kingdom)

    2015-05-07

    We explore some consequences of the crossing symmetry for defect conformal field theories, focusing on codimension one defects like flat boundaries or interfaces. We study surface transitions of the 3d Ising and other O(N) models through numerical solutions to the crossing equations with the method of determinants. In the extraordinary transition, where the low-lying spectrum of the surface operators is known, we use the bootstrap equations to obtain information on the bulk spectrum of the theory. In the ordinary transition the knowledge of the low-lying bulk spectrum allows to calculate the scale dimension of the relevant surface operator, which compares well with known results of two-loop calculations in 3d. Estimates of various OPE coefficients are also obtained. We also analyze in 4-ϵ dimensions the renormalization group interface between the O(N) model and the free theory and check numerically the results in 3d.

  1. Workshop on hadron structure from photo-reactions at intermediate energies: Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Nathan, A.M.; Sandorfi, A.M. [eds.

    1992-10-01

    This report contains papers on the following topics: The proton compton effect: Recent measurements of the electric and magnetic polorizabilities of the proton; experiments on the electric polarizability of the neutron; chiral symmetry and nucleon polarizabilities; chiral model predictions for electromagnetic polarizabilities of the nucleon, a consumer report; the polarizabilities of bound nucleons; nucleon polarizability in free space and in nuclear matter; mechanisms of photon scattering on nucleons at intermediate energies; pion polarizabilities in chiral perturbation theory; pion polarizabilities and the shielding of {sigma}(700)-meson exchange in {gamma}{gamma}{yields}{pi}{pi} processes; pion and kaon polarizabilities in the quark confinement model; radiative pion photoproduction and pion polarizabilities; pion and sigma polarizabilities and radiative transitions; the quadrupole amplitude in the {gamma}{Nu}-{Delta} transition; pion photoproduction and the {gamma}{Nu}-{Delta} amplitudes; effective- lagrangians, Watson`s theorem, and the E2/M1 mixing ratio in the excitation of the delta resonance; new measurements of the p({rvec {gamma}}, {pi}{sup o}) reaction; multipole analyses and photo-decay couplings at intermediate energies; compton scattering off the proton; connections between compton scattering and pion photoproduction in the delta region; single-pion electroproduction and the transverse one-half and scalar helicity transition form factors; relativistic effects, QCD mixing angles, and {Nu} {yields} {Nu}{gamma} and {Delta} {yields} {gamma}{Nu} transition form factors; electroproduction studies of the {Nu} {yields} {Delta} transition at bates and CEBAF.

  2. The MHD intermediate shock interaction with an intermediate wave: Are intermediate shocks physical?

    International Nuclear Information System (INIS)

    Wu, C.C.

    1988-01-01

    Contrary to the usual belief that MHD intermediate shocks are extraneous, the authors have recently shown by numerical solutions of dissipative MHD equations that intermediate shocks are admissible and can be formed through nonlinear steepening from a continuous wave. In this paper, he clarifies the differences between the conventional view and the results by studying the interaction of an MHD intermediate shock with an intermediate wave. The study reaffirms his results. In addition, the study shows that there exists a larger class of shocklike solutions in the time-dependent dissiaptive MHD equations than are given by the MHD Rankine-Hugoniot relations. it also suggests a mechanism for forming rotational discontinuities through the interaction of an intermediate shock with an intermediate wave. The results are of importance not only to the MHD shock theory but also to studies such as magnetic field reconnection models

  3. Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption.

    Science.gov (United States)

    Banerjee, Arundhati; Ray, Sujay

    2016-01-01

    Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of normal cellular behavior and malignancy. This has been earlier documented via yeast two-hybrid assays. So, with a novel outlook, this study explores the molecular level demonstration of the best satisfactory MDM2 model selection after performing manifold modeling techniques. Z-scores and other stereochemical features were estimated for comparison. Further, protein-protein docking was executed with MDM2 and the experimentally validated X-ray crystallographic DHFR. Residual disclosure from the best suited simulated protein complex disclosed 18 side chain and 3 ionic interactions to strongly accommodate MDM2 protein into the pocket-like zone in DHFR due to the positive environment by charged residues. Lysine residues from MDM2 played a predominant role. Moreover, evaluation from varied energy calculations, folding rate, and net area for solvent accessibility implied the active participation of MDM2 with DHFR. Fascinatingly, conformational transitions from coils to helices and β-sheets after interaction with DHFR affirm the conformational strength and firmer interaction of human MDM2-DHFR. Therefore, this probe instigates near-future clinical research and interactive computational investigations with mutations.

  4. Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption

    Directory of Open Access Journals (Sweden)

    Arundhati Banerjee

    2016-01-01

    Full Text Available Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of normal cellular behavior and malignancy. This has been earlier documented via yeast two-hybrid assays. So, with a novel outlook, this study explores the molecular level demonstration of the best satisfactory MDM2 model selection after performing manifold modeling techniques. Z-scores and other stereochemical features were estimated for comparison. Further, protein-protein docking was executed with MDM2 and the experimentally validated X-ray crystallographic DHFR. Residual disclosure from the best suited simulated protein complex disclosed 18 side chain and 3 ionic interactions to strongly accommodate MDM2 protein into the pocket-like zone in DHFR due to the positive environment by charged residues. Lysine residues from MDM2 played a predominant role. Moreover, evaluation from varied energy calculations, folding rate, and net area for solvent accessibility implied the active participation of MDM2 with DHFR. Fascinatingly, conformational transitions from coils to helices and β-sheets after interaction with DHFR affirm the conformational strength and firmer interaction of human MDM2-DHFR. Therefore, this probe instigates near-future clinical research and interactive computational investigations with mutations.

  5. Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories

    Science.gov (United States)

    Matsunaga, Y.; Sugita, Y.

    2018-06-01

    A data-driven modeling scheme is proposed for conformational dynamics of biomolecules based on molecular dynamics (MD) simulations and experimental measurements. In this scheme, an initial Markov State Model (MSM) is constructed from MD simulation trajectories, and then, the MSM parameters are refined using experimental measurements through machine learning techniques. The second step can reduce the bias of MD simulation results due to inaccurate force-field parameters. Either time-series trajectories or ensemble-averaged data are available as a training data set in the scheme. Using a coarse-grained model of a dye-labeled polyproline-20, we compare the performance of machine learning estimations from the two types of training data sets. Machine learning from time-series data could provide the equilibrium populations of conformational states as well as their transition probabilities. It estimates hidden conformational states in more robust ways compared to that from ensemble-averaged data although there are limitations in estimating the transition probabilities between minor states. We discuss how to use the machine learning scheme for various experimental measurements including single-molecule time-series trajectories.

  6. Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.

    Science.gov (United States)

    Chong, Song-Ho; Ham, Sihyun

    2015-10-01

    Quantifying how the rugged nature of the underlying free-energy landscape determines the entropic cost a protein must incur upon folding and ligand binding is a challenging problem. Here, we present a novel computational approach that dissects the protein configurational entropy on the basis of the classification of protein dynamics on the landscape into two separate components: short-term vibrational dynamics related to individual free-energy wells and long-term conformational dynamics associated with transitions between wells. We apply this method to separate the configurational entropy of the protein villin headpiece subdomain into its conformational and vibrational components. We find that the change in configurational entropy upon folding is dominated by the conformational entropy despite the fact that the magnitude of the vibrational entropy is the significantly larger component in each of the folded and unfolded states, which is in accord with the previous empirical estimations. The straightforward applicability of our method to unfolded proteins promises a wide range of applications, including those related to intrinsically disordered proteins.

  7. A study on the development of regulatory guide to stability conformation and classification criteria of low and intermediate level radioactive waste

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Geon Jae; Paek, Min Hoon; Park, Jong Gil; Han, Byeong Seop; Cheong, Jae Hak; Lee, Hae Chan; Yang, Jin Yeong; Hong, Hei Kwan; Park, Jin Baek [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)

    1994-01-15

    The objectives of this study are to examine basic principles and terms and to suggest and recommend definite methods and criteria necessary for the classification and stability conformation of radioactive wastes. In this study, following studies were performed : investigate the domestic regulations related with the stability conformation and classification of radioactive wastes in order to keep mutual relationship and consistency between the regulations, investigate the sources, types and characteristics of domestic radioactive wastes as a basis for this study, investigate the classification criteria and methods of others countries in a general point of view and in the view point of disposal method, select the classification criteria factors for the domestic case and general case in the both general and domestic points of view, investigate the general test items for the stability conformation of radioactive waste forms and analysis on the test items and criteria of others countries for the mined cavity disposal and shallow land disposal in the view point of disposal method, experimental leaching and immersion tests for the borate and spent resin wastes as a study on the stability conformation of waste forms, selection of acceptance criteria for the both of disposal methods in the domestic and general cases.

  8. UV Resonance Raman Elucidation of the Terminal and Internal Peptide Bond Conformations of Crystalline and Solution Oligoglycines.

    Science.gov (United States)

    Bykov, Sergei V; Asher, Sanford A

    2010-11-30

    Spectroscopic investigations of macromolecules generally attempt to interpret the measured spectra in terms of the summed contributions of the different molecular fragments. This is the basis of the local mode approximation in vibrational spectroscopy. In the case of resonance Raman spectroscopy independent contributions of molecular fragments require both a local mode-like behavior and the uncoupled electronic transitions. Here we show that the deep UV resonance Raman spectra of aqueous solution phase oligoglycines show independent peptide bond molecular fragment contributions indicating that peptide bonds electronic transitions and vibrational modes are uncoupled. We utilize this result to separately determine the conformational distributions of the internal and penultimate peptide bonds of oligoglycines. Our data indicate that in aqueous solution the oligoglycine terminal residues populate conformations similar to those found in crystals (3(1)-helices and β-strands), but with a broader distribution, while the internal peptide bond conformations are centered around the 3(1)-helix Ramachandran angles.

  9. Studies of melting, crystallization, and commensurate-incommensurate transitions in two dimensions: Third year progress report

    International Nuclear Information System (INIS)

    Mockler, R.C.; O'Sullivan, W.J.

    1988-09-01

    The free expansion melting of a 2D suspension of micron-size spheres contained between parallel silica plates has been analyzed in some detail. The translational and orientational correlation functions conform with KTHNY theory prediction of a two-step melting process. The visual observations and study of the defect structures and evolution strongly suggest the process is first order with two-phase coexistence taking the place of the intermediate (hexatic) phase. On the other hand, melting of a 2.88 μm monolayer on water is in accord with KTHNY including the observation of dislocation-pair unbinding at the first transition. However, there is no evidence of the dissociation of dislocation into free disclinations at the second transition (the defect structure is much too complex here). Dynamic light scattering experiments on a 2D crystal on the surface of water yield viscous damping factors, force constants and the Lame coefficients. 2D computer simulation, in collaboration with Noel Clark's group, reveal cooperative motion along chains of particles (''snakes''). They appear to be the principal cause of diffusion near the melting point and important in the melting process. 16 refs

  10. Louisiana SIP: LAC 33:III Ch. 14 Subchap B, 1431 to 1434--Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded, or Approved Under Title 23 U.S.C. or the Federal Transit Laws

    Science.gov (United States)

    Louisiana SIP: LAC 33:III Ch. 14 Subchap B, 1431 to 1434--Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded, or Approved Under Title 23 U.S.C. or the Federal Transit Laws

  11. Mechanism of adsorption and eclipse of bacteriophage phi X174. I. In vitro conformational change under conditions of eclipse.

    Science.gov (United States)

    Incardona, N L; Blonski, R; Feeney, W

    1972-01-01

    Bacteriophage phiX174 undergoes a conformational change during viral eclipse when virus-host cell complexes are incubated briefly at 37 C in a complex starvation buffer at pH 8. In this report, basically the same transition is demonstrated in vitro. Incubation of phiX alone for 2 to 3 hr at 35 C in 0.1 m CaCl(2) (pH 7.2) results in an irreversible decrease in S(20,w) because of an increase in the frictional coefficient that occurs during the change in conformation. The slower sedimenting conformation is noninfectious. These properties are remarkably similar to those of the eclipsed particles characterized by Newbold and Sinsheimer. Therefore, the key structural requirements for the molecular mechanism must reside within the architecture of the virus itself. This extremely simplified system uncovered the calcium ion requirement and pronounced dependence on pH between 6 and 7, both inherent properties of adsorption. This and the more than 10-fold greater rate of the in vivo conformational transition allude to the cooperative nature of attachment and eclipse for phiX.

  12. Photo-induced bleaching of sensory rhodopsin II (phoborhodopsin) from Halobacterium salinarum by hydroxylamine: identification of the responsible intermediates.

    Science.gov (United States)

    Tamogami, Jun; Kikukawa, Takashi; Ikeda, Yoichi; Demura, Makoto; Nara, Toshifumi; Kamo, Naoki

    2012-01-05

    Sensory rhodopsin II from Halobacterium salinarum (HsSRII) is a retinal protein in which retinal binds to a specific lysine residue through a Schiff base. Here, we investigated the photobleaching of HsSRII in the presence of hydroxylamine. For identification of intermediate(s) attacked by hydroxylamine, we employed the flash-induced bleaching method. In order to change the concentration of intermediates, such as M- and O-intermediates, experiments were performed under varying flashlight intensities and concentrations of azide that accelerated only the M-decay. We found the proportional relationship between the bleaching rate and area under the concentration-time curve of M, indicating a preferential attack of hydroxylamine on M. Since hydroxylamine is a water-soluble reagent, we hypothesize that for M, hydrophilicity or water-accessibility increases specifically in the moiety of Schiff base. Thus, hydroxylamine bleaching rates may be an indication of conformational changes near the Schiff base. We also considered the possibility that azide may induce a small conformational change around the Schiff base. We compared the hydroxylamine susceptibility between HsSRII and NpSRII (SRII from Natronomonas pharaonis) and found that the M of HsSRII is about three times more susceptible than that of the stable NpSRII. In addition, long illumination to HsSRII easily produced M-like photoproduct, P370. We thus infer that the instability of HsSRII under illumination may be related to this increase of hydrophilicity at M and P370. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.

    Directory of Open Access Journals (Sweden)

    Massimo Lai

    2015-01-01

    Full Text Available Calmodulin is a calcium-binding protein ubiquitous in eukaryotic cells, involved in numerous calcium-regulated biological phenomena, such as synaptic plasticity, muscle contraction, cell cycle, and circadian rhythms. It exibits a characteristic dumbell shape, with two globular domains (N- and C-terminal lobe joined by a linker region. Each lobe can take alternative conformations, affected by the binding of calcium and target proteins. Calmodulin displays considerable functional flexibility due to its capability to bind different targets, often in a tissue-specific fashion. In various specific physiological environments (e.g. skeletal muscle, neuron dendritic spines several targets compete for the same calmodulin pool, regulating its availability and affinity for calcium. In this work, we sought to understand the general principles underlying calmodulin modulation by different target proteins, and to account for simultaneous effects of multiple competing targets, thus enabling a more realistic simulation of calmodulin-dependent pathways. We built a mechanistic allosteric model of calmodulin, based on an hemiconcerted framework: each calmodulin lobe can exist in two conformations in thermodynamic equilibrium, with different affinities for calcium and different affinities for each target. Each lobe was allowed to switch conformation on its own. The model was parameterised and validated against experimental data from the literature. In spite of its simplicity, a two-state allosteric model was able to satisfactorily represent several sets of experiments, in particular the binding of calcium on intact and truncated calmodulin and the effect of different skMLCK peptides on calmodulin's saturation curve. The model can also be readily extended to include multiple targets. We show that some targets stabilise the low calcium affinity T state while others stabilise the high affinity R state. Most of the effects produced by calmodulin targets can be

  14. Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c

    Directory of Open Access Journals (Sweden)

    David S. Kliger

    2009-04-01

    Full Text Available Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t £ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-ms conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 ms timescale to a compact intermediate IC containing some native-like secondary structure. Although the existence and nature of IC as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of IC as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that IC may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.

  15. Plastocyanin conformation: an analysis of its near ultraviolet absorption and circular dichroic spectra

    International Nuclear Information System (INIS)

    Draheim, J.E.; Anderson, G.P.; Duane, J.W.; Gross, E.L.

    1986-01-01

    The near-ultraviolet absorption and circular dichroic spectra of plastocyanin are dependent upon the redox state, solution pH, and ammonium sulfate concentration. This dependency was observed in plastocyanin isolated from spinach, poplar, and lettuce. Removal of the copper atom also perturbed the near-ultraviolet spectra. Upon reduction there are increases in both extinction and ellipticity at 252 nm. Further increases at 252 nm were observed upon formation of apo plastocyanin eliminating charge transfer transitions as the cause. The spectral changes in the near-ultraviolet imply a flexible tertiary conformation for plastocyanin. There are at least two charge transfer transitions at ∼295-340 nm. One of these transitions is sensitive to low pH's and is attributed to the His 87 copper ligand. The redox state dependent changes observed in the near-ultraviolet spectra of plastocyanin are attenuated either by decreasing the pH to 5 or by increasing the ammonium sulfate concentration to 2.7 M. This attenuation cannot be easily explained by simple charge screening. Hydrophobic interactions probably play an important role in this phenomenon. The pH and redox state dependent conformational changes may play an important role in regulating electron transport

  16. Critical phenomena of static charged AdS black holes in conformal gravity

    Directory of Open Access Journals (Sweden)

    Wei Xu

    2014-09-01

    Full Text Available The extended thermodynamics of static charged AdS black holes in conformal gravity is analyzed. The P–V criticality of these black holes has some unusual features. There exists a single critical point with critical temperature Tc and critical pressure Pc. At fixed T>Tc (or at fixed P>Pc, there are two zeroth order phase transition points but no first order phase transition points. The systems favors large pressure states at constant T, or high temperature states at constant P.

  17. Magnetic re-entrance in intermediate valence compounds

    International Nuclear Information System (INIS)

    Allub, R.; Machiavelli, O.; Balseiro, C.; Alascio, B.

    1980-01-01

    The possibility is explored of magnetic re-entrance in intermediate valence compounds. Using a simplified Anderson-Lattice model the pressure-temperature magnetic phase diagram is obtained. This diagram shows that for some value of the microscopic parameters the temperature induced two transitions (non-magnetic to magnetically ordered to paramagnetic). The magnetization and the average occupation number of the localized state are calculated. Estimations of the observability of the effect in systems like CeAl 2 are made. (author)

  18. Extraction of conformal data in critical quantum spin chains using the Koo-Saleur formula

    Science.gov (United States)

    Milsted, Ashley; Vidal, Guifre

    2017-12-01

    We study the emergence of two-dimensional conformal symmetry in critical quantum spin chains on the finite circle. Our goal is to characterize the conformal field theory (CFT) describing the universality class of the corresponding quantum phase transition. As a means to this end, we propose and demonstrate automated procedures which, using only the lattice Hamiltonian H =∑jhj as an input, systematically identify the low-energy eigenstates corresponding to Virasoro primary and quasiprimary operators, and assign the remaining low-energy eigenstates to conformal towers. The energies and momenta of the primary operator states are needed to determine the primary operator scaling dimensions and conformal spins, an essential part of the conformal data that specifies the CFT. Our techniques use the action, on the low-energy eigenstates of H , of the Fourier modes Hn of the Hamiltonian density hj. The Hn were introduced as lattice representations of the Virasoro generators by Koo and Saleur [Nucl. Phys. B 426, 459 (1994), 10.1016/0550-3213(94)90018-3]. In this paper, we demonstrate that these operators can be used to extract conformal data in a nonintegrable quantum spin chain.

  19. Multi-perspective smFRET reveals rate-determining late intermediates of ribosomal translocation

    Science.gov (United States)

    Wasserman, Michael R.; Alejo, Jose L.; Altman, Roger B.; Blanchard, Scott C.

    2016-01-01

    Directional translocation of the ribosome through the messenger RNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of transfer and messenger RNA substrates with respect to the large and small ribosomal subunits. Using pre-steady state, single-molecule fluorescence resonance energy transfer imaging, we have tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations reveal direct evidence of structurally and kinetically distinct, late intermediates during substrate movement, whose resolution is rate-determining to the translocation mechanism. These steps involve intra-molecular events within the EFG(GDP)-bound ribosome, including exaggerated, reversible fluctuations of the small subunit head domain, which ultimately facilitate peptidyl-tRNA’s movement into its final post-translocation position. PMID:26926435

  20. Quantum Conformal Algebras and Closed Conformal Field Theory

    CERN Document Server

    Anselmi, D

    1999-01-01

    We investigate the quantum conformal algebras of N=2 and N=1 supersymmetric gauge theories. Phenomena occurring at strong coupling are analysed using the Nachtmann theorem and very general, model-independent, arguments. The results lead us to introduce a novel class of conformal field theories, identified by a closed quantum conformal algebra. We conjecture that they are the exact solution to the strongly coupled large-N_c limit of the open conformal field theories. We study the basic properties of closed conformal field theory and work out the operator product expansion of the conserved current multiplet T. The OPE structure is uniquely determined by two central charges, c and a. The multiplet T does not contain just the stress-tensor, but also R-currents and finite mass operators. For this reason, the ratio c/a is different from 1. On the other hand, an open algebra contains an infinite tower of non-conserved currents, organized in pairs and singlets with respect to renormalization mixing. T mixes with a se...

  1. C-metric solution for conformal gravity with a conformally coupled scalar field

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Kun, E-mail: mengkun@tjpu.edu.cn [School of Science, Tianjin Polytechnic University, Tianjin 300387 (China); Zhao, Liu, E-mail: lzhao@nankai.edu.cn [School of Physics, Nankai University, Tianjin 300071 (China)

    2017-02-15

    The C-metric solution of conformal gravity with a conformally coupled scalar field is presented. The solution belongs to the class of Petrov type D spacetimes and is conformal to the standard AdS C-metric appeared in vacuum Einstein gravity. For all parameter ranges, we identify some of the physically interesting static regions and the corresponding coordinate ranges. The solution may contain a black hole event horizon, an acceleration horizon, either of which may be cut by the conformal infinity or be hidden behind the conformal infinity. Since the model is conformally invariant, we also discussed the possible effects of the conformal gauge choices on the structure of the spacetime.

  2. Enhancement of intermediate-field two-photon absorption by rationally shaped femtosecond pulses

    International Nuclear Information System (INIS)

    Chuntonov, Lev; Rybak, Leonid; Gandman, Andrey; Amitay, Zohar

    2008-01-01

    We extend the powerful frequency-domain analysis of femtosecond two-photon absorption to the intermediate-field regime of considerable absorption yields, where additionally to the weak-field nonresonant two-photon transitions also four-photon transitions play a role. Consequently, we rationally find that the absorption is enhanced over the transform-limited pulse by any shaped pulse having a spectral phase that is antisymmetric around one-half of the transition frequency and a spectrum that is asymmetric around it (red or blue detuned according to the system). The enhancement increases as the field strength increases. The theoretical results for Na are verified experimentally

  3. Transition Metal Donor-Peptide-Acceptor Complexes: From Intramolecular Electron Transfer Reactions to the Study of Reactive Intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Isied, Stephan S.

    2003-03-11

    The trans-polyproline (PII) oligomers (Figure 1) are unusually rigid peptide structures which have been extensively studied by our group for peptide mediated intramolecular electron transfer (ET) at long distances. We have previously studied ET across a series of metal ion donor (D) acceptor (A) oligoproline peptides with different distances, driving forces and reorganizational energies. The majority of these experiments involve generating the ET intermediate using pulse radiolysis methods, although more recently photochemical methods are also used. Results of these studies showed that ET across peptides can vary by more than twelve orders of magnitude. Using ruthenium bipyridine donors, ET reaction rate constants across several proline residues (n = 4 - 9) occurred in the millisecond (ms) to {micro}s timescale, thus limiting the proline peptide conformational motions to only minor changes (far smaller than the large changes that occur on the ms to sec timescale, such as trans to cis proline isomerization). The present report describes our large data base of experimental results for D-peptide-A complexes in terms of a model where the involvement of both superexchange and hopping (hole and electron) mechanisms account for the long range ET rate constants observed. Our data shows that the change from superexchange to hopping mechanisms occurs at different distances depending on the type of D and A and their interactions with the peptides. Our model is also consistent with generalized models for superexchange and hopping which have been put forward by a number of theoretical groups to account for long range ET phenomena.

  4. Conformational targeting of fibrillar polyglutamine proteins in live cells escalates aggregation and cytotoxicity.

    Directory of Open Access Journals (Sweden)

    Erik Kvam

    2009-05-01

    Full Text Available Misfolding- and aggregation-prone proteins underlying Parkinson's, Huntington's and Machado-Joseph diseases, namely alpha-synuclein, huntingtin, and ataxin-3 respectively, adopt numerous intracellular conformations during pathogenesis, including globular intermediates and insoluble amyloid-like fibrils. Such conformational diversity has complicated research into amyloid-associated intracellular dysfunction and neurodegeneration. To this end, recombinant single-chain Fv antibodies (scFvs are compelling molecular tools that can be selected against specific protein conformations, and expressed inside cells as intrabodies, for investigative and therapeutic purposes.Using atomic force microscopy (AFM and live-cell fluorescence microscopy, we report that a human scFv selected against the fibrillar form of alpha-synuclein targets isomorphic conformations of misfolded polyglutamine proteins. When expressed in the cytoplasm of striatal cells, this conformation-specific intrabody co-localizes with intracellular aggregates of misfolded ataxin-3 and a pathological fragment of huntingtin, and enhances the aggregation propensity of both disease-linked polyglutamine proteins. Using this intrabody as a tool for modulating the kinetics of amyloidogenesis, we show that escalating aggregate formation of a pathologic huntingtin fragment is not cytoprotective in striatal cells, but rather heightens oxidative stress and cell death as detected by flow cytometry. Instead, cellular protection is achieved by suppressing aggregation using a previously described intrabody that binds to the amyloidogenic N-terminus of huntingtin. Analogous cytotoxic results are observed following conformational targeting of normal or polyglutamine-expanded human ataxin-3, which partially aggregate through non-polyglutamine domains.These findings validate that the rate of aggregation modulates polyglutamine-mediated intracellular dysfunction, and caution that molecules designed to

  5. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    International Nuclear Information System (INIS)

    Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

    2014-01-01

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space

  6. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    Energy Technology Data Exchange (ETDEWEB)

    Nedialkova, Lilia V.; Amat, Miguel A. [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de [Department of Chemical and Biological Engineering and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544 (United States); Hummer, Gerhard, E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de [Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main (Germany)

    2014-09-21

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

  7. Non-conformable, partial and conformable transposition

    DEFF Research Database (Denmark)

    König, Thomas; Mäder, Lars Kai

    2013-01-01

    and the Commission regarding a directive’s outcome, play a much more strategic role than has to date acknowledged in the transposition literature. Whereas disagreement of a member state delays conformable transposition, it speeds up non-conformable transposition. Disagreement of the Commission only prolongs...... the transposition process. We therefore conclude that a stronger focus on an effective sanctioning mechanism is warranted for safeguarding compliance with directives....

  8. Conformal Einstein spaces

    International Nuclear Information System (INIS)

    Kozameh, C.N.; Newman, E.T.; Tod, K.P.

    1985-01-01

    Conformal transformations in four-dimensional. In particular, a new set of two necessary and sufficient conditions for a space to be conformal to an Einstein space is presented. The first condition defines the class of spaces conformal to C spaces, whereas the last one (the vanishing of the Bach tensor) gives the particular subclass of C spaces which are conformally related to Einstein spaces. (author)

  9. Conformal Gravity

    International Nuclear Information System (INIS)

    Hooft, G.

    2012-01-01

    The dynamical degree of freedom for the gravitational force is the metric tensor, having 10 locally independent degrees of freedom (of which 4 can be used to fix the coordinate choice). In conformal gravity, we split this field into an overall scalar factor and a nine-component remainder. All unrenormalizable infinities are in this remainder, while the scalar component can be handled like any other scalar field such as the Higgs field. In this formalism, conformal symmetry is spontaneously broken. An imperative demand on any healthy quantum gravity theory is that black holes should be described as quantum systems with micro-states as dictated by the Hawking-Bekenstein theory. This requires conformal symmetry that may be broken spontaneously but not explicitly, and this means that all conformal anomalies must cancel out. Cancellation of conformal anomalies yields constraints on the matter sector as described by some universal field theory. Thus black hole physics may eventually be of help in the construction of unified field theories. (author)

  10. Liquid-gas phase transition and isospin fractionation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Xing Yongzhong; Liu Jianye; Guo Wenjun

    2004-01-01

    The liquid-gas phase transition in the heavy ion collisions and nuclear matter has been an important topic and got achievements, such as, based on the studies by H.Q. Song et al the critical temperature of liquid-gas phase transition enhances with increasing the mass of system and reduces as the increase of the neutron proton ratio of system. As authors know that both the liquid-gas phase transition and the isospin fractionation occur in the spinodal instability region at the nuclear density below the normal nuclear density. In particular, these two dynamical processes lead to the separation of nuclear matter into the liquid phase and gas phase. In this case to compare their dynamical behaviors is interested. The authors investigate the dependence of isospin fractionation degree on the mass and neutron proton ratio of system by using the isospin dependent quantum molecular dynamics model. The authors found that the degree of isospin fractionation (N/Z) n /(N/Z) imf decreases with increasing the mass of the system. This is just similar to the enhance of the critical temperature of liquid-gas phase transition T c as the increase of system mass. Because the enhance of T c is not favorable for the liquid-gas transition taking place, which reduces the isospin fractionation process and leads to decrease of (N/Z) n /(N/Z) imf . However the degree of isospin fractionation enhances with increasing the neutron proton ratio of the system. It is just corresponding to the reduce of T c of the liquid-gas phase transition as the increase of the isospin fractionation of the system. Because the reduce of T c enhances the liquid-gas phase transition process and also prompts the isospin fractionation process leading the increase of the isospin fractionation degree. To sum up, there are very similar dynamical behaviors for the degree of isospin fractionation and the critical temperature of the liquid-gas phase transition. So dynamical properties of the liquid-gas phase transition can

  11. Phase transitions in surfactant monolayers

    International Nuclear Information System (INIS)

    Casson, B.D.

    1998-01-01

    Two-dimensional phase transitions have been studied in surfactant monolayers at the air/water interface by sum-frequency spectroscopy and ellipsometry. In equilibrium monolayers of medium-chain alcohols C n H 2n+1 OH (n = 9-14) a transition from a two-dimensional crystalline phase to a liquid was observed at temperatures above the bulk melting point. The small population of gauche defects in the solid phase increased only slightly at the phase transition. A model of the hydrocarbon chains as freely rotating rigid rods allowed the area per molecule and chain tilt in the liquid phase to be determined. The area per molecule, chain tilt and density of the liquid phase all increased with increasing chain length, but for each chain length the density was higher than in a bulk liquid hydrocarbon. In a monolayer of decanol adsorbed at the air/water interface a transition from a two-dimensional liquid to a gas was observed. A clear discontinuity in the coefficient of ellipticity as a function of temperature showed that the transition is first-order. This result suggests that liquid-gas phase transitions in surfactant monolayers may be more widespread than once thought. A solid-liquid phase transition has also been studied in mixed monolayers of dodecanol with an anionic surfactant (sodium dodecyl sulphate) and with a homologous series of cationic surfactants (alkyltrimethylammonium bromides: C n TABs, n = 12, 14, 16). The composition and structure of the mixed monolayers was studied above and below the phase transition. At low temperatures the mixed monolayers were as densely packed as a monolayer of pure dodecanol in its solid phase. At a fixed temperature the monolayers under-went a first-order phase transition to form a phase that was less dense and more conformationally disordered. The proportion of ionic surfactant in the mixed monolayer was greatest in the high temperature phase. As the chain length of the C n TAB increased the number of conformational defects

  12. Representing environment-induced helix-coil transitions in a coarse grained peptide model

    Science.gov (United States)

    Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

    2016-10-01

    Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that

  13. AERE contracts with DoE on the treatment and disposal of intermediate level wastes

    International Nuclear Information System (INIS)

    Partridge, B.A.

    1984-11-01

    Reports are presented on work on the following topics concerned with the treatment and disposal of intermediate-level radioactive wastes: comparative evaluation of α and β γ irradiated medium level waste forms; modelling and characterisation of intermediate level waste forms based on polymers; optimisation of processing parameters for polymer and bitumen modified cements; α damage in non-reference waste form matrix materials; leaching mechanisms and modelling; inorganic ion exchange treatment of medium active effluents; electrical processes for the treatment of medium active liquid waste; fast reactor fuel element cladding; dissolver residues; effects of radiation on the properties of cemented MTR waste forms; equilibrium leach testing of cemented MTR waste forms; radiolytic oxidation of radionuclides; immobilisation of liquid organic waste; quality control, non-conformances and corrective action. (U.K.)

  14. Focused conformational sampling in proteins

    Science.gov (United States)

    Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas

    2017-11-01

    A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.

  15. Deciphering the shape and deformation of secondary structures through local conformation analysis

    Directory of Open Access Journals (Sweden)

    Camproux Anne-Claude

    2011-02-01

    Full Text Available Abstract Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

  16. Deciphering the shape and deformation of secondary structures through local conformation analysis.

    Science.gov (United States)

    Baussand, Julie; Camproux, Anne-Claude

    2011-02-01

    Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

  17. The hadron to quark/gluon transition

    International Nuclear Information System (INIS)

    Brown, G.E.; Bethe, H.A.; Pizzochero, P.M.

    1991-01-01

    In this paper we are concerned with the hadron to quark/gluon transition. We describe the equilibrium states of hadronic matter by a Hagedorn spectrum; introducing scaling masses, as dictated by the restoration of chiral invariance with increasing temperature, we show that in the chiral SU(2) f limit there is a maximum hadron temperature (T H ) max ≅ 128 MeV. Since the quark/gluon perturbative phase involves restoration of conformal invariance, we take the bag constant to be the conformal anomaly, i.e. the gluon condensate. The stability condition P QG > 0 for the pressure requires that there is a minimum temperature; we find (T QG ) min ≅ 172 MeV for SU(2) f . According to the simple Hagedorn model, there appears to be a region of temperature between (T H ) max and (T QG ) min in which no admissible equilibrium states exist. Since the two phases cannot exist at a common temperature, in this model there is no QCD phase transition. (orig.)

  18. Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.

    Directory of Open Access Journals (Sweden)

    Adrien Nicolaï

    Full Text Available ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD of Hsp70 propagates a signal to its substrate-binding domain (SBD. Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in

  19. BANKING INTERMEDIATION AND CONSEQUENCES OF FINANCIAL CRISIS

    Directory of Open Access Journals (Sweden)

    Medar Lucian-Ion

    2012-12-01

    Full Text Available The financial intermediation of bank institutions, has an essential role in mobilising of the available funds and their distribution in various products and services, for economic growth. The extent that banking system is in distress or passing through a period of crisis, then, everything turns into a general crisis, especially that, in some states, natural and legal persons have been learned ,,to live’’ on the credits.The effectiveness of banking intermediation activity in Romania depends on how fast the market is enabled under the influence of the new European regulations. The Romanian market in all its forms is the second largest in the EU, and the banking system is almost entirely made up of banks with foreign capital. The romanian banking market has not suffered so much because of the financial crisis. To the extent that banking institutions provide the necessary funds, Romania has important resources for the transition to a new economic cycle based on sustainable development.

  20. Intermediates and the folding of proteins L and G

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  1. Conformal Infinity

    Directory of Open Access Journals (Sweden)

    Frauendiener Jörg

    2000-08-01

    Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, ``conformal infinity'' is related with almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved out of physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation and how it lends itself very naturally to solve radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  2. Conformal Infinity.

    Science.gov (United States)

    Frauendiener, Jörg

    2004-01-01

    The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  3. Tilting the balance between canonical and noncanonical conformations for the H1 hypervariable loop of a llama VHH through point mutations.

    Science.gov (United States)

    Mahajan, Sai Pooja; Velez-Vega, Camilo; Escobedo, Fernando A

    2013-01-10

    Nanobodies are single-domain antibodies found in camelids. These are the smallest naturally occurring binding domains and derive functionality via three hypervariable loops (H1-H3) that form the binding surface. They are excellent candidates for antibody engineering because of their favorable characteristics like small size, high solubility, and stability. To rationally engineer antibodies with affinity for a specific target, the hypervariable loops can be tailored to obtain the desired binding surface. As a first step toward such a goal, we consider the design of loops with a desired conformation. In this study, we focus on the H1 loop of the anti-hCG llama nanobody that exhibits a noncanonical conformation. We aim to "tilt" the stability of the H1 loop structure from a noncanonical conformation to a (humanized) type 1 canonical conformation by studying the effect of selected mutations to the amino acid sequence of the H1, H2, and proximal residues. We use all-atomistic, explicit-solvent, biased molecular dynamic simulations to simulate the wild-type and mutant loops in a prefolded framework. We thus find mutants with increasing propensity to form a stable type 1 canonical conformation of the H1 loop. Free energy landscapes reveal the existence of conformational isomers of the canonical conformation that may play a role in binding different antigenic surfaces. We also elucidate the approximate mechanism and kinetics of transitions between such conformational isomers by using a Markovian model. We find that a particular three-point mutant has the strongest thermodynamic propensity to form the H1 type 1 canonical structure but also to exhibit transitions between conformational isomers, while a different, more rigid three-point mutant has the strongest propensity to be kinetically trapped in such a canonical structure.

  4. Gauge theory of glass transition

    International Nuclear Information System (INIS)

    Vasin, Mikhail

    2011-01-01

    A new analytical approach for the description of the glass transition in a frustrated system is suggested. The theory is based on the non-equilibrium dynamics technique, and takes into account the interaction of the local order field with the massive gauge field, which describes frustration-induced plastic deformation. The glass transition is regarded as a phase transition interrupted because of the premature critical slowing-down of one of the degrees of freedom caused by the frustrations. It is shown that freezing of the system appears when the correlation length and relaxation time of the gauge field diverge. The Vogel–Fulcher–Tammann relation for the transition kinetics and the critical exponent for the nonlinear susceptibility, 2.5∼ t correlation function dependence on time, and explains the boson peak appearance on this curve. In addition, the function of the glass transition temperature value with cooling rate is derived; this dependence fully conforms with known experimental data

  5. Effect of hyperons on nuclear phase transition

    International Nuclear Information System (INIS)

    Das, P.; Mallik, S.; Chaudhuri, G.

    2016-01-01

    Phase transition of nuclear system in heavy ion-collisions at intermediate energy has been studied well for many years and it has also been extended to strange nuclear matter. Recently, using the Canonical Thermodynamical Model (CTM), detailed work on multiplicity distribution of fragments produced from fragmentation of hypernuclear system shows the existence of phase transition or phase coexistence in strange system with Λ-hyperons. In present work we want to continue the investigation on phase transition with respect to some other thermodynamic observables like free energy, specific heat etc. in order to be confirmed about the nature of the transition

  6. The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.

    Directory of Open Access Journals (Sweden)

    Lili X Peng

    2014-02-01

    Full Text Available αβ-tubulin dimers need to convert between a 'bent' conformation observed for free dimers in solution and a 'straight' conformation required for incorporation into the microtubule lattice. Here, we investigate the free energy landscape of αβ-tubulin using molecular dynamics simulations, emphasizing implications for models of assembly, and modulation of the conformational landscape by colchicine, a tubulin-binding drug that inhibits microtubule polymerization. Specifically, we performed molecular dynamics, potential-of-mean force simulations to obtain the free energy profile for unpolymerized GDP-bound tubulin as a function of the ∼12° intradimer rotation differentiating the straight and bent conformers. Our results predict that the unassembled GDP-tubulin heterodimer exists in a continuum of conformations ranging between straight and bent, but, in agreement with existing structural data, suggests that an intermediate bent state has a lower free energy (by ∼1 kcal/mol and thus dominates in solution. In agreement with predictions of the lattice model of microtubule assembly, lateral binding of two αβ-tubulins strongly shifts the conformational equilibrium towards the straight state, which is then ∼1 kcal/mol lower in free energy than the bent state. Finally, calculations of colchicine binding to a single αβ-tubulin dimer strongly shifts the equilibrium toward the bent states, and disfavors the straight state to the extent that it is no longer thermodynamically populated.

  7. Post-perovskite transitions in CaB4+O3 at high pressure

    International Nuclear Information System (INIS)

    Akaogi, M; Shirako, Y; Kojitani, H; Takamori, S; Yamaura, K; Takayama-Muromachi, E

    2010-01-01

    High-pressure phase transitions in CaRhO 3 were examined using a multianvil apparatus up to 27 GPa and 1930 o C. CaRhO 3 perovskite transforms to post-perovskite via a monoclinic intermediate phase with increasing pressure. Volume changes for the transitions of perovskite - intermediate phase and of intermediate phase - post-perovskite are -1.1 and -0.7 %, respectively. CaRhO 3 post-perovskite is the fourth quenchable post-perovskite oxide found so far. By high-temperature calorimetric experiments, enthalpy of the perovskite - post-perovskite transition in CaRuO 3 was measured as 15.2±3.3 kJ/mol. Combining the datum with those of CaIrO 3 , it is shown that CaIrO 3 perovskite is energetically less stable than CaRuO 3 perovskite. This is consistent with the fact that orthorhombic distortion of CaIrO 3 perovskite is larger than CaRuO 3 , as indicated with the tilt-angle of octahedral framework of perovskite structure. The transition pressure from perovskite to post-perovskite in CaBO 3 (B = Ru, Rh, Ir) increases almost linearly with decreasing the tilt-angle, suggesting that the perovskite - post-perovskite transition may result from instability of the perovskite structure with pressure.

  8. Conformal Infinity

    Directory of Open Access Journals (Sweden)

    Frauendiener Jörg

    2004-01-01

    Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  9. Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Hui; Mustafi, Sourajit M. [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); LeMaster, David M. [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); University at Albany – SUNY, Empire State Plaza, Albany, NY 12201 (United States); Li, Zhong [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); Héroux, Annie [Brookhaven National Laboratory, Upton, NY 11973 (United States); Li, Hongmin; Hernández, Griselda, E-mail: griselda@wadsworth.org [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); University at Albany – SUNY, Empire State Plaza, Albany, NY 12201 (United States)

    2014-03-01

    Two crystal forms of unligated FKBP12.6 exhibit multiple conformations in the active site and in the 80s loop, the primary site for known protein-recognition interactions. The previously unreported NMR backbone assignment of FKBP12.6 revealed extensive doubling of amide resonances, which reflects a slow conformational transition centered in the 80s loop. The primary known physiological function of FKBP12.6 involves its role in regulating the RyR2 isoform of ryanodine receptor Ca{sup 2+} channels in cardiac muscle, pancreatic β islets and the central nervous system. With only a single previously reported X-ray structure of FKBP12.6, bound to the immunosuppressant rapamycin, structural inferences for this protein have been drawn from the more extensive studies of the homologous FKBP12. X-ray structures at 1.70 and 1.90 Å resolution from P2{sub 1} and P3{sub 1}21 crystal forms are reported for an unligated cysteine-free variant of FKBP12.6 which exhibit a notable diversity of conformations. In one monomer from the P3{sub 1}21 crystal form, the aromatic ring of Phe59 at the base of the active site is rotated perpendicular to its typical orientation, generating a steric conflict for the immunosuppressant-binding mode. The peptide unit linking Gly89 and Val90 at the tip of the protein-recognition ‘80s loop’ is flipped in the P2{sub 1} crystal form. Unlike the >30 reported FKBP12 structures, the backbone conformation of this loop closely follows that of the first FKBP domain of FKBP51. The NMR resonances for 21 backbone amides of FKBP12.6 are doubled, corresponding to a slow conformational transition centered near the tip of the 80s loop, as recently reported for 31 amides of FKBP12. The comparative absence of doubling for residues along the opposite face of the active-site pocket in FKBP12.6 may in part reflect attenuated structural coupling owing to increased conformational plasticity around the Phe59 ring.

  10. 40 Years of Experience of NIRAS / Belgoprocess on the Interim Storage of Low, Intermediate and High Level Waste

    International Nuclear Information System (INIS)

    Braeckeveldt, Marnix; Ghys, Bart

    2016-01-01

    Conclusion: • ONDRAF/NIRAS and Belgoprocess have gained over time an extended experience on the interim storage of Low-Intermediate and High level waste. • An systematic inspection strategy was developed in order the verify the conformity of the different waste-packages and corrective measures were taken to guarantee safe storage conditions. • From 2022 , ONDRAF/NIRAS will operate a surface disposal facility for LLW

  11. Two-loop conformal generators for leading-twist operators in QCD

    International Nuclear Information System (INIS)

    Braun, V.M.; Strohmaier, M.; Manashov, A.N.; Hamburg Univ.; Moch, S.

    2016-01-01

    QCD evolution equations in minimal subtraction schemes have a hidden symmetry: One can construct three operators that commute with the evolution kernel and form an SL(2) algebra, i.e. they satisfy (exactly) the SL(2) commutation relations. In this paper we find explicit expressions for these operators to two-loop accuracy going over to QCD in non-integer d=4-2ε space-time dimensions at the intermediate stage. In this way conformal symmetry of QCD is restored on quantum level at the specially chosen (critical) value of the coupling, and at the same time the theory is regularized allowing one to use the standard renormalization procedure for the relevant Feynman diagrams. Quantum corrections to conformal generators in d=4-2ε effectively correspond to the conformal symmetry breaking in the physical theory in four dimensions and the SL(2) commutation relations lead to nontrivial constraints on the renormalization group equations for composite operators. This approach is valid to all orders in perturbation theory and the result includes automatically all terms that can be identified as due to a nonvanishing QCD β-function (in the physical theory in four dimensions). Our result can be used to derive three-loop evolution equations for flavor-nonsinglet quark-antiquark operators including mixing with the operators containing total derivatives. These equations govern, e.g., the scale dependence of generalized hadron parton distributions and light-cone meson distribution amplitudes.

  12. Interconversion of two GDP-bound conformations and their selection in an Arf-family small G protein.

    Science.gov (United States)

    Okamura, Hideyasu; Nishikiori, Masaki; Xiang, Hongyu; Ishikawa, Masayuki; Katoh, Etsuko

    2011-07-13

    ADP-ribosylation factor (Arf) and other Arf-family small G proteins participate in many cellular functions via their characteristic GTP/GDP conformational cycles, during which a nucleotide(∗)Mg(2+)-binding site communicates with a remote N-terminal helix. However, the conformational interplay between the nucleotides, the helix, the protein core, and Mg(2+) has not been fully delineated. Herein, we report a study of the dynamics of an Arf-family protein, Arl8, under various conditions by means of NMR relaxation spectroscopy. The data indicated that, when GDP is bound, the protein core, which does not include the N-terminal helix, reversibly transition between an Arf-family GDP form and another conformation that resembles the Arf-family GTP form. Additionally, we found that the N-terminal helix and Mg(2+), respectively, stabilize the aforementioned former and latter conformations in a population-shift manner. Given the dynamics of the conformational changes, we can describe the Arl8 GTP/GDP cycle in terms of an energy diagram. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Logarithmic conformal field theory through nilpotent conformal dimensions

    International Nuclear Information System (INIS)

    Moghimi-Araghi, S.; Rouhani, S.; Saadat, M.

    2001-01-01

    We study logarithmic conformal field theories (LCFTs) through the introduction of nilpotent conformal weights. Using this device, we derive the properties of LCFTs such as the transformation laws, singular vectors and the structure of correlation functions. We discuss the emergence of an extra energy momentum tensor, which is the logarithmic partner of the energy momentum tensor

  14. Viscous conformal gauge theories

    DEFF Research Database (Denmark)

    Toniato, Arianna; Sannino, Francesco; Rischke, Dirk H.

    2017-01-01

    We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories.......We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories....

  15. Probing Conformational Stability and Dynamics of Erythroid and Nonerythroid Spectrin: Effects of Urea and Guanidine Hydrochloride

    Science.gov (United States)

    Patra, Malay; Mukhopadhyay, Chaitali; Chakrabarti, Abhijit

    2015-01-01

    We have studied the conformational stability of the two homologous membrane skeletal proteins, the erythroid and non-erythroid spectrins, in their dimeric and tetrameric forms respectively during unfolding in the presence of urea and guanidine hydrochloride (GuHCl). Fluorescence and circular dichroism (CD) spectroscopy have been used to study the changes of intrinsic tryptophan fluorescence, anisotropy, far UV-CD and extrinsic fluorescence of bound 1-anilinonapthalene-8-sulfonic acid (ANS). Chemical unfolding of both proteins were reversible and could be described as a two state transition. The folded erythroid spectrin and non-erythroid spectrin were directly converted to unfolded monomer without formation of any intermediate. Fluorescence quenching, anisotropy, ANS binding and dynamic light scattering data suggest that in presence of low concentrations of the denaturants (up-to 1M) hydrogen bonding network and van der Waals interaction play a role inducing changes in quaternary as well as tertiary structures without complete dissociation of the subunits. This is the first report of two large worm like, multi-domain proteins obeying twofold rule which is commonly found in small globular proteins. The free energy of stabilization (ΔGu H 2 0) for the dimeric spectrin has been 20 kcal/mol lesser than the tetrameric from. PMID:25617632

  16. Photofragment imaging study of the CH2CCH2OH radical intermediate of the OH+allene reaction

    International Nuclear Information System (INIS)

    Raman, Arjun S.; Justine Bell, M.; Lau, K.-C.; Butler, Laurie J.

    2007-01-01

    These velocity map imaging experiments characterize the photolytic generation of one of the two radical intermediates formed when OH reacts via an addition mechanism with allene. The CH 2 CCH 2 OH radical intermediate is generated photolytically from the photodissociation of 2-chloro-2-propen-1-ol at 193 nm. Detecting the Cl atoms using [2+1] resonance-enhanced multiphoton ionization evidences an isotropic angular distribution for the Cl+CH 2 CCH 2 OH photofragments, a spin-orbit branching ratio for Cl( 2 P 1/2 ):Cl( 2 P 3/2 ) of 0.28, and a bimodal recoil kinetic energy distribution. Conservation of momentum and energy allows us to determine from this data the internal energy distribution of the nascent CH 2 CCH 2 OH radical cofragment. To assess the possible subsequent decomposition pathways of this highly vibrationally excited radical intermediate, we include electronic structure calculations at the G3//B3LYP level of theory. They predict the isomerization and dissociation transition states en route from the initial CH 2 CCH 2 OH radical intermediate to the three most important product channels for the OH+allene reaction expected from this radical intermediate: formaldehyde+C 2 H 3 , H+acrolein, and ethene+CHO. We also calculate the intermediates and transition states en route from the other radical adduct, formed by addition of the OH to the center carbon of allene, to the ketene+CH 3 product channel. We compare our results to a previous theoretical study of the O+allyl reaction conducted at the CBS-QB3 level of theory, as the two reactions include several common intermediates

  17. Photofragment imaging study of the CH2CCH2OH radical intermediate of the OH +allene reaction

    Science.gov (United States)

    Raman, Arjun S.; Justine Bell, M.; Lau, Kai-Chung; Butler, Laurie J.

    2007-10-01

    These velocity map imaging experiments characterize the photolytic generation of one of the two radical intermediates formed when OH reacts via an addition mechanism with allene. The CH2CCH2OH radical intermediate is generated photolytically from the photodissociation of 2-chloro-2-propen-1-ol at 193nm. Detecting the Cl atoms using [2+1] resonance-enhanced multiphoton ionization evidences an isotropic angular distribution for the Cl +CH2CCH2OH photofragments, a spin-orbit branching ratio for Cl(P1/22):Cl(P3/22) of 0.28, and a bimodal recoil kinetic energy distribution. Conservation of momentum and energy allows us to determine from this data the internal energy distribution of the nascent CH2CCH2OH radical cofragment. To assess the possible subsequent decomposition pathways of this highly vibrationally excited radical intermediate, we include electronic structure calculations at the G3//B3LYP level of theory. They predict the isomerization and dissociation transition states en route from the initial CH2CCH2OH radical intermediate to the three most important product channels for the OH +allene reaction expected from this radical intermediate: formaldehyde+C2H3, H +acrolein, and ethene+CHO. We also calculate the intermediates and transition states en route from the other radical adduct, formed by addition of the OH to the center carbon of allene, to the ketene+CH3 product channel. We compare our results to a previous theoretical study of the O +allyl reaction conducted at the CBS-QB3 level of theory, as the two reactions include several common intermediates.

  18. Polarization control of multi-photon absorption under intermediate femtosecond laser field

    International Nuclear Information System (INIS)

    Cheng Wenjing; Liang Guo; Wu Ping; Liu Pei; Jia Tianqing; Sun Zhenrong; Zhang Shian

    2017-01-01

    It has been shown that the femtosecond laser polarization modulation is a very simple and well-established method to control the multi-photon absorption process by the light–matter interaction. Previous studies mainly focused on the multi-photon absorption control in the weak field. In this paper, we further explore the polarization control behavior of multi-photon absorption process in the intermediate femtosecond laser field. In the weak femtosecond laser field, the second-order perturbation theory can well describe the non-resonant two-photon absorption process. However, the higher order nonlinear effect (e.g., four-photon absorption) can occur in the intermediate femtosecond laser field, and thus it is necessary to establish new theoretical model to describe the multi-photon absorption process, which includes the two-photon and four-photon transitions. Here, we construct a fourth-order perturbation theory to study the polarization control behavior of this multi-photon absorption under the intermediate femtosecond laser field excitation, and our theoretical results show that the two-photon and four-photon excitation pathways can induce a coherent interference, while the coherent interference is constructive or destructive that depends on the femtosecond laser center frequency. Moreover, the two-photon and four-photon transitions have the different polarization control efficiency, and the four-photon absorption can obtain the higher polarization control efficiency. Thus, the polarization control efficiency of the whole excitation process can be increased or decreased by properly designing the femtosecond laser field intensity and laser center frequency. These studies can provide a clear physical picture for understanding and controlling the multi-photon absorption process in the intermediate femtosecond laser field, and also can provide a theoretical guidance for the future experimental realization. (paper)

  19. Conformal flight path symbology for head-up displays: Defining the distribution of visual attention in three-dimensional space

    Science.gov (United States)

    Ververs, Patricia May

    An extensive investigation of the format for head-up display (HUD) instrumentation was conducted in a two-part experiment. First, a pilot's information requirements for the tasks of approach, landing, and taxi were determined through a survey administered to professional commercial pilots via the world wide web. The results of the survey were applied in the development of two symbology sets, one set for flight navigation and the second for ground navigation. Second, twenty pilots from the University of Illinois at Urbana-Champaign were recruited to participate in a 3-day experiment. The study was designed to investigate the format for symbology on HUDs and the performance effects of using conformal and partially conformal symbology to support the pilots' tasks. In addition, two different methods were investigated for supporting the pilots' transition between the task of flying and the task of landing. A seamless transition used visual momentum techniques to smoothly guide the pilots' cognitive transition between the serial displays and the associated tasks. A seamed approach employed an abrupt change between the displays to alert the pilots of the task switch. The results indicate that incorporating a virtually conformal, tunnel-in-the-sky symbology into a complete HUD instrumentation set offers promising pilot performance effects. Pilots easily navigated the complex curved approaches with little to no deviation from the flight path (approximately 10 feet), while performing the secondary tasks of the scanning their instruments and the environment. The seamless transition between the flight and ground symbology offered the pilots a preview of the upcoming landing task, thereby preparing them for the task switch. On the ground, the perspective (scene-linked) symbology set supported landing and taxi navigation tasks with the equal efficiency to the plan view display but with much greater precision. Theories of allocation of attention were used to interpret the

  20. Conformal invariance in supergravity

    International Nuclear Information System (INIS)

    Bergshoeff, E.A.

    1983-01-01

    In this thesis the author explains the role of conformal invariance in supergravity. He presents the complete structure of extended conformal supergravity for N <= 4. The outline of this work is as follows. In chapter 2 he briefly summarizes the essential properties of supersymmetry and supergravity and indicates the use of conformal invariance in supergravity. The idea that the introduction of additional symmetry transformations can make clear the structure of a field theory is not reserved to supergravity only. By means of some simple examples it is shown in chapter 3 how one can always introduce additional gauge transformations in a theory of massive vector fields. Moreover it is shown how the gauge invariant formulation sometimes explains the quantum mechanical properties of the theory. In chapter 4 the author defines the conformal transformations and summarizes their main properties. He explains how these conformal transformations can be used to analyse the structure of gravity. The supersymmetric extension of these results is discussed in chapter 5. Here he describes as an example how N=1 supergravity can be reformulated in a conformally-invariant way. He also shows that beyond N=1 the gauge fields of the superconformal symmetries do not constitute an off-shell field representation of extended conformal supergravity. Therefore, in chapter 6, a systematic method to construct the off-shell formulation of all extended conformal supergravity theories with N <= 4 is developed. As an example he uses this method to construct N=1 conformal supergravity. Finally, in chapter 7 N=4 conformal supergravity is discussed. (Auth.)

  1. Optimal design of the cable metro with unified intermediate supports

    Directory of Open Access Journals (Sweden)

    Lagerev A.V.

    2017-12-01

    slope of the surface relief also has discrete-step type. The transition to a larger height unified intermediate supports determines the need for installation of supports with a large pitch. Its value then begins to decrease monotonically with further increase of the angle of the longitudinal slope of the surface relief until it needs to transition to the new size of supports. Synchronous change in the optimal values of the height and step of the installation of intermediate supports, depending on the angle of the longitudinal slope of the sur-face relief leads to the fact that the optimal cost characteristics of the cable metro lines are smooth functions. It has an extreme character with a minimum at angles of inclination of the surface elevation ~5 degrees, which is associated with the form of sagging of the load-bearing ropes. Unification of intermediate supports has little effect on the optimal cost characteristics of the cable metro lines. Even for a sufficiently large step of the unification the largest difference in op-timal value is almost insignificant: it lies in the range of 2...3%, increasing with increasing the angle of the longitudinal slope of the surface relief and unit cost of the intermediate support. Unification of intermediate supports according to the height and their step practically does not affect the optimal value for horizontal tension on the load-bearing ropes. It determined mainly by the angle of the longitudinal slope of the surface relief. Deviation of horizontal tension on the load-bearing ropes for the nonstandard supports and the unified supports within the range of angles of inclination of the terrain surface 0...60 degrees is not more than 0.5 to 0.8 %.

  2. Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

    Science.gov (United States)

    Min, Wei; Xie, X. Sunney; Bagchi, Biman

    2009-08-01

    Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

  3. Characteristics of Ir/Au transition edge sensor

    International Nuclear Information System (INIS)

    Kunieda, Yuichi; Ohno, Masashi; Nakazawa, Masaharu; Takahashi, Hiroyuki; Fukuda, Daiji; Ohkubo, Masataka

    2004-01-01

    A new type of microcalorimeter has been developed using a transition edge sensor (TES) and an electro-thermal feedback (ETF) method to achieve higher energy resolution and higher count rate. We are developing a superconducting Ir-based transition edge sensor (TES) microcalorimeters. To improve thermal conductivity and achieve higher energy resolution with an Ir-TES, we fabricated an Ir/Au bilayer TES by depositing gold on Ir and investigated the influence of intermediate between superconducting and normal states at the transition edge for signal responses by microscopic observation in the Ir/Au-TES. (T. Tanaka)

  4. Full conformational landscape of 3-Methoxyphenol revealed by room temperature mm-wave rotational spectroscopy supported by quantum chemical calculations.

    Science.gov (United States)

    Roucou, Anthony; Fontanari, Daniele; Dhont, Guillaume; Jabri, Atef; Bray, Cédric; Hindle, Francis; Mouret, Gaël; Bocquet, Robin; Cuisset, Arnaud

    2018-03-30

    Room temperature millimeter-wave rotational spectroscopy supported by high level of theory calculations have been employed to fully characterise the conformational landscape of 3-Methoxyphenol, a semi-volatile polar oxygenated aromatic compound precursor of secondary organic aerosols in the atmosphere arising from biomass combustion. While previous rotationally-resolved spectroscopic studies in the microwave and in the UV domains failed to observe the complete conformational landscape, the 70 - 330 GHz rotational spectrum measured in this study reveals the ground state rotational signatures of the four stable conformations theoretically predicted. Moreover, rotational transitions in the lowest energy vibrationally excited states were assigned for two conformers. While the inertial defect of methoxyphenol does not signicantly change between conformers and isomers, the excitation of the methoxy out-of-plane bending is the main contribution to the non-planarity of the molecule. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Lifetime enhancement for multiphoton absorption in intermediate band solar cells

    International Nuclear Information System (INIS)

    Bezerra, Anibal T; Studart, Nelson

    2017-01-01

    A semiconductor structure consisting of two coupled quantum wells embedded into the intrinsic region of a p – i–n junction is proposed as an intermediate band solar cell with a photon ratchet state, which would lead to increasing the cell efficiency. The conduction subband of the right-hand side quantum well works as the intermediated band, whereas the excited conduction subband of the left-hand side quantum well operates as the ratchet state. The photoelectrons in the intermediate band are scattered through the thin wells barrier and accumulated into the ratchet subband. A rate equation model for describing the charge transport properties is presented. The efficiency of the current generation is analyzed by studying the occupation of the wells subbands, taking into account the charge dynamic behavior provided by the electrical contacts connected to the cell. The current generation efficiency depends essentially from the relations between the generation, recombination rates and the scattering rate to the ratchet state. The inclusion of the ratchet states led to both an increase and a decrease in the cell current depending on the transition rates. This suggests that the coupling between the intermediate band and the ratchet state is a key point in developing an efficient solar cell. (paper)

  6. Lifetime enhancement for multiphoton absorption in intermediate band solar cells

    Science.gov (United States)

    Bezerra, Anibal T.; Studart, Nelson

    2017-08-01

    A semiconductor structure consisting of two coupled quantum wells embedded into the intrinsic region of a p-i-n junction is proposed as an intermediate band solar cell with a photon ratchet state, which would lead to increasing the cell efficiency. The conduction subband of the right-hand side quantum well works as the intermediated band, whereas the excited conduction subband of the left-hand side quantum well operates as the ratchet state. The photoelectrons in the intermediate band are scattered through the thin wells barrier and accumulated into the ratchet subband. A rate equation model for describing the charge transport properties is presented. The efficiency of the current generation is analyzed by studying the occupation of the wells subbands, taking into account the charge dynamic behavior provided by the electrical contacts connected to the cell. The current generation efficiency depends essentially from the relations between the generation, recombination rates and the scattering rate to the ratchet state. The inclusion of the ratchet states led to both an increase and a decrease in the cell current depending on the transition rates. This suggests that the coupling between the intermediate band and the ratchet state is a key point in developing an efficient solar cell.

  7. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

    International Nuclear Information System (INIS)

    Shi, Jade; Schwantes, Christian; Bilsel, Osman

    2017-01-01

    The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

  8. A pH-dependent conformational ensemble mediates proton transport through the influenza A/M2 protein†

    Science.gov (United States)

    Polishchuk, Alexei L.; Lear, James D.; Ma, Chunlong; Lamb, Robert A.; Pinto, Lawrence H.; DeGrado, William F.

    2010-01-01

    The influenza A M2 protein exhibits inwardly rectifying, pH-activated proton transport that saturates at low pH. A comparison of high-resolution structures of the transmembrane domain at high and low pH suggests that pH-dependent conformational changes may facilitate proton conduction by alternately changing the accessibility of the N-terminal and C-terminal regions of the channel as a proton transits through the transmembrane domain. Here, we show that M2 functionally reconstituted in liposomes populates at least three different conformational states over a physiologically relevant pH range, with transition midpoints that are consistent with previously reported His37 pKas. We then develop and test two similar, quantitative mechanistic models of proton transport, where protonation shifts the equilibrium between structural states having different proton affinities and solvent accessibilities. The models account well for a collection of experimental data sets over a wide range of pHs and voltages and require only a small number of adjustable parameters to accurately describe the data. While the kinetic models do not require any specific conformation for the protein, they nevertheless are consistent with a large body of structural information based on high-resolution NMR and crystallographic structures, optical spectroscopy, and MD calculations. PMID:20968306

  9. The investigation of order–disorder transition process of ZSM-5 induced by spark plasma sintering

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Liang [State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, 2999 North Renmin Road, Songjiang, Shanghai 201620 (China); Wang, Lianjun, E-mail: wanglj@dhu.edu.cn [State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, 2999 North Renmin Road, Songjiang, Shanghai 201620 (China); Jiang, Wan [Engineering Research Center of Advanced Glasses Manufacturing Technology, MOE, Donghua University, 2999 North Renmin Road, Songjiang, Shanghai 201620 (China); Lin, He, E-mail: linhe@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Pudong, Shanghai 200120 (China)

    2014-04-01

    Based on the amorphization of zeolites, an order–disorder transition method was used to prepare silica glass via Spark Plasma Sintering (SPS). In order to get a better understanding about the mechanism of amorphization induced by SPS, the intermediate products in this process were prepared and characterized by different characterization techniques. X-ray diffraction and High-energy synchrotron X-ray scattering show a gradual transformation from ordered crystal to glass. Local structural changes in glass network including Si–O bond length, O–Si–O bond angle, size of rings, coordination were detected by Infrared spectroscopy and {sup 29}Si magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy. Topologically ordered, amorphous material with a different intermediate-range structure can be obtained by precise control of intermediate process which can be expected to optimize and design material. - Graphical abstract: Low-density, ordered zeolites collapse to the rigid amorphous glass through spark plasma sintering. The intermediate-range structure formed in the process of order–disorder transition may give rise to specific property. - Highlights: • Order–disorder transition process of ZSM-5 induced by spark plasma sintering was investigated using several methods including XRD, High-energy synchrotron X-ray scattering, SAXS, IR, NMR, ect. • Order–disorder transition induced by SPS was compared with TIA and PIA. • Three stages has been divided during the whole process. • The collapse temperature range which may give rise to intermediate-range structure has been located.

  10. Freeze-quench (57)Fe-Mössbauer spectroscopy: trapping reactive intermediates.

    Science.gov (United States)

    Krebs, Carsten; Bollinger, J Martin

    2009-01-01

    (57)Fe-Mössbauer spectroscopy is a method that probes transitions between the nuclear ground state (I=1/2) and the first nuclear excited state (I=3/2). This technique provides detailed information about the chemical environment and electronic structure of iron. Therefore, it has played an important role in studies of the numerous iron-containing proteins and enzymes. In conjunction with the freeze-quench method, (57)Fe-Mössbauer spectroscopy allows for monitoring changes of the iron site(s) during a biochemical reaction. This approach is particularly powerful for detection and characterization of reactive intermediates. Comparison of experimentally determined Mössbauer parameters to those predicted by density functional theory for hypothetical model structures can then provide detailed insight into the structures of reactive intermediates. We have recently used this methodology to study the reactions of various mononuclear non-heme-iron enzymes by trapping and characterizing several Fe(IV)-oxo reaction intermediates. In this article, we summarize these findings and demonstrate the potential of the method. © Springer Science+Business Media B.V. 2009

  11. On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

    International Nuclear Information System (INIS)

    Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Fernandez-Alberti, Sebastian; Roitberg, Adrian E.

    2015-01-01

    The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data

  12. On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

    Energy Technology Data Exchange (ETDEWEB)

    Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Fernandez-Alberti, Sebastian, E-mail: sfalberti@gmail.com [Universidad Nacional de Quilmes, Roque Saenz Peña 352, B1876BXD Bernal (Argentina); Roitberg, Adrian E. [Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611 (United States)

    2015-06-28

    The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

  13. Structural analyses of polymorphic transitions of sn-1, 3-distearoyl-2-oleoylglycerol (SOS) and sn-1, 3-dioleoyl-2-stearoylglycerol (OSO): assessment on steric hindrance of unsaturated and saturated acyl chain interactions.

    Science.gov (United States)

    Yano, J; Sato, K; Kaneko, F; Small, D M; Kodali, D R

    1999-01-01

    Polymorphic transformations in two saturated-unsaturated mixed acid triacylglycerols, SOS (sn -1,3-distearoyl-2-oleoylglycerol) and OSO (sn -1,3-dioleoyl-2-stearoylglycerol), have been studied by FT-IR spectroscopy using deuterated specimens in which stearoyl chains are fully deuterated. A reversible phase transition between sub alpha and alpha and a series of irreversible transitions (alpha-->gamma-->beta'-->beta (beta2, beta1) for SOS and alpha-->beta'-->beta for OSO) were studied with an emphasis on the conformational ordering process of stearoyl and oleoyl chains. The alpha-->sub alpha reversible transition was due to the orientational change of stearoyl chains in the lateral directions from the hexagonal subcell to a perpendicularly packed one. As the first stage of the series of irreversible transitions from alpha to beta, the conformational ordering of saturated chains took place in the alpha-->gamma transition of SOS and in the alpha-->beta' transition of OSO; one stearoyl chain in SOS and OSO takes the all-trans conformation and the second stearoyl chain in SOS takes the bent conformation like those observed in the most stable beta-type. As the final stage, the ordering of unsaturated chains occurred in the beta'-->beta transition both for SOS and OSO. A conversion in the layered structure from bilayer to trilayer was also accompanied by the conformational ordering in the alpha-->gamma transition of SOS and in the beta'-->beta transition of OSO.

  14. Brillouin spectroscopy with surface acoustic waves on intermediate valent, doped SmS

    International Nuclear Information System (INIS)

    Schaerer, U.; Jung, A.; Wachter, P.

    1998-01-01

    Brillouin scattering on surface acoustic waves is a very powerful tool to determine the elastic constants of intermediate valent crystals, since the method is non-destructive and no mechanical contact is needed. A strong evidence for intermediate valence is a negative value of Poisson's ratio, which describes the behavior of the volume under uniaxial pressure. SmS by itself makes a semiconductor-metal transition at a pressure of more than 6.5 kbar. When substituting the divalent Sm by a trivalent cation, like Y, La or Tm, SmS can become - depending on the doping concentration - intermediate valent without any applied, external pressure. In this work, we will present measurements of the velocities of the surface acoustic waves and the calculation of the elastic constants of La- and Tm-doped SmS compounds. We found a clear dependence of Poisson's ratio on the doping concentration and on the valence of the materials. Furthermore, we will discuss the mechanism leading to intermediate valence when substituting Sm. Besides the internal, chemical pressure, which is produced by the built in trivalent cations with their smaller ionic radii, we have clear evidence, that the free electrons in the 5d band, induced by the substituting atoms, also play an important role in making doped SmS intermediate valent. (orig.)

  15. EVIDENCE OF LIGHT-BENDING EFFECTS AND ITS IMPLICATION FOR SPECTRAL STATE TRANSITIONS

    International Nuclear Information System (INIS)

    Reis, R. C.; Miller, J. M.; Reynolds, M. T.; Fabian, A. C.; Walton, D. J.; Steiner, J. F.; Cackett, E.

    2013-01-01

    It has long been speculated that the nature of the hard X-ray corona may be an important second driver of black hole state transitions, in addition to the mass accretion rate through the disk. However, a clear physical picture of coronal changes has not yet emerged. We present results from a systematic analysis of Rossi X-Ray Timing Explorer observations of the stellar-mass black hole binary XTE J1650-500. All spectra with significant hard X-ray detections were fit using a self-consistent, relativistically blurred disk reflection model suited to high ionization regimes. Importantly, we find evidence that both the spectral and timing properties of black hole states may be partially driven by the height of the X-ray corona above the disk, and related changes in how gravitational light bending affects the corona-disk interaction. Specifically, the evolution of the power-law, thermal disk, and relativistically convolved reflection components in our spectral analysis indicates that: (1) the disk inner radius remains constant at r in =1.65 ± 0.08 GM/c 2 (consistent with values found for the ISCO of XTE J1650-500 in other works) throughout the transition from the brighter phases of the low-hard state to the intermediate states (both the hard-intermediate and soft-intermediate), through to the soft state and back; (2) the ratio between the observed reflected X-ray flux and power-law continuum (the 'reflection fraction', R) increases sharply at the transition between the hard-intermediate and soft-intermediate states ('ballistic' jets are sometimes launched at this transition); (3) both the frequency and coherence of the high-frequency quasi-periodic oscillations observed in XTE J1650-500 increase with R. We discuss our results in terms of black hole states and the nature of black hole accretion flows across the mass scale.

  16. Synthesis of specifically 15N- and 13C-labeled antitumor (2-Haloethyl)nitrosoureas. The study of their conformations in solution by nitrogen-15 and carbon-13 nuclear magnetic resonance and evidence for stereoelectronic control in their aqueous decomposition

    International Nuclear Information System (INIS)

    Lown, J.W.; Chauhan, S.M.S.

    1981-01-01

    The synthesis of certain specifically 15 N, 13 C, and 2 H isotope labeled 1-(2-chloroethyl)-3-alkyl-1-nitrosoureas (CENUs) is described. Spectroscopic examination of CENUs and their isotope-labeled counterparts by 1 H, 15 N, and 13 C NMR and infrared spectra indicates that they adopt preferred conformations in nonpolar aprotic solvents in which the NO group is aligned toward the 2-chloroethyl group. The result is in accord with the conformation of MeCCNU in the crystalline state derived from X-ray diffraction. The chemical shifts and coupling constants in the CENUs change with both solvent polarity and basicity. In aqueous phosphate buffer there is evidence for the formation of a tetrahedral intermediate, the conformation of which alters according to the reaction conditions and ultimately controls the formation of the aqueous decomposition products of CENUs. This is revealed most clearly by 13 C NMR of carbonyl- 13 C- and nitroso- 15 N-labeled BCNU and CCNU where two distinct 15 N-coupled 13 C doublets with different chemical shifts are observed. The rate of conformational change is comparable with the rate of decomposition of CENUs (via the second conformer) and may therefore represent the critical initial step of the latter process in vivo. The intermediacy of the postulated tetrahedral intermediates for CENUs is supported by observed 18 O exchange into the carbonyl group in 18 O-enriched water. Consideration of the conformations of the intermediates and of the alignment of the heteroatom lone pairs provides a satisfactory interpretation of the reactions of CENUs in aqueous solution as well as their pH dependence in terms of strict steroelectronic control and accounts for the formation of the observed products

  17. Rotational spectrum and conformational composition of cyanoacetaldehyde, a compound of potential prebiotic and astrochemical interest.

    Science.gov (United States)

    Møllendal, Harald; Margulès, Laurent; Motiyenko, Roman A; Larsen, Niels Wessel; Guillemin, Jean-Claude

    2012-04-26

    The rotational spectrum of cyanoacetaldehyde (NCCH(2)CHO) has been investigated in the 19.5-80.5 and 150-500 GHz spectral regions. It is found that cyanoacetaldehyde is strongly preferred over its tautomer cyanovinylalcohol (NCCH═CHOH) in the gas phase. The spectra of two rotameric forms of cyanoacetaldehyde produced by rotation about the central C-C bond have been assigned. The C-C-C-O dihedral angle has an unusual value of 151(3)° from the synperiplanar (0°) position in one of the conformers denoted I, while this dihedral angle is exactly synperiplanar in the second rotamer called II, which therefore has C(s) symmetry. Conformer I is found to be preferred over II by 2.9(8) kJ/mol from relative intensity measurements. A double minimum potential for rotation about the central C-C bond with a small barrier maximum at the exact antiperiplanar (180°) position leads to Coriolis perturbations in the rotational spectrum of conformer I. Selected transitions of I were fitted to a Hamiltonian allowing for this sort of interaction, and the separation between the two lowest vibrational states was determined to be 58794(14) MHz [1.96112(5) cm(-1)]. Attempts to include additional transitions in the fits using this Hamiltonian failed, and it is concluded that it lacks interaction terms to account satisfactorily for all the observed transitions. The situation was different for II. More than 2000 transitions were assigned and fitted to the usual Watson Hamiltonian, which allowed very accurate values to be determined not only for the rotational constants, but for many centrifugal distortion constants as well. Two vibrationally excited states were also assigned for this form. Theoretical calculations were performed at the B3LYP, MP2, and CCSD levels of theory using large basis sets to augment the experimental work. The predictions of these calculations turned out to be in good agreement with most experimental results.

  18. Calibration of laboratory equipment and its intermediate verification

    International Nuclear Information System (INIS)

    Remedi, Jorge O.

    2011-01-01

    When a laboratory wants to prove that he has technical competence to carry out tests or calibrations must demonstrate that it has complied with certain requirements that establish , among others, the mandatory : calibrate or verify equipment before putting it into service in order to ensure that it meets to the specifications of laboratory equipment to keep records evidencing the checks that equipment complies with the specification ; perform intermediate checks for maintain confidence in the calibration status of the equipment , ensure that the operation is checked and calibration status of equipment when the equipment goes outside the direct control of the laboratory , before be returned to service, establish a program and procedure for the calibration of equipment; show how determined the calibration periods of their equipment as well as evidence that intermediate checks are suitable for the calibration periods. However, some confusion is observed as to the meaning of the terms 'calibration' and 'verification' of a computer. This paper analyzes applicable documentation and suggests that the differences are generated in part by translations and by characterization concepts upon its usage, that is, if it is legal metrology or assessment conformity. Therefore, this study aims to characterize both concepts , fundamentals to zoom distinguish , outline appropriate strategies for calibration and verification activities to ensure the compliance with regulatory requirements [es

  19. Conformal expansions and renormalons

    Energy Technology Data Exchange (ETDEWEB)

    Rathsman, J.

    2000-02-07

    The coefficients in perturbative expansions in gauge theories are factorially increasing, predominantly due to renormalons. This type of factorial increase is not expected in conformal theories. In QCD conformal relations between observables can be defined in the presence of a perturbative infrared fixed-point. Using the Banks-Zaks expansion the authors study the effect of the large-order behavior of the perturbative series on the conformal coefficients. The authors find that in general these coefficients become factorially increasing. However, when the factorial behavior genuinely originates in a renormalon integral, as implied by a postulated skeleton expansion, it does not affect the conformal coefficients. As a consequence, the conformal coefficients will indeed be free of renormalon divergence, in accordance with previous observations concerning the smallness of these coefficients for specific observables. The authors further show that the correspondence of the BLM method with the skeleton expansion implies a unique scale-setting procedure. The BLM coefficients can be interpreted as the conformal coefficients in the series relating the fixed-point value of the observable with that of the skeleton effective charge. Through the skeleton expansion the relevance of renormalon-free conformal coefficients extends to real-world QCD.

  20. Theoretical predictor for candidate structure assignment from IMS data of biomolecule-related conformational space.

    Science.gov (United States)

    Schenk, Emily R; Nau, Frederic; Fernandez-Lima, Francisco

    2015-06-01

    The ability to correlate experimental ion mobility data with candidate structures from theoretical modeling provides a powerful analytical and structural tool for the characterization of biomolecules. In the present paper, a theoretical workflow is described to generate and assign candidate structures for experimental trapped ion mobility and H/D exchange (HDX-TIMS-MS) data following molecular dynamics simulations and statistical filtering. The applicability of the theoretical predictor is illustrated for a peptide and protein example with multiple conformations and kinetic intermediates. The described methodology yields a low computational cost and a simple workflow by incorporating statistical filtering and molecular dynamics simulations. The workflow can be adapted to different IMS scenarios and CCS calculators for a more accurate description of the IMS experimental conditions. For the case of the HDX-TIMS-MS experiments, molecular dynamics in the "TIMS box" accounts for a better sampling of the molecular intermediates and local energy minima.

  1. Radio Detections During Two State Transitions of the Intermediate-Mass Black Hole HLX-1

    Science.gov (United States)

    Webb, Natalie; Cseh, David; Lenc, Emil; Godet, Olivier; Barret, Didier; Corbel, Stephane; Farrell, Sean; Fender, Robert; Gehrels, Neil; Heywood, Ian

    2012-01-01

    Relativistic jets are streams of plasma moving at appreciable fractions of the speed of light. They have been observed from stellar-mass black holes (approx. 3 to 20 solar masses) as well as supermassive black holes (approx.. 10(exp 6) to 10(exp 9) Solar Mass) found in the centers of most galaxies. Jets should also be produced by intermediate-mass black holes (approx. 10(exp 2) to 10(exp 5) Solar Mass), although evidence for this third class of black hole has, until recently, been weak. We report the detection of transient radio emission at the location of the intermediate-mass black hole candidate ESO 243-49 HLX-1, which is consistent with a discrete jet ejection event. These observations also allow us to refine the mass estimate of the black hole to be between approx. 9 × 10(exp 3) Solar Mass and approx. 9 × 10(exp 4) Solar Mass.

  2. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    Energy Technology Data Exchange (ETDEWEB)

    Carraher, Jack McCaslin [Iowa State Univ., Ames, IA (United States)

    2014-01-01

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding ‘greener’ sources of commodity chemicals and fuels.

  3. Crystallisation and chain conformation of long chain n-alkanes

    International Nuclear Information System (INIS)

    Gorce, J.

    2000-06-01

    Hydrocarbon chains are a basic component in a number of systems as diverse as biological membranes, phospholipids and polymers. A better understanding of the physical properties of n-alkane chains should provide a better understanding of these more complex systems. With this aim, vibrational spectroscopy has been extensively used. This technique, sensitive to molecular details, is the only one able to both identify and quantify conformational disorder present in paraffinic systems. To achieve this, methyl deformations have been widely used as ''internal standards'' for the normalisation of peak areas. However, in the case of n-alkanes with short chain length, such as n-C 44 H 90 for example, the infrared spectra recorded at liquid nitrogen temperature and reported here show the sensitivity of these latter peaks to the various crystal structures formed. Indeed, the main frequencies of the symmetric methyl bending mode were found between 1384 cm -1 and 1368 cm -1 as a function of the crystal form. Changes in the frequency of the first order of the L.A.M. present in the Raman spectra were also observed. At higher temperatures, non all-trans conformers, inferred from different infrared bands present in the wagging mode region, were found to be essentially placed at the end of the n-alkane chains. At the monoclinic phase transition, the concentration of end-gauche conformers, proportional to the area of the infrared band at 1342 cm -1 , increases abruptly. On the contrary, in the spectra recorded at liquid nitrogen temperature no such band is observed. We also studied the degree of disorder in two purely monodisperse long chain n-alkanes, namely n-C 198 H 398 and n-C 246 H 494 . The chain conformation as well as the tilt angle of the chains from the crystal surfaces were determined by means of low frequency Raman spectroscopy and S.A.X.S. measurements on solution-crystallised samples. The increase in the number of end-gauche conformers which was expected to occur with

  4. TOWARDS UNDERSTANDING OF HELIX B BASED CONFORMATIONAL DISEASES IN SERPIN

    Directory of Open Access Journals (Sweden)

    Mohamad Aman Jairajpuri

    2012-12-01

    Full Text Available Serine protease inhibitors (serpins are a unique family of protease inhibitors that are prone to polymer formation due to their metastable nature and a complex inhibition mechanism that involves large scale conformational change. Helix B is in the shutter region near the strand 2A and strand 3A of �-sheet A, where reactive centre loop inserts during the serpin inhibition mechanism. Helix B region in serpins is a mutation hotspot for naturally occurring variants that result in pathological conditions due to polymerization. Helix B residues are completely buried in the native state and loop inserted latent state but not in the inhibitory loop inserted cleaved conformation. Native to cleaved transition during inhibition forms a large cavity in the shutter region, which invariably is the largest cavity in most serpins in native state. In a recent paper we had for the first time hypothesized that exposure of helix B at the N-terminal end is important for smooth insertion of the reactive center loop during serpin inhibition mechanism. It is therefore possible that natural variant that induces conformational deformation of helix B probably alter the cavity size which increases the rate of loop-sheet interaction between the monomers resulting in increased polymerization.

  5. Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements

    Science.gov (United States)

    Onuk, A. Emre; Akcakaya, Murat; Bardhan, Jaydeep P.; Erdogmus, Deniz; Brooks, Dana H.; Makowski, Lee

    2015-01-01

    In this paper, we describe a model for maximum likelihood estimation (MLE) of the relative abundances of different conformations of a protein in a heterogeneous mixture from small angle X-ray scattering (SAXS) intensities. To consider cases where the solution includes intermediate or unknown conformations, we develop a subset selection method based on k-means clustering and the Cramér-Rao bound on the mixture coefficient estimation error to find a sparse basis set that represents the space spanned by the measured SAXS intensities of the known conformations of a protein. Then, using the selected basis set and the assumptions on the model for the intensity measurements, we show that the MLE model can be expressed as a constrained convex optimization problem. Employing the adenylate kinase (ADK) protein and its known conformations as an example, and using Monte Carlo simulations, we demonstrate the performance of the proposed estimation scheme. Here, although we use 45 crystallographically determined experimental structures and we could generate many more using, for instance, molecular dynamics calculations, the clustering technique indicates that the data cannot support the determination of relative abundances for more than 5 conformations. The estimation of this maximum number of conformations is intrinsic to the methodology we have used here. PMID:26924916

  6. Conformational analysis by intersection: CONAN.

    Science.gov (United States)

    Smellie, Andrew; Stanton, Robert; Henne, Randy; Teig, Steve

    2003-01-15

    As high throughput techniques in chemical synthesis and screening improve, more demands are placed on computer assisted design and virtual screening. Many of these computational methods require one or more three-dimensional conformations for molecules, creating a demand for a conformational analysis tool that can rapidly and robustly cover the low-energy conformational spaces of small molecules. A new algorithm of intersection is presented here, which quickly generates (on average heuristics are applied after intersection to generate a small representative collection of conformations that span the conformational space. In a study of approximately 97,000 randomly selected molecules from the MDDR, results are presented that explore these conformations and their ability to cover low-energy conformational space. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 24: 10-20, 2003

  7. Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase

    International Nuclear Information System (INIS)

    Okai, Masahiko; Yamamura, Akihiro; Hayakawa, Kou; Tsutsui, Shiho; Miyazono, Ken-ichi; Lee, Woo-Cheol; Nagata, Koji; Inoue, Yumiko; Tanokura, Masaru

    2017-01-01

    Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75–80 °C and in the pH range of 6.8–7.2. Enzyme activity was significantly enhanced by cobalt or cadmium and was moderately inhibited by Tris at 25 °C. We also determined the crystal structure of TthCP at 2.6 Å resolution. Two dimer types of TthCP are present in the crystal. One type consists of two subunits in different states, open and closed, with a C α RMSD value of 2.2 Å; the other type consists of two subunits in the same open state. This structure enables us to compare the open and closed states of an M32 carboxypeptidase. The TthCP subunit can be divided into two domains, L and S, which are separated by a substrate-binding groove. The L and S domains in the open state are almost identical to those in the closed state, with C α RMSD values of 0.84 and 0.53 Å, respectively, suggesting that the transition between the open and closed states proceeds with a large hinge-bending motion. The superimposition between the closed states of TthCP and BsuCP, another M32 family member, revealed that most putative substrate-binding residues in the grooves are oriented in the same direction. - Highlights: • The enzyme activity of TthCP was inhibited moderately by Tris molecule. • We solved the crystal structure of TthCP at 2.6 Å resolution. • The crystal structure of TthCP revealed both the open and closed conformations.

  8. Identification and characterization of the intermediate phase in hybrid organic-inorganic MAPbI3 perovskite.

    Science.gov (United States)

    Guo, Xin; McCleese, Christopher; Kolodziej, Charles; Samia, Anna C S; Zhao, Yixin; Burda, Clemens

    2016-03-07

    Perovskite films were prepared using single step solution deposition at different annealing temperatures and annealing times. The crystal structure, phases and grain size were investigated with XRD, XPS and SEM/EDX. The prepared films show a typical orientation of tetragonal perovskite phase and a gradual transition at room temperature from the yellow intermediate phase to the black perovskite phase. Films with high purity were obtained by sintering at 100 °C. In addition, the chemical composition and crystal structure of intermediate phase were investigated in detail. FTIR, UV-vis and NMR spectra revealed the occurance of DMF complexes. Interestingly, the intermediate phase could be transformed to the black perovskite phase upon X-ray irradiation. In addition, the recovery of the aged perovskite films from a yellow intermediate phase back to the black perovskite was shown to be viable via heating and X-ray irradiation.

  9. Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET.

    Science.gov (United States)

    Sikor, Martin; Mapa, Koyeli; von Voithenberg, Lena Voith; Mokranjac, Dejana; Lamb, Don C

    2013-05-29

    The numerous functions of the important class of molecular chaperones, heat shock proteins 70 (Hsp70), rely on cycles of intricate conformational changes driven by ATP-hydrolysis and regulated by cochaperones and substrates. Here, we used Förster resonance energy transfer to study the conformational dynamics of individual molecules of Ssc1, a mitochondrial Hsp70, in real time. The intrinsic dynamics of the substrate-binding domain of Ssc1 was observed to be uncoupled from the dynamic interactions between substrate- and nucleotide-binding domains. Analysis of the fluctuations in the interdomain separation revealed frequent transitions to a nucleotide-free state. The nucleotide-exchange factor Mge1 did not induce ADP release, as expected, but rather facilitated binding of ATP. These results indicate that the conformational cycle of Ssc1 is more elaborate than previously thought and provide insight into how the Hsp70s can perform a wide variety of functions.

  10. The conformal method and the conformal thin-sandwich method are the same

    International Nuclear Information System (INIS)

    Maxwell, David

    2014-01-01

    The conformal method developed in the 1970s and the more recent Lagrangian and Hamiltonian conformal thin-sandwich methods are techniques for finding solutions of the Einstein constraint equations. We show that they are manifestations of a single conformal method: there is a straightforward way to convert back and forth between the parameters for these methods so that the corresponding solutions of the Einstein constraint equations agree. The unifying idea is the need to clearly distinguish tangent and cotangent vectors to the space of conformal classes on a manifold, and we introduce a vocabulary for working with these objects without reference to a particular representative background metric. As a consequence of these conceptual advantages, we demonstrate how to strengthen previous near-CMC (constant mean curvature) existence and non-existence theorems for the original conformal method to include metrics with scalar curvatures that change sign. (paper)

  11. Kinetically Controlled Two-Step Amorphization and Amorphous-Amorphous Transition in Ice

    Science.gov (United States)

    Lin, Chuanlong; Yong, Xue; Tse, John S.; Smith, Jesse S.; Sinogeikin, Stanislav V.; Kenney-Benson, Curtis; Shen, Guoyin

    2017-09-01

    We report the results of in situ structural characterization of the amorphization of crystalline ice Ih under compression and the relaxation of high-density amorphous (HDA) ice under decompression at temperatures between 96 and 160 K by synchrotron x-ray diffraction. The results show that ice Ih transforms to an intermediate crystalline phase at 100 K prior to complete amorphization, which is supported by molecular dynamics calculations. The phase transition pathways show clear temperature dependence: direct amorphization without an intermediate phase is observed at 133 K, while at 145 K a direct Ih-to-IX transformation is observed; decompression of HDA shows a transition to low-density amorphous ice at 96 K and ˜1 Pa , to ice Ic at 135 K and to ice IX at 145 K. These observations show that the amorphization of compressed ice Ih and the recrystallization of decompressed HDA are strongly dependent on temperature and controlled by kinetic barriers. Pressure-induced amorphous ice is an intermediate state in the phase transition from the connected H-bond water network in low pressure ices to the independent and interpenetrating H-bond network of high-pressure ices.

  12. On the escape transition of a tethered Gaussian chain; exact results in two conjugate ensembles

    NARCIS (Netherlands)

    Skvortsov, A.M.; Klushin, L.I.; Leermakers, F.A.M.

    2006-01-01

    Upon compression between two pistons an end-tethered polymer chain undergoes an abrupt transition from a confined coil state to an inhomogeneous flower-like conformation that is partially escaped from the gap. In the thermodynamic limit the system demonstrates a first-order phase transition. A

  13. Parity Doubling and the S Parameter below the Conformal Window

    International Nuclear Information System (INIS)

    Appelquist, T.; Fleming, G. T.; Lin, M. F.; Neil, E. T.; Babich, R.; Brower, R. C.; Cohen, S. D.; Rebbi, C.; Schaich, D.; Cheng, M.; Vranas, P. M.; Clark, M. A.; Kiskis, J.; Osborn, J. C.

    2011-01-01

    We describe a lattice simulation of the masses and decay constants of the lowest-lying vector and axial resonances, and the electroweak S parameter, in an SU(3) gauge theory with N f =2 and 6 fermions in the fundamental representation. The spectrum becomes more parity doubled and the S parameter per electroweak doublet decreases when N f is increased from 2 to 6, motivating study of these trends as N f is increased further, toward the critical value for transition from confinement to infrared conformality.

  14. Structural Insights of the Cysteine Protease Heynein from Induction and Characterization of Non-native Intermediate States

    Directory of Open Access Journals (Sweden)

    Basant K. Patel

    2010-12-01

    Full Text Available Cysteine proteases are vital to cell physiology and many plants secrete these proteases for defense purposes. Many recent studies have reported unusually high stabilities for several plant cysteine proteases which possibly enable these proteases to function under adverse environmental conditions. Here, we have examined the conformational features of a new plant cysteine protease heynein using spectroscopic tools to understand the basis for its robust functional stability. The studies revealed structural integrity over a wide range of pH (2.5-12.0, temperature (65 oC and urea (8M. However, at pH 2.0, the protein gets acid-unfolded (UA -state with exposed hydrophobic patches, which upon addition of more protons (pH 0.5 or anions (0.5 M KCl and 0.2 M Na2 SO4 yields conformationally distinct refolded intermediates respectively termed: A-, I 1 - and I 2 -states. Strikingly, a high methanol level drives the UA -state into a predominantly -sheet rich conformation (O-state. We observed three-state unfolding kinetics of the I 2 -state by urea, possibly suggesting presence of two domains in the heynein molecule.

  15. QCD-Electroweak First-Order Phase Transition in a Supercooled Universe

    Science.gov (United States)

    Iso, Satoshi; Serpico, Pasquale D.; Shimada, Kengo

    2017-10-01

    If the electroweak sector of the standard model is described by classically conformal dynamics, the early Universe evolution can be substantially altered. It is already known that—contrarily to the standard model case—a first-order electroweak phase transition may occur. Here we show that, depending on the model parameters, a dramatically different scenario may happen: A first-order, six massless quark QCD phase transition occurs first, which then triggers the electroweak symmetry breaking. We derive the necessary conditions for this dynamics to occur, using the specific example of the classically conformal B -L model. In particular, relatively light weakly coupled particles are predicted, with implications for collider searches. This scenario is also potentially rich in cosmological consequences, such as renewed possibilities for electroweak baryogenesis, altered dark matter production, and gravitational wave production, as we briefly comment upon.

  16. QCD-Electroweak First-Order Phase Transition in a Supercooled Universe.

    Science.gov (United States)

    Iso, Satoshi; Serpico, Pasquale D; Shimada, Kengo

    2017-10-06

    If the electroweak sector of the standard model is described by classically conformal dynamics, the early Universe evolution can be substantially altered. It is already known that-contrarily to the standard model case-a first-order electroweak phase transition may occur. Here we show that, depending on the model parameters, a dramatically different scenario may happen: A first-order, six massless quark QCD phase transition occurs first, which then triggers the electroweak symmetry breaking. We derive the necessary conditions for this dynamics to occur, using the specific example of the classically conformal B-L model. In particular, relatively light weakly coupled particles are predicted, with implications for collider searches. This scenario is also potentially rich in cosmological consequences, such as renewed possibilities for electroweak baryogenesis, altered dark matter production, and gravitational wave production, as we briefly comment upon.

  17. Conformal window in QCD for large numbers of colors and flavors

    International Nuclear Information System (INIS)

    Zhitnitsky, Ariel R.

    2014-01-01

    We conjecture that the phase transitions in QCD at large number of colors N≫1 is triggered by the drastic change in the instanton density. As a result of it, all physical observables also experience some sharp modification in the θ behavior. This conjecture is motivated by the holographic model of QCD where confinement–deconfinement phase transition indeed happens precisely at temperature T=T c where θ-dependence of the vacuum energy experiences a sudden change in behavior: from N 2 cos(θ/N) at T c to cosθexp(−N) at T>T c . This conjecture is also supported by recent lattice studies. We employ this conjecture to study a possible phase transition as a function of κ≡N f /N from confinement to conformal phase in the Veneziano limit N f ∼N when number of flavors and colors are large, but the ratio κ is finite. Technically, we consider an operator which gets its expectation value solely from non-perturbative instanton effects. When κ exceeds some critical value κ>κ c the integral over instanton size is dominated by small-size instantons, making the instanton computations reliable with expected exp(−N) behavior. However, when κ c , the integral over instanton size is dominated by large-size instantons, and the instanton expansion breaks down. This regime with κ c corresponds to the confinement phase. We also compute the variation of the critical κ c (T,μ) when the temperature and chemical potential T,μ≪Λ QCD slightly vary. We also discuss the scaling (x i −x j ) −γ det in the conformal phase

  18. Intermediate treatments

    Science.gov (United States)

    John R. Jones; Wayne D. Shepperd

    1985-01-01

    Intermediate treatments are those applied after a new stand is successfully established and before the final harvest. These include not only intermediate cuttings - primarily thinning - but also fertilization, irrigation, and protection of the stand from damaging agents.

  19. A constitutively activating mutation alters the dynamics and energetics of a key conformational change in a ligand-free G protein-coupled receptor.

    Science.gov (United States)

    Tsukamoto, Hisao; Farrens, David L

    2013-09-27

    G protein-coupled receptors (GPCRs) undergo dynamic transitions between active and inactive conformations. Usually, these conversions are triggered when the receptor detects an external signal, but some so-called constitutively activating mutations, or CAMs, induce a GPCR to bind and activate G proteins in the absence of external stimulation, in ways still not fully understood. Here, we investigated how a CAM alters the structure of a GPCR and the dynamics involved as the receptor transitions between different conformations. Our approach used site-directed fluorescence labeling (SDFL) spectroscopy to compare opsin, the ligand-free form of the GPCR rhodopsin, with opsin containing the CAM M257Y, focusing specifically on key movements that occur in the sixth transmembrane helix (TM6) during GPCR activation. The site-directed fluorescence labeling data indicate opsin is constrained to an inactive conformation both in detergent micelles and lipid membranes, but when it contains the M257Y CAM, opsin is more dynamic and can interact with a G protein mimetic. Further study of these receptors using tryptophan-induced quenching (TrIQ) methods indicates that in detergent, the CAM significantly increases the population of receptors in the active state, but not in lipids. Subsequent Arrhenius analysis of the TrIQ data suggests that, both in detergent and lipids, the CAM lowers the energy barrier for TM6 movement, a key transition required for conversion between the inactive and active conformations. Together, these data suggest that the lowered energy barrier is a primary effect of the CAM on the receptor dynamics and energetics.

  20. Unbiased simulations reveal the inward-facing conformation of the human serotonin transporter and Na+ ion release

    DEFF Research Database (Denmark)

    Koldsø, Heidi; Noer, Pernille Rimmer; Grouleff, Julie

    2011-01-01

    transporter has resulted in homology models of the monoamine transporters. Here we present extended molecular dynamics simulations of an experimentally supported homology model of hSERT with and without the natural substrate yielding a total of more than 1.5 µs of simulation of the protein dimer....... The simulations reveal a transition of hSERT from an outward-facing occluded conformation to an inward-facing conformation in a one-substrate-bound state. Simulations with a second substrate in the proposed symport effector site did not lead to conformational changes associated with translocation. The central...... substrate binding site becomes fully exposed to the cytoplasm leaving both the Na+-ion in the Na2-site and the substrate in direct contact with the cytoplasm through water interactions. The simulations reveal how sodium is released and show indications of early events of substrate transport. The notion...

  1. A pH-induced conformational switch in a tyrosine kinase inhibitor identified by electronic spectroscopy and quantum chemical calculations.

    Science.gov (United States)

    Khattab, Muhammad; Wang, Feng; Clayton, Andrew H A

    2017-11-24

    Tyrosine kinase inhibitors (TKIs) are a major class of drug utilised in the clinic. During transit to their cognate kinases, TKIs will encounter different pH environments that could have a major influence on TKI structure. To address this, we report UV-Vis spectroscopic and computational studies of the TKI, AG1478, as a function of pH. The electronic absorption spectrum of AG1478 shifted by 10 nm (from 342 nm to 332 nm) from acid to neutral pH and split into two peaks (at 334 nm and 345 nm) in highly alkaline conditions. From these transitions, the pKa value was calculated as 5.58 ± 0.01. To compute structures and spectra, time-dependent density functional theory (TD-DFT) calculations were performed along with conductor-like polarizable continuum model (CPCM) to account for implicit solvent effect. On the basis of the theoretical spectra, we could assign the AG1478 experimental spectrum at acidic pH to a mixture of two twisted conformers (71% AG1478 protonated at quinazolyl nitrogen N(1) and 29% AG1478 protonated at quinazolyl nitrogen N(3)) and at neutral pH to the neutral planar conformer. The AG1478 absorption spectrum (pH 13.3) was fitted to a mixture of neutral (70%) and NH-deprotonated species (30%). These studies reveal a pH-induced conformational transition in a TKI.

  2. Superspace conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Quella, Thomas [Koeln Univ. (Germany). Inst. fuer Theoretische Physik; Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2013-07-15

    Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

  3. Superspace conformal field theory

    International Nuclear Information System (INIS)

    Quella, Thomas

    2013-07-01

    Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

  4. Prediction of isotope effects for anticipated intermediate structures in the course of bacterial denitrification

    International Nuclear Information System (INIS)

    Morgenstern, M.A.; Schowen, R.L.

    1989-01-01

    Vibrational-analysis methods have been used to estimate the equilibrium 14 N/ 15 N isotope effects to be expected for conversion of nitrite anion to thirteen possible intermediate-state and product-state structures [HONO, NO + , NO, NO - , FeNO, ON * NO 2 , O * NNO 2 , O 2 NNO 2 , ONO * N, O * NON, ONNO, * NNO, N * NO] in the reduction of nitrite ion to nitrous oxide denitrifying bacteria. The results, taken in combination with previous experimental isotope-effect and tracer studies of the Pseudomonas stutzeri and related systems, are consistent with a suggestion that a second nitrite anion enters the enzyme-catalytic cycle at the stage of a nitrosyl-ion intermediate but re-emerges after entry of the reducing electrons; the product nitrous oxide is then formed by disproportionation of enzymically generated hyponitrous acid. The calculations are consistent with contributions, under different experimental conditions, of several different transition states to limiting the rate of the enzymic reaction. These transition states (and the corresponding experimental conditions) are the transition states for N-O fission in the generation of a mononitrogen electrophilic species from nitrite anion (high reductant, high nitrite concentrations), for attack of nitrite on this electrophile (high reductant, low nitrite concentrations) and for electron transfer to a dinitrogen-trioxide-like species (low reductant concentration). (orig.)

  5. Conformal Infinity

    OpenAIRE

    Frauendiener, J?rg

    2000-01-01

    The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory...

  6. Regular-chaos transition of the energy spectrum and electromagnetic transition intensities in 44V nucleus using the framework of the nuclear shell model

    International Nuclear Information System (INIS)

    Hamoudi, A.K.; Abdul Majeed Al-Rahmani, A.

    2012-01-01

    The spectral fluctuations and the statistics of electromagnetic transition intensities and electromagnetic moments in 44 V nucleus are studied by the framework of the interacting shell model, using the FPD6 as a realistic effective interaction in the isospin formalism for 4 particles move in the fp-model space with a 40 Ca core. To look for a regular-chaos transition in 44 V nucleus, we perform shell model calculations using various interaction strengths β to the off-diagonal matrix elements of the FPD6. The nearest-neighbors level spacing distribution P(s) and the distribution of electromagnetic transition intensities [such as, B(M1) and B(E2) transitions] are found to have a regular dynamic at β=0, a chaotic dynamic at β⩾0.3 and an intermediate situation at 0 3 statistic we have found a regular dynamic at β=0, a chaotic dynamic at β⩾0.4 and an intermediate situation at 0<β<0.4. It is also found that the statistics of the squares of M1 and E2 moments, which are consistent with a Porter-Thomas distribution, have no dependence on the interaction strength β.

  7. GdnHCl-induced unfolding intermediate in the mitochondrial carbonic anhydrase VA.

    Science.gov (United States)

    Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Hassan, Md Imtaiyaz; Ahmad, Faizan

    2016-10-01

    Carbonic anhydrase VA (CAVA) is a mitochondrial enzyme belonging to the α-family of CAs, which is involved in several physiological processes including ureagenesis, lipogenesis, gluconeogenesis and neuronal transmission. Here, we have tried to understand the folding mechanism of CAVA using guanidine hydrochloride (GdnHCl)-induced denaturation at pH 8.0 and 25°C. The conformational stability was measured from the GdnHCl-induced denaturation study of CAVA monitored by circular dichroism (CD) and fluorescence measurements. On increasing the concentration of GdnHCl up to 5.0, a stable intermediate was observed between the concentrations 3.25M to 3.40M of the denaturant. However, CAVA gets completely denatured at 4.0M GdnHCl. The existence of a stable intermediate state was validated by 1-anilinonaphthalene-8-sulfonic acid (ANS binding) fluorescence and near-UV CD measurements. In silico studies were also performed to analyse the effect of GdnHCl on the structure and stability of CAVA under explicit conditions. Molecular dynamics simulations for 40ns were carried out and a well-defined correlation was established for both in vitro and in silico studies. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Conformal superalgebras via tractor calculus

    Science.gov (United States)

    Lischewski, Andree

    2015-01-01

    We use the manifestly conformally invariant description of a Lorentzian conformal structure in terms of a parabolic Cartan geometry in order to introduce a superalgebra structure on the space of twistor spinors and normal conformal vector fields formulated in purely algebraic terms on parallel sections in tractor bundles. Via a fixed metric in the conformal class, one reproduces a conformal superalgebra structure that has been considered in the literature before. The tractor approach, however, makes clear that the failure of this object to be a Lie superalgebra in certain cases is due to purely algebraic identities on the spinor module and to special properties of the conformal holonomy representation. Moreover, it naturally generalizes to higher signatures. This yields new formulas for constructing new twistor spinors and higher order normal conformal Killing forms out of existing ones, generalizing the well-known spinorial Lie derivative. Moreover, we derive restrictions on the possible dimension of the space of twistor spinors in any metric signature.

  9. Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

    International Nuclear Information System (INIS)

    Forneris, Federico; Burnley, B. Tom; Gros, Piet

    2014-01-01

    Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles. Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or ‘exosite’, region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na + and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na + ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail

  10. Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

    Science.gov (United States)

    Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.

    2013-01-01

    The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

  11. Conformal sequestering simplified

    International Nuclear Information System (INIS)

    Schmaltz, Martin; Sundrum, Raman

    2006-01-01

    Sequestering is important for obtaining flavor-universal soft masses in models where supersymmetry breaking is mediated at high scales. We construct a simple and robust class of hidden sector models which sequester themselves from the visible sector due to strong and conformally invariant hidden dynamics. Masses for hidden matter eventually break the conformal symmetry and lead to supersymmetry breaking by the mechanism recently discovered by Intriligator, Seiberg and Shih. We give a unified treatment of subtleties due to global symmetries of the CFT. There is enough review for the paper to constitute a self-contained account of conformal sequestering

  12. A perturbative RS I cosmological phase transition

    Energy Technology Data Exchange (ETDEWEB)

    Bunk, Don [Skidmore College, Department of Physics, Saratoga Springs, NY (United States); Hubisz, Jay [Syracuse University, Department of Physics, Syracuse, NY (United States); Jain, Bithika [Korea Institute for Advanced Study, School of Physics, Seoul (Korea, Republic of)

    2018-01-15

    We identify a class of Randall-Sundrum type models with a successful first order cosmological phase transition during which a 5D dual of approximate conformal symmetry is spontaneously broken. Our focus is on soft-wall models that naturally realize a light radion/dilaton and suppressed dynamical contribution to the cosmological constant. We discuss phenomenology of the phase transition after developing a theoretical and numerical analysis of these models both at zero and finite temperature. We demonstrate a model with a TeV-Planck hierarchy and with a successful cosmological phase transition where the UV value of the curvature corresponds, via AdS/CFT, to an N of 20, where 5D gravity is expected to be firmly in the perturbative regime. (orig.)

  13. Conformity index: A review

    International Nuclear Information System (INIS)

    Feuvret, Loic; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

    2006-01-01

    We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear

  14. Fermion-scalar conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

    Iliesiu, Luca [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States); Kos, Filip [Department of Physics, Yale University,217 Prospect Street, New Haven, CT 06520 (United States); Poland, David [Department of Physics, Yale University,217 Prospect Street, New Haven, CT 06520 (United States); School of Natural Sciences, Institute for Advanced Study,1 Einstein Dr, Princeton, New Jersey 08540 (United States); Pufu, Silviu S. [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States); Simmons-Duffin, David [School of Natural Sciences, Institute for Advanced Study,1 Einstein Dr, Princeton, New Jersey 08540 (United States); Yacoby, Ran [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States)

    2016-04-13

    We compute the conformal blocks associated with scalar-scalar-fermion-fermion 4-point functions in 3D CFTs. Together with the known scalar conformal blocks, our result completes the task of determining the so-called ‘seed blocks’ in three dimensions. Conformal blocks associated with 4-point functions of operators with arbitrary spins can now be determined from these seed blocks by using known differential operators.

  15. Conformational Explosion: Understanding the Complexity of the Para-Dialkylbenzene Potential Energy Surfaces

    Science.gov (United States)

    Mishra, Piyush; Hewett, Daniel M.; Zwier, Timothy S.

    2017-06-01

    This talk focuses on the single-conformation spectroscopy of small-chain para-dialkylbenzenes. This work builds on previous studies from our group on long-chain n-alkylbenzenes that identified the first folded structure in octylbenzene. The dialkylbenzenes are representative of a class of molecules that are common components of coal and aviation fuel and are known to be present in vehicle exhaust. We bring the molecules para-diethylbenzene, para-dipropylbenzene and para-dibutylbenzene into the gas phase and cool the molecules in a supersonic expansion. The jet-cooled molecules are then interrogated using laser-induced fluorescence excitation, fluorescence dip IR spectroscopy (FDIRS) and dispersed fluorescence. The LIF spectra in the S_{0}-S_{1} origin region show dramatic increases in the number of resolved transitions with increasing length of alkyl chains, reflecting an explosion in the number of unique low-energy conformations formed when two independent alkyl chains are present. Since the barriers to isomerization of the alkyl chain are similar in size, this results in an 'egg carton' shape to the potential energy surface. We use a combination of electronic frequency shift and alkyl CH stretch infrared spectra to generate a consistent set of conformational assignments.

  16. Fabrication challenges associated with conformal optics

    Science.gov (United States)

    Schaefer, John; Eichholtz, Richard A.; Sulzbach, Frank C.

    2001-09-01

    A conformal optic is typically an optical window that conforms smoothly to the external shape of a system platform to improve aerodynamics. Conformal optics can be on-axis, such as an ogive missile dome, or off-axis, such as in a free form airplane wing. A common example of conformal optics is the automotive head light window that conforms to the body of the car aerodynamics and aesthetics. The unusual shape of conformal optics creates tremendous challenges for design, manufacturing, and testing. This paper will discuss fabrication methods that have been successfully demonstrated to produce conformal missile domes and associated wavefront corrector elements. It will identify challenges foreseen with more complex free-form configurations. Work presented in this paper was directed by the Precision Conformal Optics Consortium (PCOT). PCOT is comprised of both industrial and academic members who teamed to develop and demonstrate conformal optical systems suitable for insertion into future military programs. The consortium was funded under DARPA agreement number MDA972-96-9-08000.

  17. Conformal standard model with an extended scalar sector

    Energy Technology Data Exchange (ETDEWEB)

    Latosiński, Adam [Max-Planck-Institut für Gravitationsphysik (Albert-Einstein-Institut),Mühlenberg 1, D-14476 Potsdam (Germany); Lewandowski, Adrian; Meissner, Krzysztof A. [Faculty of Physics, University of Warsaw,Pasteura 5, 02-093 Warsaw (Poland); Nicolai, Hermann [Max-Planck-Institut für Gravitationsphysik (Albert-Einstein-Institut),Mühlenberg 1, D-14476 Potsdam (Germany)

    2015-10-26

    We present an extended version of the Conformal Standard Model (characterized by the absence of any new intermediate scales between the electroweak scale and the Planck scale) with an enlarged scalar sector coupling to right-chiral neutrinos. The scalar potential and the Yukawa couplings involving only right-chiral neutrinos are invariant under a new global symmetry SU(3){sub N} that complements the standard U(1){sub B−L} symmetry, and is broken explicitly only by the Yukawa interaction, of order O(10{sup −6}), coupling right-chiral neutrinos and the electroweak lepton doublets. We point out four main advantages of this enlargement, namely: (1) the economy of the (non-supersymmetric) Standard Model, and thus its observational success, is preserved; (2) thanks to the enlarged scalar sector the RG improved one-loop effective potential is everywhere positive with a stable global minimum, thereby avoiding the notorious instability of the Standard Model vacuum; (3) the pseudo-Goldstone bosons resulting from spontaneous breaking of the SU(3){sub N} symmetry are natural Dark Matter candidates with calculable small masses and couplings; and (4) the Majorana Yukawa coupling matrix acquires a form naturally adapted to leptogenesis. The model is made perturbatively consistent up to the Planck scale by imposing the vanishing of quadratic divergences at the Planck scale (‘softly broken conformal symmetry’). Observable consequences of the model occur mainly via the mixing of the new scalars and the standard model Higgs boson.

  18. Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

    Science.gov (United States)

    Otero, Toribio F

    2017-01-18

    In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

  19. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

    Energy Technology Data Exchange (ETDEWEB)

    Knott, Michael [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Best, Robert B., E-mail: robertbe@helix.nih.gov [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States)

    2014-05-07

    Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

  20. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

    International Nuclear Information System (INIS)

    Knott, Michael; Best, Robert B.

    2014-01-01

    Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD

  1. Axiomatic conformal field theory

    International Nuclear Information System (INIS)

    Gaberdiel, M.R.; Goddard, P.

    2000-01-01

    A new rigourous approach to conformal field theory is presented. The basic objects are families of complex-valued amplitudes, which define a meromorphic conformal field theory (or chiral algebra) and which lead naturally to the definition of topological vector spaces, between which vertex operators act as continuous operators. In fact, in order to develop the theory, Moebius invariance rather than full conformal invariance is required but it is shown that every Moebius theory can be extended to a conformal theory by the construction of a Virasoro field. In this approach, a representation of a conformal field theory is naturally defined in terms of a family of amplitudes with appropriate analytic properties. It is shown that these amplitudes can also be derived from a suitable collection of states in the meromorphic theory. Zhu's algebra then appears naturally as the algebra of conditions which states defining highest weight representations must satisfy. The relationship of the representations of Zhu's algebra to the classification of highest weight representations is explained. (orig.)

  2. Conformal description of spinning particles

    International Nuclear Information System (INIS)

    Todorov, I.T.

    1986-01-01

    This book is an introduction to the application of the conformal group to quantum field theory of particles with spin. After an introduction to the twistor representations of the conformal group of a conformally flat space-time and twistor flag manifolds with Su(2,2) orbits the classical phase space of conformal spinning particles is described. Thereafter the twistor description of classical zero mass fields is considered together with the quantization. (HSI)

  3. Conformal boundaries of warped products

    DEFF Research Database (Denmark)

    Kokkendorff, Simon Lyngby

    2006-01-01

    In this note we prove a result on how to determine the conformal boundary of a type of warped product of two length spaces in terms of the individual conformal boundaries. In the situation, that we treat, the warping and conformal distortion functions are functions of distance to a base point....... The result is applied to produce examples of CAT(0)-spaces, where the conformal and ideal boundaries differ in interesting ways....

  4. Conformally connected universes

    International Nuclear Information System (INIS)

    Cantor, M.; Piran, T.

    1983-01-01

    A well-known difficulty associated with the conformal method for the solution of the general relativistic Hamiltonian constraint is the appearance of an aphysical ''bag of gold'' singularity at the nodal surface of the conformal factor. This happens whenever the background Ricci scalar is too large. Using a simple model, it is demonstrated that some of these singular solutions do have a physical meaning, and that these can be considered as initial data for Universe containing black holes, which are connected, in a conformally nonsingular way with each other. The relation between the ADM mass and the horizon area in this solution supports the cosmic censorship conjecture. (author)

  5. Magnitude of a conformational change in the glycine receptor beta1-beta2 loop is correlated with agonist efficacy

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Lynch, Joseph W

    2009-01-01

    associated with the closed-flip transition in the alpha1-glycine receptor. We employed voltage-clamp fluorometry to compare ligand-binding domain conformational changes induced by the following agonists, listed from highest to lowest affinity and efficacy: glycine > beta-alanine > taurine. Voltage...

  6. Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers.

    Science.gov (United States)

    Kriegel, Franziska; Ermann, Niklas; Lipfert, Jan

    2017-01-01

    Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level. We review several variations of magnetic tweezers, in particular conventional magnetic tweezers, freely orbiting magnetic tweezers and magnetic torque tweezers, and discuss their characteristic capabilities. We then describe the elastic rod model for DNA and RNA and discuss conformational changes induced by mechanical stress. The focus lies on the responses to torque and twist, which are crucial in the mechanics and interactions of nucleic acids and can directly be measured using magnetic tweezers. We conclude by highlighting several recent studies of nucleic acid-protein and nucleic acid-small-molecule interactions as further applications of magnetic tweezers and give an outlook of some exciting developments to come. Copyright © 2016. Published by Elsevier Inc.

  7. A unified conformational selection and induced fit approach to protein-peptide docking.

    Directory of Open Access Journals (Sweden)

    Mikael Trellet

    Full Text Available Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural components in nearly 40% of all macromolecular interactions, and are often associated with diseases, making them interesting leads for protein drug design. In recent years, large-scale technologies have enabled exhaustive studies on the peptide recognition preferences for a number of peptide-binding domain families. Yet, the paucity of data regarding their molecular binding mechanisms together with their inherent flexibility makes the structural prediction of protein-peptide interactions very challenging. This leaves flexible docking as one of the few amenable computational techniques to model these complexes. We present here an ensemble, flexible protein-peptide docking protocol that combines conformational selection and induced fit mechanisms. Starting from an ensemble of three peptide conformations (extended, a-helix, polyproline-II, flexible docking with HADDOCK generates 79.4% of high quality models for bound/unbound and 69.4% for unbound/unbound docking when tested against the largest protein-peptide complexes benchmark dataset available to date. Conformational selection at the rigid-body docking stage successfully recovers the most relevant conformation for a given protein-peptide complex and the subsequent flexible refinement further improves the interface by up to 4.5 Å interface RMSD. Cluster-based scoring of the models results in a selection of near-native solutions in the top three for ∼75% of the successfully predicted cases. This unified conformational selection and induced fit approach to protein-peptide docking should open the route to the modeling of challenging systems such as disorder-order transitions taking place upon binding, significantly expanding the applicability limit of biomolecular interaction modeling by docking.

  8. On Associative Conformal Algebras of Linear Growth

    OpenAIRE

    Retakh, Alexander

    2000-01-01

    Lie conformal algebras appear in the theory of vertex algebras. Their relation is similar to that of Lie algebras and their universal enveloping algebras. Associative conformal algebras play a role in conformal representation theory. We introduce the notions of conformal identity and unital associative conformal algebras and classify finitely generated simple unital associative conformal algebras of linear growth. These are precisely the complete algebras of conformal endomorphisms of finite ...

  9. Conformal algebra of Riemann surfaces

    International Nuclear Information System (INIS)

    Vafa, C.

    1988-01-01

    It has become clear over the last few years that 2-dimensional conformal field theories are a crucial ingredient of string theory. Conformal field theories correspond to vacuum solutions of strings; or more precisely we know how to compute string spectrum and scattering amplitudes by starting from a formal theory (with a proper value of central charge of the Virasoro algebra). Certain non-linear sigma models do give rise to conformal theories. A lot of progress has been made in the understanding of conformal theories. The author discusses a different view of conformal theories which was motivated by the development of operator formalism on Riemann surfaces. The author discusses an interesting recent work from this point of view

  10. Negative compressibility and non-equivalence of two statistical ensembles in the escape transition of a polymer chain

    NARCIS (Netherlands)

    Skvortsov, A.M.; Klushin, L.I.; Leermakers, F.A.M.

    2007-01-01

    An end-tethered polymer chain compressed between two pistons undergoes an abrupt transition from a confined coil state to an inhomogeneous flowerlike conformation partially escaped from the gap. This phase transition is first order in the thermodynamic limit of infinitely long chains. A rigorous

  11. 40 CFR 93.154 - Conformity analysis.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Conformity analysis. 93.154 Section 93...) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 93.154 Conformity analysis. Any Federal...

  12. Transverse acoustic phonon anomalies at intermediate wave vectors in MgV2O4

    Science.gov (United States)

    Weber, T.; Roessli, B.; Stock, C.; Keller, T.; Schmalzl, K.; Bourdarot, F.; Georgii, R.; Ewings, R. A.; Perry, R. S.; Böni, P.

    2017-11-01

    Magnetic spinels (with chemical formula A X2O4 , with X a 3 d transition metal ion) that also have an orbital degeneracy are Jahn-Teller active and hence possess a coupling between spin and lattice degrees of freedom. At high temperatures, MgV2O4 is a cubic spinel based on V3 + ions with a spin S =1 and a triply degenerate orbital ground state. A structural transition occurs at TOO=63 K to an orbitally ordered phase with a tetragonal unit cell followed by an antiferromagnetic transition of TN=42 K on cooling. We apply neutron spectroscopy in single crystals of MgV2O4 to show an anomaly for intermediate wave vectors at TOO associated with the acoustic phonon sensitive to the shear elastic modulus (C11-C12)/2 . On warming, the shear mode softens for momentum transfers near close to half the Brillouin zone boundary, but recovers near the zone center. High resolution spin-echo measurements further illustrate a temporal broadening with increased temperature over this intermediate range of wave vectors, indicative of a reduction in phonon lifetime. A subtle shift in phonon frequencies over the same range of momentum transfers is observed with magnetic fields. We discuss this acoustic anomaly in context of coupling to orbital and charge fluctuations.

  13. Electronic Transitions in Conformationally Controlled Tetrasilanes with a Wide Range of SiSiSiSi Dihedral Angles

    Czech Academy of Sciences Publication Activity Database

    Tsuji, H.; Fogarty, H. A.; Ehara, M.; Fukuda, R.; Casher, D. L.; Tamao, K.; Nakatsuji, H.; Michl, Josef

    2014-01-01

    Roč. 20, č. 30 (2014), s. 9431-9441 ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : conformational effects * electronic spectra * SAC-CI calculations * silicon * UV/Vis spectroscopy Subject RIV: CC - Organic Chemistry Impact factor: 5.731, year: 2014

  14. Recursion Relations for Conformal Blocks

    CERN Document Server

    Penedones, João; Yamazaki, Masahito

    2016-09-12

    In the context of conformal field theories in general space-time dimension, we find all the possible singularities of the conformal blocks as functions of the scaling dimension $\\Delta$ of the exchanged operator. In particular, we argue, using representation theory of parabolic Verma modules, that in odd spacetime dimension the singularities are only simple poles. We discuss how to use this information to write recursion relations that determine the conformal blocks. We first recover the recursion relation introduced in 1307.6856 for conformal blocks of external scalar operators. We then generalize this recursion relation for the conformal blocks associated to the four point function of three scalar and one vector operator. Finally we specialize to the case in which the vector operator is a conserved current.

  15. The logarithmic conformal field theories

    International Nuclear Information System (INIS)

    Rahimi Tabar, M.R.; Aghamohammadi, A.; Khorrami, M.

    1997-01-01

    We study the correlation functions of logarithmic conformal field theories. First, assuming conformal invariance, we explicitly calculate two- and three-point functions. This calculation is done for the general case of more than one logarithmic field in a block, and more than one set of logarithmic fields. Then we show that one can regard the logarithmic field as a formal derivative of the ordinary field with respect to its conformal weight. This enables one to calculate any n-point function containing the logarithmic field in terms of ordinary n-point functions. Finally, we calculate the operator product expansion (OPE) coefficients of a logarithmic conformal field theory, and show that these can be obtained from the corresponding coefficients of ordinary conformal theory by a simple derivation. (orig.)

  16. Electroabsorption spectra of carotenoid isomers: Conformational modulation of polarizability vs. induced dipole moments

    International Nuclear Information System (INIS)

    Krawczyk, Stanislaw; Jazurek, Beata; Luchowski, Rafal; Wiacek, Dariusz

    2006-01-01

    Electroabsorption spectra of all-trans, 13-cis and 15-cis isomers of carotenoids violaxanthin and β-carotene frozen in organic solvents were analysed in terms of changes in permanent dipole moment, Δμ, and in the linear polarizability, Δα, on electronic excitation. The spectral range investigated covered the two carotenoid absorption bands in the VIS and UV, known to originate from differently oriented transition dipole moments. In contrast with the collinearity of the apparent Δμ with Δα in the lowest-energy allowed (VIS) transition 1A g - ->1B u + , the axis of the largest polarizability change in the UV transition 1A g - ->1A g + (''cis band'') was found to make a large angle with the transition moment, while the direction of Δμ appears to be much closer to it. These data support the view that Δμ's inferred from electrochromic spectra of carotenoids are apparent and are not induced by the local matrix field in the solvent cavity, but merely result from conformational modulation of molecular polarizability

  17. Reversible and irreversible conformational transitions in myoglobin: role of hydrated amino acid ionic liquid.

    Science.gov (United States)

    Sankaranarayanan, Kamatchi; Sathyaraj, Gopal; Nair, B U; Dhathathreyan, A

    2012-04-12

    Hydrated phenylalanine ionic liquid (Phe-IL) has been used to solubilize myoglobin (Mb). Structural stability of Mb in Phe-IL analyzed using fluorescence and circular dichroism spectroscopy shows that for low levels of hydration of Phe-IL there is a large red shift in the fluorescence emission wavelength and the protein transforms to complete β sheet from its native helical conformation. Rehydration or dilution reverses the β sheet to an α helix which on aging organizes to micrometer-sized fibrils. At concentrations higher than 200 μM, the protein changes from β to a more random coiled structure. Organization of the protein in Phe-IL in a Langmuir film at the air/water interface has been investigated using the surface pressure-molecular area isotherm and shows nearly the same surface tension for both pure Mb and Mb in Phe-IL. Scanning electron microscopy of the films of Mb in Phe-IL transferred using the Langmuir-Blodgett film technique show layered morphology. This study shows that the conformation of Mb is completely reversible going from β → helix → β sheet up to 200 μM of Phe-IL. Similar surface tension values for Mb in water and in Phe-IL suggests that direct ion binding interactions with the protein coupled with the change in local viscosity from the IL seems to not only alter the secondary structure of individual proteins but also drives the self-assembly of the protein molecules leading finally to fibril formation.

  18. Comparing two tetraalkylammonium ionic liquids. II. Phase transitions

    Energy Technology Data Exchange (ETDEWEB)

    Lima, Thamires A.; Paschoal, Vitor H.; Faria, Luiz F. O.; Ribeiro, Mauro C. C., E-mail: mccribei@iq.usp.br [Laboratório de Espectroscopia Molecular, Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05513-970 São Paulo, SP (Brazil); Ferreira, Fabio F.; Costa, Fanny N. [Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP (Brazil); Giles, Carlos [Depto. de Física da Matéria Condensada, Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, 13083-859 Campinas, SP (Brazil)

    2016-06-14

    Phase transitions of the ionic liquids n-butyl-trimethylammonium bis(trifluoromethanesulfonyl)imide, [N{sub 1114}][NTf{sub 2}], and methyl-tributylammonium bis(trifluoromethanesulfonyl)imide, [N{sub 1444}][NTf{sub 2}], were investigated by differential scanning calorimetry (DSC), X-ray diffraction (XRD) measurements, and Raman spectroscopy. XRD and Raman spectra were obtained as a function of temperature at atmospheric pressure, and also under high pressure at room temperature using a diamond anvil cell (DAC). [N{sub 1444}][NTf{sub 2}] experiences glass transition at low temperature, whereas [N{sub 1114}][NTf{sub 2}] crystallizes or not depending on the cooling rate. Both the ionic liquids exhibit glass transition under high pressure. XRD and low-frequency Raman spectra provide a consistent physical picture of structural ordering-disordering accompanying the thermal events of crystallization, glass transition, cold crystallization, pre-melting, and melting. Raman spectra in the high-frequency range of some specific cation and anion normal modes reveal conformational changes of the molecular structures along phase transitions.

  19. Recent advancements in conformal gravity

    International Nuclear Information System (INIS)

    O’Brien, James G.; Chaykov, Spasen S.; Moss, Robert J.; Dentico, Jeremy; Stulge, Modestas; Stefanski, Brian

    2017-01-01

    In recent years, due to the lack of direct observed evidence of cold dark matter, coupled with the shrinking parameter space to search for new dark matter particles, there has been increased interest in Alternative Gravitational theories. This paper, addresses three recent advances in conformal gravity, a fourth order renormalizable metric theory of gravitation originally formulated by Weyl, and later advanced by Mannheim and Kazanas. The first section of the paper applies conformal gravity to the rotation curves of the LITTLE THINGS survey, extending the total number of rotation curves successfully fit by conformal gravity to well over 200 individual data sets without the need for additional dark matter. Further, in this rotation curve study, we show how MOND and conformal gravity compare for each galaxy in the sample. Second, we look at the original Zwicky problem of applying the virial theorem to the Coma cluster in order to get an estimate for the cluster mass. However, instead of using the standard Newtonian potential, here we use the weak field approximation of conformal gravity. We show that in the conformal case we can get a much smaller mass estimate and thus there is no apparent need to include dark matter. We then show that this calculation is in agreement with the observational data from other well studied clusters. Last, we explore the calculation of the deflection of starlight through conformal gravity, as a first step towards applying conformal gravity to gravitaitonal lensing. (paper)

  20. Thermally Induced Alpha-Helix to Beta-Sheet Transition in Regenerated Silk Fibers and Films

    Energy Technology Data Exchange (ETDEWEB)

    Drummy,L.; Phillips, D.; Stone, M.; Farmer, B.; Naik, R.

    2005-01-01

    The structure of thin films cast from regenerated solutions of Bombyx mori cocoon silk in hexafluoroisopropyl alcohol (HFIP) was studied by synchrotron X-ray diffraction during heating. A solid-state conformational transition from an alpha-helical structure to the well-known beta-sheet silk II structure occurred at a temperature of approximately 140 degrees C. The transition appeared to be homogeneous, as both phases do not coexist within the resolution of the current study. Modulated differential scanning calorimetry (DSC) of the films showed an endothermic melting peak followed by an exothermic crystallization peak, both occurring near 140 degrees C. Oriented fibers were also produced that displayed this helical molecular conformation. Subsequent heating above the structural transition temperature produced oriented beta-sheet fibers very similar in structure to B. mori cocoon fibers. Heat treatment of silk films at temperatures well below their degradation temperature offers a controllable route to materials with well-defined structures and mechanical behavior.

  1. Co-non-solvency: Mean-field polymer theory does not describe polymer collapse transition in a mixture of two competing good solvents

    Energy Technology Data Exchange (ETDEWEB)

    Mukherji, Debashish; Stuehn, Torsten; Kremer, Kurt [Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz (Germany); Marques, Carlos M. [Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz (Germany); Institut Charles Sadron, Université de Strasbourg, CNRS, Strasbourg (France)

    2015-03-21

    Smart polymers are a modern class of polymeric materials that often exhibit unpredictable behavior in mixtures of solvents. One such phenomenon is co-non-solvency. Co-non-solvency occurs when two (perfectly) miscible and competing good solvents, for a given polymer, are mixed together. As a result, the same polymer collapses into a compact globule within intermediate mixing ratios. More interestingly, polymer collapses when the solvent quality remains good and even gets increasingly better by the addition of the better cosolvent. This is a puzzling phenomenon that is driven by strong local concentration fluctuations. Because of the discrete particle based nature of the interactions, Flory-Huggins type mean field arguments become unsuitable. In this work, we extend the analysis of the co-non-solvency effect presented earlier [D. Mukherji et al., Nat. Commun. 5, 4882 (2014)]. We explain why co-non-solvency is a generic phenomenon, which can only be understood by the thermodynamic treatment of the competitive displacement of (co)solvent components. This competition can result in a polymer collapse upon improvement of the solvent quality. Specific chemical details are not required to understand these complex conformational transitions. Therefore, a broad range of polymers are expected to exhibit similar reentrant coil-globule-coil transitions in competing good solvents.

  2. Co-non-solvency: Mean-field polymer theory does not describe polymer collapse transition in a mixture of two competing good solvents

    International Nuclear Information System (INIS)

    Mukherji, Debashish; Stuehn, Torsten; Kremer, Kurt; Marques, Carlos M.

    2015-01-01

    Smart polymers are a modern class of polymeric materials that often exhibit unpredictable behavior in mixtures of solvents. One such phenomenon is co-non-solvency. Co-non-solvency occurs when two (perfectly) miscible and competing good solvents, for a given polymer, are mixed together. As a result, the same polymer collapses into a compact globule within intermediate mixing ratios. More interestingly, polymer collapses when the solvent quality remains good and even gets increasingly better by the addition of the better cosolvent. This is a puzzling phenomenon that is driven by strong local concentration fluctuations. Because of the discrete particle based nature of the interactions, Flory-Huggins type mean field arguments become unsuitable. In this work, we extend the analysis of the co-non-solvency effect presented earlier [D. Mukherji et al., Nat. Commun. 5, 4882 (2014)]. We explain why co-non-solvency is a generic phenomenon, which can only be understood by the thermodynamic treatment of the competitive displacement of (co)solvent components. This competition can result in a polymer collapse upon improvement of the solvent quality. Specific chemical details are not required to understand these complex conformational transitions. Therefore, a broad range of polymers are expected to exhibit similar reentrant coil-globule-coil transitions in competing good solvents

  3. Benchmarking Commercial Conformer Ensemble Generators.

    Science.gov (United States)

    Friedrich, Nils-Ole; de Bruyn Kops, Christina; Flachsenberg, Florian; Sommer, Kai; Rarey, Matthias; Kirchmair, Johannes

    2017-11-27

    We assess and compare the performance of eight commercial conformer ensemble generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE Conformation Import, and OMEGA) and one leading free algorithm, the distance geometry algorithm implemented in RDKit. The comparative study is based on a new version of the Platinum Diverse Dataset, a high-quality benchmarking dataset of 2859 protein-bound ligand conformations extracted from the PDB. Differences in the performance of commercial algorithms are much smaller than those observed for free algorithms in our previous study (J. Chem. Inf. 2017, 57, 529-539). For commercial algorithms, the median minimum root-mean-square deviations measured between protein-bound ligand conformations and ensembles of a maximum of 250 conformers are between 0.46 and 0.61 Å. Commercial conformer ensemble generators are characterized by their high robustness, with at least 99% of all input molecules successfully processed and few or even no substantial geometrical errors detectable in their output conformations. The RDKit distance geometry algorithm (with minimization enabled) appears to be a good free alternative since its performance is comparable to that of the midranked commercial algorithms. Based on a statistical analysis, we elaborate on which algorithms to use and how to parametrize them for best performance in different application scenarios.

  4. Partial inertia induces additional phase transition in the majority vote model.

    Science.gov (United States)

    Harunari, Pedro E; de Oliveira, M M; Fiore, C E

    2017-10-01

    Explosive (i.e., discontinuous) transitions have aroused great interest by manifesting in distinct systems, such as synchronization in coupled oscillators, percolation regime, absorbing phase transitions, and more recently, the majority-vote model with inertia. In the latter, the model rules are slightly modified by the inclusion of a term depending on the local spin (an inertial term). In such a case, Chen et al. [Phys Rev. E 95, 042304 (2017)2470-004510.1103/PhysRevE.95.042304] have found that relevant inertia changes the nature of the phase transition in complex networks, from continuous to discontinuous. Here we give a further step by embedding inertia only in vertices with degree larger than a threshold value 〈k〉k^{*}, 〈k〉 being the mean system degree and k^{*} the fraction restriction. Our results, from mean-field analysis and extensive numerical simulations, reveal that an explosive transition is presented in both homogeneous and heterogeneous structures for small and intermediate k^{*}'s. Otherwise, a large restriction can sustain a discontinuous transition only in the heterogeneous case. This shares some similarities with recent results for the Kuramoto model [Phys. Rev. E 91, 022818 (2015)PLEEE81539-375510.1103/PhysRevE.91.022818]. Surprisingly, intermediate restriction and large inertia are responsible for the emergence of an extra phase, in which the system is partially synchronized and the classification of phase transition depends on the inertia and the lattice topology. In this case, the system exhibits two phase transitions.

  5. Rhodium(I)-catalyzed cyclization of allenynes with a carbonyl group through unusual insertion of a C-O bond into a rhodacycle intermediate.

    Science.gov (United States)

    Oonishi, Yoshihiro; Yokoe, Takayuki; Hosotani, Akihito; Sato, Yoshihiro

    2014-01-20

    Rhodium(I)-catalyzed cyclization of allenynes with a tethered carbonyl group was investigated. An unusual insertion of a CO bond into the C(sp(2) )-rhodium bond of a rhodacycle intermediate occurs via a highly strained transition state. Direct reductive elimination from the obtained rhodacyle intermediate proceeds to give a tricyclic product containing an 8-oxabicyclo[3.2.1]octane skeleton, while β-hydride elimination from the same intermediate gives products that contain fused five- and seven-membered rings in high yields. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Antibiotic Conformity with Culture Results of Hospitalized Pneumonia Patients in Melati Ward at Dr. Hasan Sadikin General Hospital Bandung, Indonesia

    Directory of Open Access Journals (Sweden)

    Randhi Rinaldi

    2016-12-01

    Full Text Available Background: Pneumonia is an infection with the highest mortality rate in Indonesian hospitals. According to The American Thoracic Society and The Infectious Diseases Society of America (ATS/IDSA, empirical use of antibiotics is still effective for pneumonia treatment. Inappropriate use of antibiotics would cause negative effects such as prolonged hospitalization, a high cost of treatment, and increased antibiotic-resistant bacteria. The goal of this study was to clarify the empirical use of antibiotic conformity with a bacteria culture. Methods: This study was conducted from August to October 2013 using a descriptive retrospective method based on 116 medical records of pneumonia patients hospitalized in Melati Ward, Dr. Hasan Sadikin General Hospital Bandung during 2011–2012. The type of bacteria, conformity with antibiotics given to patients, and type of antibiotics were analyzed. The conformity of antibiotics was assessed based on the resistance test. If the results were sensitive, they would be put in the conforming group and in the non-conforming group if the results were resistant or intermediate. Data was derived with descriptive statistics, using percentage and frequency distribution, illustrated in tables and figures. Results: Based on culture results and sensitivity of antibiotic empirical therapy given, 55.17% cases were conformed. The most widely used antibiotic group was Third-generation Cephalosporin (60.34%. The most common bacterias were Klebsiella pneumonia (34.5% and Acinetobacter baumanni (13.8%. Conclusions: Most of the antibiotics given to pneumonia patients are still appropriate with results of the bacteria culture test and resistance test.

  7. The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain.

    Directory of Open Access Journals (Sweden)

    Christine S Schwaiger

    Full Text Available The gating of voltage-gated ion channels is controlled by the arginine-rich S4 helix of the voltage-sensor domain moving in response to an external potential. Recent studies have suggested that S4 moves in three to four steps to open the conducting pore, thus visiting several intermediate conformations during gating. However, the exact conformational changes are not known in detail. For instance, it has been suggested that there is a local rotation in the helix corresponding to short segments of a 3(10-helix moving along S4 during opening and closing. Here, we have explored the energetics of the transition between the fully open state (based on the X-ray structure and the first intermediate state towards channel closing (C1, modeled from experimental constraints. We show that conformations within 3 Å of the X-ray structure are obtained in simulations starting from the C1 model, and directly observe the previously suggested sliding 3(10-helix region in S4. Through systematic free energy calculations, we show that the C1 state is a stable intermediate conformation and determine free energy profiles for moving between the states without constraints. Mutations indicate several residues in a narrow hydrophobic band in the voltage sensor contribute to the barrier between the open and C1 states, with F233 in the S2 helix having the largest influence. Substitution for smaller amino acids reduces the transition cost, while introduction of a larger ring increases it, largely confirming experimental activation shift results. There is a systematic correlation between the local aromatic ring rotation, the arginine barrier crossing, and the corresponding relative free energy. In particular, it appears to be more advantageous for the F233 side chain to rotate towards the extracellular side when arginines cross the hydrophobic region.

  8. Conformal and Nearly Conformal Theories at Large N

    Science.gov (United States)

    Tarnoplskiy, Grigory M.

    In this thesis we present new results in conformal and nearly conformal field theories in various dimensions. In chapter two, we study different properties of the conformal Quantum Electrodynamics (QED) in continuous dimension d. At first we study conformal QED using large Nf methods, where Nf is the number of massless fermions. We compute its sphere free energy as a function of d, ignoring the terms of order 1/Nf and higher. For finite Nf we use the epsilon-expansion. Next we use a large Nf diagrammatic approach to calculate the leading corrections to CT, the coefficient of the two-point function of the stress-energy tensor, and CJ, the coefficient of the two-point function of the global symmetry current. We present explicit formulae as a function of d and check them versus the expectations in 2 and 4 - epsilon dimensions. In chapter three, we discuss vacuum stability in 1 + 1 dimensional conformal field theories with external background fields. We show that the vacuum decay rate is given by a non-local two-form. This two-form is a boundary term that must be added to the effective in/out Lagrangian. The two-form is expressed in terms of a Riemann-Hilbert decomposition for background gauge fields, and is given by its novel "functional'' version in the gravitational case. In chapter four, we explore Tensor models. Such models possess the large N limit dominated by the melon diagrams. The quantum mechanics of a real anti-commuting rank-3 tensor has a large N limit similar to the Sachdev-Ye-Kitaev (SYK) model. We also discuss the quantum mechanics of a complex 3-index anti-commuting tensor and argue that it is equivalent in the large N limit to a version of SYK model with complex fermions. Finally, we discuss models of a commuting tensor in dimension d. We study the spectrum of the large N quantum field theory of bosonic rank-3 tensors using the Schwinger-Dyson equations. We compare some of these results with the 4 - epsilon expansion, finding perfect agreement. We

  9. A key agonist-induced conformational change in the cannabinoid receptor CB1 is blocked by the allosteric ligand Org 27569.

    Science.gov (United States)

    Fay, Jonathan F; Farrens, David L

    2012-09-28

    Allosteric ligands that modulate how G protein-coupled receptors respond to traditional orthosteric drugs are an exciting and rapidly expanding field of pharmacology. An allosteric ligand for the cannabinoid receptor CB1, Org 27569, exhibits an intriguing effect; it increases agonist binding, yet blocks agonist-induced CB1 signaling. Here we explored the mechanism behind this behavior, using a site-directed fluorescence labeling approach. Our results show that Org 27569 blocks conformational changes in CB1 that accompany G protein binding and/or activation, and thus inhibit formation of a fully active CB1 structure. The underlying mechanism behind this behavior is that simultaneous binding of Org 27569 produces a unique agonist-bound conformation, one that may resemble an intermediate structure formed on the pathway to full receptor activation.

  10. Covalent dye attachment influences the dynamics and conformational properties of flexible peptides.

    Directory of Open Access Journals (Sweden)

    Manuel P Luitz

    Full Text Available Fluorescence spectroscopy techniques like Förster resonance energy transfer (FRET and fluorescence correlation spectroscopy (FCS have become important tools for the in vitro and in vivo investigation of conformational dynamics in biomolecules. These methods rely on the distance-dependent quenching of the fluorescence signal of a donor fluorophore either by a fluorescent acceptor fluorophore (FRET or a non-fluorescent quencher, as used in FCS with photoinduced electron transfer (PET. The attachment of fluorophores to the molecule of interest can potentially alter the molecular properties and may affect the relevant conformational states and dynamics especially of flexible biomolecules like intrinsically disordered proteins (IDP. Using the intrinsically disordered S-peptide as a model system, we investigate the impact of terminal fluorescence labeling on the molecular properties. We perform extensive molecular dynamics simulations on the labeled and unlabeled peptide and compare the results with in vitro PET-FCS measurements. Experimental and simulated timescales of end-to-end fluctuations were found in excellent agreement. Comparison between simulations with and without labels reveal that the π-stacking interaction between the fluorophore labels traps the conformation of S-peptide in a single dominant state, while the unlabeled peptide undergoes continuous conformational rearrangements. Furthermore, we find that the open to closed transition rate of S-peptide is decreased by at least one order of magnitude by the fluorophore attachment. Our approach combining experimental and in silico methods provides a benchmark for the simulations and reveals the significant effect that fluorescence labeling can have on the conformational dynamics of small biomolecules, at least for inherently flexible short peptides. The presented protocol is not only useful for comparing PET-FCS experiments with simulation results but provides a strategy to minimize the

  11. Conformal radiotherapy: principles and classification

    International Nuclear Information System (INIS)

    Rosenwald, J.C.; Gaboriaud, G.; Pontvert, D.

    1999-01-01

    'Conformal radiotherapy' is the name fixed by usage and given to a new form of radiotherapy resulting from the technological improvements observed during the last ten years. While this terminology is now widely used, no precise definition can be found in the literature. Conformal radiotherapy refers to an approach in which the dose distribution is more closely 'conformed' or adapted to the actual shape of the target volume. However, the achievement of a consensus on a more specific definition is hampered by various difficulties, namely in characterizing the degree of 'conformality'. We have therefore suggested a classification scheme be established on the basis of the tools and the procedures actually used for all steps of the process, i.e., from prescription to treatment completion. Our classification consists of four levels: schematically, at level 0, there is no conformation (rectangular fields); at level 1, a simple conformation takes place, on the basis of conventional 2D imaging; at level 2, a 3D reconstruction of the structures is used for a more accurate conformation; and level 3 includes research and advanced dynamic techniques. We have used our personal experience, contacts with colleagues and data from the literature to analyze all the steps of the planning process, and to define the tools and procedures relevant to a given level. The corresponding tables have been discussed and approved at the European level within the Dynarad concerted action. It is proposed that the term 'conformal radiotherapy' be restricted to procedures where all steps are at least at level 2. (author)

  12. A first order phase transition from inflationary to big bang universe

    International Nuclear Information System (INIS)

    Horwitz, G.

    1986-01-01

    The microcanonical entropy is calculated for a system of massive, conformally coupled, scalar bosons using a conformal gravitational theory. The resulting entropy is seen to indicate a first order phase transition from an inflationary expansion stage (where the amplitude of the scalar boson follows that of the scale function of the universe and the mass of the solar boson is the source of the cosmological constant) to a big bang stage (where neither of these conditions hold). Such a first order phase transition involves an entropy increase of some thirty orders of magnitude. In the author's theory, the invariant temperature (proper temperature times scale function) is not zero, nor is it the Hawking temperature, but it is tens of magnitudes smaller than the corresponding temperature of the big bang stage. A specific model for these bosons that provides the phase transition and serves as the source of the cosmological constant is also examined briefly, where the bosons are identified as spontaneously generated primordial black holes as in the cosmological model of Brout, Englert and Casher. In that case, the decay of the black holes provides a decaying cosmological constant and an explicit mechanism for heating up the universe

  13. Intermediate neutron spectrum problems and the intermediate neutron spectrum experiment

    International Nuclear Information System (INIS)

    Jaegers, P.J.; Sanchez, R.G.

    1996-01-01

    Criticality benchmark data for intermediate energy spectrum systems does not exist. These systems are dominated by scattering and fission events induced by neutrons with energies between 1 eV and 1 MeV. Nuclear data uncertainties have been reported for such systems which can not be resolved without benchmark critical experiments. Intermediate energy spectrum systems have been proposed for the geological disposition of surplus fissile materials. Without the proper benchmarking of the nuclear data in the intermediate energy spectrum, adequate criticality safety margins can not be guaranteed. The Zeus critical experiment now under construction will provide this necessary benchmark data

  14. S-Adenosylmethionine conformations in solution and in protein complexes: Conformational influences of the sulfonium group

    DEFF Research Database (Denmark)

    Markham, George D.; Norrby, Per-Ola; Bock, Charles W.

    2002-01-01

    S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR...... and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes...... with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo...

  15. Application of Semiempirical Methods to Transition Metal Complexes: Fast Results but Hard-to-Predict Accuracy.

    KAUST Repository

    Minenkov, Yury

    2018-05-22

    A series of semiempirical PM6* and PM7 methods has been tested in reproducing of relative conformational energies of 27 realistic-size complexes of 16 different transition metals (TMs). An analysis of relative energies derived from single-point energy evaluations on density functional theory (DFT) optimized conformers revealed pronounced deviations between semiempirical and DFT methods indicating fundamental difference in potential energy surfaces (PES). To identify the origin of the deviation, we compared fully optimized PM7 and respective DFT conformers. For many complexes, differences in PM7 and DFT conformational energies have been confirmed often manifesting themselves in false coordination of some atoms (H, O) to TMs and chemical transformations/distortion of coordination center geometry in PM7 structures. Despite geometry optimization with fixed coordination center geometry leads to some improvements in conformational energies, the resulting accuracy is still too low to recommend explored semiempirical methods for out-of-the-box conformational search/sampling: careful testing is always needed.

  16. The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET

    Directory of Open Access Journals (Sweden)

    Mengyi Yang

    2018-01-01

    Full Text Available Summary: Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single-molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms spontaneously transits among three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We also uncovered surprising long-range allosteric communication between the HNH domain and the RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated that a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the PAM-distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox. : Yang et al. revealed significant conformational dynamics of Cas9 at global and local scales using single-molecule FRET. They uncovered surprising long-range allosteric communication between the HNH nuclease domain and the RNA/DNA heteroduplex at the PAM-distal end that serves as a proofreading checkpoint to govern the nuclease activity and specificity of Cas9. Keywords: CRISPR, Cas9, single-molecule, FRET, conformational dynamics, proofreading, off-target, allosteric communication, genome editing

  17. Monitoring Conformational Landscape of Ovine Prion Protein Monomer Using Ion Mobility Coupled to Mass Spectrometry

    Science.gov (United States)

    Van der Rest, Guillaume; Rezaei, Human; Halgand, Frédéric

    2017-02-01

    Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry. In order to perform the analysis of a large body of data sets, we designed and evaluated the performance of a processing pipeline based on Driftscope peak detection and a homemade script for automated peak assignment, annotation, and quantification on specific multiply charged protein data. Using this approach, we showed that in the gas phase, PrPs are represented by at least three conformer families differing in both charge state distribution and collisional cross-section, in agreement with the work of Hilton et al. (2010). We also showed that this plasticity is borne both by the N- and C-terminal domains. Effect of protein concentration, pH and temperature were also assessed, showing that (1) pH does not affect conformer distributions, (2) protein concentration modifies the conformational landscape of one mutant (I208M) only, and (3) heating leads to other unfolded species and to a modification of the conformer intensity ratios.

  18. Conformal Killing vectors in Robertson-Walker spacetimes

    International Nuclear Information System (INIS)

    Maartens, R.; Maharaj, S.d.

    1986-01-01

    It is well known that Robertson-Walker spacetimes admit a conformal Killingl vector normal to the spacelike homogeneous hypersurfaces. Because these spacetimes are conformally flat, there are a further eight conformal Killing vectors, which are neither normal nor tangent to the homogeneous hypersurfaces. The authors find these further conformal Killing vectors and the Lie algebra of the full G 15 of conformal motions. Conditions on the metric scale factor are determined which reduce some of the conformal Killing vectors to homothetic Killing vectors or Killing vectors, allowing one to regain in a unified way the known special geometries. The non-normal conformal Killing vectors provide a counter-example to show that conformal motions do not, in general, map a fluid flow conformally. These non-normal vectors are also used to find the general solution of the null geodesic equation and photon Liouville equation. (author)

  19. Problems of economic security in Russian transportation and intermediate carrier infrastructure

    Directory of Open Access Journals (Sweden)

    Valeriy Anatol'evich Tsvetkov

    2012-03-01

    Full Text Available This paper reviews the basic problems of economic security in infrastructural ensuring of the implementation of transportation and intermediate carrier potential of Russia: development and reconstruction of communication lines, usage of innovative transportation methods, building a network of transportation and logistics centers, development of regional airport hubs and others. Particular attention is paid to the problems of transportation and transit potential implementation of Siberia and the Far East. It is shown that the increase of transit facilities in the territory of Russia takes place in a competitive market of infrastructure projects. At the same time it is emphasized that along with exhausting the possibilities of commodity economy development, a natural competitive advantage of Russia as a transport bridge between Europe, Asia and America will be implemented in full force.

  20. Problems of economic security in Russian transportation and intermediate carrier infrastructure

    Directory of Open Access Journals (Sweden)

    Valeriy Anatol'evich Tsvetkov

    2012-06-01

    Full Text Available This paper reviews the basic problems of economic security in infrastructural ensuring of the implementation of transportation and intermediate carrier potential of Russia: development and reconstruction of communication lines, usage of innovative transportation methods, building a network of transportation and logistics centers, development of regional airport hubs and others. Particular attention is paid to the problems of transportation and transit potential implementation of Siberia and the Far East. It is shown that the increase of transit facilities in the territory of Russia takes place in a competitive market of infrastructure projects. At the same time it is emphasized that along with exhausting the possibilities of commodity economy development, a natural competitive advantage of Russia as a transport bridge between Europe, Asia and America will be implemented in full force.

  1. Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaojing; Ren, Zhong; Kuk, Jane; Moffat, Keith (UC)

    2012-03-27

    Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C{sub 15} = C{sub 16} double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C{sub 15} methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

  2. Conformal transformations in superspace

    International Nuclear Information System (INIS)

    Dao Vong Duc

    1977-01-01

    The spinor extension of the conformal algebra is investigated. The transformation law of superfields under the conformal coordinate inversion R defined in the superspace is derived. Using R-technique, the superconformally covariant two-point and three-point correlation functions are found

  3. Statistical and dynamical aspects of intermediate energy nuclear collisions

    International Nuclear Information System (INIS)

    Ghetti, R.

    1997-01-01

    Studies of intermediate energy heavy ion reactions have revealed that the probability of emitting n-fragments is reducible to the probability of emitting a single fragment through the binomial distribution. The resulting one-fragment probability shows a dependence on the thermal energy that is characteristic of statistical decay. Similarly, the charge distributions associated with n-fragment emission are reducible to the one-fragment charge distribution, and thermal scaling is observed. The reducibility equation for the n-fragment charge distribution contains a quantity with a value that starts from zero, at low transverse energies, and saturates at high transverse energies. This evolution may signal a transition from a coexistence phase to a vapour phase. In the search for a signal of liquid-gas phase transition, the appearance of intermittency is reconsidered. Percolation calculations, as well as data analysis, indicate that an intermittent-like signal appears from classes of events that do not coincide with the critical one. 232 refs

  4. Statistical and dynamical aspects of intermediate energy nuclear collisions

    Energy Technology Data Exchange (ETDEWEB)

    Ghetti, R.

    1997-01-01

    Studies of intermediate energy heavy ion reactions have revealed that the probability of emitting n-fragments is reducible to the probability of emitting a single fragment through the binomial distribution. The resulting one-fragment probability shows a dependence on the thermal energy that is characteristic of statistical decay. Similarly, the charge distributions associated with n-fragment emission are reducible to the one-fragment charge distribution, and thermal scaling is observed. The reducibility equation for the n-fragment charge distribution contains a quantity with a value that starts from zero, at low transverse energies, and saturates at high transverse energies. This evolution may signal a transition from a coexistence phase to a vapour phase. In the search for a signal of liquid-gas phase transition, the appearance of intermittency is reconsidered. Percolation calculations, as well as data analysis, indicate that an intermittent-like signal appears from classes of events that do not coincide with the critical one. 232 refs.

  5. Towards conformal loop quantum gravity

    International Nuclear Information System (INIS)

    Wang, Charles H-T

    2006-01-01

    A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity

  6. The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET.

    Science.gov (United States)

    Yang, Mengyi; Peng, Sijia; Sun, Ruirui; Lin, Jingdi; Wang, Nan; Chen, Chunlai

    2018-01-09

    Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single-molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms spontaneously transits among three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We also uncovered surprising long-range allosteric communication between the HNH domain and the RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated that a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the PAM-distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  7. Conformational Ensembles of α-Synuclein Derived Peptide with Different Osmolytes from Temperature Replica Exchange Sampling

    Directory of Open Access Journals (Sweden)

    Salma Jamal

    2017-12-01

    Full Text Available Intrinsically disordered proteins (IDP are a class of proteins that do not have a stable three-dimensional structure and can adopt a range of conformations playing various vital functional role. Alpha-synuclein is one such IDP which can aggregate into toxic protofibrils and has been associated largely with Parkinson's disease (PD along with other neurodegenerative diseases. Osmolytes are small organic compounds that can alter the environment around the proteins by acting as denaturants or protectants for the proteins. In the present study, we have conducted a series of replica exchange molecular dynamics simulations to explore the role of osmolytes, urea which is a denaturant and TMAO (trimethylamine N-oxide, a protecting osmolyte, in aggregation and conformations of the synuclein peptide. We observed that both the osmolytes have significantly distinct impacts on the peptide and led to transitions of the conformations of the peptide from one state to other. Our findings highlighted that urea attenuated peptide aggregation and resulted in the formation of extended peptide structures whereas TMAO led to compact and folded forms of the peptide.

  8. Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry

    DEFF Research Database (Denmark)

    Petersen, Michael; Madsen, Jeppe B; Jørgensen, Thomas J D

    2017-01-01

    activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations...... are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1......Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen...

  9. The influence of charge injection from intermediate connectors on the performance of tandem organic light-emitting devices

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Dong-Ying [Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123 (China); Department of Electrical and Computer Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Siboni, Hossein Zamani; Wang, Qi; Aziz, Hany, E-mail: lsliao@suda.edu.cn, E-mail: h2aziz@uwaterloo.ca [Department of Electrical and Computer Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Liao, Liang-Sheng, E-mail: lsliao@suda.edu.cn, E-mail: h2aziz@uwaterloo.ca [Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123 (China)

    2014-12-14

    Charge generation in a typical intermediate connector, composed of “n-type doped layer/transition metal oxide (TMO)/hole transporting layer (HTL),” of a tandem organic light-emitting device (OLED) has recently been found to arise from charge transfer at the TMO/HTL interfaces. In this paper, we investigate the effect of hole injection barriers from intermediate connectors on the performance of tandem OLEDs. The hole injection barriers are caused by the offset of the highest occupied molecular orbital (HOMO) energy levels between HTLs contained in the intermediate connector and the top electroluminescence (EL) unit. We also find that although charge generation can occur at the interfaces between the TMO and a wide variety of HTLs of different HOMO values, an increase in the hole injection barrier however limits the electroluminescence efficiency of the top EL units. In the case of large hole injection barriers, significant charge accumulation in the HTLs makes the intermediate connector lose its functionality gradually over operating time, and limits device stability.

  10. Is Androgen Deprivation Therapy Necessary in All Intermediate-Risk Prostate Cancer Patients Treated in the Dose Escalation Era?

    International Nuclear Information System (INIS)

    Castle, Katherine O.; Hoffman, Karen E.; Levy, Lawrence B.; Lee, Andrew K.; Choi, Seungtaek; Nguyen, Quynh N.; Frank, Steven J.; Pugh, Thomas J.; McGuire, Sean E.; Kuban, Deborah A.

    2013-01-01

    Purpose: The benefit of adding androgen deprivation therapy (ADT) to dose-escalated radiation therapy (RT) for men with intermediate-risk prostate cancer is unclear; therefore, we assessed the impact of adding ADT to dose-escalated RT on freedom from failure (FFF). Methods: Three groups of men treated with intensity modulated RT or 3-dimensional conformal RT (75.6-78 Gy) from 1993-2008 for prostate cancer were categorized as (1) 326 intermediate-risk patients treated with RT alone, (2) 218 intermediate-risk patients treated with RT and ≤6 months of ADT, and (3) 274 low-risk patients treated with definitive RT. Median follow-up was 58 months. Recursive partitioning analysis based on FFF using Gleason score (GS), T stage, and pretreatment PSA concentration was applied to the intermediate-risk patients treated with RT alone. The Kaplan-Meier method was used to estimate 5-year FFF. Results: Based on recursive partitioning analysis, intermediate-risk patients treated with RT alone were divided into 3 prognostic groups: (1) 188 favorable patients: GS 6, ≤T2b or GS 3+4, ≤T1c; (2) 71 marginal patients: GS 3+4, T2a-b; and (3) 68 unfavorable patients: GS 4+3 or T2c disease. Hazard ratios (HR) for recurrence in each group were 1.0, 2.1, and 4.6, respectively. When intermediate-risk patients treated with RT alone were compared to intermediate-risk patients treated with RT and ADT, the greatest benefit from ADT was seen for the unfavorable intermediate-risk patients (FFF, 74% vs 94%, respectively; P=.005). Favorable intermediate-risk patients had no significant benefit from the addition of ADT to RT (FFF, 94% vs 95%, respectively; P=.85), and FFF for favorable intermediate-risk patients treated with RT alone approached that of low-risk patients treated with RT alone (98%). Conclusions: Patients with favorable intermediate-risk prostate cancer did not benefit from the addition of ADT to dose-escalated RT, and their FFF was nearly as good as patients with low-risk disease

  11. Transition State Gauche Effects Control the Torquoselectivities of the Electrocyclizations of Chiral 1-Azatrienes.

    Science.gov (United States)

    Patel, Ashay; Vella, Joseph R; Ma, Zhi-Xiong; Hsung, R P; Houk, K N

    2015-12-04

    Hsung et al. have reported a series of torquoselective electrocyclizations of chiral 1-azahexa-1E,3Z,5E-trienes that yield functionalized dihydropyridines. To understand the origins of the torquoselectivities of these azaelectrocyclizations, we modeled these electrocyclic ring closures using the M06-2X density functional. A new stereochemical model that rationalizes the observed 1,2 stereoinduction emerges from these computations. This model is an improvement and generalization of the "inside-alkoxy" model used to rationalize stereoselectivities of the 1,3-dipolar cycloaddition of chiral allyl ethers and emphasizes a stabilizing hyperconjugative effect, which we have termed a transition state gauche effect. This stereoelectronic effect controls the conformational preferences at the electrocyclization transition states, and only in one of the allowed disrotatory electrocyclization transition states is the ideal stereoelectronic arrangement achieved without the introduction of a steric clash. Computational experiments confirm the role of this effect as a stereodeterminant since substrates with electropositive groups and electronegative groups have different conformational preferences at the transition state and undergo ring closure with divergent stereochemical outcomes. This predicted reversal of stereoselectivity for the ring closures of several silyl substituted azatrienes have been demonstrated experimentally.

  12. Nearly reversible conformational change of amyloid fibrils as revealed by pH-jump experiments.

    Science.gov (United States)

    Yamaguchi, Kei-ichi; Kamatari, Yuji O; Fukuoka, Mayuko; Miyaji, Reiji; Kuwata, Kazuo

    2013-10-01

    pH-jump induced conformational transitions between substates of preformed amyloid fibrils made by a fragmented peptide of helix 2 (H2 peptide) of MoPrP were detected, and their kinetics were analyzed using a novel pH-jump apparatus specially designed for observing amyloids. Previously, we reported that H2 peptide formed ordered fibrils with a minimum at 207 nm on CD spectra at pH 2.9 (named pH 2.9 fibrils), but formed aggregate-like fibrils with a minimum at 220 nm at pH 7.5 (named pH 7.5 fibrils). When pH-jump from 2.9 to 7.5 was performed, the CD spectrum changed instantly, but the finally observed ellipticities were clearly distinct from those of pH 7.5 fibrils. Thus, the finally observed state is termed 'pH 7.5-like fibrils'. However, pH 7.5-like fibrils reverted to the conformation very similar to that of the pH 2.9 fibrils when the pH of the solution was restored to 2.9. Then, we examined the kinetics of the nearly reversible conformational changes between pH 2.9 fibrils and pH 7.5-like fibrils using ANS fluorescence stopped-flow, and we observed relatively fast phases (0.7-18 s(-1)). In contrast, the conversion between pH 7.5-like fibrils and pH 7.5 fibrils never occurred (<0.2 day(-1)). Thus, H2 fibrils can be switched readily between distinct conformations separated by a low energy barrier, while a large energy barrier clearly separated the different conformations. These conformational varieties of amyloid fibrils may explain the physical basis of the diversity in prion.

  13. Conformational dynamics of a protein in the folded and the unfolded state

    Energy Technology Data Exchange (ETDEWEB)

    Fitter, Joerg

    2003-08-01

    In a quasielastic neutron scattering experiment, the picosecond dynamics of {alpha}-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D{sub 2}O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 A; unfolded state, 1.8 A). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

  14. Infrared conformality and bulk critical points: SU(2) with heavy adjoint quarks

    CERN Document Server

    Lucini, Biagio; Rago, Antonio; Rinaldi, Enrico

    2013-01-01

    The lattice phase structure of a gauge theory can be a serious obstruction to Monte Carlo studies of its continuum behaviour. This issue is particularly delicate when numerical studies are performed to determine whether a theory is in a (near-)conformal phase. In this work we investigate the heavy mass limit of the SU(2) gauge theory with Nf=2 adjoint fermions and its lattice phase diagram, showing the presence of a critical point ending a line of first order bulk phase transition. The relevant gauge observables and the low-lying spectrum are monitored in the vicinity of the critical point with very good control over different systematic effects. The scaling properties of masses and susceptibilities open the possibility that the effective theory at criticality is a scalar theory in the universality class of the four-dimensional Gaussian model. This behaviour is clearly different from what is observed for SU(2) gauge theory with two dynamical adjoint fermions, whose (near-)conformal numerical signature is henc...

  15. Transition probabilities for two-photon H (1з–2з) and He (1 1з–2 1з ...

    Indian Academy of Sciences (India)

    Transition amplitudes and transition probabilities for the two-photon 1-2 transition in the hydrogen atom and 11-21 transition in helium atom have been calculated using a partialclosure approach. The dominant term is calculated exactly and the remaining sum over intermediate states is calculated using a mean ...

  16. Exploration of conformational changes in lactose permease upon sugar binding and proton transfer through coarse-grained simulations.

    Science.gov (United States)

    Jewel, Yead; Dutta, Prashanta; Liu, Jin

    2017-10-01

    Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H + symport process. Lactose/H + symport is a highly complex process that involves sugar translocation, H + transfer, and large-scale protein conformational changes. The complete picture of lactose/H + symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-d-galactopyranosyl-1-thio- β-d-galactopyranoside (TDG) molecule to a wild-type LacY. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from ∼5.5 µs simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with double electron-electron resonance and thiol cross-linking experiments. Our analysis suggests that the conformational changes of LacY are a cumulative consequence of interdomain H-bonds breaking at the periplasmic side, interdomain salt-bridge formation at the cytoplasmic side, and the TDG orientational changes during the transition. © 2017 Wiley Periodicals, Inc.

  17. Pressure-induced phase transitions in acentric BaHf(BO{sub 3}){sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Mączka, Mirosław, E-mail: m.maczka@int.pan.wroc.pl [Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, 50-950 Wrocław 2 (Poland); Szymborska-Małek, Katarzyna [Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, 50-950 Wrocław 2 (Poland); Sousa Pinheiro, Gardenia de [Departamento de Física, Universidade Federal do Piauí, Teresina, PI 64049-550 (Brazil); Cavalcante Freire, Paulo Tarso [Departamento de Fisica, Universidade Federal do Ceara, Fortaleza CE-60455-970 (Brazil); Majchrowski, Andrzej [Institute of Applied Physics, Military University of Technology, 2 Kaliskiego Street, 00-908 Warszawa (Poland)

    2015-08-15

    High-pressure Raman scattering studies revealed that BaHf(BO{sub 3}){sub 2} is more compressible than calcite-type orthoborates and calcite, aragonite or dolomite carbonates. It undergoes a first-order reversible pressure-induced phase transition in the 3.9–4.4 GPa pressure range. Second structural change is observed at 9.2 GPa. The intermediate phase is most likely trigonal. However, Raman results suggest increase in the number of distinct BO{sub 3} groups from two in the ambient pressure phase to at least three in the intermediate phase. This intermediate phase is also strongly compressible and strong pressure dependence of the lattice modes proves that the main changes under pressure occur within the layers built from BaO{sub 6} and HfO{sub 6} octahedra. The second phase transition leads most likely to lowering of the trigonal symmetry, as evidenced by significant increase of the number of observed bands. The pressure coefficients of the Raman bands of the high-pressure phase are relatively small, suggesting more dense arrangement of the metal–oxygen polyhedra and BO{sub 3} groups in this phase. It is worth noting that the high-pressure phase was not reached in the second compression experiment up to 10 GPa. This behavior can be most likely attributed to worse hydrostatic conditions of the first experiment. - Graphical abstract: Raman spectra of BaHf(BO{sub 3}){sub 2} recorded at different pressures during compression showing onset of pressure-induced phase transitions. - Highlights: • High-pressure Raman spectra were measured for BaHf(BO{sub 3}){sub 2.} • BaHf(BO{sub 3}){sub 2} undergoes a reversible first-order phase transition at 3.9–4.4 GPa into a trigonal phase. • The intermediate trigonal phase is strongly compressible second structural transformation is observed at 9.2 GPa under non-perfect hydrostatic conditions.

  18. Temperature and pressure dependence of the order parameter fluctuations, conformational compressibility, and the phase diagram of the PEP-PDMS diblock copolymer

    DEFF Research Database (Denmark)

    Schwahn, D.; Frielinghaus, H.; Mortensen, K.

    1996-01-01

    The structure factor of a poly(ethylene-propylene)-poly(dimethylsiloxane) diblock copolymer has been measured by small-angle neutron scattering as a function of temperature and pressure. The conformational compressibility exhibits a pronounced maximum at the order-disorder phase transition. The p...

  19. Mass generation within conformal invariant theories

    International Nuclear Information System (INIS)

    Flato, M.; Guenin, M.

    1981-01-01

    The massless Yang-Mills theory is strongly conformally invariant and renormalizable; however, when masses are introduced the theory becomes nonrenormalizable and weakly conformally invariant. Conditions which recover strong conformal invariance are discussed in the letter. (author)

  20. Conformal group actions and Segal's cosmology

    International Nuclear Information System (INIS)

    Werth, J.-E.

    1984-01-01

    A mathematical description of Segal's cosmological model in the framework of conformal group actions is presented. The relation between conformal and causal group actions on time-orientable Lorentzian manifolds is analysed and several examples are discussed. A criterion for the conformality of a map between Lorentzian manifolds is given. The results are applied to Segal's 'conformal compactification' of Minkowski space. Furthermore, the 'unitary formulation' of Segal's cosmology is regarded. (Author) [pt

  1. Conformal field theories and critical phenomena

    International Nuclear Information System (INIS)

    Xu, Bowei

    1993-01-01

    In this article we present a brief review of the conformal symmetry and the two dimensional conformal quantum field theories. As concrete applications of the conformal theories to the critical phenomena in statistical systems, we calculate the value of central charge and the anomalous scale dimensions of the Z 2 symmetric quantum chain with boundary condition. The results are compatible with the prediction of the conformal field theories

  2. New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.

    Science.gov (United States)

    Thach, Trung Thanh; Shin, Donghyuk; Han, Seungsu; Lee, Sangho

    2016-04-01

    The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such conformational flexibility remains open. Here, the crystal structure of linear Ub2 was determined in a more compact conformation than that of the previously known structure (PDB entry 3axc). The two structures differ significantly from each other, as shown by an r.m.s.d. between C(α) atoms of 3.1 Å. The compactness of the linear Ub2 structure in comparison with PDB entry 3axc is supported by smaller values of the radius of gyration (Rg; 18 versus 18.9 Å) and the maximum interatomic distance (Dmax; 55.5 versus 57.8 Å). Extra intramolecular hydrogen bonds formed among polar residues between the distal and proximal ubiquitin moieties seem to contribute to stabilization of the compact conformation of linear Ub2. An ensemble of three semi-extended and extended conformations of linear Ub2 was also observed by small-angle X-ray scattering (SAXS) analysis in solution. In addition, the conformational heterogeneity in linear polyubiquitin chains is clearly manifested by SAXS analyses of linear Ub3 and Ub4: at least three distinct solution conformations are observed in each chain, with the linear Ub3 conformations being compact. The results expand the extent of conformational space of linear polyubiquitin chains and suggest that changes in the conformational ensemble may be pivotal in mediating multiple signalling pathways.

  3. Ward identities for conformal models

    International Nuclear Information System (INIS)

    Lazzarini, S.; Stora, R.

    1988-01-01

    Ward identities which express the symmetry of conformal models are treated. Diffeomorphism invariance or locally holomorphic coordinate transformations are used. Diffeomorphism invariance is then understood in terms of Riemannian geometry. Two different sets of Ward identities expressing diffeomorphism invariance in a conformally invariant way are found for the free bosonic string. Using a geometrical argument, the correct invariance for a large class of conformal models is given

  4. Conformity and statistical tolerancing

    Science.gov (United States)

    Leblond, Laurent; Pillet, Maurice

    2018-02-01

    Statistical tolerancing was first proposed by Shewhart (Economic Control of Quality of Manufactured Product, (1931) reprinted 1980 by ASQC), in spite of this long history, its use remains moderate. One of the probable reasons for this low utilization is undoubtedly the difficulty for designers to anticipate the risks of this approach. The arithmetic tolerance (worst case) allows a simple interpretation: conformity is defined by the presence of the characteristic in an interval. Statistical tolerancing is more complex in its definition. An interval is not sufficient to define the conformance. To justify the statistical tolerancing formula used by designers, a tolerance interval should be interpreted as the interval where most of the parts produced should probably be located. This tolerance is justified by considering a conformity criterion of the parts guaranteeing low offsets on the latter characteristics. Unlike traditional arithmetic tolerancing, statistical tolerancing requires a sustained exchange of information between design and manufacture to be used safely. This paper proposes a formal definition of the conformity, which we apply successively to the quadratic and arithmetic tolerancing. We introduce a concept of concavity, which helps us to demonstrate the link between tolerancing approach and conformity. We use this concept to demonstrate the various acceptable propositions of statistical tolerancing (in the space decentring, dispersion).

  5. Dissecting the large-scale galactic conformity

    Science.gov (United States)

    Seo, Seongu

    2018-01-01

    Galactic conformity is an observed phenomenon that galaxies located in the same region have similar properties such as star formation rate, color, gas fraction, and so on. The conformity was first observed among galaxies within in the same halos (“one-halo conformity”). The one-halo conformity can be readily explained by mutual interactions among galaxies within a halo. Recent observations however further witnessed a puzzling connection among galaxies with no direct interaction. In particular, galaxies located within a sphere of ~5 Mpc radius tend to show similarities, even though the galaxies do not share common halos with each other ("two-halo conformity" or “large-scale conformity”). Using a cosmological hydrodynamic simulation, Illustris, we investigate the physical origin of the two-halo conformity and put forward two scenarios. First, back-splash galaxies are likely responsible for the large-scale conformity. They have evolved into red galaxies due to ram-pressure stripping in a given galaxy cluster and happen to reside now within a ~5 Mpc sphere. Second, galaxies in strong tidal field induced by large-scale structure also seem to give rise to the large-scale conformity. The strong tides suppress star formation in the galaxies. We discuss the importance of the large-scale conformity in the context of galaxy evolution.

  6. Influence of multiple well defined conformations on small-angle scattering of proteins in solution.

    Science.gov (United States)

    Heller, William T

    2005-01-01

    A common structural motif for many proteins comprises rigid domains connected by a flexible hinge or linker. The flexibility afforded by these domains is important for proper function and such proteins may be able to adopt more than one conformation in solution under equilibrium conditions. Small-angle scattering of proteins in solution samples all conformations that exist in the sampled volume during the time of the measurement, providing an ensemble-averaged intensity. In this paper, the influence of sampling an ensemble of well defined protein structures on the small-angle solution scattering intensity profile is examined through common analysis methods. Two tests were performed using simulated data: one with the extended and collapsed states of the bilobal calcium-binding protein calmodulin and the second with the catalytic subunit of protein kinase A, which has two globular domains connected by a glycine hinge. In addition to analyzing the simulated data for the radii of gyration Rg, distance distribution function P(r) and particle volume, shape restoration was applied to the simulated data. Rg and P(r) of the ensemble profiles could be easily mistaken for a single intermediate state. The particle volumes and models of the ensemble intensity profiles show that some indication of multiple conformations exists in the case of calmodulin, which manifests an enlarged volume and shapes that are clear superpositions of the conformations used. The effect on the structural parameters and models is much more subtle in the case of the catalytic subunit of protein kinase A. Examples of how noise influences the data and analyses are also presented. These examples demonstrate the loss of the indications of multiple conformations in cases where even broad distributions of structures exist. While the tests using calmodulin show that the ensemble states remain discernible from the other ensembles tested or a single partially collapsed state, the tests performed using the

  7. Entanglement evolution across a conformal interface

    Science.gov (United States)

    Wen, Xueda; Wang, Yuxuan; Ryu, Shinsei

    2018-05-01

    For two-dimensional conformal field theories (CFTs) in the ground state, it is known that a conformal interface along the entanglement cut can suppress the entanglement entropy from to , where L is the length of the subsystem A, and is the effective central charge which depends on the transmission property of the conformal interface. In this work, by making use of conformal mappings, we show that a conformal interface has the same effect on entanglement evolution in non-equilibrium cases, including global, local and certain inhomogeneous quantum quenches. I.e. a conformal interface suppresses the time evolution of entanglement entropy by effectively replacing the central charge c with , where is exactly the same as that in the ground state case. We confirm this conclusion by a numerical study on a critical fermion chain. Furthermore, based on the quasi-particle picture, we conjecture that this conclusion holds for an arbitrary quantum quench in CFTs, as long as the initial state can be described by a regularized conformal boundary state.

  8. Critical role of γ-phosphate in structural transition of Na,K-ATPase upon ATP binding

    Science.gov (United States)

    Petrushanko, Irina Yu.; Mitkevich, Vladimir A.; Anashkina, Anastasia A.; Klimanova, Elizaveta A.; Dergousova, Elena A.; Lopina, Olga D.; Makarov, Alexander A.

    2014-06-01

    Active transport of sodium and potassium ions by Na,K-ATPase is accompanied by the enzyme conformational transition between E1 and E2 states. ATP and ADP bind to Na,K-ATPase in the E1 conformation with similar affinity but the properties of enzyme in complexes with these nucleotides are different. We have studied thermodynamics of Na,K-ATPase binding with adenine nucleotides at different temperatures using isothermal titration calorimetry. Our data indicate that β-phosphate is involved in complex formation by increasing the affinity of adenine nucleotides to Na,K-ATPase by an order of magnitude, while γ-phosphate does not affect it. ATP binding to Na,K-ATPase in contrast to ADP binding generates a structural transition in the enzyme, which is consistent with the movement of a significant portion of the surface area to a solvent-protected state. We propose that ATP binding leads to convergence of the nucleotide-binding and phosphorylation domains transferring the enzyme from the ``E1-open'' to ``E1-closed'' conformation ready for phosphorylation.

  9. Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

    Energy Technology Data Exchange (ETDEWEB)

    Ono, Junichi [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585 (Japan); Takada, Shoji [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585 (Japan); Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Saito, Shinji, E-mail: shinji@ims.ac.jp [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585 (Japan); The Graduate University for Advanced Studies, Okazaki 444-8585 (Japan)

    2015-06-07

    An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchical conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.

  10. Long, partial-short, and special conformal fields

    Energy Technology Data Exchange (ETDEWEB)

    Metsaev, R.R. [Department of Theoretical Physics, P.N. Lebedev Physical Institute,Leninsky prospect 53, Moscow 119991 (Russian Federation)

    2016-05-17

    In the framework of metric-like approach, totally symmetric arbitrary spin bosonic conformal fields propagating in flat space-time are studied. Depending on the values of conformal dimension, spin, and dimension of space-time, we classify all conformal field as long, partial-short, short, and special conformal fields. An ordinary-derivative (second-derivative) Lagrangian formulation for such conformal fields is obtained. The ordinary-derivative Lagrangian formulation is realized by using double-traceless gauge fields, Stueckelberg fields, and auxiliary fields. Gauge-fixed Lagrangian invariant under global BRST transformations is obtained. The gauge-fixed BRST Lagrangian is used for the computation of partition functions for all conformal fields. Using the result for the partition functions, numbers of propagating D.o.F for the conformal fields are also found.

  11. Probing the Mechanism of pH-Induced Large-Scale Conformational Changes in Dengue Virus Envelope Protein Using Atomistic Simulations

    Science.gov (United States)

    Prakash, Meher K.; Barducci, Alessandro; Parrinello, Michele

    2010-01-01

    Abstract One of the key steps in the infection of the cell by dengue virus is a pH-induced conformational change of the viral envelope proteins. These envelope proteins undergo a rearrangement from a dimer to a trimer, with large conformational changes in the monomeric unit. In this article, metadynamics simulations were used to enable us to understand the mechanism of these large-scale changes in the monomer. By using all-atom, explicit solvent simulations of the monomers, the stability of the protein structure is studied under low and high pH conditions. Free energy profiles obtained along appropriate collective coordinates demonstrate that pH affects the domain interface in both the conformations of E monomer, stabilizing one and destabilizing the other. These simulations suggest a mechanism with an intermediate detached state between the two monomeric structures. Using further analysis, we comment on the key residue interactions responsible for the instability and the pH-sensing role of a histidine that could not otherwise be studied experimentally. The insights gained from this study and methodology can be extended for studying similar mechanisms in the E proteins of the other members of class II flavivirus family. PMID:20643078

  12. Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models.

    Science.gov (United States)

    Lindner, Benjamin; Yi, Zheng; Prinz, Jan-Hendrik; Smith, Jeremy C; Noé, Frank

    2013-11-07

    The dynamics of complex molecules can be directly probed by inelastic neutron scattering experiments. However, many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. Here, we show how Markov models can be used to connect structural changes observed in molecular dynamics simulation directly to the relaxation processes probed by scattering experiments. For this, a conformational dynamics theory of dynamical neutron and X-ray scattering is developed, following our previous approach for computing dynamical fingerprints of time-correlation functions [F. Noé, S. Doose, I. Daidone, M. Löllmann, J. Chodera, M. Sauer, and J. Smith, Proc. Natl. Acad. Sci. U.S.A. 108, 4822 (2011)]. Markov modeling is used to approximate the relaxation processes and timescales of the molecule via the eigenvectors and eigenvalues of a transition matrix between conformational substates. This procedure allows the establishment of a complete set of exponential decay functions and a full decomposition into the individual contributions, i.e., the contribution of every atom and dynamical process to each experimental relaxation process.

  13. An Intermediate in the evolution of superfast sonic muscles

    Directory of Open Access Journals (Sweden)

    Mok Hin-Kiu

    2011-11-01

    Full Text Available Abstract Background Intermediate forms in the evolution of new adaptations such as transitions from water to land and the evolution of flight are often poorly understood. Similarly, the evolution of superfast sonic muscles in fishes, often considered the fastest muscles in vertebrates, has been a mystery because slow bladder movement does not generate sound. Slow muscles that stretch the swimbladder and then produce sound during recoil have recently been discovered in ophidiiform fishes. Here we describe the disturbance call (produced when fish are held and sonic mechanism in an unrelated perciform pearl perch (Glaucosomatidae that represents an intermediate condition in the evolution of super-fast sonic muscles. Results The pearl perch disturbance call is a two-part sound produced by a fast sonic muscle that rapidly stretches the bladder and an antagonistic tendon-smooth muscle combination (part 1 causing the tendon and bladder to snap back (part 2 generating a higher-frequency and greater-amplitude pulse. The smooth muscle is confirmed by electron microscopy and protein analysis. To our knowledge smooth muscle attachment to a tendon is unknown in animals. Conclusion The pearl perch, an advanced perciform teleost unrelated to ophidiiform fishes, uses a slow type mechanism to produce the major portion of the sound pulse during recoil, but the swimbladder is stretched by a fast muscle. Similarities between the two unrelated lineages, suggest independent and convergent evolution of sonic muscles and indicate intermediate forms in the evolution of superfast muscles.

  14. Maxwell equations in conformal invariant electrodynamics

    International Nuclear Information System (INIS)

    Fradkin, E.S.; AN SSSR, Novosibirsk. Inst. Avtomatiki i Ehlektrometrii); Kozhevnikov, A.A.; Palchik, M.Ya.; Pomeransky, A.A.

    1983-01-01

    We consider a conformal invariant formulation of quantum electrodynamics. Conformal invariance is achieved with a specific mathematical construction based on the indecomposable representations of the conformal group associated with the electromagnetic potential and current. As a corolary of this construction modified expressions for the 3-point Green functions are obtained which both contain transverse parts. They make it possible to formulate a conformal invariant skeleton perturbation theory. It is also shown that the Euclidean Maxwell equations in conformal electrodynamics are manifestations of its kinematical structure: in the case of the 3-point Green functions these equations follow (up to constants) from the conformal invariance while in the case of higher Green functions they are equivalent to the equality of the kernels of the partial wave expansions. This is the manifestation of the mathematical fast of a (partial) equivalence of the representations associated with the potential, current and the field tensor. (orig.)

  15. Conformal symmetries of FRW accelerating cosmologies

    International Nuclear Information System (INIS)

    Kehagias, A.; Riotto, A.

    2014-01-01

    We show that any accelerating Friedmann–Robertson–Walker (FRW) cosmology with equation of state w<−1/3 (and therefore not only a de Sitter stage with w=−1) exhibits three-dimensional conformal symmetry on future constant-time hypersurfaces if the bulk theory is invariant under bulk conformal Killing vectors. We also offer an alternative derivation of this result in terms of conformal Killing vectors and show that long wavelength comoving curvature perturbations of the perturbed FRW metric are just conformal Killing motions of the FRW background. We then extend the boundary conformal symmetry to the bulk for accelerating cosmologies. Our findings indicate that one can easily generate perturbations of scalar fields which are not only scale invariant, but also fully conformally invariant on super-Hubble scales. Measuring a scale-invariant power spectrum for the cosmological perturbation does not automatically imply that the universe went through a de Sitter stage

  16. Conformal solids and holography

    Science.gov (United States)

    Esposito, A.; Garcia-Saenz, S.; Nicolis, A.; Penco, R.

    2017-12-01

    We argue that a SO( d) magnetic monopole in an asymptotically AdS space-time is dual to a d-dimensional strongly coupled system in a solid state. In light of this, it would be remiss of us not to dub such a field configuration solidon. In the presence of mixed boundary conditions, a solidon spontaneously breaks translations (among many other symmetries) and gives rise to Goldstone excitations on the boundary — the phonons of the solid. We derive the quadratic action for the boundary phonons in the probe limit and show that, when the mixed boundary conditions preserve conformal symmetry, the longitudinal and transverse sound speeds are related to each other as expected from effective field theory arguments. We then include backreaction and calculate the free energy of the solidon for a particular choice of mixed boundary conditions, corresponding to a relevant multi-trace deformation of the boundary theory. We find such free energy to be lower than that of thermal AdS. This suggests that our solidon undergoes a solid-to-liquid first order phase transition by melting into a Schwarzschild-AdS black hole as the temperature is raised.

  17. Critical Line of the Deconfinement Phase Transitions

    Science.gov (United States)

    Gorenstein, Mark I.

    Phase diagram of strongly interacting matter is discussed within the exactly solvable statistical model of the quark-gluon bags. The model predicts two phases of matter: the hadron gas at a low temperature T and baryonic chemical potential μ B , and the quark-gluon gas at a high T and/or μ B . The nature of the phase transition depends on a form of the bag massvolume spectrum (its pre-exponential factor), which is expected to change with the μ B /T ratio. It is therefore likely that the line of the 1 st order transition at a high μ B/T ratio is followed by the line of the 2 nd order phase transition at an intermediate μ B/T, and then by the lines of "higher order transitions" at a low μ B /T. This talk is based on a recent paper (Gorenstein, Gaździcki, and Greiner, 2005).

  18. Trapping and Characterization of a Reaction Intermediate in Carbapenem Hydrolysis by B. cereus Metallo-β-lactamase

    Science.gov (United States)

    Tioni, Mariana F.; Llarrull, Leticia I.; Poeylaut-Palena, Andrés A.; Martí, Marcelo A.; Saggu, Miguel; Periyannan, Gopal R.; Mata, Ernesto G.; Bennett, Brian; Murgida, Daniel H.; Vila, Alejandro J.

    2009-01-01

    Metallo-β-lactamases hydrolyze most β-lactam antibiotics. The lack of a successful inhibitor for them is related to the previous failure to characterize a reaction intermediate with a clinically useful substrate. Stopped-flow experiments together with rapid freeze-quench EPR and Raman spectroscopies were used to characterize the reaction of Co(II)-BcII with imipenem. These studies show that Co(II)-BcII is able to hydrolyze imipenem both in the mono- and dinuclear forms. In contrast to the situation met for penicillin, the species that accumulates during turnover is an enzyme-intermediate adduct in which the β-lactam bond has already been cleaved. This intermediate is a metal-bound anionic species, with a novel resonant structure, that is stabilized by the metal ion at the DCH or Zn2 site. This species has been characterized based on its spectroscopic features. This represents a novel, previously unforeseen intermediate, that is related to the chemical nature of carbapenems, as confirmed by the finding of a similar intermediate for meropenem. Since carbapenems are the only substrates cleaved by B1, B2 and B3 lactamases, the identification of this intermediate could be exploited as a first step towards the design of transition state based inhibitors for all three classes of metallo-β-lactamases. PMID:18980308

  19. Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine

    Science.gov (United States)

    Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, Rui

    2014-10-01

    The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N-H...O=C, type II by a strong O-H...N hydrogen bond, type III by weak N-H...O-H hydrogen bonds, and type IV by a C=O...H-C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O-H...N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm-1, respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG undergoes facile photofragmentation

  20. Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine

    International Nuclear Information System (INIS)

    Borba, Ana; Fausto, Rui; Gómez-Zavaglia, Andrea

    2014-01-01

    The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N–H···O=C, type II by a strong O–H···N hydrogen bond, type III by weak N–H···O–H hydrogen bonds, and type IV by a C=O···H–C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O–H···N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N 2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm −1 , respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG

  1. 40 CFR 52.2133 - General conformity.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 4 2010-07-01 2010-07-01 false General conformity. 52.2133 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South Carolina State Implementation Plan which...

  2. A Lennard-Jones-like perspective on first order transitions in biological helices

    DEFF Research Database (Denmark)

    Oskolkov, Nikolay N.; Bohr, Jakob

    2013-01-01

    Helical structures with Lennard-Jones self-interactions are studied for optimal conformations. For this purpose, their self-energy is analyzed for extrema with respect to the geometric parameters of the helices. It is found that Lennard-Jones helices exhibit a first order phase transition from...

  3. 40 CFR 91.106 - Certificate of conformity.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Certificate of conformity. 91.106... Provisions § 91.106 Certificate of conformity. (a) Every manufacturer of a new marine SI engine produced... obtain a certificate of conformity covering each engine family. The certificate of conformity must be...

  4. Physics of intermediate shocks: A review

    Science.gov (United States)

    Karimabadi, H.

    1995-01-01

    Intermediate shocks (ISs) lead to a transition from super-Alfvenic to sub-Alfvenic flow and are different from slow and fast shocks in that an IS rotates the component of the magnetic field tangent to the shock plane by 180 deg. Another peculiarity of ISs is that for the same upstream conditions an IS can have two different downstream states. There also exist a second class of ISs which rotate the magnetic field by an angle other than 180 deg. Due to their noncoplanar nature they cannot be time-stationary and are referred to as time-dependent intermediate shocks (TDIS). The existence of ISs has been the subject of much controversy over the years. Early studies questioned the physical reality of ISs. However, the studies of ISs found a new impetus when C.C. Wu showed that ISs do exist and are stable within the resistive MHD framework. In this paper, after a brief historical overview of the subject, we will review the latest developments in the study of ISs. In particular, we will address the questions of stability and structure of ISs and the relationship between ISs and other discontinuities. One of the recent developments has been the finding that ISs can be unsteady, reforming in time. Details of this process will be discussed. Finally, we examine the effect of anisotropy on the resolutions and discuss the relevance of ISs to the observed field rotations at the Earth's magnetopause.

  5. Triggering of 178Hfm2 by photoinduced electron transition

    Directory of Open Access Journals (Sweden)

    A. Ya. Dzyublik

    2013-03-01

    Full Text Available We considered the NEET (nuclear excitation by electron transition as a possible triggering mechanism of the isomer 178Hfm2 during ionization of the L3 atomic shell by x-rays. This isomer is assumed to be excited into an intermediate state by E1 electronic transition between M5 and L3 shells. Simple nonrelativistic formulas are derived for the NEET probability. The estimations show the probability to be less than the experimental data of [1] by one order of magnitude. The intermediate level is found to decay bypassing the isomeric level 16+, if the nucleus attributes a triaxial shape in the state and, besides, there exists a level 13- shifted with respect to 15- by 400 keV. We have shown also that the NEET cross section as a function of the energy of x-ray photons , has to accept constant value above the L photoionization threshold in contrast to narrow peak observed by [1].

  6. Two-Step Amyloid Aggregation: Sequential Lag Phase Intermediates

    Science.gov (United States)

    Castello, Fabio; Paredes, Jose M.; Ruedas-Rama, Maria J.; Martin, Miguel; Roldan, Mar; Casares, Salvador; Orte, Angel

    2017-01-01

    The self-assembly of proteins into fibrillar structures called amyloid fibrils underlies the onset and symptoms of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s. However, the molecular basis and mechanism of amyloid aggregation are not completely understood. For many amyloidogenic proteins, certain oligomeric intermediates that form in the early aggregation phase appear to be the principal cause of cellular toxicity. Recent computational studies have suggested the importance of nonspecific interactions for the initiation of the oligomerization process prior to the structural conversion steps and template seeding, particularly at low protein concentrations. Here, using advanced single-molecule fluorescence spectroscopy and imaging of a model SH3 domain, we obtained direct evidence that nonspecific aggregates are required in a two-step nucleation mechanism of amyloid aggregation. We identified three different oligomeric types according to their sizes and compactness and performed a full mechanistic study that revealed a mandatory rate-limiting conformational conversion step. We also identified the most cytotoxic species, which may be possible targets for inhibiting and preventing amyloid aggregation.

  7. 40 CFR 52.938 - General conformity.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 3 2010-07-01 2010-07-01 false General conformity. 52.938 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November 10, 1995, and adopted into the Kentucky State...

  8. 40 CFR 51.854 - Conformity analysis.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Conformity analysis. 51.854 Section 51... FOR PREPARATION, ADOPTION, AND SUBMITTAL OF IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 51.854 Conformity analysis. Link to an...

  9. Lie algebra of conformal Killing–Yano forms

    International Nuclear Information System (INIS)

    Ertem, Ümit

    2016-01-01

    We provide a generalization of the Lie algebra of conformal Killing vector fields to conformal Killing–Yano forms. A new Lie bracket for conformal Killing–Yano forms that corresponds to slightly modified Schouten–Nijenhuis bracket of differential forms is proposed. We show that conformal Killing–Yano forms satisfy a graded Lie algebra in constant curvature manifolds. It is also proven that normal conformal Killing–Yano forms in Einstein manifolds also satisfy a graded Lie algebra. The constructed graded Lie algebras reduce to the graded Lie algebra of Killing–Yano forms and the Lie algebras of conformal Killing and Killing vector fields in special cases. (paper)

  10. Universal hydrodynamics of non-conformal branes

    International Nuclear Information System (INIS)

    Kanitscheider, Ingmar; Skenderis, Kostas

    2009-01-01

    We examine the hydrodynamic limit of non-conformal branes using the recently developed precise holographic dictionary. We first streamline the discussion of holography for backgrounds that asymptote locally to non-conformal brane solutions by showing that all such solutions can be obtained from higher dimensional asymptotically locally AdS solutions by suitable dimensional reduction and continuation in the dimension. As a consequence, many holographic results for such backgrounds follow from the corresponding results of the Asymptotically AdS case. In particular, the hydrodynamics of non-conformal branes is fully determined in terms of conformal hydrodynamics. Using previous results on the latter we predict the form of the non-conformal hydrodynamic stress tensor to second order in derivatives. Furthermore we show that the ratio between bulk and shear viscosity is fixed by the generalized conformal structure to be ζ/η = 2(1/(d-1)-c s 2 ), where c s is the speed of sound in the fluid.

  11. Operator algebras and conformal field theory

    International Nuclear Information System (INIS)

    Gabbiani, F.; Froehlich, J.

    1993-01-01

    We define and study two-dimensional, chiral conformal field theory by the methods of algebraic field theory. We start by characterizing the vacuum sectors of such theories and show that, under very general hypotheses, their algebras of local observables are isomorphic to the unique hyperfinite type III 1 factor. The conformal net determined by the algebras of local observables is proven to satisfy Haag duality. The representation of the Moebius group (and presumably of the entire Virasoro algebra) on the vacuum sector of a conformal field theory is uniquely determined by the Tomita-Takesaki modular operators associated with its vacuum state and its conformal net. We then develop the theory of Mebius covariant representations of a conformal net, using methods of Doplicher, Haag and Roberts. We apply our results to the representation theory of loop groups. Our analysis is motivated by the desire to find a 'background-independent' formulation of conformal field theories. (orig.)

  12. 47 CFR 2.906 - Declaration of Conformity.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Declaration of Conformity. 2.906 Section 2.906... Conformity. (a) A Declaration of Conformity is a procedure where the responsible party, as defined in § 2.909... of Conformity attaches to all items subsequently marketed by the responsible party which are...

  13. AC susceptibility of thin Pb films in intermediate and mixed state

    Energy Technology Data Exchange (ETDEWEB)

    Janu, Zdenek, E-mail: janu@fzu.cz [Institute of Physics of the AS CR, v.v.i., Na Slovance 2, CZ-182 21 Prague 8 (Czech Republic); Svindrych, Zdenek [Institute of Physics of the AS CR, v.v.i., Na Slovance 2, CZ-182 21 Prague 8 (Czech Republic); Trunecek, Otakar [Charles University in Prague, Faculty of Mathematics and Physics, Ke Karlovu 3, CZ-121 16 Prague 2 (Czech Republic); Kus, Peter; Plecenik, Andrej [Komenius University in Bratislava, Faculty of Mathematics, Physics, and Informatics, Mlynska dolina, 842 48 Bratislava 4 (Slovakia)

    2011-12-15

    Thickness dependent transition in AC susceptibility between intermediate and mixed state in type-I superconducting films. The temperature induced crossover between reversible and irreversible behavior was observed in the thicker film. The temperature dependence of the AC susceptibility in mixed state follows prediction of model based on Bean critical state. The temperature dependence of the harmonics of the complex AC susceptibility in the intermediate state is explained. Thin films of type I superconductors of a thickness comparable or less than a flux penetration length behave like type II superconductors in a mixed state. With decreasing film thickness normal domains carrying a magnetic flux get smaller with smaller number of flux quanta per domain and finally transform into single quantum flux lines, i.e. quantum vortices similar to those found in type II superconductors. We give an evidence of this behavior from the measurements of the nonlinear response of a total magnetic moment to an applied AC magnetic field, directly from the temperature dependence of an AC susceptibility.

  14. Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

    Directory of Open Access Journals (Sweden)

    Jonathan Maiangwa

    2017-05-01

    Full Text Available The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent

  15. Studying multifragmentation dynamics at intermediate energies using two-fragment correlations

    International Nuclear Information System (INIS)

    Sangster, T.C.; Britt, H.C.; Namboodiri, M.N.

    1993-01-01

    One of the most challenging topics in Nuclear Physics is the multifragmentation at moderate excitation energies in large nuclear systems. Although the idea that multifragmentation is analogous to a liquid-gas like phase transition is not new, it has only been recently that highly exclusive experimental measurements have been coupled with sophisticated theoretical models like QMD and BUU/VUU to explore reaction dynamics and the process of fragment formation. Indeed, much of what is known about multifragmentation has resulted from the study of complex correlations present in both the experimental data and theoretical calculations. One of the most crucial questions in the ongoing debate concerning the liquid-gas analogy is the differentiation between simultaneous and sequential fragment emission. Clearly, the phase transition analogy breaks down if fragments are emitted sequentially as in an evaporative process. There have been a number of two-fragment correlation results published recently (including those presented in this paper) which attempt to put limits on the emission timescale using three-body Coulomb trajectory calculations with explicit emission times for sequential decays from a fixed source density. These results have been generally consistent and indicate that intermediate mass fragment (IMF) emission is nearly simultaneous in medium energy heavy ion collisions. Only very recently have calculations been performed which approach this question from the other extreme: simultaneous emission from a variable density source. When considered together, these results argue favorably for a simultaneous multifragmentation. In this paper the authors present comprehensive results on two-fragment correlations for heavy systems at intermediate energies

  16. Investigation of the intermediate- and high-density forms of amorphous ice by molecular dynamics calculations and diffraction experiments

    International Nuclear Information System (INIS)

    Tse, John S.; Klug, Dennis D.; Guthrie, Malcolm; Benmore, Chris J.; Urquidi, Jacob; Tulk, Chris A.

    2005-01-01

    The lack of an 'isosbestic' point in the oxygen-oxygen atom radial distribution functions (RDFs) for the HDA→LDA ice transformation at ambient pressure derived from molecular dynamics (MD) calculations show unequivocally that intermediate phases are not equilibrium mixtures of these two amorphous forms. This is supported by x-ray structure factor data, where it is found that linear combinations of the starting and end amorphous forms do not describe intermediate forms of amorphous ice formed during the transformation. This reflects the fact that the x-ray data are heavily weighted to O-O correlations and therefore sensitive to the basic structural changes that occur during the relaxation process. The ice Ih→HDA transformation is also reexamined using MD to identify its thermodynamic nature. This apparently first-order transition induced by a mechanical instability is investigated by compression followed by decompression to negative pressures. In this study we demonstrated that the full van der Waals loop for this transition can be identified

  17. Kinetics of disorder-to-fcc phase transition via an intermediate bcc state

    International Nuclear Information System (INIS)

    Liu Yongsheng; Nie Huifen; Bansil, Rama; Steinhart, Milos; Bang, Joona; Lodge, Timothy P.

    2006-01-01

    Time-resolved small-angle x-ray scattering measurements reveal that a long-lived intermediate bcc state forms when a poly(styrene-b-isoprene) diblock copolymer solution in an isoprene selective solvent is rapidly cooled from the disordered micellar fluid at high temperature to an equilibrium fcc state. The kinetics of the epitaxial growth of the [111] fcc peak from the [110] bcc peak was obtained by fitting the scattering data to a simple model of the transformation. The growth of the [111] fcc peak agrees with the Avrami model of nucleation and growth kinetics with an exponent n=1.4, as does the initial decay of the [110] bcc peak, with an exponent n=1.3. The data were also found to be in good agreement with the Cahn model of grain boundary nucleation and growth

  18. Optical studies of intersublevel-transitions in self-organized InGaAs/GaAs quantum dots

    International Nuclear Information System (INIS)

    Weber, A.

    2005-01-01

    In this thesis intersublevel-transitions in self-organized InGaAs/GaAs quantum dots are studied with spectroscopic methods. The charge-dependent absorption behaviour of the nanostructures in the intermediate infrared is studied by a new combination of Fourier spectroscopy and calorimetric absorption spectroscopy. Optical absorption in the quantum dots leads to a sample heating by charge-carrier relaxations, whereby non-radiative intersublevel transitions in the quantum dots are directly determined. The effects observed thereby are explained by different charge-carrier occupation, Pauli blocking, and many-=particle effects in the quantum dots. Furthermore intermediate-infrared emission from quantum dots is spectroscopically studied both under optical and electrical excitation. Each according to the structure of the waveguides in the samples emission peaks are shown, the intensity of which grows either sublinearly with the excitation power and finally saturates or exhibits a significantly superlinear growth. Simulations of an intermediate-infrared quantum-dot laser, which regard also the simultaneous intermediate-infrared emission, show that the observed superlinear growth is to be explained by intersublevel emission in the laser mode. The principal feasibility of a bipolar two-colour laser, which emits in the near- and in the intermediate infrared, is shown by this

  19. Naturality in conformal field theory

    International Nuclear Information System (INIS)

    Moore, G.; Seiberg, N.

    1989-01-01

    We discuss constraints on the operator product coefficients in diagonal and nondiagonal rational conformal field theories. Nondiagonal modular invariants always arise from automorphisms of the fusion rule algebra or from extensions of the chiral algebra. Moreover, when the chiral algebra has been maximally extended a strong form of the naturality principle of field theory can be proven for rational conformal field theory: operator product coefficients vanish if and only if the corresponding fusion rules vanish; that is, if and only if the vanishing can be understood in terms of a symmetry. We illustrate these ideas with several examples. We also generalize our ideas about rational conformal field theories to a larger class of theories: 'quasi-rational conformal field theories' and we explore some of their properties. (orig.)

  20. 21 CFR 26.70 - Conformity assessment bodies.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Conformity assessment bodies. 26.70 Section 26.70...Frameworkâ Provisions § 26.70 Conformity assessment bodies. Each party recognizes that the conformity... conformity in relation to its requirements as specified in subpart B of this part. The parties shall specify...

  1. Conformational analysis of lignin models

    International Nuclear Information System (INIS)

    Santos, Helio F. dos

    2001-01-01

    The conformational equilibrium for two 5,5' biphenyl lignin models have been analyzed using a quantum mechanical semiempirical method. The gas phase and solution structures are discussed based on the NMR and X-ray experimental data. The results obtained showed that the observed conformations are solvent-dependent, being the geometries and the thermodynamic properties correlated with the experimental information. This study shows how a systematic theoretical conformational analysis can help to understand chemical processes at a molecular level. (author)

  2. On the linear conformal gravitation

    International Nuclear Information System (INIS)

    Pal'chik, M.Ya.; Fradkin, E.S.

    1984-01-01

    Conformal gravitation is analyzed under the assumption that its solution possesses the property of conformal symmetry. This assumption has sense in the case of small distances and only for definite types of matter fields, namely: at special choice of matter fields and their interactions, providing a lack of conformal anomalies; or at definite magnitudes of binding constants, coinciding with the zeroes of the Gell-Mann-Low function. The field equations, of the group-theoretical natura are obtained

  3. Conformal Symmetry Patterns in Baryon Spectra

    International Nuclear Information System (INIS)

    Kirchbach, Mariana; Compean, Cliffor B

    2011-01-01

    Attention is drawn to the fact that the spectra of the baryons of the lightest flavors, the nucleon and the Δ, carry quantum numbers characteristic for an unitary representation of the conformal group. We show that the above phenomenon is well explained for baryons whose internal structure is dominated by a quark-diquark configuration that resides in a conformally compactified Minkowski space time, R 1 x S 3 , and is described by means of the conformal scale equation there. The R 1 x S 3 space-time represents the boundary of the conformally compactified AdS 5 , on which one expects to encounter a conformal theory in accord with the gauge-gravity duality. Within this context, our model is congruent with AdS 5 /CFT 4 .

  4. Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases

    OpenAIRE

    Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, Rui

    2006-01-01

    Dimethyl sulfite has three conformers of low energy, GG, GT and GG0, which have significant populations in the gas phase at room temperature. According to theoretical predictions, the GT and GG0 conformers are higher in energy than the GG conformer by 0.83 and 1.18 kJ molK1, respectively, while the barriers associated with the GG0/GT and GT/GG isomerizations are 1.90 and 9.64 kJ molK1, respectively. Experimental data obtained for the compound isolated in solid argon, krypton and xenon demonst...

  5. Analysis of the Intermediate-State Contributions to Neutrinoless Double β− Decays

    Directory of Open Access Journals (Sweden)

    Juhani Hyvärinen

    2016-01-01

    Full Text Available A comprehensive analysis of the structure of the nuclear matrix elements (NMEs of neutrinoless double beta-minus (0νβ-β- decays to the 0+ ground and first excited states is performed in terms of the contributing multipole states in the intermediate nuclei of 0νβ-β- transitions. We concentrate on the transitions mediated by the light (l-NMEs Majorana neutrinos. As nuclear model we use the proton-neutron quasiparticle random-phase approximation (pnQRPA with a realistic two-nucleon interaction based on the Bonn one-boson-exchange G matrix. In the computations we include the appropriate short-range correlations, nucleon form factors, and higher-order nucleonic weak currents and restore the isospin symmetry by the isoscalar-isovector decomposition of the particle-particle proton-neutron interaction parameter gpp.

  6. Comparison of Palivizumab-Like Antibody Binding to Different Conformations of the RSV F Protein in RSV-Infected Adult Hematopoietic Cell Transplant Recipients.

    Science.gov (United States)

    Ye, Xunyan; Iwuchukwu, Obinna P; Avadhanula, Vasanthi; Aideyan, Letisha O; McBride, Trevor J; Ferlic-Stark, Laura L; Patel, Kirtida D; Piedra, Felipe-Andres; Shah, Dimpy P; Chemaly, Roy F; Piedra, Pedro A

    2018-03-28

    Most respiratory syncytial virus (RSV) vaccine candidates include fusion (F) protein in different conformations. Antigenic site II found in the different F conformations is the target of palivizumab, the only US Food and Drug Administration approved monoclonal antibody (mAb). Serum palivizumab-like antibody (PLA) is a potential serologic correlate of immunity. Our objective was to determine if different conformations of F protein in a palivizumab competitive antibody (PCA) assay affect the PLA concentrations. Four PCA assays were standardized using mAbs. Each contained prefusion, postfusion, or intermediate F forms. PLA concentrations were measured in acute and convalescent sera from 22 RSV/A and 18 RSV/B-infected adult hematopoietic cell transplant (HCT) recipients. PLA concentrations were calculated using a 4-parameter logistic regression model and analyzed for statistical significance. PCA assays revealed significantly greater PLA concentrations in convalescent sera; comparable increases in PLA concentration in RSV/A and RSV/B-infected HCT recipients; and significantly reduced PLA concentrations in HCT recipients who shed RSV ≥14 days. A significant positive correlation was observed between PCA assays and RSV neutralizing antibody titers. F protein conformation does not appear to have a measurable impact on PCA assays for measuring PLA induced by RSV/A or RSV/B infection.

  7. Conformational Clusters of Phosphorylated Tyrosine.

    Science.gov (United States)

    Abdelrasoul, Maha; Ponniah, Komala; Mao, Alice; Warden, Meghan S; Elhefnawy, Wessam; Li, Yaohang; Pascal, Steven M

    2017-12-06

    Tyrosine phosphorylation plays an important role in many cellular and intercellular processes including signal transduction, subcellular localization, and regulation of enzymatic activity. In 1999, Blom et al., using the limited number of protein data bank (PDB) structures available at that time, reported that the side chain structures of phosphorylated tyrosine (pY) are partitioned into two conserved conformational clusters ( Blom, N.; Gammeltoft, S.; Brunak, S. J. Mol. Biol. 1999 , 294 , 1351 - 1362 ). We have used the spectral clustering algorithm to cluster the increasingly growing number of protein structures with pY sites, and have found that the pY residues cluster into three distinct side chain conformations. Two of these pY conformational clusters associate strongly with a narrow range of tyrosine backbone conformation. The novel cluster also highly correlates with the identity of the n + 1 residue, and is strongly associated with a sequential pYpY conformation which places two adjacent pY side chains in a specific relative orientation. Further analysis shows that the three pY clusters are associated with distinct distributions of cognate protein kinases.

  8. Kinetics of quasi-isoenergetic transition processes in biological macromolecules

    International Nuclear Information System (INIS)

    Petrov, E.G.; Teslenko, V.I.

    2010-01-01

    A master equation describing the evolution of averaged molecular state occupancies in molecular systems where alternation of molecular energy levels is caused by discrete dichotomous and trichotomous stochastic fields, is derived. This study is focused on the kinetics of quasi-isoenergetic transition processes in the presence of moderately high frequency stochastic field. A novel physical mechanism for temperature-independent transitions in flexible molecular systems is proposed. This mechanism becomes effective when the conformation transitions between quasi-isoenergetic molecular states take place. At room temperatures, stochastic broadening of molecular energy levels predominates the energy of low-frequency vibrations accompanying the transition. This leads to a cancellation of the temperature dependence in the stochastically averaged rate constants. As examples, physical interpretations of the temperature-independent onset of P2X 3 receptor desensitization in neuronal membranes, as well as degradation of PER2 protein in embrionic fibroblasts, are provided.

  9. Kinetics of quasi-isoenergetic transition processes in biological macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Petrov, E.G., E-mail: epetrov@bitp.kiev.ua [Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, Metrologichna Street, 14-b, UA-03680 Kiev (Ukraine); Teslenko, V.I. [Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, Metrologichna Street, 14-b, UA-03680 Kiev (Ukraine)

    2010-10-05

    A master equation describing the evolution of averaged molecular state occupancies in molecular systems where alternation of molecular energy levels is caused by discrete dichotomous and trichotomous stochastic fields, is derived. This study is focused on the kinetics of quasi-isoenergetic transition processes in the presence of moderately high frequency stochastic field. A novel physical mechanism for temperature-independent transitions in flexible molecular systems is proposed. This mechanism becomes effective when the conformation transitions between quasi-isoenergetic molecular states take place. At room temperatures, stochastic broadening of molecular energy levels predominates the energy of low-frequency vibrations accompanying the transition. This leads to a cancellation of the temperature dependence in the stochastically averaged rate constants. As examples, physical interpretations of the temperature-independent onset of P2X{sub 3} receptor desensitization in neuronal membranes, as well as degradation of PER2 protein in embrionic fibroblasts, are provided.

  10. Intermediality and media change

    OpenAIRE

    2012-01-01

    This book is about intermediality as an approach to analysing and understanding media change. Intermediality and Media Change is critical of technological determinism that characterises 'new media discourse' about the ongoing digitalization, framed as a revolution and creating sharp contrasts between old and new media. Intermediality instead emphasises paying attention to continuities between media of all types and privileges a comparative perspective on technological changes in media over ti...

  11. Thickenings and conformal gravity

    Science.gov (United States)

    Lebrun, Claude

    1991-07-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason [B-M].

  12. Thickenings and conformal gravity

    International Nuclear Information System (INIS)

    LeBrun, C.

    1991-01-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason [B-M]. (orig.)

  13. Angular correlations and fragmentation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Kristiansson, Anders.

    1990-05-01

    Intermediate energy heavy-ion collisions have been studied from 35 A MeV up to 94 A MeV at various accelerators. Angular correlations between light particles and detection of projectile- and target-fragments have been used to investigate the reaction mechanisms in this transition region between low- and high energy. An excess of correlations is observed in the particle-particle elastic scattering plane. This excess increases with particle mass and can be understood in terms of momentum conservation. The fragmentation measurements gives an indication that both energy and momentum transfer to the spectator volumes does occur. (author)

  14. The crystal structure and the phase transitions of pyridinium trifluoromethanesulfonate

    International Nuclear Information System (INIS)

    Jesariew, Dominik; Ilczyszyn, Maria M; Pietraszko, Adam

    2014-01-01

    The calorimetric and optical studies and the structural properties of pyridinium trifluoromethanesulfonate (abbreviated as PyHOTf) are reported. A sequence of four fully reversible solid–solid phase transitions, at 223.0, 309.0, 359.9 and 394.3 K, has been discovered. The phase transition sequence was confirmed by x-ray diffraction data. The crystal structures of three phases (V, IV and III) have been determined from the single crystal x-ray diffraction data. Structural properties of the high temperature phases are characterized using powder x-ray diffraction data measured in the 290–425 K temperature range. The structural changes triggered by the temperature change are discussed in relation to the phase transitions. Two low temperature phases (V and IV) belong to the P4 3 2 1 2 space group of the tetragonal system. The intermediate phases (III and II) are monoclinic and the prototype high temperature phase (I) is a pseudo-cubic (tetragonal) one. The low temperature phases (V and IV) are well ordered. The crystal structure of intermediate (III and II) and prototype (I) phases are characterized by high disorder of the pyridinium cations and triflate anions. (papers)

  15. Conformal symmetry inheritance in null fluid spacetimes

    International Nuclear Information System (INIS)

    Tupper, B O J; Keane, A J; Hall, G S; Coley, A A; Carot, J

    2003-01-01

    We define inheriting conformal Killing vectors for null fluid spacetimes and find the maximum dimension of the associated inheriting Lie algebra. We show that for non-conformally flat null fluid spacetimes, the maximum dimension of the inheriting algebra is seven and for conformally flat null fluid spacetimes the maximum dimension is eight. In addition, it is shown that there are two distinct classes of non-conformally flat generalized plane wave spacetimes which possess the maximum dimension, and one class in the conformally flat case

  16. Conformal maps between pseudo-Finsler spaces

    Science.gov (United States)

    Voicu, Nicoleta

    The paper aims to initiate a systematic study of conformal mappings between Finsler spacetimes and, more generally, between pseudo-Finsler spaces. This is done by extending several results in pseudo-Riemannian geometry which are necessary for field-theoretical applications and by proposing a technique that reduces some problems involving pseudo-Finslerian conformal vector fields to their pseudo-Riemannian counterparts. Also, we point out, by constructing classes of examples, that conformal groups of flat (locally Minkowskian) pseudo-Finsler spaces can be much richer than both flat Finslerian and pseudo-Euclidean conformal groups.

  17. Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Denis Bucher

    2011-04-01

    Full Text Available Periplasmic binding proteins (PBPs are a large family of molecular transporters that play a key role in nutrient uptake and chemotaxis in Gram-negative bacteria. All PBPs have characteristic two-domain architecture with a central interdomain ligand-binding cleft. Upon binding to their respective ligands, PBPs undergo a large conformational change that effectively closes the binding cleft. This conformational change is traditionally viewed as a ligand induced-fit process; however, the intrinsic dynamics of the protein may also be crucial for ligand recognition. Recent NMR paramagnetic relaxation enhancement (PRE experiments have shown that the maltose binding protein (MBP - a prototypical member of the PBP superfamily - exists in a rapidly exchanging (ns to µs regime mixture comprising an open state (approx 95%, and a minor partially closed state (approx 5%. Here we describe accelerated MD simulations that provide a detailed picture of the transition between the open and partially closed states, and confirm the existence of a dynamical equilibrium between these two states in apo MBP. We find that a flexible part of the protein called the balancing interface motif (residues 175-184 is displaced during the transformation. Continuum electrostatic calculations indicate that the repacking of non-polar residues near the hinge region plays an important role in driving the conformational change. Oscillations between open and partially closed states create variations in the shape and size of the binding site. The study provides a detailed description of the conformational space available to ligand-free MBP, and has implications for understanding ligand recognition and allostery in related proteins.

  18. Communication: A coil-stretch transition in planar elongational flow of an entangled polymeric melt

    Science.gov (United States)

    Nafar Sefiddashti, Mohammad H.; Edwards, Brian J.; Khomami, Bamin

    2018-04-01

    Virtual experimentation of atomistic entangled polyethylene melts undergoing planar elongational flow revealed an amazingly detailed depiction of individual macromolecular dynamics and the resulting effect on bistable configurational states. A clear coil-stretch transition was evident, in much the same form as first envisioned by de Gennes for dilute solutions of high polymers, resulting in an associated hysteresis in the configurational flow profile over the range of strain rates predicted by theory. Simulations conducted at steady state revealed bimodal distribution functions, in which equilibrium configurational states were simultaneously populated by relatively coiled and stretched molecules which could transition from one conformational mode to the other over a relatively long time scale at critical values of strain rates. The implication of such behavior points to a double-well conformational free energy potential with an activation barrier between the two configurational minima.

  19. Enhanced superconductivity and superconductor to insulator transition in nano-crystalline molybdenum thin films

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Shilpam; Amaladass, E.P. [Condensed Matter Physics Division, Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Sharma, Neha [Surface & Nanoscience Division, Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Harimohan, V. [Condensed Matter Physics Division, Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Amirthapandian, S. [Materials Physics Division, Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Mani, Awadhesh, E-mail: mani@igcar.gov.in [Condensed Matter Physics Division, Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India)

    2017-06-01

    Disorder driven superconductor to insulator transition via intermediate metallic regime is reported in nano-crystalline thin films of molybdenum. The nano-structured thin films have been deposited at room temperature using DC magnetron sputtering at different argon pressures. The grain size has been tuned using deposition pressure as the sole control parameter. A variation of particle sizes, room temperature resistivity and superconducting transition has been studied as a function of deposition pressure. The nano-crystalline molybdenum thin films are found to have large carrier concentration but very low mobility and electronic mean free path. Hall and conductivity measurements have been used to understand the effect of disorder on the carrier density and mobilities. Ioffe-Regel parameter is shown to correlate with the continuous metal-insulator transition in our samples. - Highlights: • Thin films of molybdenum using DC sputtering have been deposited on glass. • Argon background pressure during sputtering was used to tune the crystallite sizes of films. • Correlation in deposition pressure, disorder and particle sizes has been observed. • Disorder tuned superconductor to insulator transition along with an intermediate metallic phase has been observed. • Enhancement of superconducting transition temperature and a dome shaped T{sub C} vs. deposition pressure phase diagram has been observed.

  20. Transportation Conformity

    Science.gov (United States)

    This section provides information on: current laws, regulations and guidance, policy and technical guidance, project-level conformity, general information, contacts and training, adequacy review of SIP submissions

  1. Extended conformal algebras

    International Nuclear Information System (INIS)

    Goddard, Peter

    1990-01-01

    The algebra of the group of conformal transformations in two dimensions consists of two commuting copies of the Virasoro algebra. In many mathematical and physical contexts, the representations of ν which are relevant satisfy two conditions: they are unitary and they have the ''positive energy'' property that L o is bounded below. In an irreducible unitary representation the central element c takes a fixed real value. In physical contexts, the value of c is a characteristic of a theory. If c < 1, it turns out that the conformal algebra is sufficient to ''solve'' the theory, in the sense of relating the calculation of the infinite set of physically interesting quantities to a finite subset which can be handled in principle. For c ≥ 1, this is no longer the case for the algebra alone and one needs some sort of extended conformal algebra, such as the superconformal algebra. It is these algebras that this paper aims at addressing. (author)

  2. Families and degenerations of conformal field theories

    Energy Technology Data Exchange (ETDEWEB)

    Roggenkamp, D.

    2004-09-01

    In this work, moduli spaces of conformal field theories are investigated. In the first part, moduli spaces corresponding to current-current deformation of conformal field theories are constructed explicitly. For WZW models, they are described in detail, and sigma model realizations of the deformed WZW models are presented. The second part is devoted to the study of boundaries of moduli spaces of conformal field theories. For this purpose a notion of convergence of families of conformal field theories is introduced, which admits certain degenerated conformal field theories to occur as limits. To such a degeneration of conformal field theories, a degeneration of metric spaces together with additional geometric structures can be associated, which give rise to a geometric interpretation. Boundaries of moduli spaces of toroidal conformal field theories, orbifolds thereof and WZW models are analyzed. Furthermore, also the limit of the discrete family of Virasoro minimal models is investigated. (orig.)

  3. Intermediate Fragment

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2015-01-01

    This text and its connected exhibition are aiming to reflect both on the thoughts, the processes and the outcome of the design and production of the artefact ‘Intermediate Fragment’ and making as a contemporary architectural tool in general. Intermediate Fragment was made for the exhibition ‘Enga...... of realising an exhibition object was conceived, but expanded, refined and concretised through this process. The context of the work shown here is an interest in a tighter, deeper connection between experimentally obtained material knowledge and architectural design....

  4. Thickenings and conformal gravity

    Energy Technology Data Exchange (ETDEWEB)

    LeBrun, C. (State Univ. of New York, Stony Brook, NY (USA). Dept. of Mathematics)

    1991-07-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason (B-M). (orig.).

  5. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, C.S.; Trandum, C.; Larsen, N.

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (T-m) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal a-helix was of major importance to the conformational stability of calreticulin....

  6. The general expression for the transition amplitude of two-photon ionization of atomic hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Karule, E [Institute of Atomic Physics and Spectroscopy, University of Latvia, Raina Boulevard 19, Riga, LV-1586 (Latvia); Moine, B [Universite Paris Sud, 91405 Orsay Cedex (France)

    2003-05-28

    Two-photon ionization of atomic hydrogen with an excess photon is revisited. The non-relativistic dipole approximation and Coulomb Green function (CGF) formalism are applied. Using the CGF Sturmian expansion straightforwardly, one gets the radial transition amplitude in the form of an infinite sum over Gauss hypergeometric functions which are polynomials. It is convergent if all intermediate states are in the discrete spectrum. In the case of two-photon ionization with an excess photon, when photoionization is also possible, intermediate states are in the continuum. We performed the explicit summation over intermediate states and got a simple general expression for the radial transition amplitude in the form of a finite sum over Appell hypergeometric functions, which are not polynomials. An Appell function may be expressed as an infinite sum over Gauss functions. In the case of ionization by an excess photon, Gauss functions are transformed to give a convergent radial transition amplitude for the whole region. The generalized cross sections for two-photon above-threshold ionization of atomic hydrogen in the ground state and excited states calculated by us agree very well with results of previous calculations. Generalized cross sections for two-photon ionization of positronium in the ground state are obtained by scaling those for atomic hydrogen.

  7. Spectroscopic studies of neutral and chemically oxidized species of β-carotene, lycopene and norbixin in CH2Cl2: Fluorescence from intermediate compounds

    International Nuclear Information System (INIS)

    Alwis, D.D.D.H; Chandrika, U.G.; Jayaweera, P.M.

    2015-01-01

    Radical cations, dications and oxidized intermediate species of three carotenoids, namely, β-carotene, lycopene and norbixin, were generated in CH 2 Cl 2 solutions via chemical oxidation using anhydrous FeCl 3 . UV–vis, fluorescence and fluorescence-excitation spectroscopic studies were performed to understand and compare the nature of intermediate species generated during the chemical oxidation process and subsequent degradation. The intense emission observed at 550 nm can be assigned to the S 2 →S 0 (1 1 B u →1 1 A g ) transition of the carotenoid molecules. The 350 nm excitation during the oxidation process for β-carotene, lycopene and norbixin exhibit intense fluorescence peaks at 492 nm, 493 nm and 500 nm, respectively. These peaks are assigned to intermediate peroxy/epoxy compounds of the three molecules that are formed with molecular oxygen prior to the formation of oxidized short-chain stable compounds. - Highlights: • Fluorescence and UV–vis studies on β-carotene, lycopene and norbixin. • Oxidation, induced by FeCl 3 in CH 2 Cl 2 shows blue shifted fluorescence peaks. • Fluorescence peaks were assigned to intermediate peroxy/epoxy forms of carotenoids. • The D0→D3 transition of radical cations are observed in the near IR region

  8. Governance-Default Risk Relationship and the Demand for Intermediated and Non-Intermediated Debt

    Directory of Open Access Journals (Sweden)

    Husam Aldamen

    2012-09-01

    Full Text Available This paper explores the impact of corporate governance on the demand for intermediated debt (asset finance, bank debt, non-bank private debt and non-intermediated debt (public debt in the Australian debt market. Relative to other countries the Australian debt market is characterised by higher proportions of intermediated or private debt with a lower inherent level of information asymmetry in that private lenders have greater access to financial information (Gray, Koh & Tong 2009. Our firm level, cross-sectional evidence suggests that higher corporate governance impacts demand for debt via the mitigation of default risk. However, this relationship is not uniform across all debt types. Intermediated debt such as bank and asset finance debt are more responsive to changes in governance-default risk relationship than non-bank and non-intermediated debt. The implication is that a firm’s demand for different debt types will reflect its governance-default risk profile.

  9. Conformity in Christ | Waaijman | Acta Theologica

    African Journals Online (AJOL)

    This essay investigates the notion of conformity in Christ as it is part of a comprehensive, multilayered process of transformation. In the first part it focuses on the process of transformation in creation, re-creation, conformity, love and glory. In the second part it discusses transformation in Christ by looking at conformation and ...

  10. Liquid-vapor phase transition, collective flow and entropy determination from future measurements of intermediate mass fragments

    International Nuclear Information System (INIS)

    Coffin, J.P.

    1991-01-01

    Some global variables reflecting the highly collective character of nuclear matter produced in relativistic heavy-ion collisions are briefly reviewed on the basis of presently available experimental results and of Quantum Statistical Model and Quantum Molecular Dynamic Model predictions relative to intermediate mass fragments. Possible future measurements are suggested. (author) 27 refs., 8 figs

  11. Gauge fixing problem in the conformal QED

    International Nuclear Information System (INIS)

    Ichinose, Shoichi

    1986-01-01

    The gauge fixing problem in the conformal (spinor and scalar) QED is examined. For the analysis, we generalize Dirac's manifestly conformal-covariant formalism. It is shown that the (vector and matter) fields must obey a certain mixed (conformal and gauge) type of transformation law in order to fix the local gauge symmetry preserving the conformal invariance in the Lagrangian. (orig.)

  12. Comparative Incidence of Conformational, Neurodegenerative Disorders.

    Directory of Open Access Journals (Sweden)

    Jesús de Pedro-Cuesta

    Full Text Available The purpose of this study was to identify incidence and survival patterns in conformational neurodegenerative disorders (CNDDs.We identified 2563 reports on the incidence of eight conditions representing sporadic, acquired and genetic, protein-associated, i.e., conformational, NDD groups and age-related macular degeneration (AMD. We selected 245 papers for full-text examination and application of quality criteria. Additionally, data-collection was completed with detailed information from British, Swedish, and Spanish registries on Creutzfeldt-Jakob disease (CJD forms, amyotrophic lateral sclerosis (ALS, and sporadic rapidly progressing neurodegenerative dementia (sRPNDd. For each condition, age-specific incidence curves, age-adjusted figures, and reported or calculated median survival were plotted and examined.Based on 51 valid reported and seven new incidence data sets, nine out of eleven conditions shared specific features. Age-adjusted incidence per million person-years increased from ≤1.5 for sRPNDd, different CJD forms and Huntington's disease (HD, to 1589 and 2589 for AMD and Alzheimer's disease (AD respectively. Age-specific profiles varied from (a symmetrical, inverted V-shaped curves for low incidences to (b those increasing with age for late-life sporadic CNDDs and for sRPNDd, with (c a suggested, intermediate, non-symmetrical inverted V-shape for fronto-temporal dementia and Parkinson's disease. Frequently, peak age-specific incidences from 20-24 to ≥90 years increased with age at onset and survival. Distinct patterns were seen: for HD, with a low incidence, levelling off at middle age, and long median survival, 20 years; and for sRPNDd which displayed the lowest incidence, increasing with age, and a short median disease duration.These results call for a unified population view of NDDs, with an age-at-onset-related pattern for acquired and sporadic CNDDs. The pattern linking age at onset to incidence magnitude and survival might

  13. Comparative Incidence of Conformational, Neurodegenerative Disorders

    Science.gov (United States)

    de Pedro-Cuesta, Jesús; Rábano, Alberto; Martínez-Martín, Pablo; Ruiz-Tovar, María; Alcalde-Cabero, Enrique; Almazán-Isla, Javier; Avellanal, Fuencisla; Calero, Miguel

    2015-01-01

    Background The purpose of this study was to identify incidence and survival patterns in conformational neurodegenerative disorders (CNDDs). Methods We identified 2563 reports on the incidence of eight conditions representing sporadic, acquired and genetic, protein-associated, i.e., conformational, NDD groups and age-related macular degeneration (AMD). We selected 245 papers for full-text examination and application of quality criteria. Additionally, data-collection was completed with detailed information from British, Swedish, and Spanish registries on Creutzfeldt-Jakob disease (CJD) forms, amyotrophic lateral sclerosis (ALS), and sporadic rapidly progressing neurodegenerative dementia (sRPNDd). For each condition, age-specific incidence curves, age-adjusted figures, and reported or calculated median survival were plotted and examined. Findings Based on 51 valid reported and seven new incidence data sets, nine out of eleven conditions shared specific features. Age-adjusted incidence per million person-years increased from ≤1.5 for sRPNDd, different CJD forms and Huntington's disease (HD), to 1589 and 2589 for AMD and Alzheimer's disease (AD) respectively. Age-specific profiles varied from (a) symmetrical, inverted V-shaped curves for low incidences to (b) those increasing with age for late-life sporadic CNDDs and for sRPNDd, with (c) a suggested, intermediate, non-symmetrical inverted V-shape for fronto-temporal dementia and Parkinson's disease. Frequently, peak age-specific incidences from 20–24 to ≥90 years increased with age at onset and survival. Distinct patterns were seen: for HD, with a low incidence, levelling off at middle age, and long median survival, 20 years; and for sRPNDd which displayed the lowest incidence, increasing with age, and a short median disease duration. Interpretation These results call for a unified population view of NDDs, with an age-at-onset-related pattern for acquired and sporadic CNDDs. The pattern linking age at onset to

  14. Transportation Conformity Training and Presentations

    Science.gov (United States)

    EPA's OTAQ has provided multiple conformity training sessions in the past to assist state and local governments in implementing conformity requirements. As training information is prepared for other venues, it will be posted on this page.

  15. Two dimensional infinite conformal symmetry

    International Nuclear Information System (INIS)

    Mohanta, N.N.; Tripathy, K.C.

    1993-01-01

    The invariant discontinuous (discrete) conformal transformation groups, namely the Kleinian and Fuchsian groups Gamma (with an arbitrary signature) of H (the Poincare upper half-plane l) and the unit disc Delta are explicitly constructed from the fundamental domain D. The Riemann surface with signatures of Gamma and conformally invariant automorphic forms (functions) with Peterson scalar product are discussed. The functor, where the category of complex Hilbert spaces spanned by the space of cusp forms constitutes the two dimensional conformal field theory. (Author) 7 refs

  16. Rate of hydrolysis in ATP synthase is fine-tuned by  -subunit motif controlling active site conformation

    KAUST Repository

    Beke-Somfai, T.; Lincoln, P.; Norden, B.

    2013-01-01

    Computer-designed artificial enzymes will require precise understanding of how conformation of active sites may control barrier heights of key transition states, including dependence on structure and dynamics at larger molecular scale. F(o)F(1) ATP synthase is interesting as a model system: a delicate molecular machine synthesizing or hydrolyzing ATP using a rotary motor. Isolated F(1) performs hydrolysis with a rate very sensitive to ATP concentration. Experimental and theoretical results show that, at low ATP concentrations, ATP is slowly hydrolyzed in the so-called tight binding site, whereas at higher concentrations, the binding of additional ATP molecules induces rotation of the central γ-subunit, thereby forcing the site to transform through subtle conformational changes into a loose binding site in which hydrolysis occurs faster. How the 1-Å-scale rearrangements are controlled is not yet fully understood. By a combination of theoretical approaches, we address how large macromolecular rearrangements may manipulate the active site and how the reaction rate changes with active site conformation. Simulations reveal that, in response to γ-subunit position, the active site conformation is fine-tuned mainly by small α-subunit changes. Quantum mechanics-based results confirm that the sub-Ångström gradual changes between tight and loose binding site structures dramatically alter the hydrolysis rate.

  17. Rate of hydrolysis in ATP synthase is fine-tuned by  -subunit motif controlling active site conformation

    KAUST Repository

    Beke-Somfai, T.

    2013-01-23

    Computer-designed artificial enzymes will require precise understanding of how conformation of active sites may control barrier heights of key transition states, including dependence on structure and dynamics at larger molecular scale. F(o)F(1) ATP synthase is interesting as a model system: a delicate molecular machine synthesizing or hydrolyzing ATP using a rotary motor. Isolated F(1) performs hydrolysis with a rate very sensitive to ATP concentration. Experimental and theoretical results show that, at low ATP concentrations, ATP is slowly hydrolyzed in the so-called tight binding site, whereas at higher concentrations, the binding of additional ATP molecules induces rotation of the central γ-subunit, thereby forcing the site to transform through subtle conformational changes into a loose binding site in which hydrolysis occurs faster. How the 1-Å-scale rearrangements are controlled is not yet fully understood. By a combination of theoretical approaches, we address how large macromolecular rearrangements may manipulate the active site and how the reaction rate changes with active site conformation. Simulations reveal that, in response to γ-subunit position, the active site conformation is fine-tuned mainly by small α-subunit changes. Quantum mechanics-based results confirm that the sub-Ångström gradual changes between tight and loose binding site structures dramatically alter the hydrolysis rate.

  18. A DFT Study on Selected Physical Organic Aspects of the Fischer Carbene Intermediates [(M(CO4(C(OMeMe

    Directory of Open Access Journals (Sweden)

    Tareq Irshaidat

    2010-01-01

    Full Text Available Fischer carbenes are important starting materials for C-C bond formation via coupling reactions between carbene and wide variety of substituted alkenes or alkynes. This DFT study shed light on unique fundamental organic/organometallic aspects for the C(OMeMe carbene in the free form and in case of bonding with M(CO4 (M= Cr, Mo, W. The data illustrate that the structures of the title intermediates include a unique structure stabilizing intramolecular M…C-H interaction (agostic interaction. This conclusion was made based on calculated NMR data (for carbon and hydrogen, structural parameters, energy calculations of conformers (C-C conformation, selected IR stretching frequencies (C-O, C-C, and C-H, and atomic charges. The agostic interaction is most efficient in case of chromium and in general is described as an overlap between the σ-bond electron pair of C-H with an empty d-orbital of the metal. These characterized examples are new addition to the orbital interaction theory.

  19. Virtual and solution conformations of oligosaccharides

    International Nuclear Information System (INIS)

    Cumming, D.A.; Carver, J.P.

    1987-01-01

    The possibility that observed nuclear Overhauser enhancements and bulk longitudinal relaxation times, parameters measured by 1 H NMR and often employed in determining the preferred solution conformation of biologically important molecules, are the result of averaging over many conformational states is quantitatively evaluated. Of particular interest was to ascertain whether certain 1 H NMR determined conformations are virtual in nature; i.e., the fraction of the population of molecules actually found at any time within the subset of conformational space defined as the solution conformation is vanishingly small. A statistical mechanics approach was utilized to calculate an ensemble average relaxation matrix from which (NOE)'s and (T 1 )'s are calculated. Model glycosidic linkages in four oligosaccharides were studied. The nature of the resultant population distributions is such that 50% of the molecular population is found within 1% of available microstates, while 99% of the molecular population occupies about 10% of the ensemble microstates, a number roughly equal to that sterically allowed. From this analysis the authors conclude that in many cases quantitative interpretation of NMR relaxation data, which attempts to define a single set of allowable torsion angle values consistent with the observed data, will lead to solution conformations that are either virtual or reflect torsion angle values possessed by a minority of the molecular population. Observed values of NMR relaxation data are the result of the complex interdependence of the population distribution and NOE (or T 1 ) surfaces in conformational space. In conformational analyses, NMR data can therefore be used to test different population distributions calculated from empirical potential energy functions

  20. Phonon activity and intermediate glassy phase of YVO3

    International Nuclear Information System (INIS)

    Massa, Nestor E.; Piamonteze, Cinthia; Tolentino, Helio C.N.; Alonso, Jose Antonio; Martinez-Lope, Maria Jesus; Casais, Maria Teresa

    2004-01-01

    We show that in YVO 3 additional hard phonons gradually become zone center infrared active below ∼210 K, verifying that a lattice phase transition takes place at about that temperature. Their gradual increment in intensity between ∼210 and ∼77 K is associated with a 'glassy' behavior found in the temperature-dependent V K edge pseudoradial distribution. This translates into an increase in the Debye-Waller factors ascribed to the appearance of V local structural disorder below ∼150 K. Conflicts between various ordering mechanisms in YVO 3 bring up similarities of the intermediate phase to known results in dielectric incommensurate systems, suggesting the formation of commensurate domains below 116 K, the onset temperature of G-type antiferromagnetism. We propose that ∼210 and ∼77 K be understood as the temperatures where the commensurate-incommensurate and incommensurate-commensurate 'lock-in' phase transitions take place. We found support for this interpretation in the inverted λ shapes of the measured heat capacity and in the overall temperature dependence of the hard phonons

  1. Uniform stable conformal convolutional perfectly matched layer for enlarged cell technique conformal finite-difference time-domain method

    International Nuclear Information System (INIS)

    Wang Yue; Wang Jian-Guo; Chen Zai-Gao

    2015-01-01

    Based on conformal construction of physical model in a three-dimensional Cartesian grid, an integral-based conformal convolutional perfectly matched layer (CPML) is given for solving the truncation problem of the open port when the enlarged cell technique conformal finite-difference time-domain (ECT-CFDTD) method is used to simulate the wave propagation inside a perfect electric conductor (PEC) waveguide. The algorithm has the same numerical stability as the ECT-CFDTD method. For the long-time propagation problems of an evanescent wave in a waveguide, several numerical simulations are performed to analyze the reflection error by sweeping the constitutive parameters of the integral-based conformal CPML. Our numerical results show that the integral-based conformal CPML can be used to efficiently truncate the open port of the waveguide. (paper)

  2. Role of Met80 and Tyr67 in the low-pH conformational equilibria of cytochrome c.

    Science.gov (United States)

    Battistuzzi, Gianantonio; Bortolotti, Carlo Augusto; Bellei, Marzia; Di Rocco, Giulia; Salewski, Johannes; Hildebrandt, Peter; Sola, Marco

    2012-07-31

    The low-pH conformational equilibria of ferric yeast iso-1 cytochrome c (ycc) and its M80A, M80A/Y67H, and M80A/Y67A variants were studied from pH 7 to 2 at low ionic strength through electronic absorption, magnetic circular dichroism, and resonance Raman spectroscopies. For wild-type ycc, the protein structure, axial heme ligands, and spin state of the iron atom convert from the native folded His/Met low-spin (LS) form to a molten globule His/H(2)O high-spin (HS) form and a totally unfolded bis-aquo HS state, in a single cooperative transition with an apparent pK(a) of ~3.0. An analogous cooperative transition occurs for the M80A and M80A/Y67H variants. This is preceded by protonation of heme propionate-7, with a pK(a) of ~4.2, and by an equilibrium between a His/OH(-)-ligated LS and a His/H(2)O-ligated HS conformer, with a pK(a) of ~5.9. In the M80A/Y67A variant, the cooperative low-pH transition is split into two distinct processes because of an increased stability of the molten globule state that is formed at higher pH values than the other species. These data show that removal of the axial methionine ligand does not significantly alter the mechanism of acidic unfolding and the ranges of stability of low-pH conformers. Instead, removal of a hydrogen bonding partner at position 67 increases the stability of the molten globule and renders cytochrome c more susceptible to acid unfolding. This underlines the key role played by Tyr67 in stabilizing the three-dimensional structure of cytochrome c by means of the hydrogen bonding network connecting the Ω loops formed by residues 71-85 and 40-57.

  3. Noncommutative geometry and twisted conformal symmetry

    International Nuclear Information System (INIS)

    Matlock, Peter

    2005-01-01

    The twist-deformed conformal algebra is constructed as a Hopf algebra with twisted coproduct. This allows for the definition of conformal symmetry in a noncommutative background geometry. The twisted coproduct is reviewed for the Poincare algebra and the construction is then extended to the full conformal algebra. The case of Moyal-type noncommutativity of the coordinates is considered. It is demonstrated that conformal invariance need not be viewed as incompatible with noncommutative geometry; the noncommutativity of the coordinates appears as a consequence of the twisting, as has been shown in the literature in the case of the twisted Poincare algebra

  4. Superintegrability of d-dimensional conformal blocks

    International Nuclear Information System (INIS)

    Isachenkov, Mikhail

    2016-02-01

    We observe that conformal blocks of scalar 4-point functions in a d-dimensional conformal field theory can mapped to eigenfunctions of a 2-particle hyperbolic Calogero-Sutherland Hamiltonian. The latter describes two coupled Poeschl-Teller particles. Their interaction, whose strength depends smoothly on the dimension d, is known to be superintegrable. Our observation enables us to exploit the rich mathematical literature on Calogero-Sutherland models in deriving various results for conformal field theory. These include an explicit construction of conformal blocks in terms of Heckman-Opdam hypergeometric functions and a remarkable duality that relates the blocks of theories in different dimensions.

  5. Superintegrability of d-dimensional conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

    Isachenkov, Mikhail [Weizmann Institute of Science, Rehovot (Israel). Dept. of Particle Physics and Astronomy; Schomerus, Volker [DESY Theory Group, Hamburg (Germany)

    2016-02-15

    We observe that conformal blocks of scalar 4-point functions in a d-dimensional conformal field theory can mapped to eigenfunctions of a 2-particle hyperbolic Calogero-Sutherland Hamiltonian. The latter describes two coupled Poeschl-Teller particles. Their interaction, whose strength depends smoothly on the dimension d, is known to be superintegrable. Our observation enables us to exploit the rich mathematical literature on Calogero-Sutherland models in deriving various results for conformal field theory. These include an explicit construction of conformal blocks in terms of Heckman-Opdam hypergeometric functions and a remarkable duality that relates the blocks of theories in different dimensions.

  6. Single-Chain Conformation for Interacting Poly(N-isopropylacrylamide in Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Boualem Hammouda

    2015-04-01

    Full Text Available The demixing phase behavior of Poly(N-isopropylacrylamide (PNIPAM aqueous solution is investigated using small-angle neutron scattering. This polymer phase separates upon heating and demixes around 32 °C. The pre-transition temperature range is characterized by two scattering modes; a low-Q (large-scale signal and a high-Q dissolved chains signal. In order to get insight into this pre-transition region, especially the origin of the low-Q (large-scale structure, the zero average contrast method is used in order to isolate single-chain conformations even in the demixing polymers transition region. This method consists of measuring deuterated and non-deuterated polymers dissolved in mixtures of deuterated and non-deuterated water for which the polymer scattering length density matches the solvent scattering length density. A fixed 4% polymer mass fraction is used in a contrast variation series where the d-water/h-water fraction is varied in order to determine the match point. The zero average contrast (match point sample displays pure single-chain scattering with no interchain contributions. Our measurements prove that the large scale structure in this polymer solution is due to a transient polymer network formed through hydrophobic segment-segment interactions. Scattering intensity increases when the temperature gets close to the phase boundary. While the apparent radius of gyration increases substantially at the Lower Critical Solution Temperature (LCST transition due to strong interchain correlation, the single-chain true radius of gyration has been found to decrease slightly with temperature when approaching the transition.

  7. Induced quantum conformal gravity

    International Nuclear Information System (INIS)

    Novozhilov, Y.V.; Vassilevich, D.V.

    1988-11-01

    Quantum gravity is considered as induced by matter degrees of freedom and related to the symmetry breakdown in the low energy region of a non-Abelian gauge theory of fundamental fields. An effective action for quantum conformal gravity is derived where both the gravitational constant and conformal kinetic term are positive. Relation with induced classical gravity is established. (author). 15 refs

  8. Phase transition study in strongly correlated VO{sub 2} based sensing systems

    Energy Technology Data Exchange (ETDEWEB)

    Simo, A., E-mail: alinesimo.aline@gmail.com [UNESCO-UNISA Africa Chair in Nanoscience’s/Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk ridge, P.O. Box 392, Pretoria (South Africa); Nanosciences African Network (NANOAFNET), iThemba LABS-National Research Foundation, 1 Old Faure road, Somerset West 7129, P.O. Box 722, Somerset West, Western Cape Province (South Africa); Kaviyarasu, K. [UNESCO-UNISA Africa Chair in Nanoscience’s/Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk ridge, P.O. Box 392, Pretoria (South Africa); Nanosciences African Network (NANOAFNET), iThemba LABS-National Research Foundation, 1 Old Faure road, Somerset West 7129, P.O. Box 722, Somerset West, Western Cape Province (South Africa); Mwakikunga, B. [Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001 (South Africa); Madjoe, R. [Physics Department, University of Western Cape, 7535 Belville Cape Town (South Africa); Gibaud, A. [Laboratoire de Physique de l’Etat Condensé, Université du Maine Faculte des sciences, UPRESA 6087, 72085, Le Mans Cedex 9 (France); Maaza, M. [UNESCO-UNISA Africa Chair in Nanoscience’s/Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk ridge, P.O. Box 392, Pretoria (South Africa); Nanosciences African Network (NANOAFNET), iThemba LABS-National Research Foundation, 1 Old Faure road, Somerset West 7129, P.O. Box 722, Somerset West, Western Cape Province (South Africa)

    2017-04-15

    Highlights: • At 230 °C for about 48 h to prepare successfully VO{sub 2} nanobelts. • 1D shows good sensing performance due to the large active surface of the material. • The good selectivity of methanol compared to acetone and isopropanol. • VOC compounds was observed at room temperature. - Abstract: Intermediate phase monoclinic M2 was observed by inducing in situ X-ray thermo diffraction on VO{sub 2} (M) nanoplatelets. The solid-solid phase transition occurs at around 65 °C assisted with the percolative transition metal-insulator. The existence of an intermediate crystalline phase with room temperature insulator phase and high temperature metallic phase across MIT in VO{sub 2} could be of relevance to understand structural contributions to the phase transition dynamics. In addition, pellet of VO{sub 2} nanostructures have shown to present good sensing properties to various alcohols vapors at room temperature and good selectivity of methanol with 5.54% sensitivity and limit detection below 5 ppm, compared to isopropanol 3.2% and acetone 2.4% respectively.

  9. Improvement of radiological penumbra using intermediate energy photons (IEP) for stereotactic radiosurgery

    International Nuclear Information System (INIS)

    O'Malley, Lauren; Pignol, Jean-Philippe; Beachey, David J; Keller, Brian M; Presutti, Joseph; Sharpe, Michael

    2006-01-01

    Using efficient immobilization and dedicated beam collimation devices, stereotactic radiosurgery ensures highly conformal treatment of small tumours with limited microscopic extension. One contribution to normal tissue irradiation remains the radiological penumbra. This work aims at demonstrating that intermediate energy photons (IEP), above orthovoltage but below megavoltage, improve dose distribution for stereotactic radiosurgery for small irradiation field sizes due to a dramatic reduction of radiological penumbra. Two different simulation systems were used: (i) Monte Carlo simulation to investigate the dose distribution of monoenergetic IEP between 100 keV and 1 MeV in water phantom; (ii) the Pinnacle 3 TPS including a virtual IEP unit to investigate the dosimetry benefit of treating with 11 non-coplanar beams a 2 cm tumour in the middle of a brain adjacent to a 1 mm critical structure. Radiological penumbrae below 300 μm are generated for field size below 2 x 2 cm 2 using monoenergetic IEP beams between 200 and 400 keV. An 800 kV beam generated in a 0.5 mm tungsten target maximizes the photon intensity in this range. Pinnacle 3 confirms the dramatic reduction in penumbra size. DVHs show for a constant dose distribution conformality, improved dose distribution homogeneity and better sparing of critical structures using a 800 kV beam compared to a 6 MV beam

  10. Improvement of radiological penumbra using intermediate energy photons (IEP) for stereotactic radiosurgery

    Science.gov (United States)

    O'Malley, Lauren; Pignol, Jean-Philippe; Beachey, David J.; Keller, Brian M.; Presutti, Joseph; Sharpe, Michael

    2006-05-01

    Using efficient immobilization and dedicated beam collimation devices, stereotactic radiosurgery ensures highly conformal treatment of small tumours with limited microscopic extension. One contribution to normal tissue irradiation remains the radiological penumbra. This work aims at demonstrating that intermediate energy photons (IEP), above orthovoltage but below megavoltage, improve dose distribution for stereotactic radiosurgery for small irradiation field sizes due to a dramatic reduction of radiological penumbra. Two different simulation systems were used: (i) Monte Carlo simulation to investigate the dose distribution of monoenergetic IEP between 100 keV and 1 MeV in water phantom; (ii) the Pinnacle3 TPS including a virtual IEP unit to investigate the dosimetry benefit of treating with 11 non-coplanar beams a 2 cm tumour in the middle of a brain adjacent to a 1 mm critical structure. Radiological penumbrae below 300 µm are generated for field size below 2 × 2 cm2 using monoenergetic IEP beams between 200 and 400 keV. An 800 kV beam generated in a 0.5 mm tungsten target maximizes the photon intensity in this range. Pinnacle3 confirms the dramatic reduction in penumbra size. DVHs show for a constant dose distribution conformality, improved dose distribution homogeneity and better sparing of critical structures using a 800 kV beam compared to a 6 MV beam.

  11. Interchannel interactions in high-energetic radiationless transitions of neon-like ions

    International Nuclear Information System (INIS)

    Fritzsche, S.; Zschornack, G.; Musiol, G.; Soff, G.

    1990-07-01

    Relativistic K-LL Auger transition rates in intermediate coupling including interchannel interactions are presented for nine ions in the neon-isoelectronic sequence up to uranium. For neutral neon a comparison with experimental data is given. We demonstrate for the first time, that intercontinuum interactions result in a remarkable redistribution of individual transition rates even in high-energetic transitions. For instance, channel mixing shifts the K-L 1 L 1 rate by about 4% and the K-L 3 L 3 (J = 0) rate by about 11% in neon-like uranium, while total Auger rates are almost not affected. (orig.)

  12. Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes

    Directory of Open Access Journals (Sweden)

    Francisco eVelazquez Escobar

    2015-07-01

    Full Text Available Phytochromes are biological photoreceptors that can be reversibly photoconverted between a dark and photoactivated state. The underlying reaction sequences are initiated by the photoisomerisation of the tetrapyrrole cofactor, which in plant and cyanobacterial phytochromes are a phytochromobilin (PB and a phycocyanobilin (PCB, respectively. The transition between the two states represents an on/off-switch of the output module activating or deactivating downstream physiological processes. In addition, the photoactivated state, i.e. Pfr in canonical phytochromes, can be thermally reverted to the dark state (Pr. The present study aimed to improve our understanding of the specific reactivity of various PB- and PCB-binding phytochromes in the Pfr state by analyzing the cofactor structure by vibrational spectroscopic techniques. Resonance Raman (RR spectroscopy revealed two Pfr conformers (Pfr-I and Pfr-II forming a temperature-dependent conformational equilibrium. The two sub-states - found in all phytochromes studied, albeit with different relative contributions - differ in structural details of the C-D and A-B methine bridges. In the Pfr-I sub-state the torsion between the rings C and D is larger by ca. 10o compared to Pfr-II. This structural difference is presumably related to different hydrogen bonding interactions of ring D as revealed by time-resolved IR spectroscopic studies of the cyanobacterial phytochrome Cph1. The transitions between the two sub-states are evidently too fast (i.e., nanosecond time scale to be resolved by NMR spectroscopy which could not detect a structural heterogeneity of the chromophore in Pfr. The implications of the present findings for the dark reversion of the Pfr state are discussed.

  13. Quantifying DNA melting transitions using single-molecule force spectroscopy

    International Nuclear Information System (INIS)

    Calderon, Christopher P; Chen, W-H; Harris, Nolan C; Kiang, C-H; Lin, K-J

    2009-01-01

    We stretched a DNA molecule using an atomic force microscope (AFM) and quantified the mechanical properties associated with B and S forms of double-stranded DNA (dsDNA), molten DNA, and single-stranded DNA. We also fit overdamped diffusion models to the AFM time series and used these models to extract additional kinetic information about the system. Our analysis provides additional evidence supporting the view that S-DNA is a stable intermediate encountered during dsDNA melting by mechanical force. In addition, we demonstrated that the estimated diffusion models can detect dynamical signatures of conformational degrees of freedom not directly observed in experiments.

  14. Quantifying DNA melting transitions using single-molecule force spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Calderon, Christopher P [Department of Computational and Applied Mathematics, Rice University, Houston, TX (United States); Chen, W-H; Harris, Nolan C; Kiang, C-H [Department of Physics and Astronomy, Rice University, Houston, TX (United States); Lin, K-J [Department of Chemistry, National Chung Hsing University, Taichung, Taiwan (China)], E-mail: chkiang@rice.edu

    2009-01-21

    We stretched a DNA molecule using an atomic force microscope (AFM) and quantified the mechanical properties associated with B and S forms of double-stranded DNA (dsDNA), molten DNA, and single-stranded DNA. We also fit overdamped diffusion models to the AFM time series and used these models to extract additional kinetic information about the system. Our analysis provides additional evidence supporting the view that S-DNA is a stable intermediate encountered during dsDNA melting by mechanical force. In addition, we demonstrated that the estimated diffusion models can detect dynamical signatures of conformational degrees of freedom not directly observed in experiments.

  15. Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry

    Science.gov (United States)

    Huang, Richard Y.-C.; Iacob, Roxana E.; Sankaranarayanan, Sethu; Yang, Ling; Ahlijanian, Michael; Tao, Li; Tymiak, Adrienne A.; Chen, Guodong

    2018-01-01

    Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. [Figure not available: see fulltext.

  16. Conformal invariance in harmonic superspace

    International Nuclear Information System (INIS)

    Galperin, A.; Ivanov, E.; Ogievetsky, V.; Sokatchev, E.

    1987-01-01

    In the present paper we show how the N = 2 superconformal group is realised in harmonic superspace and examine conformal invariance of N = 2 off-shell theories. We believe that the example of N = O self-dual Yang-Mills equations can serve as an instructive introduction to the subject of harmonic superspace and this is examined. The rigid N = 2 conformal supersymmetry and its local version, i.e. N = 2 conformal supergravity is also discussed. The paper is a contribution to the book commemorating the sixtieth birthday of E.S. Fradkin. (author)

  17. Harmony of spinning conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

    Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Theory Group; Sobko, Evgeny [Stockholm Univ. (Sweden); Nordita, Stockholm (Sweden); Isachenkov, Mikhail [Weizmann Institute of Science, Rehovoth (Israel). Dept. of Particle Physics and Astrophysics

    2016-12-07

    Conformal blocks for correlation functions of tensor operators play an increasingly important role for the conformal bootstrap programme. We develop a universal approach to such spinning blocks through the harmonic analysis of certain bundles over a coset of the conformal group. The resulting Casimir equations are given by a matrix version of the Calogero-Sutherland Hamiltonian that describes the scattering of interacting spinning particles in a 1-dimensional external potential. The approach is illustrated in several examples including fermionic seed blocks in 3D CFT where they take a very simple form.

  18. Harmony of spinning conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

    Schomerus, Volker [DESY Hamburg, Theory Group,Notkestraße 85, 22607 Hamburg (Germany); Sobko, Evgeny [Nordita and Stockholm University,Roslagstullsbacken 23, SE-106 91 Stockholm (Sweden); Isachenkov, Mikhail [Department of Particle Physics and Astrophysics, Weizmann Institute of Science,Rehovot 7610001 (Israel)

    2017-03-15

    Conformal blocks for correlation functions of tensor operators play an increasingly important role for the conformal bootstrap programme. We develop a universal approach to such spinning blocks through the harmonic analysis of certain bundles over a coset of the conformal group. The resulting Casimir equations are given by a matrix version of the Calogero-Sutherland Hamiltonian that describes the scattering of interacting spinning particles in a 1-dimensional external potential. The approach is illustrated in several examples including fermionic seed blocks in 3D CFT where they take a very simple form.

  19. Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases

    Science.gov (United States)

    Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, Rui

    2006-08-01

    Dimethyl sulfite has three conformers of low energy, GG, GT and GG', which have significant populations in the gas phase at room temperature. According to theoretical predictions, the GT and GG' conformers are higher in energy than the GG conformer by 0.83 and 1.18 kJ mol -1, respectively, while the barriers associated with the GG'→GT and GT→GG isomerizations are 1.90 and 9.64 kJ mol -1, respectively. Experimental data obtained for the compound isolated in solid argon, krypton and xenon demonstrated that the GG'→GT energy barrier is low enough to allow an extensive conversion of the GG' form into the GT conformer during deposition of the matrices, the extent of the conversion increasing along the series Arconformers could be trapped in both argon and krypton matrices, but, at a given temperature, the amount of GG' form trapped in krypton is considerably smaller than in argon, while the amount of GT form increases in relation to the most stable GG form. In addition, when xenon is used, no bands due to GG' are observed in the as-deposited spectra ( Tsubstrate≥10 K, the minimum substrate temperature accessible to our experimental set up), indicating that when the best relaxant gas is used the GG'→GT conversion during deposition of the matrix is complete even at 10 K. Annealing of the argon and krypton matrices shows that the increase of the temperature of the matrix first promotes the GG'→GT isomerization, and only at higher temperatures the GT→GG conversion starts to occur, in consonance with the relative energy barriers associated with these two processes. The results also indicate that dimethyl sulfite exhibits conformation selective aggregation, with the most stable form, which has the highest dipole moment, aggregating more easily than the remaining experimentally relevant conformers (GT and GG').

  20. Conformal hyperbolicity of Lorentzian warped products

    International Nuclear Information System (INIS)

    Markowitz, M.J.

    1982-01-01

    A space-time M is said to be conformally hyperbolic if the intrinsic conformal Lorentz pseudodistance dsub(M) is a true distance. In this paper criteria are derived which insure the conformal hyperbolicity of certain space-times which are generalizations of the Robertson-Walker spaces. Then dsub(M) is determined explicitly for Einstein-de Sitter space, and important cosmological model. (author)