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

General shape and hapten-induced conformational changes of pig anti-dinitrophenyl antibody. A small-angle scattering study

International Nuclear Information System (INIS)

Cher, L.; Gladkikh, I.A.; Franek, F.; Kunchenko, A.B.; Ostanevich, Yu.M.

1980-01-01

Pig anti-dinitrophenyl antibodies were studied by neutron and X-ray small-angle scattering. Observed scattering curves show that the shapes of two antibody types, precipitating and non-precipitating, are similar, however the latter being more compact. A hapten binding induced conformational change of antibody is observed. This conformational change might be described as a contraction of the whole molecule via similarity transformation. The spatial models of pig antibody molecule based on the existing experimental data were designed. Most probable models have a cavity in the Fsub(c) part and the Fsub(ab) parts are either fully extended or slightly bent down to the Fsub(c) part

Investigating ion channel conformational changes using voltage clamp fluorometry.

Science.gov (United States)

Talwar, Sahil; Lynch, Joseph W

2015-11-01

Ion channels are membrane proteins whose functions are governed by conformational changes. The widespread distribution of ion channels, coupled with their involvement in most physiological and pathological processes and their importance as therapeutic targets, renders the elucidation of these conformational mechanisms highly compelling from a drug discovery perspective. Thanks to recent advances in structural biology techniques, we now have high-resolution static molecular structures for members of the major ion channel families. However, major questions remain to be resolved about the conformational states that ion channels adopt during activation, drug modulation and desensitization. Patch-clamp electrophysiology has long been used to define ion channel conformational states based on functional criteria. It achieves this by monitoring conformational changes at the channel gate and cannot detect conformational changes occurring in regions distant from the gate. Voltage clamp fluorometry involves labelling cysteines introduced into domains of interest with environmentally sensitive fluorophores and inferring structural rearrangements from voltage or ligand-induced fluorescence changes. Ion channel currents are monitored simultaneously to verify the conformational status. By defining real time conformational changes in domains distant from the gate, this technique provides unexpected new insights into ion channel structure and function. This review aims to summarise the methodology and highlight recent innovative applications of this powerful technique. This article is part of the Special Issue entitled 'Fluorescent Tools in Neuropharmacology'. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conformational change of spin labelled myoglobin

International Nuclear Information System (INIS)

Wajnberg, E.; Ribeiro, P.C.; Nascimento, O.R.; Bemski, G.

1978-01-01

A conformational change of spin labelled myoglobin have been followed by measuring the spin label's (isothiocyanate) correlation time for temperatures between 18 0 C and 44 0 C. The correlation time was calculated from Electrom Paramagnetic Ressonance Spectra using the components of the espectroscopic and hiperfine tensors obtained by fitting the powder spectra using Lefebvre and Maruani's program- [pt

Beam-induced temperature changes in HVEM irradiations

International Nuclear Information System (INIS)

Garner, F.A.; Thomas, L.E.; Gelles, D.S.

1975-01-01

The peak value of the temperature distribution induced by energy loss of 1.0 MeV electrons in traversing a typical HVEM irradiation specimen can be very substantial. The origin and various features of this distribution were analyzed for a variety of specimen geometries. The major parametric dependencies are shown to be relatively independent of specimen geometry, however, and allow the definition of a scaling relationship that can be employed to predict temperature rises in materials that cannot be measured directly. The use of this scaling relationship requires that the experimenter minimize perturbations of the heat flow due to proximity of the central hole in the specimen. An experimental method of determining directly the magnitude and distribution of beam-induced temperature profiles was developed which utilizes the order-disorder transformation in Fe 3 Al and Cu 3 Au. Scaling of experimentally determined temperature changes leads to more realistic estimates of the total temperature rise than are currently available in various literature tabulations. The factors which determine the optimum selection of irradiation parameters for a given experiment are also discussed

Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

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Keskin Ozlem

2007-05-01

Full Text Available Abstract Background How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium. Results Here, two antibodies, a germline antibody of 36–65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones. Conclusion Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.

Envelope conformational changes induced by human immunodeficiency virus type 1 attachment inhibitors prevent CD4 binding and downstream entry events.

Science.gov (United States)

Ho, Hsu-Tso; Fan, Li; Nowicka-Sans, Beata; McAuliffe, Brian; Li, Chang-Ben; Yamanaka, Gregory; Zhou, Nannan; Fang, Hua; Dicker, Ira; Dalterio, Richard; Gong, Yi-Fei; Wang, Tao; Yin, Zhiwei; Ueda, Yasutsugu; Matiskella, John; Kadow, John; Clapham, Paul; Robinson, James; Colonno, Richard; Lin, Pin-Fang

2006-04-01

BMS-488043 is a small-molecule human immunodeficiency virus type 1 (HIV-1) CD4 attachment inhibitor with demonstrated clinical efficacy. The compound inhibits soluble CD4 (sCD4) binding to the 11 distinct HIV envelope gp120 proteins surveyed. Binding of BMS-488043 and that of sCD4 to gp120 are mutually exclusive, since increased concentrations of one can completely block the binding of the other without affecting the maximal gp120 binding capacity. Similarly, BMS-488043 inhibited virion envelope trimers from binding to sCD4-immunoglobulin G (IgG), with decreasing inhibition as the sCD4-IgG concentration increased, and BMS-488043 blocked the sCD4-induced exposure of the gp41 groove in virions. In both virion binding assays, BMS-488043 was active only when added prior to sCD4. Collectively, these results indicate that obstruction of gp120-sCD4 interactions is the primary inhibition mechanism of this compound and that compound interaction with envelope must precede CD4 binding. By three independent approaches, BMS-488043 was further shown to induce conformational changes within gp120 in both the CD4 and CCR5 binding regions. These changes likely prevent gp120-CD4 interactions and downstream entry events. However, BMS-488043 could only partially inhibit CD4 binding to an HIV variant containing a specific envelope truncation and altered gp120 conformation, despite effectively inhibiting the pseudotyped virus infection. Taken together, BMS-488043 inhibits viral entry primarily through altering the envelope conformation and preventing CD4 binding, and other downstream entry events could also be inhibited as a result of these induced conformational changes.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

Energy Technology Data Exchange (ETDEWEB)

Justino, Licínia L. G., E-mail: liciniaj@ci.uc.pt; Reva, Igor; Fausto, Rui [CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal)

2016-07-07

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N{sub 2}, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

Science.gov (United States)

Justino, Licínia L. G.; Reva, Igor; Fausto, Rui

2016-07-01

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N2, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

International Nuclear Information System (INIS)

Justino, Licínia L. G.; Reva, Igor; Fausto, Rui

2016-01-01

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N 2 , Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

Supramolecular engineering through temperature-induced chemical modification of 2H-tetraphenylporphyrin on Ag(111): flat phenyl conformation and possible dehydrogenation reactions.

Science.gov (United States)

Di Santo, Giovanni; Blankenburg, Stephan; Castellarin-Cudia, Carla; Fanetti, Mattia; Borghetti, Patrizia; Sangaletti, Luigi; Floreano, Luca; Verdini, Alberto; Magnano, Elena; Bondino, Federica; Pignedoli, Carlo A; Nguyen, Manh-Thuong; Gaspari, Roberto; Passerone, Daniele; Goldoni, Andrea

2011-12-16

Scratching the surface: Formation of a monolayer of 2H-tetraphenylporphyrins (2H-TPP) on Ag(111), either by sublimation of a multilayer in the range 525-600 K or by annealing (at the same temperature) a monolayer deposited at room temperature, induces a chemical modification of the molecules. Rotation of the phenyl rings into a flat conformation is observed and tentatively explained, by using DFT calculations, as a peculiar reaction due to molecular dehydrogenation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An all optical system for studying temperature induced changes in diamond

CSIR Research Space (South Africa)

Masina, B

2010-01-01

Full Text Available .csir.co.za An all optical system for studying temperature induced changes in diamond Bathusile Masina and Andrew Forbes 1 September 2010 © CSIR 2010 Slide 2 It is acknowledged that temperature induces damage in the diamond bits due to friction during the drilling...

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...

Outside-In Signal Transmission by Conformational Changes in Integrin Mac-11

Science.gov (United States)

Lefort, Craig T.; Hyun, Young-Min; Schultz, Joanne B.; Law, Foon-Yee; Waugh, Richard E.; Knauf, Philip A.; Kim, Minsoo

2010-01-01

Intracellular signals associated with or triggered by integrin ligation can control cell survival, differentiation, proliferation, and migration. Despite accumulating evidence that conformational changes regulate integrin affinity to its ligands, how integrin structure regulates signal transmission from the outside to the inside of the cell remains elusive. Using fluorescence resonance energy transfer, we addressed whether conformational changes in integrin Mac-1 are sufficient to transmit outside-in signals in human neutrophils. Mac-1 conformational activation induced by ligand occupancy or activating Ab binding, but not integrin clustering, triggered similar patterns of intracellular protein tyrosine phosphorylation, including Akt phosphorylation, and inhibited spontaneous neutrophil apoptosis, indicating that global conformational changes are critical for Mac-1-dependent outside-in signal transduction. In neutrophils and myeloid K562 cells, ligand ICAM-1 or activating Ab binding promoted switchblade-like extension of the Mac-1 extracellular domain and separation of the αM and β2 subunit cytoplasmic tails, two structural hallmarks of integrin activation. These data suggest the primacy of global conformational changes in the generation of Mac-1 outside-in signals. PMID:19864611

Conformational changes of fibrinogen in dispersed carbon nanotubes

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Park SJ

2012-08-01

Full Text Available Sung Jean Park,1 Dongwoo Khang21College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea; 2School of Nano and Advanced Materials Science Engineering and Center for PRC and RIGET, Gyeongsang National University, Jinju, South KoreaAbstract: The conformational changes of plasma protein structures in response to carbon nanotubes are critical for determining the nanotoxicity and blood coagulation effects of carbon nanotubes. In this study, we identified that the functional intensity of carboxyl groups on carbon nanotubes, which correspond to the water dispersity or hydrophilicity of carbon nanotubes, can induce conformational changes in the fibrinogen domains. Also, elevation of carbon nanotube density can alter the secondary structures (ie, helices and beta sheets of fibrinogen. Furthermore, fibrinogen that had been in contact with the nanoparticle material demonstrated a different pattern of heat denaturation compared with free fibrinogen as a result of a variation in hydrophilicity and concentration of carbon nanotubes. Considering the importance of interactions between carbon nanotubes and plasma proteins in the drug delivery system, this study elucidated the correlation between nanoscale physiochemical material properties of carbon nanotubes and associated structural changes in fibrinogen.Keywords: carbon nanotubes, fibrinogen, nanotoxicity, conformational change, denaturation

Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II?

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Nørholm, Ann-Beth; Hendus-Altenburger, Ruth

2010-01-01

temperature, which most likely reflects formation of transient alpha-helices or loss of polyproline II (PPII) content. Using three IDPs, ACTR, NHE1, and Spd1, we show that the temperature-induced structural change is common among IDPs and is accompanied by a contraction of the conformational ensemble...... with increasing temperature, and accordingly these were not responsible for the change in the CD spectra. In contrast, the nonhelical regions exhibited a general temperature-dependent structural change that was independent of long-range interactions. The temperature-dependent CD spectroscopic signature of IDPs...

Effects of macromolecular crowding on protein conformational changes.

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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

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

Localized frustration and binding-induced conformational change in recognition of 5S RNA by TFIIIA zinc finger.

Science.gov (United States)

Tan, Cheng; Li, Wenfei; Wang, Wei

2013-12-19

Protein TFIIIA is composed of nine tandemly arranged Cys2His2 zinc fingers. It can bind either to the 5S RNA gene as a transcription factor or to the 5S RNA transcript as a chaperone. Although structural and biochemical data provided valuable information on the recognition between the TFIIIIA and the 5S DNA/RNA, the involved conformational motions and energetic factors contributing to the binding affinity and specificity remain unclear. In this work, we conducted MD simulations and MM/GBSA calculations to investigate the binding-induced conformational changes in the recognition of the 5S RNA by the central three zinc fingers of TFIIIA and the energetic factors that influence the binding affinity and specificity at an atomistic level. Our results revealed drastic interdomain conformational changes between these three zinc fingers, involving the exposure/burial of several crucial DNA/RNA binding residues, which can be related to the competition between DNA and RNA for the binding of TFIIIA. We also showed that the specific recognition between finger 4/finger 6 and the 5S RNA introduces frustrations to the nonspecific interactions between finger 5 and the 5S RNA, which may be important to achieve optimal binding affinity and specificity.

MOLECULAR MODELING INDICATES THAT HOMOCYSTEINE INDUCES CONFORMATIONAL CHANGES IN THE STRUCTURE OF PUTATIVE TARGET PROTEINS

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Yumnam Silla

2015-09-01

Full Text Available An elevated level of homocysteine, a reactive thiol containing amino acid is associated with a multitude of complex diseases. A majority (>80% of homocysteine in circulation is bound to protein cysteine residues. Although, till date only 21 proteins have been experimentally shown to bind with homocysteine, using an insilico approach we had earlier identified several potential target proteins that could bind with homocysteine. Shomocysteinylation of proteins could potentially alter the structure and/or function of the protein. Earlier studies have shown that binding of homocysteine to protein alters its function. However, the effect of homocysteine on the target protein structure has not yet been documented. In the present work, we assess conformational or structural changes if any due to protein homocysteinylation using two proteins, granzyme B (GRAB and junctional adhesion molecule 1 (JAM1, which could potentially bind to homocysteine. We, for the first time, constructed computational models of homocysteine bound to target proteins and monitored their structural changes using explicit solvent molecular dynamic (MD simulation. Analysis of homocysteine bound trajectories revealed higher flexibility of the active site residues and local structural perturbations compared to the unbound native structure’s simulation, which could affect the stability of the protein. In addition, secondary structure analysis of homocysteine bound trajectories also revealed disappearance of â-helix within the G-helix and linker region that connects between the domain regions (as defined in the crystal structure. Our study thus captures the conformational transitions induced by homocysteine and we suggest these structural alterations might have implications for hyperhomocysteinemia induced pathologies.

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.

Conformational changes in matrix-isolated 6-methoxyindole: Effects of the thermal and infrared light excitations

Energy Technology Data Exchange (ETDEWEB)

Lopes Jesus, A. J. [CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal); CQC, Faculty of Pharmacy, University of Coimbra, 3004-295 Coimbra (Portugal); Reva, I., E-mail: reva@qui.uc.pt; Fausto, R. [CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal); Araujo-Andrade, C. [CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal); Unidad Académica de Física de la Universidad Autónoma de Zacatecas, Zacatecas (Mexico); ICFO–The Institute of Photonic Sciences, 08860 Castelldefels (Barcelona) (Spain)

2016-03-28

Conformational changes induced thermally or upon infrared excitation of matrix-isolated 6-methoxyindole were investigated. Narrowband near-infrared excitation of the first overtone of the N–H stretching vibration of each one of the two identified conformers is found to induce a selective large-scale conversion of the pumped conformer into the other one. This easily controllable bidirectional process consists in the intramolecular reorientation of the methoxy group and allowed a full assignment of the infrared spectra of the two conformers. Matrices with different conformational compositions prepared by narrow-band irradiations were subsequently used to investigate the effects of both thermal and broadband infrared excitations on the conformational mixtures. Particular attention is given to the influence of the matrix medium (Ar vs. Xe) and conformational effects of exposition of the sample to the spectrometer light source during the measurements.

Kinetics of conformational changes of fibronectin adsorbed onto model surfaces.

Science.gov (United States)

Baujard-Lamotte, L; Noinville, S; Goubard, F; Marque, P; Pauthe, E

2008-05-01

Fibronectin (FN), a large glycoprotein found in body fluids and in the extracellular matrix, plays a key role in numerous cellular behaviours. We investigate FN adsorption onto hydrophilic bare silica and hydrophobic polystyrene (PS) surfaces using Fourier transform infrared spectroscopy-attenuated total reflection (FTIR-ATR) in aqueous medium. Adsorption kinetics using different bulk concentrations of FN were followed for 2h and the surface density of adsorbed FN and its time-dependent conformational changes were determined. When adsorption occurs onto the hydrophilic surface, FN molecules keep their native conformation independent of the adsorption conditions, but the amount of adsorbed FN increases with time and the bulk concentration. Although the protein surface density is the same on the hydrophobic PS surface, this has a strong impact on the average conformation of the adsorbed FN layer. Indeed, interfacial hydration changes induced by adsorption onto the hydrophobic surface lead to a decrease in unhydrated beta-sheet content and cause an increase in hydrated beta-strand and hydrated random domain content of adsorbed FN. This conformational change is mainly dependent on the bulk concentration. Indeed, at low bulk concentrations, the secondary structures of adsorbed FN molecules undergo strong unfolding, allowing an extended and hydrated conformation of the protein. At high bulk concentrations, the molecular packing reduces the unfolding of the stereoregular structures of the FN molecules, preventing stronger spreading of the protein.

Lanthanide ions induce hydrolysis of hemoglobin-bound 2,3-diphosphoglycerate (2,3-DPG), conformational changes of globin and bidirectional changes of 2,3-DPG-hemoglobin's oxygen affinity.

Science.gov (United States)

Cheng, Y; Lin, H; Xue, D; Li, R; Wang, K

2001-02-14

The changes in structure and function of 2,3-diphosphoglycerate-hemoglobin (2,3-DPG-Hb) induced by Ln(3+) binding were studied by spectroscopic methods. The binding of lanthanide cations to 2,3-DPG is prior to that to Hb. Ln(3+) binding causes the hydrolysis of either one from the two phosphomonoester bonds in 2,3-DPG non-specifically. The results using the ultrafiltration method indicate that Ln(3+) binding sites for Hb can be classified into three categories: i.e. positive cooperative sites (N(I)), non-cooperative strong sites (N(S)) and non-cooperative weak sites (N(W)) with binding constants in decreasing order: K(I)>K(S)>K(W). The total number of binding sites amounts to about 65 per Hb tetramer. Information on reaction kinetics was obtained from the change of intrinsic fluorescence in Hb monitored by stopped-flow fluorometry. Fluctuation of fluorescence dependent on Ln(3+) concentration and temperature was observed and can be attributed to the successive conformational changes induced by Ln(3+) binding. The results also reveal the bidirectional changes of the oxygen affinity of Hb in the dependence on Ln(3+) concentration. At the range of [Ln(3+)]/[Hb]<2, the marked increase of oxygen affinity (P(50) decrease) with the Ln(3+) concentration can be attributed to the hydrolysis of 2,3-DPG, while the slight rebound of oxygen affinity in higher Ln(3+) concentration can be interpreted by the transition to the T-state of the Hb tetramer induced by Ln(3+) binding. This was indicated by the changes in secondary structure characterized by the decrease of alpha-helix content.

Radiation-induced conductivity and high-temperature Q changes in quartz resonators

International Nuclear Information System (INIS)

Koehler, D.R.

1981-01-01

While high temperature electrolysis has proven beneficial as a technique to remove interstitial impurities from quartz, reliable indices to measure the efficacy of such a processing step are still under development. The present work is directed toward providing such an index. Two techniques have been investigated - one involves measurement of the radiation induced conductivity in quartz along the optic axis, and the second involves measurement of high temperature Q changes. Both effects originate when impurity charge compensators are released from their traps, in the first case resulting in ionic conduction and in the second case resulting in increased acoustic losses. Radiation induced conductivity measurements have been carried out with a 200 kV, 14 mA x-ray machine producing 5 rads/s. With electric fields of the order of 10 4 V/cm, the noise level in the current measuring system is equivalent to an ionic current generated by quartz impurities in the 1 ppB range. The accuracy of the high temperature ( 300 to 800 0 K) Q -1 measurement technique will be determined. A number of resonators constructed of quartz material of different impurity contents have been tested and both the radiation induced conductivity and the high temperature Q -1 results compared with earlier radiation induced frequency and resonator resistance changes. 10 figures

A chemometric analysis of ligand-induced changes in intrinsic fluorescence of folate binding protein indicates a link between altered conformational structure and physico-chemical characteristics

DEFF Research Database (Denmark)

Bruun, Susanne W; Holm, Jan; Hansen, Steen Ingemann

2009-01-01

Ligand binding alters the conformational structure and physico-chemical characteristics of bovine folate binding protein (FBP). For the purpose of achieving further information we analyzed ligand (folate and methotrexate)-induced changes in the fluorescence landscape of FBP. Fluorescence excitation...... of folate accords fairly well with the disappearance of strongly hydrophobic tryptophan residues from the solvent-exposed surface of FBP. The PARAFAC has thus proven useful to establish a hitherto unexplained link between parallel changes in conformational structure and physico-chemical characteristics...... of FBP induced by folate binding. Parameters for ligand binding derived from PARAFAC analysis of the fluorescence data were qualitatively and quantitatively similar to those obtained from binding of radiofolate to FBP. Herein, methotrexate exhibited a higher affinity for FBP than in competition...

Conformational change of adenosine deaminase during ligand-exchange in a crystal.

Science.gov (United States)

Kinoshita, Takayoshi; Tada, Toshiji; Nakanishi, Isao

2008-08-15

Adenosine deaminase (ADA) perpetuates chronic inflammation by degrading extracellular adenosine which is toxic for lymphocytes. ADA has two distinct conformations: open form and closed form. From the crystal structures with various ligands, the non-nucleoside type inhibitors bind to the active site occupying the critical water-binding-position and sustain the open form of apo-ADA. In contrast, substrate mimics do not occupy the critical position, and induce the large conformational change to the closed form. However, it is difficult to predict the binding of (+)-erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA), as it possesses characteristic parts of both the substrate and the non-nucleoside inhibitors. The crystal structure shows that EHNA binds to the open form through a novel recognition of the adenine base accompanying conformational change from the closed form of the PR-ADA complex in crystalline state.

In silico analysis of conformational changes induced by mutation of aromatic binding residues: consequences for drug binding in the hERG K+ channel.

Directory of Open Access Journals (Sweden)

Kirsten Knape

Full Text Available Pharmacological inhibition of cardiac hERG K(+ channels is associated with increased risk of lethal arrhythmias. Many drugs reduce hERG current by directly binding to the channel, thereby blocking ion conduction. Mutation of two aromatic residues (F656 and Y652 substantially decreases the potency of numerous structurally diverse compounds. Nevertheless, some drugs are only weakly affected by mutation Y652A. In this study we utilize molecular dynamics simulations and docking studies to analyze the different effects of mutation Y652A on a selected number of hERG blockers. MD simulations reveal conformational changes in the binding site induced by mutation Y652A. Loss of π-π-stacking between the two aromatic residues induces a conformational change of the F656 side chain from a cavity facing to cavity lining orientation. Docking studies and MD simulations qualitatively reproduce the diverse experimentally observed modulatory effects of mutation Y652A and provide a new structural interpretation for the sensitivity differences.

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

Water Evaporation and Conformational Changes from Partially Solvated Ubiquitin

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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.

Modulation of cadmium-induced mitochondrial dysfunction and volume changes by temperature in rainbow trout (Oncorhynchus mykiss)

International Nuclear Information System (INIS)

Onukwufor, John O.; Kibenge, Fred; Stevens, Don; Kamunde, Collins

2015-01-01

Highlights: • Interactions of Cd and temperature exacerbate mitochondrial dysfunction and enhance Cd accumulation. • Cd uptake by mitochondria occurs through the Ca uniporter. • Temperature exacerbates Cd-induced mitochondrial volume changes. • Low concentrations of Cd inhibit mitochondrial swelling. - Abstract: We investigated how temperature modulates cadmium (Cd)-induced mitochondrial bioenergetic disturbances, metal accumulation and volume changes in rainbow trout (Oncorhynchus mykiss). In the first set of experiments, rainbow trout liver mitochondrial function and Cd content were measured in the presence of complex I substrates, malate and glutamate, following exposure to Cd (0–100 μM) at three (5, 13 and 25 °C) temperatures. The second set of experiments assessed the effect of temperature on Cd-induced mitochondrial volume changes, including the underlying mechanisms, at 15 and 25 °C. Although temperature stimulated both state 3 and 4 rates of respiration, the coupling efficiency was reduced at temperature extremes due to greater inhibition of state 3 at low temperature and greater stimulation of state 4 at the high temperature. Cadmium exposure reduced the stimulatory effect of temperature on state 3 respiration but increased that on state 4, consequently exacerbating mitochondrial uncoupling. The interaction of Cd and temperature yielded different responses on thermal sensitivity of state 3 and 4 respiration; the Q 10 values for state 3 respiration increased at low temperature (5–13 °C) while those for state 4 increased at high temperature (13–25 °C). Importantly, the mitochondria accumulated more Cd at high temperature suggesting that the observed greater impairment of oxidative phosphorylation with temperature was due, at least in part, to a higher metal burden. Cadmium-induced mitochondrial volume changes were characterized by an early phase of contraction followed by swelling, with temperature changing the kinetics and intensifying

Modulation of cadmium-induced mitochondrial dysfunction and volume changes by temperature in rainbow trout (Oncorhynchus mykiss)

Energy Technology Data Exchange (ETDEWEB)

Onukwufor, John O. [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada C1A 4P3 (Canada); Kibenge, Fred [Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada C1A 4P3 (Canada); Stevens, Don [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada C1A 4P3 (Canada); Kamunde, Collins, E-mail: ckamunde@upei.ca [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada C1A 4P3 (Canada)

2015-01-15

Highlights: • Interactions of Cd and temperature exacerbate mitochondrial dysfunction and enhance Cd accumulation. • Cd uptake by mitochondria occurs through the Ca uniporter. • Temperature exacerbates Cd-induced mitochondrial volume changes. • Low concentrations of Cd inhibit mitochondrial swelling. - Abstract: We investigated how temperature modulates cadmium (Cd)-induced mitochondrial bioenergetic disturbances, metal accumulation and volume changes in rainbow trout (Oncorhynchus mykiss). In the first set of experiments, rainbow trout liver mitochondrial function and Cd content were measured in the presence of complex I substrates, malate and glutamate, following exposure to Cd (0–100 μM) at three (5, 13 and 25 °C) temperatures. The second set of experiments assessed the effect of temperature on Cd-induced mitochondrial volume changes, including the underlying mechanisms, at 15 and 25 °C. Although temperature stimulated both state 3 and 4 rates of respiration, the coupling efficiency was reduced at temperature extremes due to greater inhibition of state 3 at low temperature and greater stimulation of state 4 at the high temperature. Cadmium exposure reduced the stimulatory effect of temperature on state 3 respiration but increased that on state 4, consequently exacerbating mitochondrial uncoupling. The interaction of Cd and temperature yielded different responses on thermal sensitivity of state 3 and 4 respiration; the Q{sub 10} values for state 3 respiration increased at low temperature (5–13 °C) while those for state 4 increased at high temperature (13–25 °C). Importantly, the mitochondria accumulated more Cd at high temperature suggesting that the observed greater impairment of oxidative phosphorylation with temperature was due, at least in part, to a higher metal burden. Cadmium-induced mitochondrial volume changes were characterized by an early phase of contraction followed by swelling, with temperature changing the kinetics and

Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change.

Science.gov (United States)

Mandal, Soumit Sankar; Merz, Dale R; Buchsteiner, Maximilian; Dima, Ruxandra I; Rief, Matthias; Žoldák, Gabriel

2017-06-06

Owing to the cooperativity of protein structures, it is often almost impossible to identify independent subunits, flexible regions, or hinges simply by visual inspection of static snapshots. Here, we use single-molecule force experiments and simulations to apply tension across the substrate binding domain (SBD) of heat shock protein 70 (Hsp70) to pinpoint mechanical units and flexible hinges. The SBD consists of two nanomechanical units matching 3D structural parts, called the α- and β-subdomain. We identified a flexible region within the rigid β-subdomain that gives way under load, thus opening up the α/β interface. In exactly this region, structural changes occur in the ATP-induced opening of Hsp70 to allow substrate exchange. Our results show that the SBD's ability to undergo large conformational changes is already encoded by passive mechanics of the individual elements.

Variable-temperature NMR and conformational analysis of Oenothein B

International Nuclear Information System (INIS)

Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de

2014-01-01

Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

Variable-temperature NMR and conformational analysis of Oenothein B

Energy Technology Data Exchange (ETDEWEB)

Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de, [Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Instituto de Quimica

2014-02-15

Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

pH-induced conformational changes of AcrA, the membrane fusion protein of Escherichia coli multidrug efflux system.

Science.gov (United States)

Ip, Hermia; Stratton, Kelly; Zgurskaya, Helen; Liu, Jun

2003-12-12

The multidrug efflux system AcrA-AcrB-TolC of Escherichia coli expels a wide range of drugs directly into the external medium from the bacterial cell. The mechanism of the efflux process is not fully understood. Of an elongated shape, AcrA is thought to span the periplasmic space coordinating the concerted operation of the inner and outer membrane proteins AcrB and TolC. In this study, we used site-directed spin labeling (SDSL) EPR (electron paramagnetic resonance) spectroscopy to investigate the molecular conformations of AcrA in solution. Ten AcrA mutants, each with an alanine to cysteine substitution, were engineered, purified, and labeled with a nitroxide spin label. EPR analysis of spin-labeled AcrA variants indicates that the side chain mobilities are consistent with the predicted secondary structure of AcrA. We further demonstrated that acidic pH induces oligomerization and conformational change of AcrA, and that the structural changes are reversible. These results suggest that the mechanism of action of AcrA in drug efflux is similar to the viral membrane fusion proteins, and that AcrA actively mediates the efflux of substrates.

Conformational changes induced by Mg2+ on the multiple forms of glutamine synthetase from Bacillus brevis Bb G1

Directory of Open Access Journals (Sweden)

Suja Abraham

2013-01-01

Full Text Available Conformational changes play an important role in the function of proteins. Glutamine synthetase, an important enzyme of nitrogen metabolism, was purified under sporulating (GSala and non-sporulating (GSpyr conditions and the effect of Mg2+ on these multiple forms was studied by fluorescence spectroscopy to detect possible conformational changes that occur in the presenceof Mg2+. The substantial changes in the fluorescence emission maximum, fluorescence intensity and lifetime that occur in the presence of different concentrations of Mg2+, indicated major changes in molecular conformations in both forms of this enzyme. The fluorescent changes produced by the effect of Mg2+ in GSala was much more prominent than in GSpyr. These observations strongly support the possibility that GSala and GSpyr undergoes a conformational change on binding with Mg2+.

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

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

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.

Small angle X-ray scattering study of thermodynamic and conformational changes in ion-containing symmetric diblock copolymers

Energy Technology Data Exchange (ETDEWEB)

Gunkel, Ilja [Max Planck Institute of Microstructure Physics, Halle (Germany); Institute of Physics, Martin Luther University Halle Wittenberg, Halle (Germany); Thurn-Albrecht, Thomas [Institute of Physics, Martin Luther University Halle Wittenberg, Halle (Germany)

2010-07-01

We present temperature-dependent SAXS measurements on two different symmetric block copolymers with added salt (lithiumtriflate, LiCF{sub 3}SO{sub 3}). For both studied systems, polystyrene-b-poly-2-vinylpyridine (PS-b-P2VP) and Polystyrene-b-Polyethyleneoxide (PS-b-PEO), the salt selectively dissolved in one block leading to large increases of the order-disorder transition temperatures (T{sub ODT}). In addition, the lamellar thickness of these ion-containing block copolymers nontrivially changed above a certain salt concentration - in PS-b-P2VP the lamellae became thicker whereas their thickness decreased in PS-b-PEO. Using basic arguments of the thermodynamics of block copolymers we were able to separate the ion-induced increase of T{sub ODT} due to a higher incompatibility between the different blocks from changes in the thickness of the lamellae at T{sub ODT} resulting from changes in the conformation of the ion-containing blocks.

Probing the interaction of ferrocene containing hyperbranched poly-ester with model plasma protein: Effect on the interaction mechanism and conformational change

Energy Technology Data Exchange (ETDEWEB)

Xiao, Fengjuan, E-mail: xfj66@126.com; Gu, Muqing; Liang, Ye; Li, Lanlan; Yu, Xiaolei; Wu, Xiangfeng

2014-05-01

Interaction mechanism and conformational change of model plasma protein-bovine serum albumin (BSA) induced by ferrocenyl-functionalized hyperbranched polyester (HBPE-Fc) were investigated using cyclicvoltammetry (CV), differential pulsed voltammetry (DPV), fluorescence, UV–vis absorption spectrometry and circular dichroism (CD). Some complicated interactions occurred between BSA and HBPE-Fc and the new redox centers appeared in the BSA/HBPE-Fc complex that changed and hindered the electron transfer of Fe/Fe{sup 2+}. Fluorescence quenching data showed that the fluorescence of BSA was statically quenched by HBPE-Fc, which implied that ground state complex formed between BSA and HBPE-Fc. van der Waals force and hydrogen bond played major roles in the interaction of HBPE-Fc with BSA. The binding constant Ka for HBPE-Fc–protein interaction is in the order of 10{sup 6} at room temperature indicates that there is a strong interaction between HBPE-Fc and BSA. Synchronous, three-dimensional fluorescence and CD studies indicated that the interaction of BSA with HBPE-Fc induced conformational changes in BSA with overall decrease in the α-helical structure and increase in β-pleated sheet structure. The molecular model of the interaction between HBPE-Fc and BSA was also presented according to the results in this study. - Highlights: • A novel ferrocenyl-functionalized hyperbranched polymer (HBPE-Fc) with potential anticancer effects. • New redox centers appear in the BSA/HBPE-Fc complex that changed and hindered the electron transfer of Fe/Fe{sup 2+}. • BSA fluorescence was statically quenched by HBPE-Fc. • BSA/HBPE-Fc ground state complex was mainly formed by the hydrogen bonds and van der Waals force. • HBPE-Fc induced conformational changes in BSA with overall decrease in the α-helical structure and increase in β-pleated sheet structure. • The molecular model of the interaction was presented according to the results in this study.

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.

Recognition of conformational changes in beta-lactoglobulin by molecularly imprinted thin films.

Science.gov (United States)

Turner, Nicholas W; Liu, Xiao; Piletsky, Sergey A; Hlady, Vladimir; Britt, David W

2007-09-01

Pathogenesis in protein conformational diseases is initiated by changes in protein secondary structure. This molecular restructuring presents an opportunity for novel shape-based detection approaches, as protein molecular weight and chemistry are otherwise unaltered. Here we apply molecular imprinting to discriminate between distinct conformations of the model protein beta-lactoglobulin (BLG). Thermal- and fluoro-alcohol-induced BLG isoforms were imprinted in thin films of 3-aminophenylboronic acid on quartz crystal microbalance chips. Enhanced rebinding of the template isoform was observed in all cases when compared to the binding of nontemplate isoforms over the concentration range of 1-100 microg mL(-1). Furthermore, it was observed that the greater the changes in the secondary structure of the template protein the lower the binding of native BLG challenges to the imprint, suggesting a strong steric influence in the recognition system. This feasibility study is a first demonstration of molecular imprints for recognition of distinct conformations of the same protein.

Recognition of Conformational Changes in β-Lactoglobulin by Molecularly Imprinted Thin Films

Science.gov (United States)

Turner, Nicholas W.; Liu, Xiao; Piletsky, Sergey A.; Hlady, Vladimir; Britt, David W.

2008-01-01

Pathogenesis in protein conformational diseases is initiated by changes in protein secondary structure. This molecular restructuring presents an opportunity for novel shape-based detection approaches, as protein molecular weight and chemistry are otherwise unaltered. Here we apply molecular imprinting to discriminate between distinct conformations of the model protein β-lactoglobulin (BLG). Thermal- and fluoro-alcohol-induced BLG isoforms were imprinted in thin films of 3-aminophenylboronic acid on quartz crystal microbalance chips. Enhanced rebinding of the template isoform was observed in all cases when compared to the binding of nontemplate isoforms over the concentration range of 1–100 µg mL−1. Furthermore, it was observed that the greater the changes in the secondary structure of the template protein the lower the binding of native BLG challenges to the imprint, suggesting a strong steric influence in the recognition system. This feasibility study is a first demonstration of molecular imprints for recognition of distinct conformations of the same protein. PMID:17665947

Telemetry pill versus rectal and esophageal temperature during extreme rates of exercise-induced core temperature change

International Nuclear Information System (INIS)

Teunissen, L P J; Daanen, H A M; De Haan, A; De Koning, J J

2012-01-01

Core temperature measurement with an ingestible telemetry pill has been scarcely investigated during extreme rates of temperature change, induced by short high-intensity exercise in the heat. Therefore, nine participants performed a protocol of rest, (sub)maximal cycling and recovery at 30 °C. The pill temperature (T pill ) was compared with the rectal temperature (T re ) and esophageal temperature (T es ). T pill corresponded well to T re during the entire trial, but deviated considerably from T es during the exercise and recovery periods. During maximal exercise, the average ΔT pill −T re and ΔT pill −T es were 0.13 ± 0.26 and −0.57 ± 0.53 °C, respectively. The response time from the start of exercise, the rate of change during exercise and the peak temperature were similar for T pill and T re. T es responded 5 min earlier, increased more than twice as fast and its peak value was 0.42 ± 0.46 °C higher than T pill . In conclusion, also during considerable temperature changes at a very high rate, T pill is still a representative of T re . The extent of the deviation in the pattern and peak values between T pill and T es (up to >1 °C) strengthens the assumption that T pill is unsuited to evaluate central blood temperature when body temperatures change rapidly. (paper)

Temperature-induced changes in neuromuscular function: central and peripheral mechanisms.

Science.gov (United States)

Goodman, D; Hancock, P A; Runnings, D W; Brown, S L

1984-10-01

Three series of experimental tests were conducted on subjects under both elevated and depressed thermal conditions. Tripartite series consisted of whole-body immersion excepting the head, whole-body immersion excepting the head and response limb, and immersion of the discrete-response limb. Measures of physiological and behavioural responses were made at sequential .4 degrees C changes during whole-body immersions and approximately 5 degrees C changes of water temperature during the immersion of a limb only. Results suggested that velocity of nerve conduction decreased with thermal depression. Premotor, motor, simple, and choice reaction times varied differentially as a function of the hot and cold conditions. Implications of these differential effects on neuromuscular function are examined with respect to person-machine performance in artificially induced or naturally occurring extremes of ambient temperature.

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.

Conformational changes in DNA caused by DNA-ase I, gamma and ultraviolet radiation as revealed by differential pulse polarography

International Nuclear Information System (INIS)

Vorlickova, M.

1979-01-01

The height, potential and half width of differential pulse-polarographic peaks of DNA were investigated in dependence on degradation by DNA-ase I and gamma and UV radiation. It was found that in all cases studied growth of peak II (reflecting conformational changes in the DNA double helix) was limited, and only after it reached a certain height further degradation induced the appearance of peak III of single-stranded DNA. This course is explained as reflecting the limited extent of conformational changes in the framework of the double helix, which probably follows from a limited number of sites that can undergo certain types of conformational changes. The character of the conformational changes is dependent on the chemical nature of the damage. (author)

Stress-induced core temperature changes in pigeons (Columba livia).

Science.gov (United States)

Bittencourt, Myla de Aguiar; Melleu, Fernando Falkenburger; Marino-Neto, José

2015-02-01

Changes in body temperature are significant physiological consequences of stressful stimuli in mammals and birds. Pigeons (Columba livia) prosper in (potentially) stressful urban environments and are common subjects in neurobehavioral studies; however, the thermal responses to stress stimuli by pigeons are poorly known. Here, we describe acute changes in the telemetrically recorded celomatic (core) temperature (Tc) in pigeons given a variety of potentially stressful stimuli, including transfer to a novel cage (ExC) leading to visual isolation from conspecifics, the presence of the experimenter (ExpR), gentle handling (H), sham intracelomatic injections (SI), and the induction of the tonic immobility (TI) response. Transfer to the ExC cage provoked short-lived hyperthermia (10-20 min) followed by a long-lasting and substantial decrease in Tc, which returned to baseline levels 2 h after the start of the test. After a 2-hour stay in the ExC, the other potentially stressful stimuli evoked only weak, marginally significant hyperthermic (ExpR, IT) or hypothermic (SI) responses. Stimuli delivered 26 h after transfer to the ExC induced definite and intense increases in Tc (ExpR, H) or hypothermic responses (SI). These Tc changes appear to be unrelated to modifications in general activity (as measured via telemetrically recorded actimetric data). Repeated testing failed to affect the hypothermic responses to the transference to the ExC, even after nine trials and at 1- or 8-day intervals, suggesting that the social (visual) isolation from conspecifics may be a strong and poorly controllable stimulus in this species. The present data indicated that stress-induced changes in Tc may be a consistent and reliable physiological parameter of stress but that they may also show stressor type-, direction- and species-specific attributes. Copyright © 2014 Elsevier Inc. All rights reserved.

pH-induced conformational change of the rotavirus VP4 spike: implications for cell entry and antibody neutralization.

Science.gov (United States)

Pesavento, Joseph B; Crawford, Sue E; Roberts, Ed; Estes, Mary K; Prasad, B V Venkataram

2005-07-01

The rotavirus spike protein, VP4, is a major determinant of infectivity and neutralization. Previously, we have shown that trypsin-enhanced infectivity of rotavirus involves a transformation of the VP4 spike from a flexible to a rigid bilobed structure. Here we show that at elevated pH the spike undergoes a drastic, irreversible conformational change and becomes stunted, with a pronounced trilobed appearance. These particles with altered spikes, at a normal pH of 7.5, despite the loss of infectivity and the ability to hemagglutinate, surprisingly exhibit sialic acid (SA)-independent cell binding in contrast to the SA-dependent cell binding exhibited by native virions. Remarkably, a neutralizing monoclonal antibody that remains bound to spikes throughout the pH changes (pH 7 to 11 and back to pH 7) completely prevents this conformational change, preserving the SA-dependent cell binding and hemagglutinating functions of the virion. A hypothesis that emerges from the present study is that high-pH treatment triggers a conformational change that mimics a post-SA-attachment step to expose an epitope recognized by a downstream receptor in the rotavirus cell entry process. This process involves sequential interactions with multiple receptors, and the mechanism by which the antibody neutralizes is by preventing this conformational change.

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.

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

New insights into heat induced structural changes of pectin methylesterase on fluorescence spectroscopy and molecular modeling basis

Science.gov (United States)

Nistor, Oana Viorela; Stănciuc, Nicoleta; Aprodu, Iuliana; Botez, Elisabeta

2014-07-01

Heat-induced structural changes of Aspergillus oryzae pectin methylesterase (PME) were studied by means of fluorescence spectroscopy and molecular modeling, whereas the functional enzyme stability was monitored by inactivation studies. The fluorescence spectroscopy experiments were performed at two pH value (4.5 and 7.0). At both pH values, the phase diagrams were linear, indicating the presence of two molecular species induced by thermal treatment. A red shift of 7 nm was observed at neutral pH by increasing temperature up to 60 °C, followed by a blue shift of 4 nm at 70 °C, suggesting significant conformational rearrangements. The quenching experiments using acrylamide and iodide demonstrate a more flexible conformation of enzyme with increasing temperature, especially at neutral pH. The experimental results were complemented with atomic level observations on PME model behavior after performing molecular dynamics simulations at different temperatures. The inactivation kinetics of PME in buffer solutions was fitted using a first-order kinetics model, resulting in activation energy of 241.4 ± 7.51 kJ mol-1.

Conformational variation of proteins at room temperature is not dominated by radiation damage

International Nuclear Information System (INIS)

Russi, Silvia; González, Ana; Kenner, Lillian R.; Keedy, Daniel A.; Fraser, James S.; Bedem, Henry van den

2017-01-01

Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. Recent studies have shown that flash-cooling decreases the heterogeneity of the conformational ensemble and can hide important functional mechanisms from observation. These discoveries have motivated increasing numbers of experiments to be carried out at room temperature. However, the trade-offs between increased risk of radiation damage and increased observation of alternative conformations at room temperature relative to cryogenic temperature have not been examined. A considerable amount of effort has previously been spent studying radiation damage at cryo-temperatures, but the relevance of these studies to room temperature diffraction is not well understood. Here, the effects of radiation damage on the conformational landscapes of three different proteins (T. danielli thaumatin, hen egg-white lysozyme and human cyclophilin A) at room (278 K) and cryogenic (100 K) temperatures are investigated. Increasingly damaged datasets were collected at each temperature, up to a maximum dose of the order of 10 7 Gy at 100 K and 10 5 Gy at 278 K. Although it was not possible to discern a clear trend between damage and multiple conformations at either temperature, it was observed that disorder, monitored by B-factor-dependent crystallographic order parameters, increased with higher absorbed dose for the three proteins at 100 K. At 278 K, however, the total increase in this disorder was only statistically significant for thaumatin. A correlation between specific radiation damage affecting side chains and the amount of disorder was not observed. Lastly, this analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation

On induced action for conformal higher spins in curved background

Energy Technology Data Exchange (ETDEWEB)

Beccaria, Matteo, E-mail: matteo.beccaria@le.infn.it [Dipartimento di Matematica e Fisica Ennio De Giorgi, Università del Salento & INFN, Via Arnesano, 73100 Lecce (Italy); Tseytlin, Arkady A., E-mail: tseytlin@imperial.ac.uk [The Blackett Laboratory, Imperial College, London SW7 2AZ (United Kingdom)

2017-06-15

We continue the investigation of the structure of the action for a tower of conformal higher spin fields in non-trivial 4d background metric recently discussed in Grigoriev and Tseytlin (2016). The action is defined as an induced one from path integral of a conformal scalar field in curved background coupled to higher spin fields. We analyze in detail the dependence of the quadratic part of the induced action on the spin 1 and spin 3 fields, determining the presence of a curvature-dependent mixed spin 1–3 term. One consequence is that the pure spin 3 kinetic term cannot be gauge-invariant on its own beyond the leading term in small curvature expansion. We also compute the non-zero contribution of the 1–3 mixing term to the conformal anomaly c-coefficient. One is thus to determine all such mixing terms before addressing the question of possible vanishing of the total c-coefficient in the conformal higher spin theory.

On induced action for conformal higher spins in curved background

Directory of Open Access Journals (Sweden)

Matteo Beccaria

2017-06-01

Full Text Available We continue the investigation of the structure of the action for a tower of conformal higher spin fields in non-trivial 4d background metric recently discussed in Grigoriev and Tseytlin (2016 [15]. The action is defined as an induced one from path integral of a conformal scalar field in curved background coupled to higher spin fields. We analyze in detail the dependence of the quadratic part of the induced action on the spin 1 and spin 3 fields, determining the presence of a curvature-dependent mixed spin 1–3 term. One consequence is that the pure spin 3 kinetic term cannot be gauge-invariant on its own beyond the leading term in small curvature expansion. We also compute the non-zero contribution of the 1–3 mixing term to the conformal anomaly c-coefficient. One is thus to determine all such mixing terms before addressing the question of possible vanishing of the total c-coefficient in the conformal higher spin theory.

Ratiometric Sensing of Hydrogen Peroxide Utilizing Conformational Change in Fluorescent Boronic Acid Polymers

Directory of Open Access Journals (Sweden)

Kan Takeshima

2017-01-01

Full Text Available We demonstrate that the copolymers containing boronic acid and pyrene units can be utilized for the fluorometric sensing of hydrogen peroxide (H2O2 in aqueous solutions. The copolymer exists in a relatively extended conformation in the absence of H2O2, whereas the polymer chain is contracted by the reaction of boronic acid moieties with H2O2 to form phenol groups. This conformational change induces aggregation of the originally isolated pyrene groups. As a result, relative intensity of excimer emission with respect to monomer emission increases with H2O2 concentration. Accordingly, the present methodology enables us to measure H2O2 by means of ratiometric fluorescence change in the range of 0–30 μM.

Ligand-specific conformational changes in the alpha1 glycine receptor ligand-binding domain

DEFF Research Database (Denmark)

Pless, Stephan Alexander; Lynch, Joseph W

2009-01-01

, and by the antagonist, strychnine. Voltage-clamp fluorometry involves labeling introduced cysteines with environmentally sensitive fluorophores and inferring structural rearrangements from ligand-induced fluorescence changes. In the inner beta-sheet, we labeled residues in loop 2 and in binding domain loops D and E....... At each position, strychnine and glycine induced distinct maximal fluorescence responses. The pre-M1 domain responded similarly; at each of four labeled positions glycine produced a strong fluorescence signal, whereas strychnine did not. This suggests that glycine induces conformational changes...... in the inner beta-sheet and pre-M1 domain that may be important for activation, desensitization, or both. In contrast, most labeled residues in loops C and F yielded fluorescence changes identical in magnitude for glycine and strychnine. A notable exception was H201C in loop C. This labeled residue responded...

Chain conformation change upon heating for Pauci-chain polystyrene microsphere made by microemulsion polymerization

NARCIS (Netherlands)

Ming, W.; Zhao, Y.Q.; Zhao, Jun; Fu, Shoukuan; Jones, F.N.

2000-01-01

The conformation change of pauci-chain polystyrene microsphere (micro-PS) upon heating was investigated by in-situ FTIR. For the peaks at 1492 and 1452 cm-1 due to phenyl ring semicircle stretch, there are two discontinuities in the plots of peak height versus temperature. The first discontinuity at

Cation diffusion facilitators transport initiation and regulation is mediated by cation induced conformational changes of the cytoplasmic domain.

Directory of Open Access Journals (Sweden)

Natalie Zeytuni

Full Text Available Cation diffusion facilitators (CDF are part of a highly conserved protein family that maintains cellular divalent cation homeostasis in all domains of life. CDF's were shown to be involved in several human diseases, such as Type-II diabetes and neurodegenerative diseases. In this work, we employed a multi-disciplinary approach to study the activation mechanism of the CDF protein family. For this we used MamM, one of the main ion transporters of magnetosomes--bacterial organelles that enable magnetotactic bacteria to orientate along geomagnetic fields. Our results reveal that the cytosolic domain of MamM forms a stable dimer that undergoes distinct conformational changes upon divalent cation binding. MamM conformational change is associated with three metal binding sites that were identified and characterized. Altogether, our results provide a novel auto-regulation mode of action model in which the cytosolic domain's conformational changes upon ligand binding allows the priming of the CDF into its transport mode.

Time-resolved circular dichroism: Application to the study of conformal changes in biomolecules

Science.gov (United States)

Hache, F.

2010-06-01

Circular dichroism (CD) is known to be a very sensitive probe of the conformation of molecules and biomolecules. It is therefore tempting to implement CD in a pump-probe experiment in order to measure ultrarapid conformational changes which occur in photochemical processes. We present two technical developments of such time-resolved CD experiments. The first one relies on the modulation of the probe polarization from left to right circular whereas the second one measures the pump-induced ellipticity of the probe with a Babinet-Soleil compensator. Some applications are described and extension of these techniques towards the study of elementary protein folding processes is discussed.

Time-resolved circular dichroism: Application to the study of conformal changes in biomolecules

Directory of Open Access Journals (Sweden)

Hache F.

2010-06-01

Full Text Available Circular dichroism (CD is known to be a very sensitive probe of the conformation of molecules and biomolecules. It is therefore tempting to implement CD in a pump-probe experiment in order to measure ultrarapid conformational changes which occur in photochemical processes. We present two technical developments of such time-resolved CD experiments. The first one relies on the modulation of the probe polarization from left to right circular whereas the second one measures the pump-induced ellipticity of the probe with a Babinet-Soleil compensator. Some applications are described and extension of these techniques towards the study of elementary protein folding processes is discussed.

Modelling property changes in graphite irradiated at changing irradiation temperature

CSIR Research Space (South Africa)

Kok, S

2011-01-01

Full Text Available A new method is proposed to predict the irradiation induced property changes in nuclear; graphite, including the effect of a change in irradiation temperature. The currently used method; to account for changes in irradiation temperature, the scaled...

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.

Radiation-induced cytogenetic damage in relation to changes in interphase chromosome conformation

International Nuclear Information System (INIS)

Pantelias, G.E.

1986-01-01

The premature chromosome condensation (PCC) technique was used to study several factors that determine the yield of chromosome fragments as observed in interphase cells after irradiation. In addition to absorbed dose and the extent of chromosome condensation at the time of irradiation, changes in chromosome conformation as cells progressed through the cell cycle after irradiation affected dramatically the yield of chromosome fragments observed. As a test of the effect of chromosome decondensation, irradiated metaphase Chinese hamster ovary (CHO) cells were allowed to divide, and the prematurely condensed chromosomes in the daughter cells were analyzed in their G1 phase. The yield of chromosome fragments increased as the daughter cells progressed toward S phase and chromosome decondensation occurred. When early G1 CHO cells were irradiated and analyzed at later times in G1 phase, an increase in chromosome fragmentation again followed the gradual increase in chromosome decondensation. As a test of the effect of chromosome condensation, G0 human lymphocytes were irradiated and analyzed at various times after fusion with mitotic CHO cells, i.e., as condensation proceeded. The yield of fragments observed was directly related to the amount of chromosome condensation allowed to take place after irradiation and inversely related to the extent of chromosome condensation at the time of irradiation. It can be concluded that changes in chromosome conformation interfered with rejoining processes. In contrast, resting chromosomes (as in G0 lymphocytes irradiated before fusion) showed efficient rejoining. These results support the hypothesis that cytogenetic lesions become observable chromosome breaks when chromosome condensation or decondensation occurs during the cell cycle

Evidence for distinct sodium-, dopamine-, and cocaine-dependent conformational changes in transmembrane segments 7 and 8 of the dopamine transporter

DEFF Research Database (Denmark)

Norregaard, Lene; Loland, Claus Juul; Gether, Ulrik

2003-01-01

. Inhibitors such as cocaine did not alter the effect of MTSET in M371C. The protection of M371C inactivation by dopamine required Na+. Because dopamine binding is believed to be Na+-independent, this suggests that dopamine induces a transport-associated conformational change that decreases the reactivity of M......371C with MTSET. In contrast to M371C, cocaine decreased the reaction rate of A399C with MTSET, whereas dopamine had no effect. The protection by cocaine can either reflect that Ala-399 lines the cocaine binding crevice or that cocaine induces a conformational change that decreases the reactivity of A...

Radiatively induced breaking of conformal symmetry in a superpotential

International Nuclear Information System (INIS)

Arbuzov, A.B.; Cirilo-Lombardo, D.J.

2016-01-01

Radiatively induced symmetry breaking is considered for a toy model with one scalar and one fermion field unified in a superfield. It is shown that the classical quartic self-interaction of the superfield possesses a quantum infrared singularity. Application of the Coleman–Weinberg mechanism for effective potential leads to the appearance of condensates and masses for both scalar and fermion components. That induces a spontaneous breaking of the initial classical symmetries: the supersymmetry and the conformal one. The energy scales for the scalar and fermion condensates appear to be of the same order, while the renormalization scale is many orders of magnitude higher. A possibility to relate the considered toy model to conformal symmetry breaking in the Standard Model is discussed.

BcL-xL Conformational Changes upon Fragment Binding Revealed by NMR

Science.gov (United States)

Aguirre, Clémentine; ten Brink, Tim; Walker, Olivier; Guillière, Florence; Davesne, Dany; Krimm, Isabelle

2013-01-01

Protein-protein interactions represent difficult but increasingly important targets for the design of therapeutic compounds able to interfere with biological processes. Recently, fragment-based strategies have been proposed as attractive approaches for the elaboration of protein-protein surface inhibitors from fragment-like molecules. One major challenge in targeting protein-protein interactions is related to the structural adaptation of the protein surface upon molecular recognition. Methods capable of identifying subtle conformational changes of proteins upon fragment binding are therefore required at the early steps of the drug design process. In this report we present a fast NMR method able to probe subtle conformational changes upon fragment binding. The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding. We illustrate the method by the retrospective analysis of the complex between the anti-apoptotic Bcl-xL protein and the fragment 4′-fluoro-[1,1′-biphenyl]-4-carboxylic acid that was previously shown to bind one of the Bcl-xL hot spots. The CSP-based approach shows that the protein undergoes a subtle conformational rearrangement upon interaction, for residues located in helices 2, 3 and the very beginning of 5. Our observations are corroborated by residual dipolar coupling measurements performed on the free and fragment-bound forms of the Bcl-xL protein. These NMR-based results are in total agreement with previous molecular dynamic calculations that evidenced a high flexibility of Bcl-xL around the binding site. Here we show that CSP of protein amine protons are useful and reliable structural probes. Therefore, we propose to use CSP simulation to assess protein conformational changes upon ligand binding in the fragment-based drug design approach. PMID:23717610

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.

Biospectroscopy of Nanodiamond-Induced Alterations in Conformation of Intra- and Extracellular Proteins: A Nanoscale IR Study.

Science.gov (United States)

Khanal, Dipesh; Kondyurin, Alexey; Hau, Herman; Knowles, Jonathan C; Levinson, Olga; Ramzan, Iqbal; Fu, Dong; Marcott, Curtis; Chrzanowski, Wojciech

2016-08-02

The toxicity of nanomaterials raises major concerns because of the impact that nanomaterials may have on health, which remains poorly understood. We need to explore the fate of individual nanoparticles in cells at nano and molecular levels to establish their safety. Conformational changes in secondary protein structures are one of the main indicators of impaired biological function, and hence, the ability to identify these changes at a nanoscale level offers unique insights into the nanotoxicity of materials. Here, we used nanoscale infrared spectroscopy and demonstrated for the first time that nanodiamond-induced alterations in both extra- and intracellular secondary protein structures lead to the formation of antiparallel β-sheet, β-turns, intermolecular β-sheet, and aggregation of proteins. These conformational changes of the protein structure may result in the loss of functionality of proteins and in turn lead to adverse effects.

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...

Tetrahymena telomerase protein p65 induces conformational changes throughout telomerase RNA (TER) and rescues telomerase reverse transcriptase and TER assembly mutants.

Science.gov (United States)

Berman, Andrea J; Gooding, Anne R; Cech, Thomas R

2010-10-01

The biogenesis of the Tetrahymena telomerase ribonucleoprotein particle (RNP) is enhanced by p65, a La family protein. Single-molecule and biochemical studies have uncovered a hierarchical assembly of the RNP, wherein the binding of p65 to stems I and IV of telomerase RNA (TER) causes a conformational change that facilitates the subsequent binding of telomerase reverse transcriptase (TERT) to TER. We used purified p65 and variants of TERT and TER to investigate the conformational rearrangements that occur during RNP assembly. Nuclease protection assays and mutational analysis revealed that p65 interacts with and stimulates conformational changes in regions of TER beyond stem IV. Several TER mutants exhibited telomerase activity only in the presence of p65, revealing the importance of p65 in promoting the correct RNP assembly pathway. In addition, p65 rescued TERT assembly mutants but not TERT activity mutants. Taken together, these results suggest that p65 stimulates telomerase assembly and activity in two ways. First, by sequestering stems I and IV, p65 limits the ensemble of structural conformations of TER, thereby presenting TERT with the active conformation of TER. Second, p65 acts as a molecular buttress within the assembled RNP, mutually stabilizing TER and TERT in catalytically active conformations.

Classification of conformal representations induced from the maximal cuspidal parabolic

Energy Technology Data Exchange (ETDEWEB)

Dobrev, V. K., E-mail: dobrev@inrne.bas.bg [Scuola Internazionale Superiore di Studi Avanzati (Italy)

2017-03-15

In the present paper we continue the project of systematic construction of invariant differential operators on the example of representations of the conformal algebra induced from the maximal cuspidal parabolic.

Glycerin-Induced Conformational Changes in Bombyx mori Silk Fibroin Film Monitored by (13)C CP/MAS NMR and ¹H DQMAS NMR.

Science.gov (United States)

Asakura, Tetsuo; Endo, Masanori; Hirayama, Misaki; Arai, Hiroki; Aoki, Akihiro; Tasei, Yugo

2016-09-09

In order to improve the stiff and brittle characteristics of pure Bombyx mori (B. mori) silk fibroin (SF) film in the dry state, glycerin (Glyc) has been used as a plasticizer. However, there have been very limited studies on the structural characterization of the Glyc-blended SF film. In this study, (13)C Cross Polarization/Magic Angle Spinning nuclear magnetic resonance (CP/MAS NMR) was used to monitor the conformational changes in the films by changing the Glyc concentration. The presence of only 5 wt % Glyc in the film induced a significant conformational change in SF where Silk I* (repeated type II β-turn and no α-helix) newly appeared. Upon further increase in Glyc concentration, the percentage of Silk I* increased linearly up to 9 wt % Glyc and then tended to be almost constant (30%). This value (30%) was the same as the fraction of Ala residue within the Silk I* form out of all Ala residues of SF present in B. mori mature silkworm. The ¹H DQMAS NMR spectra of Glyc-blended SF films confirmed the appearance of Silk I* in the Glyc-blended SF film. A structural model of Glyc-SF complex including the Silk I* form was proposed with the guidance of the Molecular Dynamics (MD) simulation using ¹H-¹H distance constraints obtained from the ¹H Double-Quantum Magic Angle Spinning (DQMAS) NMR spectra.

Time-Resolved Fluorescence of Water-Soluble Pyridinium Salt: Sensitive Detection of the Conformational Changes of Bovine Serum Albumin.

Science.gov (United States)

Li, Lei; Yi, Hua; Jia, Menghui; Chang, Mengfang; Zhou, Zhongneng; Zhang, Sanjun; Pan, Haifeng; Chen, Yan; Chen, Jinquan; Xu, Jianhua

2016-06-20

In this paper, we report a pyridinium salt "turn-on" fluorescent probe, 4-[2-(4-Dimethylamino-phenyl)-vinyl]-1-methylpyridinium iodide (p-DASPMI), and applied its time-resolved fluorescence (TRF) to monitor the protein conformational changes. Both the fluorescence lifetime and quantum yield (QY) of p-DASPMI were increased about two orders of magnitude after binding to the protein bovine serum albumin (BSA). The free p-DASPMI in solution presents an ultrashort fluorescence lifetime (12.4 ps), thus it does not interfere the detection of bound p-DASPMI which has nanosecond fluorescence lifetime. Decay-associated spectra (DAS) show that p-DASPMI molecules bind to subdomains IIA and IIIA of BSA. The TRF decay profiles of p-DASPMI can be described by multi-exponential decay function ([Formula: see text]), and the obtained parameters, such as lifetimes ([Formula: see text]), fractional amplitudes ([Formula: see text]), and fractional intensities ([Formula: see text]), may be used to deduce the conformational changes of BSA. The pH and Cu 2+ induced conformational changes of BSA were investigated through the TRF of p-DASPMI. The results show that the p-DASPMI is a candidate fluorescent probe in studying the conformational changes of proteins through TRF spectroscopy and microscopy in the visible range. © The Author(s) 2016.

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.

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

Temperature-induced structural changes in fluorozirconate glasses and liquids

International Nuclear Information System (INIS)

Sen, S.; Youngman, R.E.

2002-01-01

The atomic structure and its temperature dependence in fluorozirconate glasses and supercooled liquids have been studied with high-resolution and high-temperature 19 F and 23 Na nuclear-magnetic-resonance (NMR) spectroscopy. The 19 F NMR spectra in these glasses show the presence of multiple F environments. Temperature dependence of the 19 F magic-angle-spinning NMR spectra indicates a progressive change in the average F coordination environment in the glass structure, besides motional narrowing due to substantial mobility of F - ions. The observed change in the average 19 F NMR chemical shift is consistent with progressive breaking of the Zr-F-Zr linkages in the glass structure with increasing temperature. The onset of such a change in F speciation is observed at temperatures well below T g . This result is evidence of changes in the average equilibrium structure in an inorganic glass-forming liquid at T g , albeit on a local scale. The 23 Na NMR spectra indicate that the cations in these glasses become significantly mobile only at temperatures T≥T g , which allows for the onset of global structural relaxation and viscous flow

Small-angle reflectometry of milk protein (β -casein) at the air/serum interface and its conformational changes due to fat content and temperature

International Nuclear Information System (INIS)

Heidari, R.; White, J.W.

2003-01-01

Full text: The surface structure of dispersed emulsions play a key role in stability of the system. Proteins being one of the most important surface-active components in foods stabilise interfaces by self-interaction, resulting in a stiff visco-elastic adsorbed layer. These interactions are sensitive to disruptive effects of lipids. Previous kinetics studies by the group 1 using the X-ray reflectivity method to investigate the surface adsorption of milk proteins indicate that β -casein had a stronger affinity for the air-liquid interface compared to whey proteins. It has been shown that initially a dense protein layer, with the thickness of 20 Angstroms is formed then a second more diffuse layer with lower volume density of protein follows. Here we report the conformational changes (with particular emphasise on the β -casein tail) occurred at the air-milk serum interface due to the effects of milk fat content, temperature and the milk preparation technique (ie homogenisation vs microfluidisation). In the effect of fat content on the adsorption of protein into the interface the key conclusion is that at lower temperatures the surface composition remains unchanged. The compositional changes, however, become significant at room temperature indicating adsorption of less reflective-water-soluble components into the surface layer. Repulsive interactions between casein aggregates are also involved. Microfluidised samples having the advantage of smaller particle size prove to be more stable to fat or temperature effects compared to the corresponding homogenised milks

Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

Science.gov (United States)

Doyle, Colleen M; Rumfeldt, Jessica A; Broom, Helen R; Sekhar, Ashok; Kay, Lewis E; Meiering, Elizabeth M

2016-03-08

The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.

Conformational transformations induced by the charge-curvature interaction: Mean-field approach

DEFF Research Database (Denmark)

Gaididei, Yu B.; Christiansen, Peter Leth; Zakrzewski, W.J.

2006-01-01

A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom of closed molecular aggregates may act as drivers giving ...... impetus to conformational dynamics of biopolymers. It is demonstrated that initially circular aggregates may undergo transformation to polygonal shapes and possible application to aggregates of bacteriochlorophyl a molecules is considered....

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.

Phosphorylation-induced conformational changes in short peptides probed by fluorescence resonance energy transfer in the 10A domain.

Science.gov (United States)

Sahoo, Harekrushna; Nau, Werner M

2007-03-26

Phosphorylation-induced conformational changes in short polypeptides were probed by a fluorescence resonance energy transfer (FRET) method by employing a short-distance FRET pair (R(0) approximately 10 A) based on tryptophan as natural donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as synthetic acceptor. Two substrates for kinases, LeuArgArgTrpSerLeuGly-Dbo (peptide I) and TrpLysArgThrLeuArgArg-Dbo (peptide II), were investigated, with serine and threonine, respectively, as phosphorylation sites. Steady-state and time-resolved fluorescence experiments in H(2)O revealed a decrease in FRET efficiency for peptide I and an increase for peptide II; this suggested that the effective distances between donor and acceptor increased and decreased, respectively. The same trends and similar absolute variations in effective donor-acceptor distances were observed in propylene glycol, a less polar and highly viscous solvent; this suggested that the variations are due to intrinsic structural preferences. Fitting of the time-resolved decay traces according to a distribution function model (Gaussian distribution) provided the mean donor-acceptor distances, which showed an increase upon phosphorylation for peptide I (from 9.7 to 10.5 A) and a decrease for peptide II (from 10.9 to 9.3 A) in H(2)O. The broadness (half-width) of the distributions, which provides a measure of the rigidity of the peptides, remained similar upon phosphorylation of peptide I (3.0 versus 3.1 A), but decreased for peptide II (from 3.1 to 0.73 A in H(2)O); this suggests a more compact, structured conformation upon phosphorylation of the latter peptide. The elongation of the peptide backbone (by ca. 0.7 A) for peptide I is attributed to an increase in steric demand upon phosphorylation, which favors an extended conformation. The contraction (by ca. 1.4 A) and structural rigidification of peptide II is attributed to attractive Coulombic interactions and hydrogen bonding between the

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...

Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

KAUST Repository

Wang, Wei

2017-10-06

The function of complex biomolecular machines relies heavily on their conformational changes. Investigating these functional conformational changes is therefore essential for understanding the corresponding biological processes and promoting bioengineering applications and rational drug design. Constructing Markov State Models (MSMs) based on large-scale molecular dynamics simulations has emerged as a powerful approach to model functional conformational changes of the biomolecular system with sufficient resolution in both time and space. However, the rapid development of theory and algorithms for constructing MSMs has made it difficult for nonexperts to understand and apply the MSM framework, necessitating a comprehensive guidance toward its theory and practical usage. In this study, we introduce the MSM theory of conformational dynamics based on the projection operator scheme. We further propose a general protocol of constructing MSM to investigate functional conformational changes, which integrates the state-of-the-art techniques for building and optimizing initial pathways, performing adaptive sampling and constructing MSMs. We anticipate this protocol to be widely applied and useful in guiding nonexperts to study the functional conformational changes of large biomolecular systems via the MSM framework. We also discuss the current limitations of MSMs and some alternative methods to alleviate them.

The possible role of chromatin conformation changes in adaptive responses to ionizing radiation

International Nuclear Information System (INIS)

Ekhtiar, A.; Ammer, A.; Jbawi, A.; Othman, A.

2012-05-01

Organisms are affected by different DNA damaging agents naturally present in the environment or released as a result of human activity. Many defense mechanisms have evolved in organisms to minimize genotoxic damage. One of them is induced radioresistance or adaptive response. The adaptive response could be considered as a nonspecific phenomenon in which exposure to minimal stress could result in increased resistance to higher levels of the same or to other types of stress some hours later. A better understanding of the molecular mechanism underlying the adaptive response may lead to an improvement of cancer treatment, risk assessment and risk management strategies, radiation protection. The aim of current study was to study the possible role of chromatin conformation changes induced by ionizing radiation on the adaptive responses in human lymphocyte. For this aim the chromatin conformation have been studied in human lymphocytes from three non-smoking and three smoking healthy volunteers prior, and after espouser to gamma radiation (adaptive dose 0.1 Gy, challenge dose 1.5 Gy and adaptive + dose challenge). Chromosomal aberrations and micronucleus have been used as end point to study radio cytotoxicity and adaptive response. Our results indicated individual differences in radio adaptive response and the level of this response was dependent of chromatin de condensation induced by a adaptive small dose.The results showed that different dose of gamma rays induce a chromatin de condensation in human lymphocyte. The maximum chromatin relaxation were record when lymphocyte exposed to adaptive dose (0.1 Gy.). Results also showed that Adaptive dose have affected on the induction of challenge dose (1.5 Gy) of chromosome aberration and micronucleus . The comparison of results of chromatin de condensation induction as measured by flow cytometry and cytogenetic damages measured by chromosomal aberrations or micronucleus, was showed a proportionality of adaptive response with

Conformational change of oil contaminants adhered onto crystalline alpha-alumina surface in aqueous solution

International Nuclear Information System (INIS)

Xie, Wenkun; Sun, Yazhou; Liu, Haitao; Fu, Hongya; Liang, Yingchun

2016-01-01

Graphical abstract: - Highlights: • Dynamic conformational change process of oil contaminations adhered onto Al-terminated α-Al_2O_3 surface in aqueous solution is given. • Effect of water penetration on the conformational change and even detachment of oil contaminants is considered. • Change of driving forces leading to the conformational change of oil contaminants is described. - Abstract: Microscopic conformational change of oil contaminants adhered onto perfect α-Al_2O_3 (0001) surface in the aqueous solution was simulated by means of detailed fully atomistic molecular dynamics simulations. The main driving forces of the conformation change process of the oil contaminants were explored. The simulation results indicate that with submerging of the contaminated α-Al_2O_3 (0001) surface into the aqueous solution, the oil contaminants undertake an evident conformational change process. The dynamic process can be divided into several stages, including early penetration of water molecules, formation and widening of water channel, and generation of molecularly adsorbed hydration layers. Moreover, the oil contaminants on the α-Al_2O_3 surface are not fully removed from solid surface after a 10 ns relaxation, while a relatively stable oil/water/solid three-phase interface is gradually formed. Further, the residual oil contaminants are finally divided into several new ordered molecular adsorption layers. In addition, by systemically analyzing the driving forces for the conformational change of the oil contaminants, the penetration of water molecules is found to be the most important driving force. With penetrating of the water molecules, the dominating interactions controlling the conformational change of the oil contaminants have been changing over the whole simulation.

Effect of ethanol concentrations on temperature driven structural changes of chymotrypsin inhibitor 2

Energy Technology Data Exchange (ETDEWEB)

Mohanta, Dayanidhi; Jana, Madhurima, E-mail: janam@nitrkl.ac.in [Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008 (India)

2016-04-28

A series of atomistic molecular dynamics (MD) simulations of a small enzymatic protein Chymotrypsin Inhibitor 2 (CI2) in water-ethanol mixed solutions were carried out to explore the underlying mechanism of ethanol driven conformational changes of the protein. Efforts have been made to probe the influence of ethanol concentrations ranging from 0% to 75% (v/v) at ambient condition (300 K (T1)) and at elevated temperatures (375 K (T2) and 450 K (T3)) to investigate the temperature induced conformational changes of the protein further. Our study showed that the effect of varying ethanol concentrations on protein’s structure is almost insignificant at T1 and T2 temperatures whereas at T3 temperature, partial unfolding of CI2 in 10% ethanol solution followed by full unfolding of the protein at ethanol concentrations above 25% occurs. However, interestingly, at T3 temperature CI2’s native structure was found to be retained in pure water (0% ethanol solution) indicating that the cosolvent ethanol do play an important role in thermal denaturation of CI2. Such observations were quantified in the light of root-mean-square deviations (RMSDs) and radius of gyration. Although higher RMSD values of β-sheet over α-helix indicate complete destruction of the β-structure of CI2 at high ethanol concentrations, the associated time scale showed that the faster melting of α-helix happens over β-sheet. Around 60%-80% of initial native contacts of the protein were found broken with the separation of hydrophobic core consisting eleven residues at ethanol concentrations greater than 25%. This leads protein to expand with the increase in solvent accessible surface area. The interactions between protein and solvent molecules showed that protein’s solvation shell preferred to accommodate ethanol molecules as compared to water thereby excluded water molecules from CI2’s surface. Further, concentration dependent differential self-aggregation behavior of ethanol is likely to regulate

A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport

Science.gov (United States)

Chopra, Paras; Bender, Andreas

The bgl operon is responsible for the metabolism of β-glucoside sugars such as salicin or arbutin in E. coli. Its regulatory system involves both positive and negative feedback mechanisms and it can be assumed to be more complex than that of the more closely studied lac and trp operons. We have developed a quantitative model for the regulation of the bgl operon which is subject to in silico experiments investigating its behavior under different hypothetical conditions. Upon administration of 5mM salicin as an inducer our model shows 80-fold induction, which compares well with the 60-fold induction measured experimentally. Under practical conditions 5-10mM inducer are employed, which is in line with the minimum inducer concentration of 1mM required by our model. The necessity of BglF conformational change for sugar transport has been hypothesized previously, and in line with those hypotheses our model shows only minor induction if conformational change is not allowed. Overall, this first quantitative model for the bgl operon gives reasonable predictions that are close to experimental results (where measured). It will be further refined as values of the parameters are determined experimentally. The model was developed in Systems Biology Markup Language (SBML) and it is available from the authors and from the Biomodels repository [www.ebi.ac.uk/biomodels].

Acetylcholinesterase in motion : Visualizing conformational changes in crystal structures by a morphing procedure

NARCIS (Netherlands)

Zeev-Ben-Mordehai, T; Silman, I.; Sussman, J.L.

In order to visualize and appreciate conformational changes between homologous three-dimensional (3D) protein structures or protein/inhibitor complexes, we have developed a user-friendly morphing procedure. It enabled us to detect coordinated conformational changes not easily discernible by analytic

Temperature sensitivity of drought-induced tree mortality portends increased regional die-off under global-change-type drought

Science.gov (United States)

Adams, Henry D.; Guardiola-Claramonte, Maite; Barron-Gafford, Greg A.; Villegas, Juan Camilo; Breshears, David D.; Zou, Chris B.; Troch, Peter A.; Huxman, Travis E.

2009-01-01

Large-scale biogeographical shifts in vegetation are predicted in response to the altered precipitation and temperature regimes associated with global climate change. Vegetation shifts have profound ecological impacts and are an important climate-ecosystem feedback through their alteration of carbon, water, and energy exchanges of the land surface. Of particular concern is the potential for warmer temperatures to compound the effects of increasingly severe droughts by triggering widespread vegetation shifts via woody plant mortality. The sensitivity of tree mortality to temperature is dependent on which of 2 non-mutually-exclusive mechanisms predominates—temperature-sensitive carbon starvation in response to a period of protracted water stress or temperature-insensitive sudden hydraulic failure under extreme water stress (cavitation). Here we show that experimentally induced warmer temperatures (≈4 °C) shortened the time to drought-induced mortality in Pinus edulis (piñon shortened pine) trees by nearly a third, with temperature-dependent differences in cumulative respiration costs implicating carbon starvation as the primary mechanism of mortality. Extrapolating this temperature effect to the historic frequency of water deficit in the southwestern United States predicts a 5-fold increase in the frequency of regional-scale tree die-off events for this species due to temperature alone. Projected increases in drought frequency due to changes in precipitation and increases in stress from biotic agents (e.g., bark beetles) would further exacerbate mortality. Our results demonstrate the mechanism by which warmer temperatures have exacerbated recent regional die-off events and background mortality rates. Because of pervasive projected increases in temperature, our results portend widespread increases in the extent and frequency of vegetation die-off. PMID:19365070

Detection of small conformational changes of proteins by small-angle scattering

International Nuclear Information System (INIS)

Durchschlag, H.; Purr, G.; Zipper, P.; Wilfing, R.

1991-01-01

In the past the technique of small-angle scattering has been a powerful tool for studying conformational changes of protein which occur, for example, upon binding with ligands. Results obtained by different authors from X-ray and neutron experiments on a variety of proteins and under various conditions have been compiled. This offers the possibility of comparing the extent of changes in the molecular parameters investigated (e.g. change of the radius of gyration). Problems encountered with the detection of small changes are discussed. As an example, conformational changes of the enzyme citrate synthase upon substrate binding (oxaloacetate) are presented. X-ray crystallography had already found distinct changes between open and closed forms of the enzyme. Small-angle X-ray scattering studies registered slight changes of some parameters in solution. These changes could be paralleled with the results of other solution techniques (UV absorption, fluorescence and circular dichroism spectroscopy, analytical ultracentrifugation). The results found for citrate synthase are also compared with previous findings for malate synthase, an enzyme of similar enzymatic function. Above all, this study shows that care has to be taken when studying small conformational changes. It is absolutely necessary to use different methods and conditions and to study the problem from different points of view to avoid pitfalls. (orig.)

Property changes in graphite irradiated at changing irradiation temperature

International Nuclear Information System (INIS)

Price, R.J.; Haag, G.

1979-07-01

Design data for irradiated graphite are usually presented as families of isothermal curves showing the change in physical property as a function of fast neutron fluence. In this report, procedures for combining isothermal curves to predict behavior under changing irradiation temperatures are compared with experimental data on irradiation-induced changes in dimensions, Young's modulus, thermal conductivity, and thermal expansivity. The suggested procedure fits the data quite well and is physically realistic

Changes in myosin S1 orientation and force induced by a temperature increase.

Science.gov (United States)

Griffiths, Peter J; Bagni, Maria A; Colombini, Barbara; Amenitsch, Heinz; Bernstorff, Sigrid; Ashley, Christopher C; Cecchi, Giovanni; Ameritsch, Heinz

2002-04-16

Force generation in myosin-based motile systems is thought to result from an angular displacement of the myosin subfragment 1 (S1) tail domain with respect to the actin filament axis. In muscle, raised temperature increases the force generated by S1, implying a greater change in tail domain angular displacement. We used time-resolved x-ray diffraction to investigate the structural corollary of this force increase by measuring M3 meridional reflection intensity during sinusoidal length oscillations. This technique allows definition of S1 orientation with respect to the myofilament axis. M3 intensity changes were approximately sinusoid at low temperatures but became increasingly distorted as temperature was elevated, with the formation of a double intensity peak at maximum shortening. This increased distortion could be accounted for by assuming a shift in orientation of the tail domain of actin-bound S1 toward the orientation at which M3 intensity is maximal, which is consistent with a tail domain rotation model of force generation in which the tail approaches a more perpendicular projection from the thin filament axis at higher temperatures. In power stroke simulations, the angle between S1 tail mean position during oscillations and the position at maximum intensity decreased by 4.7 degrees, corresponding to a mean tail displacement toward the perpendicular of 0.73 nm for a temperature-induced force increase of 0.28 P(0) from 4 to 22 degrees C. Our findings suggest that at least 62% of crossbridge compliance is associated with the tail domain.

Torsional Arming of Thiomannosyl Donors & Conformational Control of Hexahydropyridazines via pH

DEFF Research Database (Denmark)

Olsen, Jacob Ingemar

The overall objective of the research presented in this PhD thesis was to investigate torsional arming of thiogalacto- and thiomannosyl donors (part 1) and to investigate the possible synthesis and attachment of a pH regulated conformational switch to an α-cyclodextrin (part 2). Part 1: It is well...... demonstrated their ability to change conformation under different conditions. These conformational changes are connected to various intramolecular interactions and can to some extent, be controlled by pH (Chapter 3). Fusing these conformationally labile compounds to the rim of a cyclodextrin would create...... compounds that could release molecules at a specified change in pH conditions. To investigate this, four hexahydropyridazines were synthesized and investigated for their pH induced conformational change (Chapter 4). Out of the four compounds, one revealed to flip between two conformations depending on pH...

Distinct conformational changes in activated agonist-bound and agonist-free glycine receptor subunits

DEFF Research Database (Denmark)

Pless, Stephan Alexander; Lynch, Joseph W

2009-01-01

Ligand binding to Cys-loop receptors produces either global conformational changes that lead to activation or local conformational changes that do not. We found that the fluorescence of a fluorophore tethered to R271C in the extracellular M2 region of the alpha1 glycine receptor increases during ...

Proton transfer and complex formation of angiotensin I ions with gaseous molecules at various temperature

International Nuclear Information System (INIS)

Nonose, Shinji; Yamashita, Kazuki; Sudo, Ayako; Kawashima, Minami

2013-01-01

Highlights: • Proton transfer from angiotensin I ions (z = 2, 3) to gaseous molecules was studied. • Temperature dependence of absolute reaction rate constants was measured. • Remarkable changes were obtained for distribution of product ions and reaction rate constants. • Proton transfer reaction was enhanced and reduced by complex formation. • Conformation changes are induced by complex formation and or by thermal collision with He. - Abstract: Proton transfer reactions of angiotensin I ions for +2 charge state, [M + 2H] 2+ , to primary, secondary and aromatic amines were examined in the gas phase. Absolute reaction rate constants for proton transfer were determined from intensities of parent and product ions in the mass spectra. Temperature dependence of the reaction rate constants was measured. Remarkable change was observed for distribution of product ions and reaction rate constants. Proton transfer reaction was enhanced or reduced by complex formation of [M + 2H] 2+ with gaseous molecules. The results relate to conformation changes of [M + 2H] 2+ with change of temperature, which are induced by complex formation and or by thermal collision with He. Proton transfer reactions of angiotensin I ions for +3 charge state, [M + 3H] 3+ , were also studied. The reaction rates did not depend on temperature so definitely

Coarse-grained Simulations of Sugar Transport and Conformational Changes of Lactose Permease

Science.gov (United States)

Liu, Jin; Jewel, S. M. Yead; Dutta, Prashanta

2016-11-01

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, as well as 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 transport of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule across a wild-type LacY during lactose/H+ symport process. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Protonation of Glu325 stabilizes the TDG and inward-facing conformation of LacY. Protonation of Glu269 induces a dramatic protein structural reorganization and causes the expulsion of TDG from LacY to both sides of the membrane. The structural changes occur primarily in the N-terminal domain of LacY. This work is supported by NSF Grants: CBET-1250107 and CBET -1604211.

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.

Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

Science.gov (United States)

Flechsig, Holger

2016-02-01

ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter

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...

Canine Plasminogen: Spectral Responses to Changes in 6-Aminohexanoate and Temperature

Directory of Open Access Journals (Sweden)

Jack A. Kornblatt

2007-01-01

Full Text Available We studied the near UV absorption spectrum of canine plasminogen. There are 19 tryptophans, 19 phenylalanines and 34 tyrosines in the protein. 4th derivative spectra optimized for either tryptophan or tyrosine give a measure of the polarity of the environments of these two aromatic amino acids. Plasminogen at temperatures between 0 °C and 37 °C exists as a mixture of four conformations: closed-relaxed, open-relaxed, closed-compact, and open-compact. The closed to open transition is driven by addition of ligand to a site on the protein. The relaxed to compact transition is driven by increasing temperature from 0 °C to above 15–20 °C.When the conformation of plasminogen is mainly closed-relaxed, the 4th derivative spectra suggest that the average tryptophan environment is similar to a solution of 20% methanol at the same temperature. Under the same conditions, 4th derivative spectra suggest that the average tyrosine environment is similar to water. These apparent polarities change as the plasminogen is forced to assume the other conformations. We try to rationalize the information based on the known portions of the plasminogen structure.Abbreviations: 6-AH: 6-aminohexanoate, a homolog of lysine; DPGN: dog plasminogen; HPGN: human plasminogen. NTP: the N-terminal peptide of DPGN (It consists of the fi rst 77 amino acids in the protein.

Detecting climate change oriented and human induced changes in stream temperature across the Southeastern U.S.

Science.gov (United States)

Zhang, X.; Voisin, N.; Cheng, Y.; Niemeyer, R. J.; Nijssen, B.; Yearsley, J. R.; Zhou, T.

2017-12-01

In many areas, climate change is expected to alter the flow regime and increase stream temperature, especially during summer low flow periods. During these low flow periods, water management increases flows in order to sustain human activities such as water for irrigation and hydroelectric power generation. Water extraction from rivers during warm season can increase stream temperature while reservoir regulation may cool downstream river temperatures by releasing cool water from deep layers. Thus, it is reasonable to hypothesize that water management changes the sensitivity of the stream temperature regime to climate change when compared to unmanaged resources. The time of emergence of change refers to the point in time when observations, or model simulations, show statistically significant changes from a given baseline period, i.e. above natural variability. Here we aim to address two questions by investigating the time of emergence of changes in stream temperature in the southeastern United States: what is the sensitivity of stream temperature under regulated flow conditions to climate change and what is the contribution of water management in increasing or decreasing stream temperature sensitivity to climate change. We simulate regulated flow by using runoff from the Variable Infiltration Capacity (VIC) macroscale hydrological model as input into a large scale river routing and reservoir model MOSART-WM. The River Basin Model (RBM), a distributed stream temperature model, includes a two-layer thermal stratification module to simulate stream temperature in regulated river systems. We evaluate the timing of emergence of changes in flow and stream temperature based on climate projections from two representative concentration pathways (RCPs; RCP4.5 and RCP8.5) from the Coupled Model Intercomparison Project Phase 5 (CMIP5). We analyze the difference in emergence of change between natural and regulated streamflow. Insights will be provided toward applications for

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.

Role and structural mechanism of WASP-triggered conformational changes in branched actin filament nucleation by Arp2/3 complex.

Science.gov (United States)

Rodnick-Smith, Max; Luan, Qing; Liu, Su-Ling; Nolen, Brad J

2016-07-05

The Arp2/3 (Actin-related proteins 2/3) complex is activated by WASP (Wiskott-Aldrich syndrome protein) family proteins to nucleate branched actin filaments that are important for cellular motility. WASP recruits actin monomers to the complex and stimulates movement of Arp2 and Arp3 into a "short-pitch" conformation that mimics the arrangement of actin subunits within filaments. The relative contribution of these functions in Arp2/3 complex activation and the mechanism by which WASP stimulates the conformational change have been unknown. We purified budding yeast Arp2/3 complex held in or near the short-pitch conformation by an engineered covalent cross-link to determine if the WASP-induced conformational change is sufficient for activity. Remarkably, cross-linked Arp2/3 complex bypasses the need for WASP in activation and is more active than WASP-activated Arp2/3 complex. These data indicate that stimulation of the short-pitch conformation is the critical activating function of WASP and that monomer delivery is not a fundamental requirement for nucleation but is a specific requirement for WASP-mediated activation. During activation, WASP limits nucleation rates by releasing slowly from nascent branches. The cross-linked complex is inhibited by WASP's CA region, even though CA potently stimulates cross-linking, suggesting that slow WASP detachment masks the activating potential of the short-pitch conformational switch. We use structure-based mutations and WASP-Arp fusion chimeras to determine how WASP stimulates movement toward the short-pitch conformation. Our data indicate that WASP displaces the autoinhibitory Arp3 C-terminal tail from a hydrophobic groove at Arp3's barbed end to destabilize the inactive state, providing a mechanism by which WASP stimulates the short-pitch conformation and activates Arp2/3 complex.

47 CFR 68.348 - Changes in equipment and circuitry subject to a Supplier's Declaration of Conformity.

Science.gov (United States)

2010-10-01

... Supplier's Declaration of Conformity. 68.348 Section 68.348 Telecommunication FEDERAL COMMUNICATIONS... a Supplier's Declaration of Conformity. (a) No change shall be made in terminal equipment or... Declaration of Conformity Statement furnished to users. (b) Any other changes in terminal equipment or...

A unified conformational selection and induced fit approach to protein-peptide docking.

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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.

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

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

Conformational studies of the (+)-trans, (-)-trans, (+)-cis, and (-)-cis adducts of anti-benzo[a]pyrene diolepoxide to N2-dG in duplex oligonucleotides using polyacrylamide gel electrophoresis and low-temperature fluorescence spectroscopy

NARCIS (Netherlands)

Suh, Myungkoo; Ariese, Freek; Small, Gerald J.; Jankowiak, Ryszard; Liu, Tong Ming; Geacintov, Nicholas E.

1995-01-01

Using polyacrylamide gel electrophoresis (PAGE) and low-temperature, laser-induced fluorescence line narrowing (FLN) and non-line narrowing (NLN) spectroscopic methods, the conformational characteristics of stereochemically defined and site-specific adducts derived from the binding of

Non-invasive SFG spectroscopy: a tool to reveal the conformational change of grafted chains due to bacterial adhesion

Science.gov (United States)

Bulard, Emilie; Dubost, Henri; Fontaine-Aupart, Marie-Pierre; Zheng, Wanquan; Herry, Jean-Marie; Bellon-Fontaine, Marie-No"lle; Briandet, Romain; Bourguignon, Bernard

2011-07-01

In many fields such as biomedical or food industry, surface colonization by micro-organisms leads to biofilms formation that are tridimentional biostructures highly resistant to the action of antimicrobials, by mechanisms still unclear. In order to deepen our understanding of the initial interaction of bacteria cells with a solid surface, we analyze by in situ vibrational Sum Frequency Generation (SFG) spectroscopy the effect of the adhesion of hydrophilic Lactoccocus lactis bacteria and its hydrophobic mutants in distilled water on a self-assembled monolayer (SAM) of octadecanethiol (ODT) on a gold film. When a homogeneous bacterial monolayer is deposited on this ordered surface, SFG spectrum of the ODT SAM shows significant intensity changes from that in air or in water. Its modelling as a function of conformation allows to distinguish optical effects due to the water solution surrounding bacteria from conformational changes of the ODT SAM due to the presence of the bacteria cells. Futhermore, bacterial adhesion induces different measurable effects on the ODT SAM conformation, depending on the hydrophobic / hydrophilic character of the bacterial surface. Such a result deserves to be taken into account for the design of new materials with improved properties or to control biofilm formation.

Protein adsorption on tailored substrates: long-range forces and conformational changes

Energy Technology Data Exchange (ETDEWEB)

Bellion, M; Santen, L [Department of Theoretical Physics, Saarland University, 66041 Saarbruecken (Germany); Mantz, H; Haehl, H; Quinn, A; Nagel, A; Gilow, C; Weitenberg, C; Schmitt, Y; Jacobs, K [Department of Experimental Physics, Saarland University, 66041 Saarbruecken (Germany)], E-mail: k.jacobs@physik.uni-saarland.de

2008-10-08

Adsorption of proteins onto solid surfaces is an everyday phenomenon that is not yet fully understood. To further the current understanding, we have performed in situ ellipsometry studies to reveal the adsorption kinetics of three different proteins, lysozyme, {alpha}-amylase and bovine serum albumin. As substrates we offer Si wafers with a controlled Si oxide layer thickness and a hydrophilic or hydrophobic surface functionalization, allowing the tailoring of the influence of short- and long-range interactions. Our studies show that not only the surface chemistry determines the properties of an adsorbed protein layer but also the van der Waals contributions of a composite substrate. We compare the experimental findings to results of a colloidal Monte Carlo approach that includes conformational changes of the adsorbed proteins induced by density fluctuations.

Influence of DNA conformation on radiation-induced single-strand breaks

International Nuclear Information System (INIS)

Barone, F.; Belli, M.; Mazzei, F.

1994-01-01

We performed experiments on two DNA fragments of about 300 bp having different conformation to test whether radiation-induced single-strand breakage is dependent on DNA conformation. Breakage analysis was carried out by denaturing polyacrylamide gel electrophoresis, which allows determination of the broken site at single nucleotide resolution. We found uniform cutting patterns in B-form regions. On the contrary, X- or γ-irradiation of curved fragments of kinetoplast DNA showed that the distribution of single-strand breaks was not uniform along the fragment, as the cleavage pattern was modulated in phase with the runs of A-T pairs. This modulation likely reflected the reduced accessibility of the sites which on hydroxyl-radical attack give rise to strand breaks. The cleavage pattern was phased with the runs of A-T pairs. Moreover, the overall yield of strand breaks was considerably lower in curved DNA fragments than in those with extended straight regions. The conformation effect found here indicates that the cleavage pattern reflects the fine structural features of DNA. (orig./MG)

The influence of N-terminal acetylation on micelle-induced conformational changes and aggregation of α-Synuclein.

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David Ruzafa

Full Text Available The biological function of α-Synuclein has been related to binding to lipids and membranes but these interactions can also mediate α-Synuclein aggregation, which is associated to Parkinson's disease and other neuropathologies. In brain tissue α-Synuclein is constitutively N-acetylated, a modification that plays an important role in its conformational propensity, lipid and membrane binding, and aggregation propensity. We studied the interactions of the lipid-mimetic SDS with N-acetylated and non-acetylated α-Synuclein, as well as their early-onset Parkinson's disease variants A30P, E46K and A53T. At low SDS/protein ratios α-Synuclein forms oligomeric complexes with SDS micelles with relatively low α-helical structure. These micellar oligomers can efficiently nucleate aggregation of monomeric α-Synuclein, with successive formation of oligomers, protofibrils, curly fibrils and mature amyloid fibrils. N-acetylation reduces considerably the rate of aggregation of WT α-Synuclein. However, in presence of any of the early-onset Parkinson's disease mutations the protective effect of N-acetylation against micelle-induced aggregation becomes impaired. At higher SDS/protein ratios, N-acetylation favors another conformational transition, in which a second type of α-helix-rich, non-aggregating oligomers become stabilized. Once again, the Parkinson's disease mutations disconnect the influence of N-acetylation in promoting this transition. These results suggest a cooperative link between the N-terminus and the region of the mutations that may be important for α-Synuclein function.

Molecular Dynamics Simulations of Insulin: Elucidating the Conformational Changes that Enable Its Binding.

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Anastasios Papaioannou

Full Text Available A sequence of complex conformational changes is required for insulin to bind to the insulin receptor. Recent experimental evidence points to the B chain C-terminal (BC-CT as the location of these changes in insulin. Here, we present molecular dynamics simulations of insulin that reveal new insights into the structural changes occurring in the BC-CT. We find three key results: 1 The opening of the BC-CT is inherently stochastic and progresses through an open and then a "wide-open" conformation--the wide-open conformation is essential for receptor binding, but occurs only rarely. 2 The BC-CT opens with a zipper-like mechanism, with a hinge at the Phe24 residue, and is maintained in the dominant closed/inactive state by hydrophobic interactions of the neighboring Tyr26, the critical residue where opening of the BC-CT (activation of insulin is initiated. 3 The mutation Y26N is a potential candidate as a therapeutic insulin analogue. Overall, our results suggest that the binding of insulin to its receptor is a highly dynamic and stochastic process, where initial docking occurs in an open conformation and full binding is facilitated through interactions of insulin receptor residues with insulin in its wide-open conformation.

Mangiferin binding to serum albumin is non-saturable and induces conformational changes at high concentrations

Energy Technology Data Exchange (ETDEWEB)

Freitas, P.G.; Barbosa, A.F. [Biochemistry Laboratory, Institute of Exact Sciences, Federal University of Alfenas, Unifal-MG, R. Gabriel Monteiro da Silva, 700, 37130-000 Alfenas, MG (Brazil); Saraiva, L.A. [Phytochemistry and Medicinal Chemistry Laboratory, Institute of Exact Sciences, Unifal-MG (Brazil); Camps, I. [Physics Laboratory, Institute of Exact Sciences, Unifal-MG (Brazil); Silveira, N.J.F. da [Bioinformatics Laboratory, Institute of Exact Sciences, Unifal-MG (Brazil); Veloso, M.P. [Phytochemistry and Medicinal Chemistry Laboratory, Institute of Exact Sciences, Unifal-MG (Brazil); Santos, M.H., E-mail: poliany.santos@gmail.com [Phytochemistry and Medicinal Chemistry Laboratory, Institute of Exact Sciences, Unifal-MG (Brazil); Schneedorf, J.M., E-mail: zemasfs@gmail.com [Biochemistry Laboratory, Institute of Exact Sciences, Federal University of Alfenas, Unifal-MG, R. Gabriel Monteiro da Silva, 700, 37130-000 Alfenas, MG (Brazil)

2012-11-15

The binding interaction between mangiferin (MGF), which a natural xanthone isolated from mangoes, and bovine serum albumin (BSA) was studied with absorbance and fluorescence spectroscopy, cyclic voltammetry and molecular modeling. The data were analyzed to assess the binding mechanism, effect of pH and ionic strength, conformational changes in the protein and electrical charge transfer involved. The MGF-BSA complex exhibited positive cooperativity with a 1:1 stoichiometry (K{sub d}=0.38 mmol L{sup -1}) for the first binding site and a non-saturable binding at high ligand concentrations. Furthermore, the data also suggest an increase in drug bioavailability in the acidic region and relatively low ionic strength values, which are close to physiological levels. The data suggest a specific electrostatic interaction together with hydrophobic effects and H-bonding displayed in MGF binding to the BSA IIA subdomain. Synchronous fluorescence spectra indicate that there are conformational changes in the polypeptide backbone upon ligand binding. Cyclic voltammetry indicates that there is an irreversible charge transfer between MGF and BSA that is modulated by diffusion on the electrode surface, where two electrons are transferred. These results can help the knowledge of the pharmacokinetic activities of natural or chemical xanthone-based drugs. - Highlights: Black-Right-Pointing-Pointer The MGF-BSA complex exhibited positive cooperativity beyond 1:1 stoichiometry. Black-Right-Pointing-Pointer The interaction of MGF with BSA is non-saturable at higher ligand concentration. Black-Right-Pointing-Pointer The binding was accomplished by H-bonding, hydrophobic and electrostatic forces. Black-Right-Pointing-Pointer The apparent binding constant for MGF-BSA was 0.38 mmol L{sup -1}. Black-Right-Pointing-Pointer MGF binds electrostatically to BSA, different from a hydrophobic interaction to HSA.

ATP-induced conformational changes of nucleotide-binding domains in an ABC transporter. Importance of the water-mediated entropic force.

Science.gov (United States)

Hayashi, Tomohiko; Chiba, Shuntaro; Kaneta, Yusuke; Furuta, Tadaomi; Sakurai, Minoru

2014-11-06

ATP binding cassette (ABC) proteins belong to a superfamily of active transporters. Recent experimental and computational studies have shown that binding of ATP to the nucleotide binding domains (NBDs) of ABC proteins drives the dimerization of NBDs, which, in turn, causes large conformational changes within the transmembrane domains (TMDs). To elucidate the active substrate transport mechanism of ABC proteins, it is first necessary to understand how the NBD dimerization is driven by ATP binding. In this study, we selected MalKs (NBDs of a maltose transporter) as a representative NBD and calculated the free-energy change upon dimerization using molecular mechanics calculations combined with a statistical thermodynamic theory of liquids, as well as a method to calculate the translational, rotational, and vibrational entropy change. This combined method is applied to a large number of snapshot structures obtained from molecular dynamics simulations containing explicit water molecules. The results suggest that the NBD dimerization proceeds with a large gain of water entropy when ATP molecules bind to the NBDs. The energetic gain arising from direct NBD-NBD interactions is canceled by the dehydration penalty and the configurational-entropy loss. ATP hydrolysis induces a loss of the shape complementarity between the NBDs, which leads to the dissociation of the dimer, due to a decrease in the water-entropy gain and an increase in the configurational-entropy loss. This interpretation of the NBD dimerization mechanism in concert with ATP, especially focused on the water-mediated entropy force, is potentially applicable to a wide variety of the ABC transporters.

Conformational lock and dissociative thermal inactivation of lentil seedling amine oxidase.

Science.gov (United States)

Moosavi-Nejad, S Zahra; Moosavi-Movahedi, Ali-Akbar; Rezaei-Tavirani, Mostafa; Floris, Giovanni; Medda, Rosaria

2003-03-31

The kinetics of thermal inactivation of copper-containing amine oxidase from lentil seedlings were studied in a 100 mM potassium phosphate buffer, pH 7, using putrescine as the substrate. The temperature range was between 47-60 degrees C. The thermal inactivation curves were not linear at 52 and 57 degrees C; three linear phases were shown. The first phase gave some information about the number of dimeric forms of the enzyme that were induced by the higher temperatures using the "conformational lock" pertaining theory to oligomeric enzyme. The "conformational lock" caused two additional dimeric forms of the enzyme when the temperature increased to 57 degrees C. The second and third phases were interpreted according to a dissociative thermal inactivation model. These phases showed that lentil amine oxidase was reversibly-dissociated before the irreversible thermal inactivation. Although lentil amine oxidase is not a thermostable enzyme, its dimeric structure can form "conformational lock," conferring a structural tolerance to the enzyme against heat stress.

Conformation evolution of oil contaminants onto aluminum oxide surface in aqueous solution: The effect of surface coverage

Energy Technology Data Exchange (ETDEWEB)

Xie, Wenkun; Liu, Haitao, E-mail: xwk584523412@126.com; Sun, Yazhou; Fu, Hongya; Liang, Yingchun

2017-01-15

Highlights: • The dynamic conformational change of oil contaminations, at various surface coverages onto perfect α-Al{sub 2}O{sub 3}(0001) surface in aqueous solution is given. • The effect of surface coverage of oil molecules on the driving forces for the conformational change of oil contaminations is described. • The effect of interfacial water on the conformational change and even detachment of oil contaminations is considered. - Abstract: The microscopic conformational change process of oil contaminants adhered onto perfect α-Al{sub 2}O{sub 3} (0001) surface in aqueous solution was investigated by using all-atom classic molecular dynamics simulations. The change in removal mechanism of oil contaminants induced by surface coverage (surface area per molecule) was emphatically explored. Our simulation results strongly reveal that the increase in oil surface coverage induces an evident difference in microscopic detachment processes of oil contaminants. At a low surface coverage, oil contaminants can be thoroughly detached from solid surface. The whole detachment process could be divided into multi stages, including conformational change of oil contaminants on solid surface, dynamic motion of those in bulk solution and rapid migration of those from bulk solution to air/water interface. With surface coverage increasing, water diffusion becomes the key to induce conformational change and promote the detachment of oil contaminants. When oil surface coverage exceeds a threshold value, oil contaminants also undertake an evident conformational change process exhibiting typical characteristics but an incomplete detachment process occurs. All findings of the present study are helpful for the interpretation of the removal mechanism of oil contaminants on solid surface.

Cholesterol-induced conformational changes in the sterol-sensing domain of the Scap protein suggest feedback mechanism to control cholesterol synthesis.

Science.gov (United States)

Gao, Yansong; Zhou, Yulian; Goldstein, Joseph L; Brown, Michael S; Radhakrishnan, Arun

2017-05-26

Scap is a polytopic protein of endoplasmic reticulum (ER) membranes that transports sterol regulatory element-binding proteins to the Golgi complex for proteolytic activation. Cholesterol accumulation in ER membranes prevents Scap transport and decreases cholesterol synthesis. Previously, we provided evidence that cholesterol inhibition is initiated when cholesterol binds to loop 1 of Scap, which projects into the ER lumen. Within cells, this binding causes loop 1 to dissociate from loop 7, another luminal Scap loop. However, we have been unable to demonstrate this dissociation when we added cholesterol to isolated complexes of loops 1 and 7. We therefore speculated that the dissociation requires a conformational change in the intervening polytopic sequence separating loops 1 and 7. Here we demonstrate such a change using a protease protection assay in sealed membrane vesicles. In the absence of cholesterol, trypsin or proteinase K cleaved cytosolic loop 4, generating a protected fragment that we visualized with a monoclonal antibody against loop 1. When cholesterol was added to these membranes, cleavage in loop 4 was abolished. Because loop 4 is part of the so-called sterol-sensing domain separating loops 1 and 7, these results support the hypothesis that cholesterol binding to loop 1 alters the conformation of the sterol-sensing domain. They also suggest that this conformational change helps transmit the cholesterol signal from loop 1 to loop 7, thereby allowing separation of the loops and facilitating the feedback inhibition of cholesterol synthesis. These insights suggest a new structural model for cholesterol-mediated regulation of Scap activity. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

An event-based account of conformity.

Science.gov (United States)

Kim, Diana; Hommel, Bernhard

2015-04-01

People often change their behavior and beliefs when confronted with deviating behavior and beliefs of others, but the mechanisms underlying such phenomena of conformity are not well understood. Here we suggest that people cognitively represent their own actions and others' actions in comparable ways (theory of event coding), so that they may fail to distinguish these two categories of actions. If so, other people's actions that have no social meaning should induce conformity effects, especially if those actions are similar to one's own actions. We found that female participants adjusted their manual judgments of the beauty of female faces in the direction consistent with distracting information without any social meaning (numbers falling within the range of the judgment scale) and that this effect was enhanced when the distracting information was presented in movies showing the actual manual decision-making acts. These results confirm that similarity between an observed action and one's own action matters. We also found that the magnitude of the standard conformity effect was statistically equivalent to the movie-induced effect. © The Author(s) 2015.

Insight the C-site pocket conformational changes responsible for sirtuin 2 activity using molecular dynamics simulations.

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Sugunadevi Sakkiah

Full Text Available Sirtuin belongs to a family of typical histone deacetylase which regulates the fundamental cellular biological processes including gene expression, genome stability, mitosis, nutrient metabolism, aging, mitochondrial function, and cell motility. Michael et. al. reported that B-site mutation (Q167A and H187A decreased the SIRT2 activity but still the structural changes were not reported. Hence, we performed 5 ns molecular dynamics (MD simulation on SIRT2 Apo-form and complexes with substrate/NAD(+ and inhibitor of wild type (WT, Q167A, and H187A. The results revealed that the assembly and disassembly of C-site induced by presence of substrate/NAD(+ and inhibitor, respectively. This assembly and disassembly was mainly due to the interaction between the substrate/NAD(+ and inhibitor and F96 and the distance between F96 and H187 which are present at the neck of the C-site. MD simulations suggest that the conformational change of L3 plays a major role in assembly and disassembly of C-site. Our current results strongly suggest that the distinct conformational change of L3 as well as the assembly and disassembly of C-site plays an important role in SIRT2 deacetylation function. Our study unveiled the structural changes of SIRT2 in presence of NAD(+ and inhibitor which should be helpful to improve the inhibitory potency of SIRT2.

Thermal Performance Study of Composite Phase Change Material with Polyacrylicand Conformal Coating.

Science.gov (United States)

Kee, Shin Yiing; Munusamy, Yamuna; Ong, Kok Seng; Cornelis Metselaar, Hendrik Simon; Chee, Swee Yong; Lai, Koon Chun

2017-07-28

The composite PCM was prepared by blending polymethyl methacrylate (PMMA) and myristic acid (MA) in different weight percentages. The MA and PMMA were selected as PCM and supporting material, respectively. As liquid MA may leak out during the phase transition, this study proposes the use of two coatings, namely a polyacrylic coating and a conformal coating to overcome the leakage problem. Both coatings were studied in terms of the leakage test, chemical compatibility, thermal stability, morphology, and reliability. No leakage was found in the PCMs with coatings compared to those without under the same proportions of MA/PMMA, thus justifying the use of coatings in the present study. The chemically compatibility was confirmed by FTIR spectra: the functional groups of PCMs were in accordance with those of coatings. DSC showed that the coatings did not significantly change the melting and freezing temperatures, however, they improved the thermal stability of composite PCMs as seen in TGA analysis. Furthermore, the composite PCMs demonstrated good thermal reliability after 1000 times thermal cycling. The latent heat of melting reduced by only 0.16% and 1.02% for the PCMs coated with conformal coating and polyacrylic coating, respectively. Therefore, the proposed coatings can be considered in preparing fatty acid/PMMA blends attributed to the good stability, compatibility and leakage prevention.

Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures.

Science.gov (United States)

Silvaroli, Josie A; Arne, Jason M; Chelstowska, Sylwia; Kiser, Philip D; Banerjee, Surajit; Golczak, Marcin

2016-04-15

Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by CRBP1 remain unclear. Here we report the first structure of CRBP1 in a ligand-free form as well as ultra-high resolution structures of this protein bound to either all-trans-retinol or retinylamine, the latter a therapeutic retinoid that prevents light-induced retinal degeneration. Superpositioning of human apo- and holo-CRBP1 revealed major differences within segments surrounding the entrance to the retinoid-binding site. These included α-helix II and hairpin turns between β-strands βC-βD and βE-βF as well as several side chains, such as Phe-57, Tyr-60, and Ile-77, that change their orientations to accommodate the ligand. Additionally, we mapped hydrogen bond networks inside the retinoid-binding cavity and demonstrated their significance for the ligand affinity. Analyses of the crystallographic B-factors indicated several regions with higher backbone mobility in the apoprotein that became more rigid upon retinoid binding. This conformational flexibility of human apo-CRBP1 facilitates interaction with the ligands, whereas the more rigid holoprotein structure protects the labile retinoid moiety during vitamin A transport. These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular retinol-binding proteins. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Light induces petal color change in Quisqualis indica (Combretaceae

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Juan Yan

2018-02-01

Full Text Available Petal color change, a common phenomenon in angiosperms, is induced by various environmental and endogenous factors. Interestingly, this phenomenon is important for attracting pollinators and further reproductive success. Quisqualis indica L. (Combretaceae is a tropical Asian climber that undergoes sequential petal color change from white to pink to red. This color changing process is thought to be a good strategy to attract more pollinators. However, the underlying physiological and biochemical mechanisms driving this petal color change phenomenon is still underexplored. In this context, we investigated whether changes in pH, pollination, light, temperature or ethylene mediate petal color change. We found that the detected changes in petal pH were not significant enough to induce color alterations. Additionally, pollination and temperatures of 20–30 °C did not alter the rate of petal color change; however, flowers did not open when exposed to constant temperatures at 15 °C or 35 °C. Moreover, the application of ethylene inhibitor, i.e., silver thiosulphate, did not prevent color change. It is worth mentioning here that in our study we found light as a strong factor influencing the whole process of petal color change, as petals remained white under dark conditions. Altogether, the present study suggests that petal color change in Q. indica is induced by light and not by changes in petal pH, pollination, ethylene, or temperature, while extremely low or high temperatures affect flower anthesis. In summary, our findings represent the probable mechanism underlying the phenomenon of petal color change, which is important for understanding flower color evolution.

A Conformational Change in C-Reactive Protein Enhances Leukocyte Recruitment and Reactive Oxygen Species Generation in Ischemia/Reperfusion Injury

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Jan R. Thiele

2018-04-01

Full Text Available IntroductionC-reactive protein circulates as a pentameric protein (pCRP. pCRP is a well-established diagnostic marker as plasma levels rise in response to tissue injury and inflammation. We recently described pro-inflammatory properties of CRP, which are mediated by conformational changes from pCRP to bioactive isoforms expressing pro-inflammatory neo-epitopes [pCRP* and monomeric C-reactive protein (mCRP]. Here, we investigate the role of CRP isoforms in renal ischemia/reperfusion injury (IRI.MethodsRat kidneys in animals with and without intraperitoneally injected pCRP were subjected to IRI by the time of pCRP exposure and were subsequently analyzed for monocyte infiltration, caspase-3 expression, and tubular damage. Blood urea nitrogen (BUN was analyzed pre-ischemia and post-reperfusion. CRP effects on leukocyte recruitment were investigated via intravital imaging of rat-striated muscle IRI. Localized conformational CRP changes were analyzed by immunohistochemistry using conformation specific antibodies. 1,6-bis(phosphocholine-hexane (1,6-bisPC, which stabilizes CRP in its native pentameric form was used to validate CRP effects. Leukocyte activation was assessed by quantification of reactive oxygen species (ROS induction by CRP isoforms ex vivo and in vitro through electron spin resonance spectroscopy. Signaling pathways were analyzed by disrupting lipid rafts with nystatin and subsequent ROS detection. In order to confirm the translational relevance of our findings, biopsies of microsurgical human free tissue transfers before and after IRI were examined by immunofluorescence for CRP deposition and co-localization of CD68+ leukocytes.ResultsThe application of pCRP aggravates tissue damage in renal IRI. 1,6-bisPC reverses these effects via inhibition of the conformational change that leads to exposure of pro-inflammatory epitopes in CRP (pCRP* and mCRP. Structurally altered CRP induces leukocyte–endothelial interaction and induces ROS

Amplification and dampening of soil respiration by changes in temperature variability

Science.gov (United States)

C.A. Sierra; M.E. Harmon; E.A. Thomann; S.S. Perakis; H.W. Loescher

2011-01-01

Accelerated release of carbon from soils is one of the most important feedbacks related to anthropogenically induced climate change. Studies addressing the mechanisms for soil carbon release through organic matter decomposition have focused on the effect of changes in the average temperature, with little attention to changes in temperature variability. Anthropogenic...

Temperature-induced plasticity in egg size and resistance of eggs to temperature stress in a soil arthropod.

NARCIS (Netherlands)

Liefting, M.; Weerenbeck, M.; van Dooremalen, J.A.; Ellers, J.

2010-01-01

Temperature is considered one of the most important mediators of phenotypic plasticity in ectotherms, resulting in predictable changes in egg size. However, the fitness consequences of temperature-induced plasticity in egg size are not well understood and are often assessed at mild temperatures,

Exploring the relationship between the conformation and pK_a

DEFF Research Database (Denmark)

Olsen, Jacob Ingemar; Sauer, Stephan P. A.; Pedersen, Christian Marcus

2015-01-01

Four substituted cis and trans-4,5-dihydroxyhexahydropyridazines that were expected to undergo pH induced conformational switching were synthesized and carefully investigated by NMR analyses and calculations. For two of the compounds a large difference in pKa existed between the two possible chair...... conformers and for one compound this resulted in conformational switching as a result of pH change. For the first time it is shown that the pKa directly reflects the conformational equilibrium of conformers....

Anion induced conformational preference of Cα NN motif residues in functional proteins.

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Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

2017-12-01

Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

Temperature Dependence of Faraday Effect-Induced Bias Error in a Fiber Optic Gyroscope.

Science.gov (United States)

Li, Xuyou; Liu, Pan; Guang, Xingxing; Xu, Zhenlong; Guan, Lianwu; Li, Guangchun

2017-09-07

Improving the performance of interferometric fiber optic gyroscope (IFOG) in harsh environments, such as magnetic field and temperature field variation, is necessary for its practical applications. This paper presents an investigation of Faraday effect-induced bias error of IFOG under varying temperature. Jones matrix method is utilized to formulize the temperature dependence of Faraday effect-induced bias error. Theoretical results show that the Faraday effect-induced bias error changes with the temperature in the non-skeleton polarization maintaining (PM) fiber coil. This phenomenon is caused by the temperature dependence of linear birefringence and Verdet constant of PM fiber. Particularly, Faraday effect-induced bias errors of two polarizations always have opposite signs that can be compensated optically regardless of the changes of the temperature. Two experiments with a 1000 m non-skeleton PM fiber coil are performed, and the experimental results support these theoretical predictions. This study is promising for improving the bias stability of IFOG.

Interfacial adsorption of insulin - Conformational changes and reversibility of adsorption

NARCIS (Netherlands)

Mollmann, SH; Jorgensen, L; Bukrinsky, JT; Elofsson, U; Norde, W; Frokjaer, S

The adsorption of human insulin to Teflon particles was studied with respect to conformational changes and the reversibility of adsorption was examined by total internal reflection fluorescence (TIRF). Adsorption isotherms for the adsorption of human insulin indicated high affinity adsorption, even

A Dualistic Conformational Response to Substrate Binding in the Human Serotonin Transporter Reveals a High Affinity State for Serotonin*

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Bjerregaard, Henriette; Severinsen, Kasper; Said, Saida; Wiborg, Ove; Sinning, Steffen

2015-01-01

Serotonergic neurotransmission is modulated by the membrane-embedded serotonin transporter (SERT). SERT mediates the reuptake of serotonin into the presynaptic neurons. Conformational changes in SERT occur upon binding of ions and substrate and are crucial for translocation of serotonin across the membrane. Our understanding of these conformational changes is mainly based on crystal structures of a bacterial homolog in various conformations, derived homology models of eukaryotic neurotransmitter transporters, and substituted cysteine accessibility method of SERT. However, the dynamic changes that occur in the human SERT upon binding of ions, the translocation of substrate, and the role of cholesterol in this interplay are not fully elucidated. Here we show that serotonin induces a dualistic conformational response in SERT. We exploited the substituted cysteine scanning method under conditions that were sensitized to detect a more outward-facing conformation of SERT. We found a novel high affinity outward-facing conformational state of the human SERT induced by serotonin. The ionic requirements for this new conformational response to serotonin mirror the ionic requirements for translocation. Furthermore, we found that membrane cholesterol plays a role in the dualistic conformational response in SERT induced by serotonin. Our results indicate the existence of a subpopulation of SERT responding differently to serotonin binding than hitherto believed and that membrane cholesterol plays a role in this subpopulation of SERT. PMID:25614630

Conformational Footprint in Hydrolysis-Induced Nanofibrillation and Crystallization of Poly(lactic acid).

Science.gov (United States)

Xu, Huan; Yang, Xi; Xie, Lan; Hakkarainen, Minna

2016-03-14

The origin of hydrolysis-induced nanofibrillation and crystallization, at the molecular level, was revealed by mapping the conformational ordering during long-term hydrolytic degradation of initially amorphous poly(lactic acid) (PLA), a representative model for degradable aliphatic polyesters generally displaying strong interplay between crystallization and hydrolytic erosion. The conformational regularization of chain segments was essentially the main driving force for the morphological evolution of PLA during hydrolytic degradation. For hydrolysis at 37 °C, no significant structural variations were observed due to the immobilization of "frozen" PLA chains. In contrast, conformational ordering in PLA was immediately triggered during hydrolysis at 60 °C and was responsible for the transition from random coils to disordered trans and, further, to quasi-crystalline nanospheres. On the surfaces, the head-by-head absorption and joining of neighboring nanospheres led to nanofibrillar assemblies following a "gluttonous snake"-like manner. The length and density of nanofibers formed were in close relation to the hydrolytic evolution, both of which showed a direct rise in the initial 60 days and then a gradual decline. In the interior, presumably the high surface energy of the nanospheres allowed for the preferential anchoring and packing of conformationally ordered chains into lamellae. In accordance with the well-established hypothesis, the amorphous regions were attacked prior to the erosion of crystalline entities, causing a rapid increase of crystallinity during the initial 30 days, followed by a gradual fall until 90 days. In addition to adequate illustration of hydrolysis-induced variations of crystallinity, our proposed model elucidates the formation of spherulitic nuclei featuring an extremely wide distribution of diameters ranging from several nanometers to over 5 μm, as well as the inferior resistance to hydrolysis observed for the primary nuclei. Our work

Induced helical backbone conformations of self-organizable dendronized polymers.

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Rudick, Jonathan G; Percec, Virgil

2008-12-01

information to rationalize function as retrostructural analysis. Retrostructural analysis validates our hypothesis that the self-assembling dendrons induce a helical backbone conformation in cylindrical self-organizable dendronized polymers. This helical conformation mediates unprecedented functions. Self-organizable dendronized polymers have emerged as powerful building blocks for nanoscience by virtue of their dimensions and ability to self-organize. Discrete cylindrical and spherical structures with well-defined dimensions can be visualized and manipulated individually. More importantly, they provide a robust framework for elucidating functions available only at the nanoscale. This Account will highlight structures and functions generated from self-organizable dendronized polymers that enable integration of the nanoworld with its macroscopic universe. Emphasis is placed on those structures and functions derived from the induced helical backbone conformation of cylindrical self-organizable dendronized polymers.

Conformation and activity alteration of horseradish peroxidase induced by the interaction with gene carrier polyethyleneimines

Science.gov (United States)

Huang, Aimin; Wei, Bangzhi; Mo, Junyong; Wang, Yajing; Ma, Lin

2018-01-01

Polyethyleneimine (PEI) has long been considered as "golden standard" for polymeric gene delivery carriers. However the molecular basis of the cytotoxicity of PEI is poorly understood. Little is known about the effects of PEI on the structure and functions of biomacromolecules. In this work, fluorescence, UV-vis absorption, circular dichroism spectroscopy were conducted to investigate the influence of PEI of average molecular weight 25, 10 and 1.8 kDa (denoted as PEI25k, PEI10k and PEI1.8k) on the conformation of horseradish peroxidase (HRP) and its catalytic efficiency. Zeta-potential measurement and isothermal titration calorimetry were used to reveal the mechanism of the interaction between PEIs and HRP. PEIs were found to bind onto the surface of HRP predominantly via hydrophobic interaction and hydrogen bond or van der Waals interaction. The complex formation between HRP and PEI induced a more compact conformation of the enzyme and an increased hydrophobicity of the microenvironment surrounding heme pocket. The conformational change of HRP had little impact on the affinity towards H2O2 and phenol. However, the increase in the non-planarity of porphyrin ring in the heme group led to an increase in the exposure degree of the active center and thus an enhancement of catalytic efficiency of HRP in the presence of high molecular weight PEIs (PEI25k and PEI10k). The polymer size played an important role in PEI-HRP interaction. PEI of low molecular weight (PEI1.8k) was less efficient to alter the conformation and catalytic activity of HRP in aqueous solutions.

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 Artemperatures lower than ca. 30 K, the three conformers 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').

A combined variable temperature 600 MHz NMR/MD study of the calcium release agent cyclic adenosine diphosphate ribose (cADPR): Structure, conformational analysis, and thermodynamics of the conformational equilibria.

Science.gov (United States)

Javornik, Uroš; Plavec, Janez; Wang, Baifan; Graham, Steven M

2018-01-02

A combined variable temperature 600 MHz NMR/molecular dynamics study of the Ca 2+ -release agent cyclic adenosine 5'-diphosphate ribose (cADPR) was conducted. In addition to elucidating the major and minor orientations of the conformationally flexible furanose rings, γ- (C4'-C5'), and β- (C5'-O5') bonds, the thermodynamics (ΔH o , ΔS o ) associated with each of these conformational equilibria were determined. Both furanose rings were biased towards a south conformation (64-74%) and both β-bonds heavily favored trans conformations. The R-ring γ-bond was found to exist almost exclusively as the γ + conformer, whereas the A-ring γ-bond was a mixture of the γ + and γ t conformers, with the trans conformer being slightly favored. Enthalpic factors accounted for most of the observed conformational preferences, although the R-ring furanose exists as its major conformation based solely on entropic factors. There was excellent agreement between the NMR and MD results, particularly with regard to the conformer identities, but the MD showed a bias towards γ + conformers. The MD results showed that both N-glycosidic χ-bonds are exclusively syn. Collectively the data allowed for the construction of a model for cADPR in which many of the conformationally flexible units in fact effectively adopt single orientations and where most of the conformational diversity resides in its A-ring furanose and γ-bond. Copyright © 2017 Elsevier Ltd. All rights reserved.

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...

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....

Specific phosphopeptide binding regulates a conformational change in the PI 3-kinase SH2 domain associated with enzyme activation.

Science.gov (United States)

Shoelson, S E; Sivaraja, M; Williams, K P; Hu, P; Schlessinger, J; Weiss, M A

1993-01-01

SH2 (src-homology 2) domains define a newly recognized binding motif that mediates the physical association of target phosphotyrosyl proteins with downstream effector enzymes. An example of such phosphoprotein-effector coupling is provided by the association of phosphatidylinositol 3-kinase (PI 3-kinase) with specific phosphorylation sites within the PDGF receptor, the c-Src/polyoma virus middle T antigen complex and the insulin receptor substrate IRS-1. Notably, phosphoprotein association with the SH2 domains of p85 also stimulates an increase in catalytic activity of the PI 3-kinase p110 subunit, which can be mimicked by phosphopeptides corresponding to targeted phosphoprotein phosphorylation sites. To investigate how phosphoprotein binding to the p85 SH2 domain stimulates p110 catalytic activation, we have examined the differential effects of phosphotyrosine and PDGF receptor-, IRS-1- and c-Src-derived phosphopeptides on the conformation of an isolated SH2 domain of PI 3-kinase. Although phosphotyrosine and both activating and non-activating phosphopeptides bind to the SH2 domain, activating phosphopeptides bind with higher affinity and induce a qualitatively distinct conformational change as monitored by CD and NMR spectroscopy. Amide proton exchange and protease protection assays further show that high affinity, specific phosphopeptide binding induces non-local dynamic SH2 domain stabilization. Based on these findings we propose that specific phosphoprotein binding to the p85 subunit induces a change in SH2 domain structure which is transmitted to the p110 subunit and regulates enzymatic activity by an allosteric mechanism. Images PMID:8382612

Cold temperature blocks thyroid hormone-induced changes in lipid and energy metabolism in the liver of Lithobates catesbeianus tadpoles.

Science.gov (United States)

Suzuki, Shunsuke; Awai, Koichiro; Ishihara, Akinori; Yamauchi, Kiyoshi

2016-01-01

Exposure of the American bullfrog Lithobates catesbeianus tadpoles to low temperature affects many biological processes including lipid metabolism and the thyroid hormone (TH) signaling pathway, resulting in arrest of TH-induced metamorphosis. To clarify what molecular events occur in this phenomenon, we investigated the glycerophospholipid and fatty acid (FA) compositions, the activities of mitochondrial enzymes and the transcript levels of related genes in the liver of control (26 °C) and cold-treated (4 °C) tadpoles with or without 5 nM 3,3',5-triiodothyronine (T3). Exposure to T3 decreased the tail height and polyunsaturation of FAs in the glycerophospholipids, and increased plasma glucose levels and transcript levels of primary TH-response genes including TH receptor, and some energy metabolic (cox4, srebp1 and fas) and FA chain elongase genes (elovl3 and elovl5). However, these T3-induced responses were abolished at 4 °C. Exposure to cold temperature enhanced plasma glucose, triglyceride and free FA levels, monounsaturation of FAs, mitochondrial enzymes activities (cytochrome c oxidase and carnitine palmitoyltransferase; U/g liver), with the upregulation of the genes involved in glycogenolysis (pygl), gluconeogenesis (pck1 and g6pc2), FA β-oxidation (acadl), and cholesterol uptake and synthesis (hmgcr, srebp2 and ldlr1), glycerophospholipids synthesis (pcyt1, pcyt2, pemt, and pparg), and FA monounsaturation (scd1) and chain elongation (elovl1 and elovl2). T3 had little effect on the cold-induced changes. Our study demonstrated that exposures to T3 and cold temperature exert different effects on lipid metabolism, resulting in changes in the FA composition in glycerophospholipids, and suggests that a cold-induced signal may block TH-signaling pathway around primary TH-response genes.

Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion

International Nuclear Information System (INIS)

Martín-García, Fernando; Mendieta-Moreno, Jesús Ignacio; Mendieta, Jesús; Gómez-Puertas, Paulino

2012-01-01

Highlights: ► Initial conformational change of paramyxovirus F protein is caused only by mechanical forces. ► HRA region undergoes a structural change from a beta + alpha conformation to an extended coil and then to an all-alpha conformation. ► HRS domains of F protein form three single α-helices prior to generation of the coiled coil. -- Abstract: The fusion of paramyxovirus to the cell membrane is mediated by fusion protein (F protein) present in the virus envelope, which undergoes a dramatic conformational change during the process. Unlike hemagglutinin in orthomyxovirus, this change is not mediated by an alteration of environmental pH, and its cause remains unknown. Steered molecular dynamics analysis leads us to suggest that the conformational modification is mediated only by stretching mechanical forces once the transmembrane fusion peptide of the protein is anchored to the cell membrane. Such elongating forces will generate major secondary structure rearrangement in the heptad repeat A region of the F protein; from β-sheet conformation to an elongated coil and then spontaneously to an α-helix. In addition, it is proposed that the heptad repeat A region adopts a final three-helix coiled coil and that this structure appears after the formation of individual helices in each monomer.

Ultrafast Electric Field Pulse Control of Giant Temperature Change in Ferroelectrics

Science.gov (United States)

Qi, Y.; Liu, S.; Lindenberg, A. M.; Rappe, A. M.

2018-01-01

There is a surge of interest in developing environmentally friendly solid-state-based cooling technology. Here, we point out that a fast cooling rate (≈1011 K /s ) can be achieved by driving solid crystals to a high-temperature phase with a properly designed electric field pulse. Specifically, we predict that an ultrafast electric field pulse can cause a giant temperature decrease up to 32 K in PbTiO3 occurring on few picosecond time scales. We explain the underlying physics of this giant electric field pulse-induced temperature change with the concept of internal energy redistribution: the electric field does work on a ferroelectric crystal and redistributes its internal energy, and the way the kinetic energy is redistributed determines the temperature change and strongly depends on the electric field temporal profile. This concept is supported by our all-atom molecular dynamics simulations of PbTiO3 and BaTiO3 . Moreover, this internal energy redistribution concept can also be applied to understand electrocaloric effect. We further propose new strategies for inducing giant cooling effect with ultrafast electric field pulse. This Letter offers a general framework to understand electric-field-induced temperature change and highlights the opportunities of electric field engineering for controlled design of fast and efficient cooling technology.

Conformational flexibility of avidin: the influence of biotin binding

International Nuclear Information System (INIS)

Soledad Celej, M.; Montich, Guillermo G.; Fidelio, Gerardo D.

2004-01-01

Ligand binding to proteins is a key process in cell biochemistry. The interaction usually induces modifications in the unfolding thermodynamic parameters of the macromolecule due to the coupling of unfolding and binding equilibria. In addition, these modifications can be attended by changes in protein structure and/or conformational flexibility induced by ligand binding. In this work, we have explored the effect of biotin binding on conformation and dynamic properties of avidin by using infrared spectroscopy including kinetics of hydrogen/deuterium exchange. Our results, along with previously thermodynamic published data, indicate a clear correlation between thermostability and protein compactness. In addition, our results also help to interpret the thermodynamic binding parameters of the exceptionally stable biotin:AVD complex

Spectroscopic and theoretical investigation of conformational changes of proteins by synthesized pyrimidine derivative and its sensitivity towards FRET application

Science.gov (United States)

Ghosh, Swadesh; Singharoy, Dipti; Bhattacharya, Subhash Chandra

2018-04-01

Interest in synthesizing and characterizing (IR, NMR and HRMS spectroscopic methods) a pyrimidine based Schiff-base ligand, 2-(2-(Anthracen-9-ylmethylene) hydrazinyl)-4,6-dimethyl pyrimidine (ANHP) has been developed for its application to ascertain the conformational change of protein and sensitivity towards fluorescence resonance energy transfer (FRET) process. Location of ANHP in bovine serum albumin (BSA) and human serum albumin (HSA) proteins environment has been determined using different spectroscopic techniques. Weakly fluorescent ANHP have shown greater protein induced fluorescence enhancement (PIFE) in case of HSA than BSA, though in both cases energy transfer efficiency are almost same but difference in binding constant values encourages us to find the location of ANHP within the complex protein environment. From the FRET parameter and α-helicity change, it has been found that ANHP bound with Trp-214 of HSA and surface Trp-134 of BSA. Conformational changes of proteins have been observed more for HSA than BSA in presence of ANHP, which has confirmed the location of ANHP in both the protein environments. Coupled with experimental studies, molecular docking analysis has also been done to explain the locations and distance dependent FRET process of ANHP in both proteins.

Multilayer conformal applicator for microwave heating and brachytherapy treatment of superficial tissue disease.

Science.gov (United States)

Juang, T; Stauffer, P R; Neuman, D G; Schlorff, J L

2006-11-01

The purpose of this study was to construct and perform preliminary functionality evaluations of a multilayer conformal applicator with provisions for thermal monitoring, tight conformity and simultaneous microwave heating and brachytherapy treatment of large-area contoured surfaces. The multilayer conformal applicator consists of thermal monitoring catheters for fibre-optic monitoring of skin temperatures, a waterbolus, a PCB microwave antenna array, a dielectric spacer for brachytherapy considerations, brachytherapy catheters for delivering HDR radiation and an inflatable air bladder for improving conformity to contoured surfaces. The applicator also includes an elastic attachment structure to hold the applicator securely in place on the patient. The conformity of the applicator to irregular surfaces was evaluated through CT imaging of the applicator fitted onto a life-sized human torso phantom. The fluid flow dynamics of the waterbolus, which impact the effectiveness of temperature control, were evaluated with thermometry during a 19 degrees C step change temperature of the circulating water. CT imaging showed improved conformity to the torso phantom surface following the application of gentle inward pressure from inflating the outer air bladder. Only a small number of 1-5 mm sized air gaps separated the conformal applicator and tissue surface. Thermometry testing of the bolus fluid flow dynamics demonstrated temperature uniformity within +/-0.82 degrees C across a 19 x 34 x 0.6 cm area bolus and +/-0.85 degrees C across a large 42 x 32 x 0.6 cm area bolus. CT scans of the applicator confirmed that the applicator conforms well to complex body contours and should maintain good conformity and positional stability even when worn on a mobile patient. Thermometry testing of two different waterbolus geometries demonstrated that uniform circulation and temperature control can be maintained throughout large, complex bolus shapes.

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.

Cohort Removal Induces Changes in Body Temperature, Pain Sensitivity, and Anxiety-Like Behavior

Science.gov (United States)

Takao, Keizo; Shoji, Hirotaka; Hattori, Satoko; Miyakawa, Tsuyoshi

2016-01-01

Mouse behavior is analyzed to elucidate the effects of various experimental manipulations, including gene mutation and drug administration. When the effect of a factor of interest is assessed, other factors, such as age, sex, temperature, apparatus, and housing, are controlled in experiments by matching, counterbalancing, and/or randomizing. One such factor that has not attracted much attention is the effect of sequential removal of animals from a common cage (cohort removal). Here we evaluated the effects of cohort removal on rectal temperature, pain sensitivity, and anxiety-like behavior by analyzing the combined data of a large number of C57BL/6J mice that we collected using a comprehensive behavioral test battery. Rectal temperature increased in a stepwise manner according to the position of sequential removal from the cage, consistent with previous reports. In the hot plate test, the mice that were removed first from the cage had a significantly longer latency to show the first paw response than the mice removed later. In the elevated plus maze, the mice removed first spent significantly less time on the open arms compared to the mice removed later. The results of the present study demonstrated that cohort removal induces changes in body temperature, pain sensitivity, and anxiety-like behavior in mice. Cohort removal also increased the plasma corticosterone concentration in mice. Thus, the ordinal position in the sequence of removal from the cage should be carefully counterbalanced between groups when the effect of experimental manipulations, including gene manipulation and drug administration, are examined using behavioral tests. PMID:27375443

Cohort removal induces changes in body temperature, pain sensitivity, and anxiety-like behavior

Directory of Open Access Journals (Sweden)

Keizo eTakao

2016-06-01

Full Text Available Mouse behavior is analyzed to elucidate the effects of various experimental manipulations, including gene mutation and drug administration. When the effect of a factor of interest is assessed, other factors, such as age, sex, temperature, apparatus, and housing, are controlled in experiments by matching, counterbalancing, and/or randomizing. One such factor that has not attracted much attention is the effect of sequential removal of animals from a common cage (cohort removal. Here we evaluated the effects of cohort removal on rectal temperature, pain sensitivity, and anxiety-like behavior by analyzing the combined data of a large number of C57BL/6J mice that we collected using a comprehensive behavioral test battery. Rectal temperature increased in a stepwise manner according to the position of sequential removal from the cage, consistent with previous reports. In the hot plate test, the mice that were removed first from the cage had a significantly longer latency to show the first paw response than the mice removed later. In the elevated plus maze, the mice removed first spent significantly less time on the open arms compared to the mice removed later. The results of the present study demonstrated that cohort removal induces changes in body temperature, pain sensitivity, and anxiety-like behavior in mice. Cohort removal also increased the plasma corticosterone concentration in mice. Thus, the ordinal position in the sequence of removal from the cage should be carefully counterbalanced between groups when the effect of experimental manipulations, including gene manipulation and drug administration, are examined using behavioral tests.

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

Conformational changes in the G protein Gs induced by the β2 adrenergic receptor

DEFF Research Database (Denmark)

Chung, Ka Young; Rasmussen, Søren Gøgsig Faarup; Liu, Tong

2011-01-01

and initiation of downstream signalling cascades. Despite a wealth of biochemical and biophysical studies on inactive and active conformations of several heterotrimeric G proteins, the molecular underpinnings of G protein activation remain elusive. To characterize this mechanism, we applied peptide amide...

Substrate and Inhibitor-Specific Conformational Changes in the Human Serotonin Transporter Revealed by Voltage-Clamp Fluorometry

DEFF Research Database (Denmark)

Söderhielm, Pella C; Andersen, Jacob; Munro, Lachlan

2015-01-01

of TM6, Ala419 in the interface between TM8 and extracellular loop (EL) 4, and Leu481 in EL5. The reporter positions were used for time-resolved measurement of conformational changes during 5-HT transport and binding of cocaine and the selective serotonin reuptake inhibitors fluoxetine and escitalopram...... changes overall, which included movements within or around TM1b, EL4, and EL5. Taken together, our data lead us to suggest that competitive inhibitors stabilize hSERT in a state that is different from the apo outward-open conformation as well as inward-facing conformations....

Temperature induced alternative splicing is affected in sdg8 and sdg26

OpenAIRE

Pajoro, A.; Severing, E.I.; Immink, G.H.

2017-01-01

Plants developed a plasticity to environmental conditions, such as temperature, that allows their adaptation. A change in ambient temperature leads to changes in the transcriptome in plants, such as the production of different splicing isoforms. Here we study temperature induced alternative splicing events in Arabidopsis thaliana wild-type and two epigenetic mutants, sdg8-2 and sdg26-1 using an RNA-seq approach.

Phosphorylation- and nucleotide-binding-induced changes to the stability and hydrogen exchange patterns of JNK1ß1 provide insight into its mechanisms of activation

CSIR Research Space (South Africa)

Owen, GR

2014-10-01

Full Text Available –deuterium exchange (HX) mass spectrometry were used to investigate the changes to the stability and conformation/conformational dynamics of JNK1ß1 induced by phosphorylative activation. Equivalent studies were also employed to determine the effects of nucleotide...

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.

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

An extension of the counterion condensation theory to conformational changes of flexible polymers

International Nuclear Information System (INIS)

Benegas, J.C.; Cesaro, A.

1988-01-01

A full report on a statistical model is presented in which an ionic polymer is taken as an aggregate of linear flexible segments (similar to the spring-bead model). This model is thought to represent fairly well some flexible ionic polymers in solution. The model assumes two factorizable energy contributions, one purely conformational the other electrostatic. The first contribution is calculated from distribution function of the end-to-end distances and can be obtained from numerical Monte Carlo calculations of chain conformations. The second contribution is the excess thermodynamic property and is calculated, by using Manning's theory of linear polyelectrolytes, as a function of the degree of ionization and of a number of physical variables. Procedures to evaluate changes in the chain conformation of polysaccharides and polypeptides bearing ionizable charged groups are presented. The results show excellent quantitative agreement of averaged functions and experimental data. They also show that statistical average over the conformational states is not equivalent to the thermodynamic property of the averaged conformation. (author). 37 refs, 17 figs

Health Impacts of Climate Change-Induced Subzero Temperature Fires.

Science.gov (United States)

Metallinou, Maria-Monika; Log, Torgrim

2017-07-20

General fire risk and the special risk related to cold climate cellulosic drying processes are outlined. Four recent subzero temperatures fires are studied with respect to health impacts: a wooden village fire, a single wood structure fire, a wildland urban interface (WUI) fire and a huge wildland fire. The health impacts range from stress related to loss of jobs, psychological effects of lost possessions, exposure to smoke and heat as well as immediate, or delayed, loss of lives. These four fires resulted in 32 fatalities, 385 persons hospitalized for shorter or longer periods, 104 structures lost and 1015 km² of wildland burned north of, and just south of, the Arctic Circle. It is shown that the combination of subzero temperature dry weather, strong winds, changing agricultural activities and declining snowpack may lead to previously anticipated threats to people and the environment. There are reasons to believe that these fires are a result of the ongoing climate changes. Risk impacts are discussed. Rural districts and/or vulnerable populations seem to be most affected. Training methods to identify and better monitor critical fire risk parameters are suggested to mitigate the health impacts of a possibly increasing number of such fires.

Raman Spectroscopy of Conformational Changes in Membrane-Bound Sodium Potassium ATPase

DEFF Research Database (Denmark)

Helix Nielsen, Claus; Abdali, Salim; Lundbæk, Jens August

2007-01-01

In this investigation we assess the potential of Raman spectroscopy as a tool for probing conformational changes in membrane-spanning proteins — in this case, the sodium potassium adenosine triphosphatase (Na+,K+-ATPase). Spectral analysis of protein-lipid complexes is complicated by the presence...

Relationship between phase development and swelling of AISI 316 during temperature changes

International Nuclear Information System (INIS)

Yang, W.J.S.; Garner, F.A.

1982-04-01

The effect of temperature changes on radiation-induced swelling and phase development of AISI 316 has been examined for specimens irradiated in two different experiments. The formation of radiation-stable phases at low temperature appears to precede swelling but these phases tend to dissolve when subsequently subjected to higher temperature. Phases which develop at high temperature persist when the temperature is subsequently lowered. Once nucleated at low temperatures, voids tend to persist without reduction in density at higher temperatures. However, a new round of void nucleation occurs when the temperature is decreased during irradiation. If the swelling has entered the steady-state swelling regime prior to the temperature change, there is no effect on the subsequent swelling rate. For temperature changes that occur before the end of the transient swelling regime, substantial changes can occur in the swelling behavior, particularly if the changes occur in the range around 500 0 . The isothermal swelling behavior of AISI 316 is much less sensitive to irradiation temperature than previously envisioned

Conformational impact of structural modifications in 2-fluorocyclohexanone

Directory of Open Access Journals (Sweden)

Francisco A. Martins

2017-08-01

Full Text Available 2-Haloketones are building blocks that combine physical, chemical and biological features of materials and bioactive compounds, while organic fluorine plays a fundamental role in the design of performance organic molecules. Since these features are dependent on the three-dimensional chemical structure of a molecule, simple structural modifications can affect its conformational stability and, consequently, the corresponding physicochemical/biological property of interest. In this work, structural changes in 2-fluorocyclohexanone were theoretically studied with the aim at finding intramolecular interactions that induce the conformational equilibrium towards the axial or equatorial conformer. The interactions evaluated were hydrogen bonding, hyperconjugation, electrostatic and steric effects. While the gauche effect, originated from hyperconjugative interactions, does not appear to cause some preferences for the axial conformation of organofluorine heterocycles, more classical effects indeed rule the conformational equilibrium of the compounds. Spectroscopic parameters (NMR chemical shifts and coupling constants, which can be useful to determine the stereochemistry and the interactions operating in the series of 2-fluorocyclohexanone derivatives, were also calculated.

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Directory of Open Access Journals (Sweden)

Bhattacharyya Moitrayee

2010-08-01

Full Text Available Abstract Background One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results In this study, we have explored the ligand induced conformational changes in H.pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H.pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co-operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in

Past temperature reconstructions from deep ice cores: relevance for future climate change

Directory of Open Access Journals (Sweden)

V. Masson-Delmotte

2006-01-01

Full Text Available Ice cores provide unique archives of past climate and environmental changes based only on physical processes. Quantitative temperature reconstructions are essential for the comparison between ice core records and climate models. We give an overview of the methods that have been developed to reconstruct past local temperatures from deep ice cores and highlight several points that are relevant for future climate change. We first analyse the long term fluctuations of temperature as depicted in the long Antarctic record from EPICA Dome C. The long term imprint of obliquity changes in the EPICA Dome C record is highlighted and compared to simulations conducted with the ECBILT-CLIO intermediate complexity climate model. We discuss the comparison between the current interglacial period and the long interglacial corresponding to marine isotopic stage 11, ~400 kyr BP. Previous studies had focused on the role of precession and the thresholds required to induce glacial inceptions. We suggest that, due to the low eccentricity configuration of MIS 11 and the Holocene, the effect of precession on the incoming solar radiation is damped and that changes in obliquity must be taken into account. The EPICA Dome C alignment of terminations I and VI published in 2004 corresponds to a phasing of the obliquity signals. A conjunction of low obliquity and minimum northern hemisphere summer insolation is not found in the next tens of thousand years, supporting the idea of an unusually long interglacial ahead. As a second point relevant for future climate change, we discuss the magnitude and rate of change of past temperatures reconstructed from Greenland (NorthGRIP and Antarctic (Dome C ice cores. Past episodes of temperatures above the present-day values by up to 5°C are recorded at both locations during the penultimate interglacial period. The rate of polar warming simulated by coupled climate models forced by a CO2 increase of 1% per year is compared to ice

Temperature-induced transitions between domain structures of ultrathin magnetic films

International Nuclear Information System (INIS)

Polyakova, T.; Zablotskii, V.

2005-01-01

Full text: Understanding of the influence of temperature on behavior of domain patterns of ultrathin magnetic films is of high significance for the fundamental physics of nanomagnetism as well as for technological applications. A thickness-dependent Curie temperature of ultrathin films may cause many interesting phenomena in the thermal evolution of domain structures (DS): i) nontrivial changes of the anisotropy constants as a function of the film thickness; ii) so-called inverse melting of DSs (processes where a more symmetric domain phase is found at lower temperatures than at higher temperatures - the inverse phase sequence) [1]; iii) temperature-induced transitions between domain structures. The possibility of such transitions is determined by lowering of the potential barriers separating different magnetization states as the film temperature approaches the Curie point. In this case with an increase of temperature, due to a significant decrease of the anisotropy constant, the domain wall energy is low enough and allows the system to reach equilibrium by a change of the domain wall number in the sample. This manifests itself in a transition from a metastable DS to a more stable DS which corresponds to new values of the anisotropy constant and magnetizations saturation. Thus, the temperature-induced transitions are driven by temperature changes of the magnetic parameters of the film. The key parameters controlling the DS geometry and period are the characteristic length, l c =σ/4πM S 2 (the ratio between the domain wall and demagnetization energies), and the quality factor Q =K/2πM S 2 (K is the first anisotropy constant). We show that for films with a pronounced nonmonotonic temperature dependence of l c one can expect a counter thermodynamic behavior: the inverse phase sequence and cooling-induced disordering. On changing temperature the existing domain structure should accommodate itself under new magnitudes of l c and Q. There are the two possible

Structural mechanisms of high-temperature shape changes in titanium-nickel alloys after low-temperature thermomechanical treatment

International Nuclear Information System (INIS)

Prokoshkin, S.D.; Turenne, S.; Khmelevskaya, I.Yu.; Brailovski, V.; Trochu, F.

2000-01-01

High-Temperature Shape Memory Effect (HTSME) in Ti-Ni alloys and corresponding structural and internal stress changes were studied using dilatometry, in situ electron microscope and X-ray diffractometry. The HTSME induced by the Low Temperature Thermomechanical Treatment (LTMT) consists of two stages. The temperature range of the first stage is limited to 250 o C, while the second stage extends to 400-500 o C. The first stage is caused by the oriented reverse martensite transformation. The heterogeneous residual stress field causes a different thermal stability for the different martensite orientations. During the reverse transformation an anisotropic shift of martensite and austenite X-ray lines is observed that can be due to a relaxation of the orientated stresses and to changes in the martensite lattice. The second stage of HTSME is caused by internal stress relaxation during recovery and polygonization of austenite that are not typical shape memory mechanisms. The possible reasons for the martensite stabilization induced by LTMT will be discussed. (author)

Amine oxidase from lentil seedlings: energetic domains and effect of temperature on activity.

Science.gov (United States)

Moosavi-Nejad, S Z; Rezaei-Tavirani, M; Padiglia, A; Floris, G; Moosavi-Movahedi, A A

2001-07-01

Copper/TPQ amine oxidases from mammalian and plant sources have shown many differences in substrate specificity and molecular properties. In this work the activity of lentil seedling amine oxidase was followed at various temperatures in 100 mM potassium phosphate buffer, pH 7, using benzylamine as substrate. The discontinuous Arrhenius plot of lentil amine oxidase showed two distinct phases with a jump between them. Thermal denaturation of the enzyme, using differential scanning calorimetry under the same experimental conditions, showed a transition at the same temperature ranges in the absence of substrate, indicating the occurrence of conformational changes, with an enthalpy change of about 175.9 kJ/mole. The temperature-induced changes of the activity of lentil amine oxidase are compared with those of bovine serum amine oxidase (taken from the literature).

Rational design of a conformation-switchable Ca2+- and Tb3+-binding protein without the use of multiple coupled metal-binding sites.

Science.gov (United States)

Li, Shunyi; Yang, Wei; Maniccia, Anna W; Barrow, Doyle; Tjong, Harianto; Zhou, Huan-Xiang; Yang, Jenny J

2008-10-01

Ca2+, as a messenger of signal transduction, regulates numerous target molecules via Ca2+-induced conformational changes. Investigation into the determinants for Ca2+-induced conformational change is often impeded by cooperativity between multiple metal-binding sites or protein oligomerization in naturally occurring proteins. To dissect the relative contributions of key determinants for Ca2+-dependent conformational changes, we report the design of a single-site Ca2+-binding protein (CD2.trigger) created by altering charged residues at an electrostatically sensitive location on the surface of the host protein rat Cluster of Differentiation 2 (CD2).CD2.trigger binds to Tb3+ and Ca2+ with dissociation constants of 0.3 +/- 0.1 and 90 +/- 25 microM, respectively. This protein is largely unfolded in the absence of metal ions at physiological pH, but Tb3+ or Ca2+ binding results in folding of the native-like conformation. Neutralization of the charged coordination residues, either by mutation or protonation, similarly induces folding of the protein. The control of a major conformational change by a single Ca2+ ion, achieved on a protein designed without reliance on sequence similarity to known Ca2+-dependent proteins and coupled metal-binding sites, represents an important step in the design of trigger proteins.

Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

Science.gov (United States)

Paul, Fabian; Noé, Frank; Weikl, Thomas R

2018-03-27

Unstructured proteins and peptides typically fold during binding to ligand proteins. A challenging problem is to identify the mechanism and kinetics of these binding-induced folding processes in experiments and atomistic simulations. In this Article, we present a detailed picture for the folding of the inhibitor peptide PMI into a helix during binding to the oncoprotein fragment 25-109 Mdm2 obtained from atomistic, explicit-water simulations and Markov state modeling. We find that binding-induced folding of PMI is highly parallel and can occur along a multitude of pathways. Some pathways are induced-fit-like with binding occurring prior to PMI helix formation, while other pathways are conformational-selection-like with binding after helix formation. On the majority of pathways, however, binding is intricately coupled to folding, without clear temporal ordering. A central feature of these pathways is PMI motion on the Mdm2 surface, along the binding groove of Mdm2 or over the rim of this groove. The native binding groove of Mdm2 thus appears as an asymmetric funnel for PMI binding. Overall, binding-induced folding of PMI does not fit into the classical picture of induced fit or conformational selection that implies a clear temporal ordering of binding and folding events. We argue that this holds in general for binding-induced folding processes because binding and folding events in these processes likely occur on similar time scales and do exhibit the time-scale separation required for temporal ordering.

Conformal Coating of a Phase Change Material on Ordered Plasmonic Nanorod Arrays for Broadband All-Optical Switching

Energy Technology Data Exchange (ETDEWEB)

Guo, Peijun; Weimer, Matthew S. [Department; Emery, Jonathan D.; Diroll, Benjamin T.; Chen, Xinqi; Hock, Adam S. [Department; Chang, Robert P. H.; Martinson, Alex B. F.; Schaller, Richard D.

2016-12-19

Actively tunable optical transmission through artificial metamaterials holds great promise for next-generation nanophotonic devices and metasurfaces. Plasmonic nanostructures and phase change materials have been extensively studied to this end due to their respective strong interactions with light and tunable dielectric constants under external stimuli. Seamlessly integrating plasmonic components with phase change materials, as demonstrated in the present work, can facilitate phase change by plasmonically enabled light confinement and meanwhile make use of the high sensitivity of plasmon resonances to the variation of dielectric constant associated with the phase change. The hybrid platform here is composed of plasmonic indium tin-oxide nanorod arrays (ITO-NRAs) conformally coated with an ultrathin layer of a prototypical phase change material, vanadium dioxide (VO2), which enables all-optical modulation of the infrared as well as the visible spectral ranges. The interplay between the intrinsic plasmonic nonlinearity of ITO-NRAs and the phase transition induced permittivity change of VO2 gives rise to spectral and temporal responses that cannot be achieved with individual material components alone.

Conformal Coating of a Phase Change Material on Ordered Plasmonic Nanorod Arrays for Broadband All-Optical Switching.

Science.gov (United States)

Guo, Peijun; Weimer, Matthew S; Emery, Jonathan D; Diroll, Benjamin T; Chen, Xinqi; Hock, Adam S; Chang, Robert P H; Martinson, Alex B F; Schaller, Richard D

2017-01-24

Actively tunable optical transmission through artificial metamaterials holds great promise for next-generation nanophotonic devices and metasurfaces. Plasmonic nanostructures and phase change materials have been extensively studied to this end due to their respective strong interactions with light and tunable dielectric constants under external stimuli. Seamlessly integrating plasmonic components with phase change materials, as demonstrated in the present work, can facilitate phase change by plasmonically enabled light confinement and meanwhile make use of the high sensitivity of plasmon resonances to the variation of dielectric constant associated with the phase change. The hybrid platform here is composed of plasmonic indium-tin-oxide nanorod arrays (ITO-NRAs) conformally coated with an ultrathin layer of a prototypical phase change material, vanadium dioxide (VO 2 ), which enables all-optical modulation of the infrared as well as the visible spectral ranges. The interplay between the intrinsic plasmonic nonlinearity of ITO-NRAs and the phase transition induced permittivity change of VO 2 gives rise to spectral and temporal responses that cannot be achieved with individual material components alone.

Radiation-induced changes of liposomes and lecithin in non-aqueous media

International Nuclear Information System (INIS)

Nakazawa, T.; Nagatsuka, S.; Sakurai, T.

1981-01-01

Radiation-induced changes of lipids in non-aqueous media were studied to elucidate the process of radiation damage in biological membranes. The lipid peroxidation progressed linearly with increasing dose and decreasing dose rate of γ-irradiation in soyabean lecithin in chloroform. The fatty acid composition of lecithin also changed, especially in linoleic and linolenic acids. Lower dose rate radiation enhanced these changes in oxic condition. Lipid peroxidation was also shown in lipids extracted from irradiated liposomes or in liposomes prepared from irradiated lecithin in chloroform. The dose-dependent glucose efflux was seen in liposomes prepared from irradiated lecithin in chloroform. These results indicate that the peroxidation of lipid molecules might cause radiation damage to the membrane conformation. (author)

Switch region for pathogenic structural change in conformational disease and its prediction.

Directory of Open Access Journals (Sweden)

Xin Liu

2010-01-01

Full Text Available Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1 influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1 it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2 it provides an ideal target for clinical treatment.

Conformation sensitive charge transport in conjugated polymers

International Nuclear Information System (INIS)

Mattias Andersson, L.; Hedström, Svante; Persson, Petter

2013-01-01

Temperature dependent charge carrier mobility measurements using field effect transistors and density functional theory calculations are combined to show how the conformation dependent frontier orbital delocalization influences the hole- and electron mobilities in a donor-acceptor based polymer. A conformationally sensitive lowest unoccupied molecular orbital results in an electron mobility that decreases with increasing temperature above room temperature, while a conformationally stable highest occupied molecular orbital is consistent with a conventional hole mobility behavior and also proposed to be one of the reasons for why the material works well as a hole transporter in amorphous bulk heterojunction solar cells

Thermal conditions influence changes in body temperature induced by intragastric administration of capsaicin in mice.

Science.gov (United States)

Mori, Noriyuki; Urata, Tomomi; Fukuwatari, Tsutomu

2016-08-01

Capsaicin has been reported to have unique thermoregulatory actions. However, changes in core temperature after the administration of capsaicin are a controversial point. Therefore, we investigated the effects of environmental thermal conditions on changes in body temperature caused by capsaicin in mice. We showed that intragastric administration of 10 and 15 mg/kg capsaicin increased tail temperature and decreased colonic temperatures in the core temperature (CT)-constant and CT-decreasing conditions. In the CT-increasing condition, 15 mg/kg capsaicin increased tail temperature and decreased colonic temperature. However, 10 mg/kg capsaicin increased colonic temperature. Furthermore, the amount of increase in tail temperature was greater in the CT-decreasing condition and lower in the CT-increasing condition, compared with that of the CT-constant condition. These findings suggest that the changes in core temperature were affected by the environmental thermal conditions and that preliminary thermoregulation state might be more important than the constancy of temperature to evaluate the effects of heat diffusion and thermogensis.

Emission properties of MEH-PPV in thin films simultaneously illuminated and annealed at different temperatures

KAUST Repository

Botiz, Ioan; Freyberg, Paul; Leordean, Cosmin; Gabudean, Ana-Maria; Astilean, Simion; Yang, Arnold Chang-Mou; Stingelin, Natalie

2015-01-01

© 2014 Elsevier B.V. All rights reserved. We report on the enhancement of photoluminescence in thin films of poly[2-methoxy-5-((2′-ethylhexyl)oxy)-1,4-phenylenvinylene], neat or embedded in polystyrene, upon illumination with light as a function of annealing temperature, with our data emphasizing the picture of a light-induced conformation change that leads to the altered photophysical response of this polymer.

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

Volcanic influence on centennial to millennial Holocene Greenland temperature change.

Science.gov (United States)

Kobashi, Takuro; Menviel, Laurie; Jeltsch-Thömmes, Aurich; Vinther, Bo M; Box, Jason E; Muscheler, Raimund; Nakaegawa, Toshiyuki; Pfister, Patrik L; Döring, Michael; Leuenberger, Markus; Wanner, Heinz; Ohmura, Atsumu

2017-05-03

Solar variability has been hypothesized to be a major driver of North Atlantic millennial-scale climate variations through the Holocene along with orbitally induced insolation change. However, another important climate driver, volcanic forcing has generally been underestimated prior to the past 2,500 years partly owing to the lack of proper proxy temperature records. Here, we reconstruct seasonally unbiased and physically constrained Greenland Summit temperatures over the Holocene using argon and nitrogen isotopes within trapped air in a Greenland ice core (GISP2). We show that a series of volcanic eruptions through the Holocene played an important role in driving centennial to millennial-scale temperature changes in Greenland. The reconstructed Greenland temperature exhibits significant millennial correlations with K + and Na + ions in the GISP2 ice core (proxies for atmospheric circulation patterns), and δ 18 O of Oman and Chinese Dongge cave stalagmites (proxies for monsoon activity), indicating that the reconstructed temperature contains hemispheric signals. Climate model simulations forced with the volcanic forcing further suggest that a series of large volcanic eruptions induced hemispheric-wide centennial to millennial-scale variability through ocean/sea-ice feedbacks. Therefore, we conclude that volcanic activity played a critical role in driving centennial to millennial-scale Holocene temperature variability in Greenland and likely beyond.

Analysis of calcium-induced conformational changes in calcium-binding allergens and quantitative determination of their IgE binding properties.

Science.gov (United States)

Parody, Nuria; Fuertes, Miguel Angel; Alonso, Carlos; Pico de Coaña, Yago

2013-01-01

The polcalcin family is one of the most epidemiologically relevant families of calcium-binding allergens. Polcalcins are potent plant allergens that contain one or several EF-hand motifs and their allergenicity is primarily associated with the Ca(2+)-bound form of the protein. Conformation, stability, as well as IgE recognition of calcium-binding allergens greatly depend on the presence of protein-bound calcium ions. We describe a protocol that uses three techniques (SDS-PAGE, circular dichroism spectroscopy, and ELISA) to describe the effects that calcium has on the structural changes in an allergen and its IgE binding properties.

A lipid-mediated conformational switch modulates the thermosensing activity of DesK.

Science.gov (United States)

Inda, María Eugenia; Vandenbranden, Michel; Fernández, Ariel; de Mendoza, Diego; Ruysschaert, Jean-Marie; Cybulski, Larisa Estefanía

2014-03-04

The thermosensor DesK is a multipass transmembrane histidine-kinase that allows the bacterium Bacillus subtilis to adjust the levels of unsaturated fatty acids required to optimize membrane lipid fluidity. The cytoplasmic catalytic domain of DesK behaves like a kinase at low temperature and like a phosphatase at high temperature. Temperature sensing involves a built-in instability caused by a group of hydrophilic residues located near the N terminus of the first transmembrane (TM) segment. These residues are buried in the lipid phase at low temperature and partially "buoy" to the aqueous phase at higher temperature with the thinning of the membrane, promoting the required conformational change. Nevertheless, the core question remains poorly understood: How is the information sensed by the transmembrane region converted into a rearrangement in the cytoplasmic catalytic domain to control DesK activity? Here, we identify a "linker region" (KSRKERERLEEK) that connects the TM sensor domain with the cytoplasmic catalytic domain involved in signal transmission. The linker adopts two conformational states in response to temperature-dependent membrane thickness changes: (i) random coiled and bound to the phospholipid head groups at the water-membrane interface, promoting the phosphatase state or (ii) unbound and forming a continuous helix spanning a region from the membrane to the cytoplasm, promoting the kinase state. Our results uphold the view that the linker is endowed with a helix/random coil conformational duality that enables it to behave like a transmission switch, with helix disruption decreasing the kinase/phosphatase activity ratio, as required to modulate the DesK output response.

CONFORMATION CHANGES OF HUMAN SERUM γ–GLOBULIN IN THE PRESENCE OF ZINC IONS

Directory of Open Access Journals (Sweden)

S. B. Cheknev

2005-01-01

Full Text Available Abstract. Conformational changes of human serum γ–globulin during interaction with the zinc ions were studied in a solution. It has been shown that the presence of zinc in over its physiological concentrations led to increase in optical density across the whole spectrum of γ–globulin ultraviolet absorption. On the contrary, hypochromia in the spectrum was registered after interaction of the protein with zinc used in subphisiological concentrations. Possible role of divalent metal cations in changes in conformation of the blood serum γ–globulins, and thereby in regulation of their effector functions was discussed. (Med. Immunol., 2005, vol.7, № 4, pp. 375–380

Amplification and dampening of soil respiration by changes in temperature variability

Directory of Open Access Journals (Sweden)

C. A. Sierra

2011-04-01

Full Text Available Accelerated release of carbon from soils is one of the most important feedbacks related to anthropogenically induced climate change. Studies addressing the mechanisms for soil carbon release through organic matter decomposition have focused on the effect of changes in the average temperature, with little attention to changes in temperature variability. Anthropogenic activities are likely to modify both the average state and the variability of the climatic system; therefore, the effects of future warming on decomposition should not only focus on trends in the average temperature, but also variability expressed as a change of the probability distribution of temperature. Using analytical and numerical analyses we tested common relationships between temperature and respiration and found that the variability of temperature plays an important role determining respiration rates of soil organic matter. Changes in temperature variability, without changes in the average temperature, can affect the amount of carbon released through respiration over the long-term. Furthermore, simultaneous changes in the average and variance of temperature can either amplify or dampen the release of carbon through soil respiration as climate regimes change. These effects depend on the degree of convexity of the relationship between temperature and respiration and the magnitude of the change in temperature variance. A potential consequence of this effect of variability would be higher respiration in regions where both the mean and variance of temperature are expected to increase, such as in some low latitude regions; and lower amounts of respiration where the average temperature is expected to increase and the variance to decrease, such as in northern high latitudes.

Amplification and dampening of soil respiration by changes in temperature variability

Science.gov (United States)

Sierra, C.A.; Harmon, M.E.; Thomann, E.; Perakis, S.S.; Loescher, H.W.

2011-01-01

Accelerated release of carbon from soils is one of the most important feed backs related to anthropogenically induced climate change. Studies addressing the mechanisms for soil carbon release through organic matter decomposition have focused on the effect of changes in the average temperature, with little attention to changes in temperature vari-ability. Anthropogenic activities are likely to modify both the average state and the variability of the climatic system; therefore, the effects of future warming on decomposition should not only focus on trends in the average temperature, but also variability expressed as a change of the probability distribution of temperature.Using analytical and numerical analyses we tested common relationships between temperature and respiration and found that the variability of temperature plays an important role determining respiration rates of soil organic matter. Changes in temperature variability, without changes in the average temperature, can affect the amount of carbon released through respiration over the long term. Furthermore, simultaneous changes in the average and variance of temperature can either amplify or dampen there release of carbon through soil respiration as climate regimes change. The effects depend on the degree of convexity of the relationship between temperature and respiration and the magnitude of the change in temperature variance. A potential consequence of this effect of variability would be higher respiration in regions where both the mean and variance of temperature are expected to increase, such as in some low latitude regions; and lower amounts of respiration where the average temperature is expected to increase and the variance to decrease, such as in northern high latitudes.

Attributing Changing Rates of Temperature Record Breaking to Anthropogenic Influences

Science.gov (United States)

King, Andrew D.

2017-11-01

Record-breaking temperatures attract attention from the media, so understanding how and why the rate of record breaking is changing may be useful in communicating the effects of climate change. A simple methodology designed for estimating the anthropogenic influence on rates of record breaking in a given time series is proposed here. The frequency of hot and cold record-breaking temperature occurrences is shown to be changing due to the anthropogenic influence on the climate. Using ensembles of model simulations with and without human-induced forcings, it is demonstrated that the effect of climate change on global record-breaking temperatures can be detected as far back as the 1930s. On local scales, a climate change signal is detected more recently at most locations. The anthropogenic influence on the increased occurrence of hot record-breaking temperatures is clearer than it is for the decreased occurrence of cold records. The approach proposed here could be applied in rapid attribution studies of record extremes to quantify the influence of climate change on the rate of record breaking in addition to the climate anomaly being studied. This application is demonstrated for the global temperature record of 2016 and the Central England temperature record in 2014.

Modulation of Amyloid-β Conformation by Charge State of N-Terminal Disordered Region

International Nuclear Information System (INIS)

Xi Wen-Hui; Li Wen-Fei; Wang Wei

2012-01-01

Based on molecular dynamics simulations, we show that variations of the charge states of the histidines, which are the main effects of pH-value change and metal binding, can lead to a drastic change of the intra-peptide interactions of the segment 17–42 and the conformational distribution of the monomeric amyloid-β (Aβ). Since we already knew that the conformational distribution of monomeric Aβ can largely affect Aβ fibrillar aggregation, our results suggest that the pH value change and metal binding can affect the Aβ aggregation by much more complex mechanism than just affecting the inter-peptide interactions. To fully understand the mechanism of metal binding and pH-value induced Aβ aggregation, we also need to consider their effects on the conformational distribution of monomeric Aβ. (cross-disciplinary physics and related areas of science and technology)

Conformational Selection and Induced Fit for RNA Polymerase and RNA/DNA Hybrid Backtracked Recognition

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Haifeng eChen

2015-11-01

Full Text Available RNA polymerase catalyzes transcription with a high fidelity. If DNA/RNA mismatch or DNA damage occurs downstream, a backtracked RNA polymerase can proofread this situation. However, the backtracked mechanism is still poorly understood. Here we have performed multiple explicit-solvent molecular dynamics (MD simulations on bound and apo DNA/RNA hybrid to study backtracked recognition. MD simulations at room temperature suggest that specific electrostatic interactions play key roles in the backtracked recognition between the polymerase and DNA/RNA hybrid. Kinetics analysis at high temperature shows that bound and apo DNA/RNA hybrid unfold via a two-state process. Both kinetics and free energy landscape analyses indicate that bound DNA/RNA hybrid folds in the order of DNA/RNA contracting, the tertiary folding and polymerase binding. The predicted Φ-values suggest that C7, G9, dC12, dC15 and dT16 are key bases for the backtracked recognition of DNA/RNA hybrid. The average RMSD values between the bound structures and the corresponding apo ones and Kolmogorov-Smirnov (KS P test analyses indicate that the recognition between DNA/RNA hybrid and polymerase might follow an induced fit mechanism for DNA/RNA hybrid and conformation selection for polymerase. Furthermore, this method could be used to relative studies of specific recognition between nucleic acid and protein.

Increased Risk of Drug-Induced Hyponatremia during High Temperatures

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Anna K Jönsson

2017-07-01

Full Text Available Purpose: To investigate the relationship between outdoor temperature in Sweden and the reporting of drug-induced hyponatremia to the Medical Products Agency (MPA. Methods: All individual adverse drug reactions (ADR reported to MPA from 1 January 2010 to 31 October 2013 of suspected drug-induced hyponatremia and random controls were identified. Reports where the ADR had been assessed as having at least a possible relation to the suspected drug were included. Information on administered drugs, onset date, causality assessment, sodium levels, and the geographical origin of the reports was extracted. A case-crossover design was used to ascertain the association between heat exposure and drug-induced hyponatremia at the individual level, while linear regression was used to study its relationship to sodium concentration in blood. Temperature exposure data were obtained from the nearest observation station to the reported cases. Results: During the study period, 280 reports of hyponatremia were identified. More cases of drug-induced hyponatremia were reported in the warmer season, with a peak in June, while other ADRs showed an opposite annual pattern. The distributed lag non-linear model indicated an increasing odds ratio (OR with increasing temperature in the warm season with a highest odds ratio, with delays of 1–5 days after heat exposure. A cumulative OR for a lag time of 1 to 3 days was estimated at 2.21 at an average daily temperature of 20 °C. The change in sodium per 1 °C increase in temperature was estimated to be −0.37 mmol/L (95% CI: −0.02, −0.72. Conclusions: Warm weather appears to increase the risk of drug-induced hyponatremia

Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

KAUST Repository

Wang, Wei; Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

2017-01-01

bioengineering applications and rational drug design. Constructing Markov State Models (MSMs) based on large-scale molecular dynamics simulations has emerged as a powerful approach to model functional conformational changes of the biomolecular system

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....

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.

Reversible conformational change in herpes simplex virus glycoprotein B with fusion-from-without activity is triggered by mildly acidic pH

Directory of Open Access Journals (Sweden)

Nicola Anthony V

2010-12-01

Full Text Available Abstract Background The pre-fusion form of the herpes simplex virus (HSV fusion protein gB undergoes pH-triggered conformational change in vitro and during viral entry (Dollery et al., J. Virol. 84:3759-3766, 2010. The antigenic structure of gB from the fusion-from-without (FFWO strain of HSV-1, ANG path, resembles wild type gB that has undergone pH-triggered changes. Together, changes in the antigenic and oligomeric conformation of gB correlate with fusion activity. We tested whether the pre-fusion form of FFWO gB undergoes altered conformational change in response to low pH. Results A pH of 5.5 - 6.0 altered the conformation of Domains I and V of FFWO gB, which together comprise the functional region containing the hydrophobic fusion loops. The ANG path gB oligomer was altered at a similar pH. All changes were reversible. In wild type HSV lacking the UL45 protein, which has been implicated in gB-mediated fusion, gB still underwent pH-triggered changes. ANG path entry was inactivated by pretreatment of virions with low pH. Conclusion The pre-fusion conformation of gB with enhanced fusion activity undergoes alteration in antigenic structure and oligomeric conformation in response to acidic pH. We propose that endosomal pH triggers conformational change in mutant gB with FFWO activity in a manner similar to wild type. Differences apart from this trigger may account for the increased fusion activity of FFWO gB.

Effect of temperature changes on swelling and creep of AISI 316

International Nuclear Information System (INIS)

Garner, F.A.; Gilbert, E.R.; Gelles, D.S.; Foster, J.P.

1980-04-01

A number of previous publications have shown that the swelling of cold-worked AISI 316 is quite sensitive to changes in temperature which occur during irradiation. In this report those data are expanded and reanalyzed to show that the concurrent irradiation creep is also quite sensitive to changes in irradiation temperature. An explanation is advanced to explain this behavior in terms of the sensitivity to temperture history of the radiation-induced microchemical evolution of this steel. In particular, the sensitivity to temperature history of the radiation-stabilized gamma prime phase is invoked to explain the enhanced creep and swelling behavior of AISI 316 components which experienced either gradual or abrupt decreases in temperature. The phase development observed in this steel in response to temperature changes during irradiation is also compared to the similar behavior found in aged specimens subjected to isothermal irradiation

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

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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.

Temperature-induced viral resistance in Emiliania huxleyi (Prymnesiophyceae).

Science.gov (United States)

Kendrick, B Jacob; DiTullio, Giacomo R; Cyronak, Tyler J; Fulton, James M; Van Mooy, Benjamin A S; Bidle, Kay D

2014-01-01

Annual Emiliania huxleyi blooms (along with other coccolithophorid species) play important roles in the global carbon and sulfur cycles. E. huxleyi blooms are routinely terminated by large, host-specific dsDNA viruses, (Emiliania huxleyi Viruses; EhVs), making these host-virus interactions a driving force behind their potential impact on global biogeochemical cycles. Given projected increases in sea surface temperature due to climate change, it is imperative to understand the effects of temperature on E. huxleyi's susceptibility to viral infection and its production of climatically active dimethylated sulfur species (DSS). Here we demonstrate that a 3°C increase in temperature induces EhV-resistant phenotypes in three E. huxleyi strains and that successful virus infection impacts DSS pool sizes. We also examined cellular polar lipids, given their documented roles in regulating host-virus interactions in this system, and propose that alterations to membrane-bound surface receptors are responsible for the observed temperature-induced resistance. Our findings have potential implications for global biogeochemical cycles in a warming climate and for deciphering the particular mechanism(s) by which some E. huxleyi strains exhibit viral resistance.

Substantial conformational change mediated by charge-triad residues of the death effector domain in protein-protein interactions.

Directory of Open Access Journals (Sweden)

Edward C Twomey

Full Text Available Protein conformational changes are commonly associated with the formation of protein complexes. The non-catalytic death effector domains (DEDs mediate protein-protein interactions in a variety of cellular processes, including apoptosis, proliferation and migration, and glucose metabolism. Here, using NMR residual dipolar coupling (RDC data, we report a conformational change in the DED of the phosphoprotein enriched in astrocytes, 15 kDa (PEA-15 protein in the complex with a mitogen-activated protein (MAP kinase, extracellular regulated kinase 2 (ERK2, which is essential in regulating ERK2 cellular distribution and function in cell proliferation and migration. The most significant conformational change in PEA-15 happens at helices α2, α3, and α4, which also possess the highest flexibility among the six-helix bundle of the DED. This crucial conformational change is modulated by the D/E-RxDL charge-triad motif, one of the prominent structural features of DEDs, together with a number of other electrostatic and hydrogen bonding interactions on the protein surface. Charge-triad motif promotes the optimal orientation of key residues and expands the binding interface to accommodate protein-protein interactions. However, the charge-triad residues are not directly involved in the binding interface between PEA-15 and ERK2.

Relationship between conformational changes in the dopamine transporter and cocaine-like subjective effects of uptake inhibitors

DEFF Research Database (Denmark)

Løland, Claus Juul; Desai, Rajeev I; Zou, Mu-Fa

2007-01-01

Cocaine exerts its stimulatory effect by inhibiting the dopamine transporter (DAT). However, novel benztropine- and rimcazole-based inhibitors show reduced stimulant effects compared with cocaine, despite higher affinity and selectivity for DAT. To investigate possible mechanisms, we compared...... the extracellular transporter gate is open but inaccessible when it is closed. The data indicated that cocaine analogs bind an open conformation, whereas benztropine and rimcazole analogs bind a closed conformation. Next, we investigated the changes in inhibition potency of [(3)H]dopamine uptake of the compounds...... at a mutant DAT (Y335A) characterized by a global change in the conformational equilibrium. We observed a close relationship between the decrease in potencies of inhibitors at this mutant and cocaine-like responding in rats trained to discriminate cocaine from saline injections. Our data suggest...

Lipid- and temperature-dependent structural changes in Acholeplasma laidlawii cell membrances

Energy Technology Data Exchange (ETDEWEB)

James, R.; Branton, D.

1973-01-01

The lipids in cell membranes of Acholeplasma laidlawii were enriched with different fatty acids selected to produce membranes showing molecular motion discontinuities at temperatures between 10 and 35/sup 0/C. Molecular motion in these membranes was probed by ESR after labelling with 12-nitroxide stearate, and structure in these membranes was examined by electron microscopy after freeze-etching. Freeze-etching and electron microscopy showed that under certain conditions the particles in the A. laidlawii membranes aggregated, resulting in particle-rich and particle-depleted regions in the cell membrane. Depending upon the lipid content of the membrane, this aggregation could begin at temperatures well above the ESR-determined discontinuity. Aggregation increased with decreasing temperature but was completed at or near the discontinuity. However, cell membranes grown and maintained well below their ESR-determined discontinuity did not show maximum particle aggregation until after they had been exposed to temperatures at or above the discontinuity. The results show that temperatures at or near a phase transition temperature can induce aggregation of the membrane particles. This suggests that temperature-induced changes in the lipid phase of a biological membrane can induce phase separations which affect the topography of associated proteins.

Hidden conformal symmetry of extremal black holes

International Nuclear Information System (INIS)

Chen Bin; Long Jiang; Zhang Jiaju

2010-01-01

We study the hidden conformal symmetry of extremal black holes. We introduce a new set of conformal coordinates to write the SL(2,R) generators. We find that the Laplacian of the scalar field in many extremal black holes, including Kerr(-Newman), Reissner-Nordstrom, warped AdS 3 , and null warped black holes, could be written in terms of the SL(2,R) quadratic Casimir. This suggests that there exist dual conformal field theory (CFT) descriptions of these black holes. From the conformal coordinates, the temperatures of the dual CFTs could be read directly. For the extremal black hole, the Hawking temperature is vanishing. Correspondingly, only the left (right) temperature of the dual CFT is nonvanishing, and the excitations of the other sector are suppressed. In the probe limit, we compute the scattering amplitudes of the scalar off the extremal black holes and find perfect agreement with the CFT prediction.

Conformational Assessment of Adnectin and Adnectin-Drug Conjugate by Hydrogen/Deuterium Exchange Mass Spectrometry

Science.gov (United States)

Huang, Richard Y.-C.; O'Neil, Steven R.; Lipovšek, Daša; Chen, Guodong

2018-05-01

Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region. HDX-MS dataset revealed the ability of peptide-based payload/linker to retain deuterium in HDX experiments. Combined results from intact, top-down, and bottom-up HDX indicated no significant conformational changes of adnectin 1 upon payload conjugation. [Figure not available: see fulltext.

Enhancing Architecture-Implementation Conformance with Change Management and Support for Behavioral Mapping

Science.gov (United States)

Zheng, Yongjie

2012-01-01

Software architecture plays an increasingly important role in complex software development. Its further application, however, is challenged by the fact that software architecture, over time, is often found not conformant to its implementation. This is usually caused by frequent development changes made to both artifacts. Against this background,…

Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3

International Nuclear Information System (INIS)

Diehl, Carl; Genheden, Samuel; Modig, Kristofer; Ryde, Ulf; Akke, Mikael

2009-01-01

The conformational entropy of proteins can make significant contributions to the free energy of ligand binding. NMR spin relaxation enables site-specific investigation of conformational entropy, via order parameters that parameterize local reorientational fluctuations of rank-2 tensors. Here we have probed the conformational entropy of lactose binding to the carbohydrate recognition domain of galectin-3 (Gal3), a protein that plays an important role in cell growth, cell differentiation, cell cycle regulation, and apoptosis, making it a potential target for therapeutic intervention in inflammation and cancer. We used 15 N spin relaxation experiments and molecular dynamics simulations to monitor the backbone amides and secondary amines of the tryptophan and arginine side chains in the ligand-free and lactose-bound states of Gal3. Overall, we observe good agreement between the experimental and computed order parameters of the ligand-free and lactose-bound states. Thus, the 15 N spin relaxation data indicate that the molecular dynamics simulations provide reliable information on the conformational entropy of the binding process. The molecular dynamics simulations reveal a correlation between the simulated order parameters and residue-specific backbone entropy, re-emphasizing that order parameters provide useful estimates of local conformational entropy. The present results show that the protein backbone exhibits an increase in conformational entropy upon binding lactose, without any accompanying structural changes

Voltage-Driven Conformational Switching with Distinct Raman Signature in a Single-Molecule Junction.

Science.gov (United States)

Bi, Hai; Palma, Carlos-Andres; Gong, Yuxiang; Hasch, Peter; Elbing, Mark; Mayor, Marcel; Reichert, Joachim; Barth, Johannes V

2018-04-11

Precisely controlling well-defined, stable single-molecule junctions represents a pillar of single-molecule electronics. Early attempts to establish computing with molecular switching arrays were partly challenged by limitations in the direct chemical characterization of metal-molecule-metal junctions. While cryogenic scanning probe studies have advanced the mechanistic understanding of current- and voltage-induced conformational switching, metal-molecule-metal conformations are still largely inferred from indirect evidence. Hence, the development of robust, chemically sensitive techniques is instrumental for advancement in the field. Here we probe the conformation of a two-state molecular switch with vibrational spectroscopy, while simultaneously operating it by means of the applied voltage. Our study emphasizes measurements of single-molecule Raman spectra in a room-temperature stable single-molecule switch presenting a signal modulation of nearly 2 orders of magnitude.

Observed changes of temperature extremes during 1960-2005 in China: natural or human-induced variations?

Science.gov (United States)

Zhang, Qiang; Li, Jianfeng; David Chen, Yongqin; Chen, Xiaohong

2011-12-01

The purpose of this study was to statistically examine changes of surface air temperature in time and space and to analyze two factors potentially influencing air temperature changes in China, i.e., urbanization and net solar radiation. Trends within the temperature series were detected by using Mann-Kendall trend test technique. The scientific problem this study expected to address was that what could be the role of human activities in the changes of temperature extremes. Other influencing factors such as net solar radiation were also discussed. The results of this study indicated that: (1) increasing temperature was observed mainly in the northeast and northwest China; (2) different behaviors were identified in the changes of maximum and minimum temperature respectively. Maximum temperature seemed to be more influenced by urbanization, which could be due to increasing urban albedo, aerosol, and air pollutions in the urbanized areas. Minimum temperature was subject to influences of variations of net solar radiation; (3) not significant increasing and even decreasing temperature extremes in the Yangtze River basin and the regions south to the Yangtze River basin could be the consequences of higher relative humidity as a result of increasing precipitation; (4) the entire China was dominated by increasing minimum temperature. Thus, we can say that the warming process of China was reflected mainly by increasing minimum temperature. In addition, consistently increasing temperature was found in the upper reaches of the Yellow River basin, the Yangtze River basin, which have the potential to enhance the melting of permafrost in these areas. This may trigger new ecological problems and raise new challenges for the river basin scale water resource management.

Climate-induced changes in river water temperature in North Iberian Peninsula

Science.gov (United States)

Soto, Benedicto

2017-06-01

This study evaluates the effects of climate change on the thermal regime of 12 rivers in the Northern Iberian Peninsula by using a non-linear regression model that employs air temperature as the only input variable. Prediction of future air temperature was obtained from five regional climate models (RCMs) under emission scenario Special Report on Emissions Scenarios A1B. Prior to simulation of water temperature, air temperature was bias-corrected (B-C) by means of variance scaling (VS) method. This procedure allows an improvement of fit between observed and estimated air temperature for all climate models. The simulation of water temperature for the period 1990-2100 shows an increasing trend, which is higher for the period of June-August (summer) and September-November (autumn) (0.0275 and 0.0281 °C/year) than that of winter (December-February) and spring (March-May) (0.0181 and 0.0218 °C/year). In the high air temperature range, daily water temperature is projected to increase on average by 2.2-3.1 °C for 2061-2090 relative to 1961-1990. During the coldest days, the increment of water temperature would range between 1.0 and 1.7 °C. In fact, employing the numbers of days that water temperature exceeded the upper incipient lethal temperature (UILT) for brown trout (24.7 °C) has been noted that this threshold is exceeded 14.5 days per year in 2061-2090 while in 1961-1990, this values was exceeded 2.6 days per year of mean and 3.6 days per year in observation period (2000-2014).

Conformational changes in IpaD from Shigella flexneri upon binding bile salts provide insight into the second step of type III secretion.

Science.gov (United States)

Dickenson, Nicholas E; Zhang, Lingling; Epler, Chelsea R; Adam, Philip R; Picking, Wendy L; Picking, William D

2011-01-18

Shigella flexneri uses its type III secretion apparatus (TTSA) to inject host-altering proteins into targeted eukaryotic cells. The TTSA is composed of a basal body and an exposed needle with invasion plasmid antigen D (IpaD) forming a tip complex that controls secretion. The bile salt deoxycholate (DOC) stimulates recruitment of the translocator protein IpaB into the maturing TTSA needle tip complex. This process appears to be triggered by a direct interaction between DOC and IpaD. Fluorescence spectroscopy and NMR spectroscopy are used here to confirm the DOC-IpaD interaction and to reveal that IpaD conformational changes upon DOC binding trigger the appearance of IpaB at the needle tip. Förster resonance energy transfer between specific sites on IpaD was used here to identify changes in distances between IpaD domains as a result of DOC binding. To further explore the effects of DOC binding on IpaD structure, NMR chemical shift mapping was employed. The environments of residues within the proposed DOC binding site and additional residues within the "distal" globular domain were perturbed upon DOC binding, further indicating that conformational changes occur within IpaD upon DOC binding. These events are proposed to be responsible for the recruitment of IpaB at the TTSA needle tip. Mutation analyses combined with additional spectroscopic analyses confirm that conformational changes in IpaD induced by DOC binding contribute to the recruitment of IpaB to the S. flexneri TTSA needle tip. These findings lay the foundation for determining how environmental factors promote TTSA needle tip maturation prior to host cell contact.

Conformational Changes in IpaD from Shigella flexneri Upon Binding Bile Salts Provide Insight into the Second Step of Type III Secretion†

Science.gov (United States)

Dickenson, Nicholas E.; Zhang, Lingling; Epler, Chelsea R.; Adam, Philip R.; Picking, Wendy L.; Picking, William D.

2011-01-01

Shigella flexneri uses its type III secretion apparatus (TTSA) to inject host-altering proteins into targeted eukaryotic cells. The TTSA is composed of a basal body and an exposed needle with invasion plasmid antigen D (IpaD) forming a tip complex that controls secretion. The bile salt deoxycholate (DOC) stimulates recruitment of the translocator protein IpaB into the maturing TTSA needle tip complex. This process appears to be triggered by a direct interaction between DOC and IpaD. Fluorescence spectroscopy and NMR spectroscopy are used here to confirm the DOC-IpaD interaction and to reveal that IpaD conformational changes upon DOC binding trigger the appearance of IpaB at the needle tip. Förster resonance energy transfer between specific sites on IpaD was used here to identify changes in distances between IpaD domains as a result of DOC binding. To further explore the effects of DOC binding on IpaD structure, NMR chemical shift mapping was employed. The environments of residues within the proposed DOC binding site and additional residues within the “distal” globular domain were perturbed upon DOC binding, further indicating that conformational changes occur within IpaD upon DOC binding. These events are proposed to be responsible for the recruitment of IpaB at the TTSA needle tip. Mutation analyses combined with additional spectroscopic analyses confirms that conformational changes in IpaD induced by DOC binding contribute to the recruitment of IpaB to the S. flexneri TTSA needle tip. These findings lay the foundation for determining how environmental factors promote TTSA needle tip maturation prior to host cell contact. PMID:21126091

Radiatively induced symmetry breaking and the conformally coupled magnetic monopole in AdS space

Science.gov (United States)

Edery, Ariel; Graham, Noah

2013-11-01

We implement quantum corrections for a magnetic monopole in a classically conformally invariant theory containing gravity. This yields the trace (conformal) anomaly and introduces a length scale in a natural fashion via the process of renormalization. We evaluate the one-loop effective potential and extract the vacuum expectation value (VEV) from it; spontaneous symmetry breaking is radiatively induced. The VEV is set at the renormalization scale M and we exchange the dimensionless scalar coupling constant for the dimensionful VEV via dimensional transmutation. The asymptotic (background) spacetime is anti-de Sitter (AdS) and its Ricci scalar is determined entirely by the VEV. We obtain analytical asymptotic solutions to the coupled set of equations governing gravitational, gauge and scalar fields that yield the magnetic monopole in an AdS spacetime.

75 FR 76260 - Conforming Changes to Applicant Submission Requirements; Implementing Federal Financial Report...

Science.gov (United States)

2010-12-08

... HUD regulations to reference the new governmentwide Federal Financial Report (FFR) approved by the... task of filing required financial reports. Similarly, CCR registration has been required of applicants...] RIN 2501-AD50 Conforming Changes to Applicant Submission Requirements; Implementing Federal Financial...

On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A

Science.gov (United States)

Chopade, Prashant D.; Sarma, Bipul; Santiso, Erik E.; Simpson, Jeffrey; Fry, John C.; Yurttas, Nese; Biermann, Kari L.; Chen, Jie; Trout, Bernhardt L.; Myerson, Allan S.

2015-12-01

The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.

On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A

International Nuclear Information System (INIS)

Chopade, Prashant D.; Sarma, Bipul; Santiso, Erik E.; Chen, Jie; Trout, Bernhardt L.; Myerson, Allan S.; Simpson, Jeffrey; Fry, John C.; Biermann, Kari L.; Yurttas, Nese

2015-01-01

The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described

On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A

Energy Technology Data Exchange (ETDEWEB)

Chopade, Prashant D.; Sarma, Bipul; Santiso, Erik E.; Chen, Jie; Trout, Bernhardt L.; Myerson, Allan S., E-mail: myerson@mit.edu [Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 66-568, Cambridge, Massachusetts 02139 (United States); Simpson, Jeffrey [Department of Chemistry Instrumentation Facility, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 18-0090, Cambridge, Massachusetts 02139 (United States); Fry, John C.; Biermann, Kari L. [Connect Consulting, 6 Hollands Field, Horsham RH123HQ (United Kingdom); Yurttas, Nese [Cargill, Inc., Global Food Technology, 2301 Crosby Road, Wayzata, Minnesota 55391 (United States)

2015-12-28

The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.

Irradiation-induced dimensional changes of poorly crystalline carbons

International Nuclear Information System (INIS)

Bullock, R.E.

1979-01-01

Data are presented on irradiation-induced changes of poorly crystalline carbons at high temperatures(>900 0 C). The materials surveyed include: (1) carbon fibers, (2) glassy carbons, (3) carbonaceous matrix materials for HTGR fuel rods and (4) pyrocarbons. The materials are listed in order of increasing stability, with maximum strains ranging from more than 50% for fibers to less than 10% for pyrocarbons. Dimensional changes of highly anisotropic carbon fibers appear to be sensitive to irradiation temperature, as slightly anisotropic pyrocarbons are, whereas temperature seems to have little influence on the behavior of isotropic glassy carbons over the range from 600 to 1350 0 C. Dimensional changes for graphite-filled matrix materials were roughly isotropic on the average and did not seem to be strongly temperature dependent for the lower fluences investigated. Increased graphite filler lowered volumetric dimensional changes of the matrix in agreement with a rule-of-mixtures relationship between change components for the filler and the less-stable binder phases. Instabilities of all of the poorly crystalline materials were generally greater than those for more crystalline carbons under the same conditions, including highly orientated graphites that approximate single-crystal behavior. (author)

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

Temperature-dependent changes in the host-seeking behaviors of parasitic nematodes.

Science.gov (United States)

Lee, Joon Ha; Dillman, Adler R; Hallem, Elissa A

2016-05-06

Entomopathogenic nematodes (EPNs) are lethal parasites of insects that are of interest as biocontrol agents for insect pests and disease vectors. Although EPNs have been successfully commercialized for pest control, their efficacy in the field is often inconsistent for reasons that remain elusive. EPN infective juveniles (IJs) actively search for hosts to infect using a diverse array of host-emitted odorants. Here we investigate whether their host-seeking behavior is subject to context-dependent modulation. We find that EPN IJs exhibit extreme plasticity of olfactory behavior as a function of cultivation temperature. Many odorants that are attractive for IJs grown at lower temperatures are repulsive for IJs grown at higher temperatures and vice versa. Temperature-induced changes in olfactory preferences occur gradually over the course of days to weeks and are reversible. Similar changes in olfactory behavior occur in some EPNs as a function of IJ age. EPNs also show temperature-dependent changes in their host-seeking strategy: IJs cultured at lower temperatures appear to more actively cruise for hosts than IJs cultured at higher temperatures. Furthermore, we find that the skin-penetrating rat parasite Strongyloides ratti also shows temperature-dependent changes in olfactory behavior, demonstrating that such changes occur in mammalian-parasitic nematodes. IJs are developmentally arrested and long-lived, often surviving in the environment through multiple seasonal temperature changes. Temperature-dependent modulation of behavior may enable IJs to optimize host seeking in response to changing environmental conditions, and may play a previously unrecognized role in shaping the interactions of both beneficial and harmful parasitic nematodes with their hosts.

Cdc6-Induced Conformational Changes in ORC Bound to Origin DNA Revealed by Cryo-Electron Microscopy

Energy Technology Data Exchange (ETDEWEB)

Sun J.; Li H.; Kawakami, H.; Zech, J.; Speck, C.; Stillman, B.

2012-03-07

The eukaryotic origin recognition complex (ORC) interacts with and remodels origins of DNA replication prior to initiation in S phase. Here, we report a single-particle cryo-EM-derived structure of the supramolecular assembly comprising Saccharomyces cerevisiae ORC, the replication initiation factor Cdc6, and double-stranded ARS1 origin DNA in the presence of ATP{gamma}S. The six subunits of ORC are arranged as Orc1:Orc4:Orc5:Orc2:Orc3, with Orc6 binding to Orc2. Cdc6 binding changes the conformation of ORC, in particular reorienting the Orc1 N-terminal BAH domain. Segmentation of the 3D map of ORC-Cdc6 on DNA and docking with the crystal structure of the homologous archaeal Orc1/Cdc6 protein suggest an origin DNA binding model in which the DNA tracks along the interior surface of the crescent-like ORC. Thus, ORC bends and wraps the DNA. This model is consistent with the observation that binding of a single Cdc6 extends the ORC footprint on origin DNA from both ends.

Conformational analysis of HAMLET, the folding variant of human alpha-lactalbumin associated with apoptosis.

Science.gov (United States)

Casbarra, Annarita; Birolo, Leila; Infusini, Giuseppe; Dal Piaz, Fabrizio; Svensson, Malin; Pucci, Piero; Svanborg, Catharina; Marino, Gennaro

2004-05-01

A combination of hydrogen/deuterium (H/D) exchange and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the conformation in solution of HAMLET, the folding variant of human alpha-lactalbumin, complexed to oleic acid, that induces apoptosis in tumor and immature cells. Although near- and far-UV CD and fluorescence spectroscopy were not able to discriminate between HAMLET and apo-alpha-lactalbumin, H/D exchange experiments clearly showed that they correspond to two distinct conformational states, with HAMLET incorporating a greater number of deuterium atoms than the apo and holo forms. Complementary proteolysis experiments revealed that HAMLET and apo are both accessible to proteases in the beta-domain but showed substantial differences in accessibility to proteases at specific sites. The overall results indicated that the conformational changes associated with the release of Ca2+ are not sufficient to induce the HAMLET conformation. Metal depletion might represent the first event to produce a partial unfolding in the beta-domain of alpha-lactalbumin, but some more unfolding is needed to generate the active conformation HAMLET, very likely allowing the protein to bind the C18:1 fatty acid moiety. On the basis of these data, a putative binding site of the oleic acid, which stabilizes the HAMLET conformation, is proposed.

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...

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

Temperature dependent rapid annealing effect induces amorphous aggregation of human serum albumin.

Science.gov (United States)

Ishtikhar, Mohd; Ali, Mohd Sajid; Atta, Ayman M; Al-Lohedan, Hammad; Badr, Gamal; Khan, Rizwan Hasan

2016-01-01

This study represents an analysis of the thermal aggregation of human serum albumin (HSA) induced by novel rosin modified compounds. The aggregation process causes conformational alterations in the secondary and tertiary structures of the proteins. The conversion of globular protein to amorphous aggregates was carried out by spectroscopic, calorimetric and microscopic techniques to investigate the factors that are responsible for the structural, conformational and morphological alteration in the protein. Our outcome results show that the aggregation of HSA was dependent on the hydrophobicity, charge and temperature, because the formation of amorphous aggregates occurs in the presence of a novel cationic rosin compound, quaternary amine of rosin diethylaminoethyl ester (QRMAE), at 40°C and pH 7.4 (but at 25°C on similar pH value, there was no evidence of aggregate formation). In addition, the parent compound of QRMAE, i.e., abietic acid, and other derivatives such as nonionic rosin compounds [(RMPEG-750) and (RMA-MPEG-750)] do not shows the aggregating property. This work provides precise and necessary information that aid in the understanding the effects of rosin derivative compounds on HSA. This study also restrains important information for athletes, health providers, pharmaceutical companies, industries, and soft drink-processing companies. Copyright © 2015 Elsevier B.V. All rights reserved.

Single-molecule fluorescence polarization study of conformational change in archaeal group II chaperonin.

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Ryo Iizuka

Full Text Available Group II chaperonins found in archaea and in eukaryotic cytosol mediate protein folding without a GroES-like cofactor. The function of the cofactor is substituted by the helical protrusion at the tip of the apical domain, which forms a built-in lid on the central cavity. Although many studies on the change in lid conformation coupled to the binding and hydrolysis of nucleotides have been conducted, the molecular mechanism of lid closure remains poorly understood. Here, we performed a single-molecule polarization modulation to probe the rotation of the helical protrusion of a chaperonin from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1. We detected approximately 35° rotation of the helical protrusion immediately after photorelease of ATP. The result suggests that the conformational change from the open lid to the closed lid state is responsible for the approximately 35° rotation of the helical protrusion.

G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch.

Science.gov (United States)

Yan, Yi-Yong; Tan, Jia-Heng; Lu, Yu-Jing; Yan, Siu-Cheong; Wong, Kwok-Yin; Li, Ding; Gu, Lian-Quan; Huang, Zhi-Shu

2013-10-01

G-Quadruplex is a highly polymorphic structure, and its behavior in acidic condition has not been well studied. Circular dichroism (CD) spectra were used to study the conformational change of G-quadruplex. The thermal stabilities of the G-quadruplex were measured with CD melting. Interconversion kinetics profiles were investigated by using CD kinetics. The fluorescence of the inserted 2-Aminopurine (Ap) was monitored during pH change and acrylamide quenching, indicating the status of the loop. Proton NMR was adopted to help illustrate the change of the conformation. G-Quadruplex of specific loop was found to be able to transform upon pH variation. The transformation was resulted from the loop rearrangement. After screening of a library of diverse G-quadruplex, a sequence exhibiting the best transformation property was found. A pH-driven nanoswitch with three gears was obtained based on this transition cycle. Certain G-quadruplex was found to go through conformational change at low pH. Loop was the decisive factor controlling the interconversion upon pH variation. G-Quadruplex with TT central loop could be converted in a much milder condition than the one with TTA loop. It can be used to design pH-driven nanodevices such as a nanoswitch. These results provide more insights into G-quadruplex polymorphism, and also contribute to the design of DNA-based nanomachines and logic gates. © 2013.

Self-induced temperature gradients in Brownian dynamics

Science.gov (United States)

Devine, Jack; Jack, M. W.

2017-12-01

Brownian systems often surmount energy barriers by absorbing and emitting heat to and from their local environment. Usually, the temperature gradients created by this heat exchange are assumed to dissipate instantaneously. Here we relax this assumption to consider the case where Brownian dynamics on a time-independent potential can lead to self-induced temperature gradients. In the same way that externally imposed temperature gradients can cause directed motion, these self-induced gradients affect the dynamics of the Brownian system. The result is a coupling between the local environment and the Brownian subsystem. We explore the resulting dynamics and thermodynamics of these coupled systems and develop a robust method for numerical simulation. In particular, by focusing on one-dimensional situations, we show that self-induced temperature gradients reduce barrier-crossing rates. We also consider a heat engine and a heat pump based on temperature gradients induced by a Brownian system in a nonequilibrium potential.

Vibrational spectrum, ab initio calculations, conformational stabilities and assignment of fundamentals of 1,2-dibromopropane

Science.gov (United States)

LaPlante, Arthur J.; Stidham, Howard D.

2009-10-01

The mid and far infrared and the Raman spectrum of 1,2-dibromopropane is reported in solid, liquid and gas. Several bands reported by earlier workers are not present in the spectrum of the purified material. Ab initio calculations of optimized geometry, energy, dipole moment, molar volume, vibrational spectrum and normal coordinate calculation were performed using the density functional B3LYP/6-311++g(3df,2pd), and the results used to assist a complete assignment of the 81 fundamental modes of vibrations of the three conformers of 1,2-dibromopropane. Relative energies found conformer A the lowest with G and G' at 815.6 and 871.4 cm -1 higher. The temperature dependence of the Raman spectrum of the liquid was investigated in the CCC bending region and the relative energies determined. It was found that the G' and G conformers lie 236 ± 11 and 327 ±11 cm -1, respectively above the A conformer, leading to the room temperature composition of the liquid as A, 65 ± 1; G', 21 ± 1; G, 14 ± 1%. It is apparent that the calculated highest energy conformer G' is stabilized more than the G conformer in the liquid. The G' conformer has the lowest molar volume effectively changing the interaction distance between conformers in the liquid, and enhancing the effect of its dipole moment.

Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

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Soares Alexei S

2007-11-01

Full Text Available Abstract Background Ricin is a potent toxin and known bioterrorism threat with no available antidote. The ricin A-chain (RTA acts enzymatically to cleave a specific adenine base from ribosomal RNA, thereby blocking translation. To understand better the relationship between ligand binding and RTA active site conformational change, we used a fragment-based approach to find a minimal set of bonding interactions able to induce rearrangements in critical side-chain positions. Results We found that the smallest ligand stabilizing an open conformer of the RTA active site pocket was an amide group, bound weakly by only a few hydrogen bonds to the protein. Complexes with small amide-containing molecules also revealed a switch in geometry from a parallel towards a splayed arrangement of an arginine-tryptophan cation-pi interaction that was associated with an increase and red-shift in tryptophan fluorescence upon ligand binding. Using the observed fluorescence signal, we determined the thermodynamic changes of adenine binding to the RTA active site, as well as the site-specific binding of urea. Urea binding had a favorable enthalpy change and unfavorable entropy change, with a ΔH of -13 ± 2 kJ/mol and a ΔS of -0.04 ± 0.01 kJ/(K*mol. The side-chain position of residue Tyr80 in a complex with adenine was found not to involve as large an overlap of rings with the purine as previously considered, suggesting a smaller role for aromatic stacking at the RTA active site. Conclusion We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the

Climatic impact of aircraft induced ozone changes

Energy Technology Data Exchange (ETDEWEB)

Sausen, R; Feneberg, B; Ponater, M [Deutsche Forschungs- und Versuchsanstalt fuer Luft- und Raumfahrt e.V., Oberpfaffenhofen (Germany). Inst. fuer Physik der Atmosphaere

1998-12-31

The effect of aircraft induced ozone changes on the global climate is studied by means of the general circulation model ECHAM4. The zonal mean temperature signal is considered. In order to estimate the statistical significance of the climatic impact a multivariate statistical test hierarchy combined with the fingerprint method has been applied. Sensitivity experiments show a significant coherent temperature response pattern in the northern extra-tropics for mid-latitude summer conditions. It consists of a tropospheric warming of about 0.2 K with a corresponding stratospheric cooling of the same magnitude. (author) 16 refs.

Climatic impact of aircraft induced ozone changes

Energy Technology Data Exchange (ETDEWEB)

Sausen, R.; Feneberg, B.; Ponater, M. [Deutsche Forschungs- und Versuchsanstalt fuer Luft- und Raumfahrt e.V., Oberpfaffenhofen (Germany). Inst. fuer Physik der Atmosphaere

1997-12-31

The effect of aircraft induced ozone changes on the global climate is studied by means of the general circulation model ECHAM4. The zonal mean temperature signal is considered. In order to estimate the statistical significance of the climatic impact a multivariate statistical test hierarchy combined with the fingerprint method has been applied. Sensitivity experiments show a significant coherent temperature response pattern in the northern extra-tropics for mid-latitude summer conditions. It consists of a tropospheric warming of about 0.2 K with a corresponding stratospheric cooling of the same magnitude. (author) 16 refs.

Eliminating Age Differences in Children's and Adults' Suggestibility and Memory Conformity Effects

Science.gov (United States)

Otgaar, Henry; Howe, Mark L.; Brackmann, Nathalie; van Helvoort, Daniël H. J.

2017-01-01

We examined whether typical developmental trends in suggestion-induced false memories (i.e., age-related decrease) could be changed. Using theoretical principles from the spontaneous false memory field, we adapted 2 often-used false memory procedures: misinformation (Experiment 1) and memory conformity (Experiment 2). In Experiment 1, 7- to…

Conformational changes of the amyloid beta-peptide (1-40) adsorbed on solid surfaces

NARCIS (Netherlands)

Giacomelli, CE; Norde, W

2005-01-01

The conformational change of the 39-43 residues of the amyloid beta-peptide (A beta) toward a beta-sheet enriched state promotes self-aggregation of the peptide molecules and constitutes the major peptide component of the amyloid plaques in Alzheimer patients. The crucial question behind the

Conformational changes of the amyloid beta-peptide (1-40) adsorbed on solid surfaces

NARCIS (Netherlands)

Giacomelli, C.E.; Norde, W.

2005-01-01

The conformational change of the 39-43 residues of the amyloid beta -peptide (A beta) toward a beta -sheet enriched state promotes self-aggregation of the peptide molecules and constitutes the major peptide component of the amyloid plaques in Alzheimer patients. The crucial question behind the

Electron paramagnetic resonance in myoglobin single crystals doped with Cu(II) : conformational changes

International Nuclear Information System (INIS)

Nascimento, O.R.

1976-03-01

Single crystals of sperm whale met-Myoglobin were doped with Cu (II) by immersion in a saturaded solution of NH 3 (SO 4 ) containing diluted Cu (SO 4 ).Two isotropic EPR spectra with different parameters and three anisotropic EPR spectra corresponding to three distinct types of Cu(II) : Mb complexes were identified. A fitting of the angular variation of the EPR spectrum of one of the complexes named here Cu(II)A : Mb was done using a spin Hamiltonian with axial symmetry calculated up to second order which gave the EPR hyperfine parameters.A study of the thermal variation of the complex Cu (II)A : Mb EPR spectrum in the temperature range of 25 0 C to 55 0 C allowed an identification of a conformational variation of the molecule the spectrum evolved from the anisotropic to isotropic spectrum with different parameters. A model of the Cu(II)A : Mb complex is proposed to explain the conformational change of the molecule by means of EPR spectra before and after thermal treatment. The isotropic spectrum obtained with the crystal at 55 0 C presents the EPR parameters very similar to the same parameters obtained with the Cu (II) : Mb complex in aqueous solution at 77 0 K, whereas the isotropic spectra parameters obtained with the dried crystal are quite different. It was possible to identify two different tertiary structures of the myoglobin molecule : one corresponding to the molecule in the crystal at 55 0 C and other to the dry crystal. A slight difference in the crystalline and solution structure of the myoglobin mollecule is observed. (Author) [pt

Climate Impacts of Fire-Induced Land-Surface Changes

Science.gov (United States)

Liu, Y.; Hao, X.; Qu, J. J.

2017-12-01

One of the consequences of wildfires is the changes in land-surface properties such as removal of vegetation. This will change local and regional climate through modifying the land-air heat and water fluxes. This study investigates mechanism by developing and a parameterization of fire-induced land-surface property changes and applying it to modeling of the climate impacts of large wildfires in the United States. Satellite remote sensing was used to quantitatively evaluate the land-surface changes from large fires provided from the Monitoring Trends in Burning Severity (MTBS) dataset. It was found that the changes in land-surface properties induced by fires are very complex, depending on vegetation type and coverage, climate type, season and time after fires. The changes in LAI are remarkable only if the actual values meet a threshold. Large albedo changes occur in winter for fires in cool climate regions. The signs are opposite between the first post-fire year and the following years. Summer day-time temperature increases after fires, while nigh-time temperature changes in various patterns. The changes are larger in forested lands than shrub / grassland lands. In the parameterization scheme, the detected post-fire changes are decomposed into trends using natural exponential functions and fluctuations of periodic variations with the amplitudes also determined by natural exponential functions. The final algorithm is a combination of the trends, periods, and amplitude functions. This scheme is used with Earth system models to simulate the local and regional climate effects of wildfires.

Analysis of calcium-induced effects on the conformation of fengycin.

Science.gov (United States)

Nasir, Mehmet Nail; Laurent, Pascal; Flore, Christelle; Lins, Laurence; Ongena, Marc; Deleu, Magali

2013-06-01

Fengycin is a natural lipopeptide with antifungal and eliciting properties and able to inhibit the activity of phospholipase A2. A combination of CD, FT-IR, NMR and fluorescence spectroscopic techniques was applied to elucidate its conformation in a membrane-mimicking environment and to investigate the effect of calcium ions on it. We mainly observed that fengycin adopts a turn conformation. Our results showed that calcium ions are bound by the two charged glutamates. The calcium binding has an influence on the fengycin conformation and more particularly, on the environment of the tyrosine residues. The modulation of the fengycin conformation by the environmental conditions may influence its biological properties. Copyright © 2013 Elsevier B.V. All rights reserved.

Temperature responsive porous silicon nanoparticles for cancer therapy - spatiotemporal triggering through infrared and radiofrequency electromagnetic heating.

Science.gov (United States)

Tamarov, Konstantin; Xu, Wujun; Osminkina, Liubov; Zinovyev, Sergey; Soininen, Pasi; Kudryavtsev, Andrey; Gongalsky, Maxim; Gaydarova, Azha; Närvänen, Ale; Timoshenko, Victor; Lehto, Vesa-Pekka

2016-11-10

One critical functionality of the carrier system utilized in targeted drug delivery is its ability to trigger the release of the therapeutic cargo once the carrier has reached its target. External triggering is an alluring approach as it can be applied in a precise spatiotemporal manner. In the present study, we achieved external triggering through the porous silicon (PSi) nanoparticles (NPs) by providing a pulse of infrared or radiofrequency radiation. The NPs were grafted with a temperature responsive polymer whose critical temperature was tailored to be slightly above 37°C. The polymer coating improved the biocompatibility of the NPs significantly in comparison with their uncoated counterparts. Radiation induced a rapid temperature rise, which resulted in the collapse of the polymer chains facilitating the cargo release. Both infrared and radiofrequency radiation were able to efficiently trigger the release of the encapsulated drug in vitro and induce significant cell death in comparison to the control groups. Radiofrequency radiation was found to be more efficient in vitro, and the treatment efficacy was verified in vivo in a lung carcinoma (3LL) mice model. After a single intratumoral administration of the carrier system combined with radiofrequency radiation, there was clear suppression of the growth of the carcinoma and a prolongation of the survival time of the animals. The temperature responsive (TR) polymer grafted on the surface of porous silicon nanoparticles (PSi NPs) changes its conformation in response to the heating induced by infrared or radiofrequency radiation. The conformation change allows the loaded doxorubicin to escape from the pores, achieving controlled drug release from TR PSi NPs, which displayed efficacy against malignant cells both in vitro and in vivo. Copyright © 2016 Elsevier B.V. All rights reserved.

Binding of Cimetidine to Balb/C Mouse Liver Catalase; Kinetics and Conformational Studies.

Science.gov (United States)

Jahangirvand, Mahboubeh; Minai-Tehrani, Dariush; Yazdi, Fatemeh; Minai-Tehrani, Arash; Razmi, Nematollah

2016-01-01

Catalase is responsible for converting hydrogen peroxide (H2O2) into water and oxygen in cells. This enzyme has high affinity for hydrogen peroxide and can protect the cells from oxidative stress damage. Catalase is a tetramer protein and each monomer contains a heme group. Cimetidine is a histamine H2 receptor blocker which inhibits acid release from stomach and is used for gasterointestinal diseases. In this research, effect of cimetidine on the activity of liver catalase was studied and the kinetic parameters of this enzyme and its conformational changes were investigated. Cell free extract of mouse liver was used for the catalase assay. The activity of the catalase was detected in the absence and presence of cimetidine by monitoring hydrogen peroxide reduction absorbance at 240 nm. The purified enzyme was used for conformational studies by Fluorescence spectrophotometry. The data showed that cimetidine could inhibit the enzyme in a non-competitive manner. Ki and IC50 values of the drug were determined to be about 0.75 and 0.85 uM, respectively. The Arrhenius plot showed that activation energy was 6.68 and 4.77 kJ/mol in the presence and absence of the drug, respectively. Fluorescence spectrophotometry revealed that the binding of cimetidine to the purified enzyme induced hyperchromicity and red shift which determined the conformational change on the enzyme. Cimetidine could non-competitively inhibit the liver catalase with high affinity. Binding of cimetidine to the enzyme induced conformational alteration in the enzyme.

Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1.

Science.gov (United States)

Stamogiannos, Athanasios; Maben, Zachary; Papakyriakou, Athanasios; Mpakali, Anastasia; Kokkala, Paraskevi; Georgiadis, Dimitris; Stern, Lawrence J; Stratikos, Efstratios

2017-03-14

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that is important for the generation of antigenic epitopes and major histocompatibility class I-restricted adaptive immune responses. ERAP1 processes a vast variety of different peptides but still shows length and sequence selectivity, although the mechanism behind these properties is poorly understood. X-ray crystallographic analysis has revealed that ERAP1 can assume at least two distinct conformations in which C-terminal domain IV is either proximal or distal to active site domain II. To improve our understanding of the role of this conformational change in the catalytic mechanism of ERAP1, we used site-directed mutagenesis to perturb key salt bridges between domains II and IV. Enzymatic analysis revealed that these mutations, although located away from the catalytic site, greatly reduce the catalytic efficiency and change the allosteric kinetic behavior. The variants were more efficiently activated by small peptides and bound a competitive inhibitor with weaker affinity and faster dissociation kinetics. Molecular dynamics analysis suggested that the mutations affect the conformational distribution of ERAP1, reducing the population of closed states. Small-angle X-ray scattering indicated that both the wild type and the ERAP1 variants are predominantly in an open conformational state in solution. Overall, our findings suggest that electrostatic interactions between domains II and IV in ERAP1 are crucial for driving a conformational change that regulates the structural integrity of the catalytic site. The extent of domain opening in ERAP1 probably underlies its specialization for antigenic peptide precursors and should be taken into account in inhibitor development efforts.

Conformational changes in a hyperthermostable glycoside hydrolase: enzymatic activity is a consequence of the loop dynamics and protonation balance.

Directory of Open Access Journals (Sweden)

Leandro C de Oliveira

Full Text Available Endo-β-1, 4-mannanase from Thermotoga petrophila (TpMan is a modular hyperthermostable enzyme involved in the degradation of mannan-containing polysaccharides. The degradation of these polysaccharides represents a key step for several industrial applications. Here, as part of a continuing investigation of TpMan, the region corresponding to the GH5 domain (TpManGH5 was characterized as a function of pH and temperature. The results indicated that the enzymatic activity of the TpManGH5 is pH-dependent, with its optimum activity occurring at pH 6. At pH 8, the studies demonstrated that TpManGH5 is a molecule with a nearly spherical tightly packed core displaying negligible flexibility in solution, and with size and shape very similar to crystal structure. However, TpManGH5 experiences an increase in radius of gyration in acidic conditions suggesting expansion of the molecule. Furthermore, at acidic pH values, TpManGH5 showed a less globular shape, probably due to a loop region slightly more expanded and flexible in solution (residues Y88 to A105. In addition, molecular dynamics simulations indicated that conformational changes caused by pH variation did not change the core of the TpManGH5, which means that only the above mentioned loop region presents high degree of fluctuations. The results also suggested that conformational changes of the loop region may facilitate polysaccharide and enzyme interaction. Finally, at pH 6 the results indicated that TpManGH5 is slightly more flexible at 65°C when compared to the same enzyme at 20°C. The biophysical characterization presented here is well correlated with the enzymatic activity and provide new insight into the structural basis for the temperature and pH-dependent activity of the TpManGH5. Also, the data suggest a loop region that provides a starting point for a rational design of biotechnological desired features.

The effects of information and social conformity on opinion change.

Science.gov (United States)

Mallinson, Daniel J; Hatemi, Peter K

2018-01-01

Extant research shows that social pressures influence acts of political participation, such as turning out to vote. However, we know less about how conformity pressures affect one's deeply held political values and opinions. Using a discussion-based experiment, we untangle the unique and combined effects of information and social pressure on a political opinion that is highly salient, politically charged, and part of one's identity. We find that while information plays a role in changing a person's opinion, the social delivery of that information has the greatest effect. Thirty three percent of individuals in our treatment condition change their opinion due to the social delivery of information, while ten percent respond only to social pressure and ten percent respond only to information. Participants that change their opinion due to social pressure in our experiment are more conservative politically, conscientious, and neurotic than those that did not.

The effects of information and social conformity on opinion change

Science.gov (United States)

Hatemi, Peter K.

2018-01-01

Extant research shows that social pressures influence acts of political participation, such as turning out to vote. However, we know less about how conformity pressures affect one’s deeply held political values and opinions. Using a discussion-based experiment, we untangle the unique and combined effects of information and social pressure on a political opinion that is highly salient, politically charged, and part of one’s identity. We find that while information plays a role in changing a person’s opinion, the social delivery of that information has the greatest effect. Thirty three percent of individuals in our treatment condition change their opinion due to the social delivery of information, while ten percent respond only to social pressure and ten percent respond only to information. Participants that change their opinion due to social pressure in our experiment are more conservative politically, conscientious, and neurotic than those that did not. PMID:29718958

Thermally induced changes of optical and vital parameters in human cancer cells

Science.gov (United States)

Dressler, C.; Schwandt, D.; Beuthan, J.; Mildaziene, V.; Zabarylo, U.; Minet, O.

2010-11-01

Minimally invasive laser-induced thermotherapy (LITT) presents an alternative method to conventional tumor therapeutically interventions, such as surgery, chemotherapy, radiotherapy or nuclear medicine. Optical tissue characteristics of tumor cells and their heat-induced changes are essential issues for controlling LITT progressions. Therefore, it is indispensable to exactly know the absorption coefficient μa, the scattering coefficient μs and the anisotropy factor g as well as their changes under rising temperatures in order to simulate the treatment parameters successfully. Optical parameters of two different cancer model tissues - breast cancer cells species MX1 and colon cancer cells species CX1 - were measured in the spectral range 400 - 1100 nm as well as in the temperature range 37 - 60°C. The absorption coefficient of both cell species was low throughout the spectral range analyzed, while μs of both species rose with increasing temperatures. The anisotropy factor g however dropped for both tissues with increasing temperatures. Light scatterings inside tissues proceeded continuously forward for all species tested. It was demonstrated that optical tissue properties undergo significant changes along with the vital status of the cells when the temperature increases.

The carbon monoxide stretching modes in camphor-bound cytochrome P-450cam. The effect of solvent conditions, temperature, and pressure.

Science.gov (United States)

Schulze, H; Ristau, O; Jung, C

1994-09-15

The effect of pH, monovalent cations, glycerol, temperature, and pressure on the carbonmonoxy (CO) stretching mode of camphor-bound cytochrome P-450cam (CYP 101) was studied. Two effects, band overlap and frequency shift, have been observed. The CO stretch infrared band located at about 1940 cm-1 is asymmetric because of the overlap of three bands at about 1931 cm-1, 1939 cm-1, and 1942 cm-1 with strongly different populations. Reducing the temperature or increasing the pressure leads to splitting the band or switching the asymmetry from the lower energy side to the higher energy side of the infrared band. The overlap of several CO stretch bands indicates conformational substates within the heme pocket. A frequency shift of the predominantly populated band is observed by changing all the parameters mentioned. The pH-induced frequency shift follows an S-shape with the pK at 6.2, which matches the pK observed for the pH-induced high-spin/low-spin transition. Conformational changes on the proximal heme side are suggested to be the origin. Monovalent cations at saturating concentration induce a small frequency shift depending on the ion radius. The potassium ion is the one that induces a CO stretch frequency with the highest wave-number while sodium and lithium (smaller radii) and rubidium and caesium ion (larger radii) have diminished values, which is supporting evidence for the special function of the potassium ion within the structure. Glycerol and hydrostatic pressure induce a red shift of the CO stretching frequency. Forced contact of the polar hydroxyl group of Thr252 of the I helix induced by pressure and indirectly by glycerol is suggested to change the CO dipole moment, reflecting in the decreased CO stretching frequency.

Experimental evaluation of the pressure and temperature dependence of ion-induced nucleation.

Science.gov (United States)

Munir, Muhammad Miftahul; Suhendi, Asep; Ogi, Takashi; Iskandar, Ferry; Okuyama, Kikuo

2010-09-28

An experimental system for the study of ion-induced nucleation in a SO(2)/H(2)O/N(2) gas mixture was developed, employing a soft x-ray at different pressure and temperature levels. The difficulties associated with these experiments included the changes in physical properties of the gas mixture when temperature and pressure were varied. Changes in the relative humidity (RH) as a function of pressure and temperature also had a significant effect on the different behaviors of the mobility distributions of particles. In order to accomplish reliable measurement and minimize uncertainties, an integrated on-line control system was utilized. As the pressure decreased in a range of 500-980 hPa, the peak concentration of both ions and nanometer-sized particles decreased, which suggests that higher pressure tended to enhance the growth of particles nucleated by ion-induced nucleation. Moreover, the modal diameters of the measured particle size distributions showed a systematic shift to larger sizes with increasing pressure. However, in the temperature range of 5-20 °C, temperature increases had no significant effects on the mobility distribution of particles. The effects of residence time, RH (7%-70%), and SO(2) concentration (0.08-6.7 ppm) on ion-induced nucleation were also systematically investigated. The results show that the nucleation and growth were significantly dependent on the residence time, RH, and SO(2) concentration, which is in agreement with both a previous model and previous observations. This research will be inevitable for a better understanding of the role of ions in an atmospheric nucleation mechanism.

Pressure and temperature induced electrical resistance change in nano-carbon/epoxy composites

NARCIS (Netherlands)

Shen, J. T.; Buschhorn, S. T.; De Hosson, J. Th. M.; Schulte, K.; Fiedler, B.

2015-01-01

In this study, we investigate the changes of electrical resistance of the carbon black (CB) and carbon nanotube (CNT) filled epoxy composites upon compression, swelling and temperature variation. For all samples we observe a decrease of electrical resistance under compression, while an increase of

Induced-fit Mechanism for Prolyl Endopeptidase

Energy Technology Data Exchange (ETDEWEB)

Li, Min; Chen, Changqing; Davies, David R.; Chiu, Thang K. (NIH); (LSU); (Chinese Aca. Sci.)

2010-11-15

Prolyl peptidases cleave proteins at proline residues and are of importance for cancer, neurological function, and type II diabetes. Prolyl endopeptidase (PEP) cleaves neuropeptides and is a drug target for neuropsychiatric diseases such as post-traumatic stress disorder, depression, and schizophrenia. Previous structural analyses showing little differences between native and substrate-bound structures have suggested a lock-and-key catalytic mechanism. We now directly demonstrate from seven structures of Aeromonus punctata PEP that the mechanism is instead induced fit: the native enzyme exists in a conformationally flexible opened state with a large interdomain opening between the {beta}-propeller and {alpha}/{beta}-hydrolase domains; addition of substrate to preformed native crystals induces a large scale conformational change into a closed state with induced-fit adjustments of the active site, and inhibition of this conformational change prevents substrate binding. Absolute sequence conservation among 28 orthologs of residues at the active site and critical residues at the interdomain interface indicates that this mechanism is conserved in all PEPs. This finding has immediate implications for the use of conformationally targeted drug design to improve specificity of inhibition against this family of proline-specific serine proteases.

Analysis of the dynamics of Rhizomucor miehei lipase at different temperatures

DEFF Research Database (Denmark)

Peters, Günther H.j.; Toxvaerd, S.; Andersen, K.V.

1999-01-01

The dynamics of Rhizomucor miehei lipase has been studied by molecular dynamics simulations at temperatures ranging from 200-500K. Simulations carried out in periodic boundary conditions and using explicit water molecules were performed for 400 ps at each temperature. Our results indicate...... that conformational changes and internal motions in the protein are significantly influenced by the temperature increase. With increasing temperature, the number of internal hydrogen bonds decreases, while surface accessibility, radius of gyration and the number of residues in random coil conformation increase...

Novel inhibitors induce large conformational changes of GAB1 pleckstrin homology domain and kill breast cancer cells.

Directory of Open Access Journals (Sweden)

Lu Chen

2015-01-01

Full Text Available The Grb2-associated binding protein 1 (GAB1 integrates signals from different signaling pathways and is over-expressed in many cancers, therefore representing a new therapeutic target. In the present study, we aim to target the pleckstrin homology (PH domain of GAB1 for cancer treatment. Using homology models we derived, high-throughput virtual screening of five million compounds resulted in five hits which exhibited strong binding affinities to GAB1 PH domain. Our prediction of ligand binding affinities is also in agreement with the experimental KD values. Furthermore, molecular dynamics studies showed that GAB1 PH domain underwent large conformational changes upon ligand binding. Moreover, these hits inhibited the phosphorylation of GAB1 and demonstrated potent, tumor-specific cytotoxicity against MDA-MB-231 and T47D breast cancer cell lines. This effort represents the discovery of first-in-class GAB1 PH domain inhibitors with potential for targeted breast cancer therapy and provides novel insights into structure-based approaches to targeting this protein.

A user-friendly web portal for analyzing conformational changes in structures of Mycobacterium tuberculosis.

Science.gov (United States)

Hassan, Sameer; Thangam, Manonanthini; Vasudevan, Praveen; Kumar, G Ramesh; Unni, Rahul; Devi, P K Gayathri; Hanna, Luke Elizabeth

2015-10-01

Initiation of the Tuberculosis Structural Consortium has resulted in the expansion of the Mycobacterium tuberculosis (MTB) protein structural database. Currently, 969 experimentally solved structures are available for 354 MTB proteins. This includes multiple crystal structures for a given protein under different functional conditions, such as the presence of different ligands or mutations. In depth analysis of the multiple structures reveal that subtle differences exist in conformations of a given protein under varied conditions. Therefore, it is immensely important to understand the conformational differences between the multiple structures of a given protein in order to select the most suitable structure for molecular docking and structure-based drug designing. Here, we introduce a web portal ( http://bmi.icmr.org.in/mtbsd/torsion.php ) that we developed to provide comparative data on the ensemble of available structures of MTB proteins, such as Cα root means square deviation (RMSD), sequence identity, presence of mutations and torsion angles. Additionally, torsion angles were used to perform principal component analysis (PCA) to identify the conformational differences between the structures. Additionally, we present a few case studies to demonstrate this database. Graphical Abstract Conformational changes seen in the structures of the enoyl-ACP reductase protein encoded by the Mycobacterial gene inhA.

Fluctuations in Brain Temperature Induced by Lypopolysaccharides: Central and Peripheral Contributions

Directory of Open Access Journals (Sweden)

Jeremy S. Tang

2010-01-01

Full Text Available In this study, we examined changes in central (anterior-preoptic hypothalamus and peripheral (temporal muscle and facial skin temperatures in freely moving rats following intravenous administration of bacterial lipopolysaccharides (LPS at low doses (1 and 10 μg/kg at thermoneutral conditions (28˚C. Recordings were made with high temporal resolution (5-s bin and the effects of LPS were compared with those induced by a tail-pinch, a standard arousing somato-sensory stimulus. At each dose, LPS moderately elevated brain, muscle and skin temperatures. In contrast to rapid, monophasic and relatively short hyperthermic responses induced by a tail-pinch, LPS-induced increases in brain and muscle temperatures occurred with ~40 min onset latencies, showed three not clearly defined phases, were slightly larger with the 10 μm/kg dose and maintained for the entire 4-hour post-injection recording duration. Based on dynamics of brain-muscle and skin-muscle temperature differentials, it appears that the hyperthermic response induced by LPS at the lowest dose originates from enhanced peripheral heat production, with no evidence of brain metabolic activation and skin vasoconstriction. While peripheral heat production also appears to determine the first phase of brain and body temperature elevation with LPS at 10 μg/kg, a further prolonged increase in brain-muscle differentials (onset at ~100 min suggests metabolic brain activation as a factor contributing to brain and body hyperthermia. At this dose, skin temperature increase was weaker than in temporal muscle, suggesting vasoconstriction as another contributor to brain/ body hyperthermia. Therefore, although both LPS at low doses and salient sensory stimuli moderately increase brain and body temperatures, these hyperthermic responses have important qualitative differences, reflecting unique underlying mechanisms.

Fluctuations in brain temperature induced by lipopolysaccharides: central and peripheral contributions.

Science.gov (United States)

Tang, Jeremy S; Kiyatkin, Eugene A

2010-01-01

In this study, we examined changes in central (anterior-preoptic hypothalamus) and peripheral (temporal muscle and facial skin) temperatures in freely moving rats following intravenous administration of bacterial lipopolysaccharides (LPS) at low doses (1 and 10 μg/kg) at thermoneutral conditions (28°C). Recordings were made with high temporal resolution (5-s bin) and the effects of LPS were compared with those induced by a tail-pinch, a standard arousing somato-sensory stimulus. At each dose, LPS moderately elevated brain, muscle, and skin temperatures. In contrast to rapid, monophasic and relatively short hyperthermic responses induced by a tail-pinch, LPS-induced increases in brain and muscle temperatures occurred with ~40 min onset latencies, showed three not clearly defined phases, were slightly larger with the 10 μm/kg dose, and maintained for the entire 4-hour post-injection recording duration. Based on dynamics of brain-muscle and skin-muscle temperature differentials, it appears that the hyperthermic response induced by LPS at the lowest dose originates from enhanced peripheral heat production, with no evidence of brain metabolic activation and skin vasoconstriction. While peripheral heat production also appears to determine the first phase of brain and body temperature elevation with LPS at 10 μg/kg, a further prolonged increase in brain-muscle differentials (onset at ~100 min) suggests metabolic brain activation as a factor contributing to brain and body hyperthermia. At this dose, skin temperature increase was weaker than in temporal muscle, suggesting vasoconstriction as another contributor to brain/body hyperthermia. Therefore, although both LPS at low doses and salient sensory stimuli moderately increase brain and body temperatures, these hyperthermic responses have important qualitative differences, reflecting unique underlying mechanisms.

A new general method for simultaneous fitting of temperature and concentration dependence of reaction rates yields kinetic and thermodynamic parameters for HIV reverse transcriptase specificity.

Science.gov (United States)

Li, An; Ziehr, Jessica L; Johnson, Kenneth A

2017-04-21

Recent studies have demonstrated the dominant role of induced fit in enzyme specificity of HIV reverse transcriptase and many other enzymes. However, relevant thermodynamic parameters are lacking, and equilibrium thermodynamic methods are of no avail because the key parameters can only be determined by kinetic measurement. By modifying KinTek Explorer software, we present a new general method for globally fitting data collected over a range of substrate concentrations and temperatures and apply it to HIV reverse transcriptase. Fluorescence stopped-flow methods were used to record the kinetics of enzyme conformational changes that monitor nucleotide binding and incorporation. The nucleotide concentration dependence was measured at temperatures ranging from 5 to 37 °C, and the raw data were fit globally to derive a single set of rate constants at 37 °C and a set of activation enthalpy terms to account for the kinetics at all other temperatures. This comprehensive analysis afforded thermodynamic parameters for nucleotide binding ( K d , Δ G , Δ H , and Δ S at 37 °C) and kinetic parameters for enzyme conformational changes and chemistry (rate constants and activation enthalpy). Comparisons between wild-type enzyme and a mutant resistant to nucleoside analogs used to treat HIV infections reveal that the ground state binding is weaker and the activation enthalpy for the conformational change step is significantly larger for the mutant. Further studies to explore the structural underpinnings of the observed thermodynamics and kinetics of the conformational change step may help to design better analogs to treat HIV infections and other diseases. Our new method is generally applicable to enzyme and chemical kinetics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Simulation of regional temperature change effect of land cover change in agroforestry ecotone of Nenjiang River Basin in China

Science.gov (United States)

Liu, Tingxiang; Zhang, Shuwen; Yu, Lingxue; Bu, Kun; Yang, Jiuchun; Chang, Liping

2017-05-01

The Northeast China is one of typical regions experiencing intensive human activities within short time worldwide. Particularly, as the significant changes of agriculture land and forest, typical characteristics of pattern and process of agroforestry ecotone change formed in recent decades. The intensive land use change of agroforestry ecotone has made significant change for regional land cover, which had significant impact on the regional climate system elements and the interactions among them. This paper took agroforestry ecotone of Nenjiang River Basin in China as study region and simulated temperature change based on land cover change from 1950s to 1978 and from 1978 to 2010. The analysis of temperature difference sensitivity to land cover change based on Weather Research and Forecasting (WRF) model showed that the land cover change from 1950s to 1978 induced warming effect over all the study area, including the change of grassland to agriculture land, grassland to deciduous broad-leaved forest, and deciduous broad-leaved forest to shrub land. The land cover change from 1978 to 2010 induced cooling effect over all the study area, including the change of deciduous broad-leaved forest to agriculture land, grassland to agriculture land, shrub land to agriculture land, and deciduous broad-leaved forest to grassland. In addition, the warming and cooling effect of land cover change was more significant in the region scale than specific land cover change area.

Temperature fluctuations superimposed on background temperature change

International Nuclear Information System (INIS)

Otto, James; Roberts, J.A.

2016-01-01

Proxy data allows the temperature of the Earth to be mapped over long periods of time. In this work the temperature fluctuations for over 200 proxy data sets were examined and from this set 50 sets were analyzed to test for periodic and quasi-periodic fluctuations in the data sets. Temperature reconstructions over 4 different time scales were analyzed to see if patterns emerged. Data were put into four time intervals; 4,000 years, 14,000 years, 1,000,000 years, and 3,000,000 years and analyzed with a goal to understanding periodic and quasi-periodic patterns in global temperature change superimposed on a “background” average temperature change. Quasi-periodic signatures were identified that predate the Industrial Revolution, during much of which direct data on temperature are not available. These data indicate that Earth temperatures have undergone a number of periodic and quasi-periodic intervals that contain both global warming and global cooling cycles. The fluctuations are superimposed on a background of temperature change that has a declining slope during the two periods, pre-ice age and post ice age with a transition about 12,000 BCE. The data are divided into “events” that span the time periods 3,000,000 BCE to “0” CE, 1,000,000 BCE to “0” CE, 12,000 BCE to 2,000 CE and 2,000 BCE to 2,000 CE. An equation using a quasi-periodic (frequency modulated sine waves) patterns was developed to analyze the date sets for quasi-periodic patterns. “Periodicities” which show reasonable agreement with the predictions of Milankovitch and other investigators were found in the data sets.

Conformational changes and translocation of tissue-transglutaminase to the plasma membranes: role in cancer cell migration

International Nuclear Information System (INIS)

Kumar, Ambrish; Hu, Jianjun; LaVoie, Holly A; Walsh, Kenneth B; DiPette, Donald J; Singh, Ugra S

2014-01-01

membrane fractions and sensitive to intracellular Ca 2+ concentration suggesting a calcium requirement in TG2-regulated cell migration. Taken together, we conclude that resveratrol induces conformational changes in TG2, and that Ca 2+ -mediated TG2 association with the plasma membrane is responsible for the inhibitory effects of resveratrol on cell migration

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.

Temperature in the throat

Directory of Open Access Journals (Sweden)

Dariush Kaviani

2016-09-01

Full Text Available We study the temperature of extended objects in string theory. Rotating probe D-branes admit horizons and temperatures a la Unruh effect. We find that the induced metrics on slow rotating probe D1-branes in holographic string solutions including warped Calabi–Yau throats have distinct thermal horizons with characteristic Hawking temperatures even if there is no black hole in the bulk Calabi–Yau. Taking the UV/IR limits of the solution, we show that the world volume black hole nucleation depends on the deformation and the warping of the throat. We find that world volume horizons and temperatures of expected features form not in the regular confining IR region but in the singular nonconfining UV solution. In the conformal limit of the UV, we find horizons and temperatures similar to those on rotating probes in the AdS throat found in the literature. In this case, we also find that activating a background gauge field form the U(1 R-symmetry modifies the induced metric with its temperature describing two different classes of black hole solutions.

Complexation of triptycene-derived macrotricyclic polyether with paraquat derivatives, diquat, and a 2,7-diazapyrenium salt: guest-induced conformational changes of the host.

Science.gov (United States)

Han, Ying; Cao, Jing; Li, Peng-Fei; Zong, Qian-Shou; Zhao, Jian-Min; Guo, Jia-Bin; Xiang, Jun-Feng; Chen, Chuan-Feng

2013-04-05

Complexation between a triptycene-derived macrotricyclic polyether containing two dibenzo-[30]-crown-10 cavities and different functionalized paraquat derivatives, diquat, and a 2,7-diazapyrenium salt in both solution and solid state was investigated in detail. It was found that depending on the guests with different terminal functional groups and structures, the macrotricyclic polyether could form 1:1 or 1:2 complexes with the guests in different complexation modes in solution and also in the solid state. Especially, the conformation of the macrotricyclic polyether was efficiently adjusted by the encapsulated guests, which was to some extent similar to substrate-induced fit of enzymes. Moreover, the binding and releasing of the guests in the complexes could be controlled by potassium ions.

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.

Synchrotron radiation structure analyses of the light-induced radical pair of a hexaarylbiimidazolyl derivative. Origin of the spin-multiplicity change

CERN Document Server

Kawano, M; Matsubara, K; Imabayashi, H; Mitsumi, M; Toriumi, K; Ohashi, Y

2002-01-01

In situ synchrotron radiation structure analyses of a light-induced radical pair from o-Cl-HABI were performed by using an X-ray vacuum camera at 23-70K at the BL02B1 station of SPring-8. The combined results of X-ray analysis with theoretical calculation, IR, and UV-vis spectroscopy reveal that a slight conformational change of the radical pair causes the drastic spin-multiplicity change during 2-140K. (author)

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)

Dosimetry analysis on radiation-induced acute esophagitis after three-dimensional conformal radiotherapy for non-small cell lung cancer

International Nuclear Information System (INIS)

ZZhu Shuchai; Cui Yanli; Li Juan; Liu Zhikun; Shen Wenbin; Su Jingwei; Wang Yuxiang

2010-01-01

Objective: To analyze the related factors with radiation-induced esophagitis after threedimensional conformal radiotherapy for non-small cell lung cancer (NSCLC), in order to explore the predictors for optimizing the treatment planning of NSCLC. Methods: From Aug 2000 to Dec 2004, 104 NSCLC patients received radiotherapy and were eligible for this study, 45 cases squamous cell carcinoma, 20 cases adenocarcinoma, 33 cases carrying with cancer cells by test and 6 case with no definitive pathologic feature.46 patients were treated with three dimensional conformal radiotherapy (3DCRT), the other 58 patients conventional radiotherapy (CRT) before later-course 3DCRT. All the patients received the prescribed dose between 60-78 Gy and the median dose 66 Gy. The correlation of the variables were evaluated by Spearman relationship analysis. The morbidity of radiation-induced esophagitis was analyzed by X 2 test. The multivariate effect on radiation-induced esophagitis was statistically processed by Logistic regression model. Results: In 104 patients, the morbidity of radiation- induced esophagitis was 46.2%, including 32 cases at grade 1, 15 cases at grade 2, 1 case at grade 3. Univariate analysis showed the maximal and mean dose of esophagus, the volume of esophagus irradiated, the values of V 40 , V 45 , V 50 , V 55 , V 60 , LETT 45 , LETT 50 , LETT 55 , LETT 60 for the esophagus were correlated with radiation-induced esophagitis. Logistic regression model showed that the maximum dose received by the esophagus was the independent factor of ≥ 2 grade radiation-induced esophagitis. Conclusions: The maxmal dose of esophagus received might be the important factor of radiation-induced esophagitis. (authors)

Polyploidization mechanisms: temperature environment can induce diploid gamete formation in Rosa sp.

Science.gov (United States)

Pécrix, Yann; Rallo, Géraldine; Folzer, Hélène; Cigna, Mireille; Gudin, Serge; Le Bris, Manuel

2011-06-01

Polyploidy is an important evolutionary phenomenon but the mechanisms by which polyploidy arises still remain underexplored. There may be an environmental component to polyploidization. This study aimed to clarify how temperature may promote diploid gamete formation considered an essential element for sexual polyploidization. First of all, a detailed cytological analysis of microsporogenesis and microgametogenesis was performed to target precisely the key developmental stages which are the most sensitive to temperature. Then, heat-induced modifications in sporad and pollen characteristics were analysed through an exposition of high temperature gradient. Rosa plants are sensitive to high temperatures with a developmental sensitivity window limited to meiosis. Moreover, the range of efficient temperatures is actually narrow. 36 °C at early meiosis led to a decrease in pollen viability, pollen ectexine defects but especially the appearance of numerous diploid pollen grains. They resulted from dyads or triads mainly formed following heat-induced spindle misorientations in telophase II. A high temperature environment has the potential to increase gamete ploidy level. The high frequencies of diplogametes obtained at some extreme temperatures support the hypothesis that polyploidization events could have occurred in adverse conditions and suggest polyploidization facilitating in a global change context.

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.

Electrostatics effects on Ca(2+) binding and conformational changes in EF-hand domains: Functional implications for EF-hand proteins.

Science.gov (United States)

Ababou, Abdessamad; Zaleska, Mariola

2015-12-01

Mutations of Gln41 and Lys75 with nonpolar residues in the N-terminal domain of calmodulin (N-Cam) revealed the importance of solvation energetics in conformational change of Ca(2+) sensor EF-hand domains. While in general these domains have polar residues at these corresponding positions yet the extent of their conformational response to Ca(2+) binding and their Ca(2+) binding affinity can be different from N-Cam. Consequently, here we address the charge state of the polar residues at these positions. The results show that the charge state of these polar residues can affect substantially the conformational change and the Ca(2+) binding affinity of our N-Cam variants. Since all the variants kept their conformational activity in the presence of Ca(2+) suggests that the differences observed among them mainly originate from the difference in their molecular dynamics. Hence we propose that the molecular dynamics of Ca(2+) sensor EF-hand domains is a key factor in the multifunctional aspect of EF-hand proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

Stress- and Magnetic Field-Induced Martensitic Transformation at Cryogenic Temperatures in Fe-Mn-Al-Ni Shape Memory Alloys

Science.gov (United States)

Xia, Ji; Xu, Xiao; Miyake, Atsushi; Kimura, Yuta; Omori, Toshihiro; Tokunaga, Masashi; Kainuma, Ryosuke

2017-12-01

Stress-induced and magnetic-field-induced martensitic transformation behaviors at low temperatures were investigated for Fe-Mn-Al-Ni alloys. The magnetic-field-induced reverse martensitic transformation was directly observed by in situ optical microscopy. Magnetization measurements under pulsed magnetic fields up to 50 T were carried out at temperatures between 4.2 and 125 K on a single-crystal sample; full magnetic-field-induced reverse martensitic transformation was confirmed at all tested temperatures. Compression tests from 10 to 100 K were conducted on a single-crystal sample; full shape recovery was obtained at all tested temperatures. It was found that the temperature dependence of both the critical stress and critical magnetic field is small and that the transformation hysteresis is less sensitive to temperature even at cryogenic temperatures. The temperature dependence of entropy change during martensitic transformation up to 100 K was then derived using the Clausius-Clapeyron relation with critical stresses and magnetic fields.

Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes

Energy Technology Data Exchange (ETDEWEB)

Matei, Iulia; Ionescu, Sorana [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania); Hillebrand, Mihaela, E-mail: mihh@gw-chimie.math.unibuc.ro [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania)

2011-08-15

The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 10{sup 5} M{sup -1} was evidenced. Foerster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes in the CD band of HSA indicate a decrease in the {alpha}-helix content upon binding. An induced CD signal for bound fisetin was observed and rationalized in terms of density functional theory calculations. - Highlights: > Fisetin-BSA system was studied by fluorescence spectroscopy. > Binding parameters, association constant and number of sites were estimated. > Binding site of fisetin was identified by competitive experiments. > Conformational changes in HSA and fisetin were evidenced by circular dichroism. > TDDFT calculated CD spectra supported the experimental data.

Climate-Induced Boreal Forest Change: Predictions versus Current Observations

Science.gov (United States)

Soja, Amber J.; Tchebakova, Nadezda M.; French, Nancy H. F.; Flannigan, Michael D.; Shugart, Herman H.; Stocks, Brian J.; Sukhinin, Anatoly I.; Parfenova, E. I.; Chapin, F. Stuart, III; Stackhouse, Paul W., Jr.

2007-01-01

For about three decades, there have been many predictions of the potential ecological response in boreal regions to the currently warmer conditions. In essence, a widespread, naturally occurring experiment has been conducted over time. In this paper, we describe previously modeled predictions of ecological change in boreal Alaska, Canada and Russia, and then we investigate potential evidence of current climate-induced change. For instance, ecological models have suggested that warming will induce the northern and upslope migration of the treeline and an alteration in the current mosaic structure of boreal forests. We present evidence of the migration of keystone ecosystems in the upland and lowland treeline of mountainous regions across southern Siberia. Ecological models have also predicted a moisture-stress-related dieback in white spruce trees in Alaska, and current investigations show that as temperatures increase, white spruce tree growth is declining. Additionally, it was suggested that increases in infestation and wildfire disturbance would be catalysts that precipitate the alteration of the current mosaic forest composition. In Siberia, five of the last seven years have resulted in extreme fire seasons, and extreme fire years have also been more frequent in both Alaska and Canada. In addition, Alaska has experienced extreme and geographically expansive multi-year outbreaks of the spruce beetle, which had been previously limited by the cold, moist environment. We suggest that there is substantial evidence throughout the circumboreal region to conclude that the biosphere within the boreal terrestrial environment has already responded to the transient effects of climate change. Additionally, temperature increases and warming-induced change are progressing faster than had been predicted in some regions, suggesting a potential non-linear rapid response to changes in climate, as opposed to the predicted slow linear response to climate change.

Asymetric change of daily temperature range: Proceedings

Energy Technology Data Exchange (ETDEWEB)

Kukla, G. [ed.] [Columbia Univ., Palisades, NY (United States). Lamont-Doherty Earth Observatory; Karl, T.R. [ed.] [National Climatic Data Center, Asheville, NC (United States); Riches, M.R. [ed.] [USDOE, Washington, DC (United States)

1994-04-01

This report is a compilation of abstracts of papers presented at the MINIMAX workshop. Topics include; temperature fluxes, influence of clouds on temperature, anthropogenic influences on temperature flux, and carbon dioxide and aerosol induced greenhouse effect.

Asymetric change of daily temperature range: Proceedings

International Nuclear Information System (INIS)

Kukla, G.; Riches, M.R.

1994-04-01

This report is a compilation of abstracts of papers presented at the MINIMAX workshop. Topics include; temperature fluxes, influence of clouds on temperature, anthropogenic influences on temperature flux, and carbon dioxide and aerosol induced greenhouse effect

Effects of land cover change on temperature and rainfall extremes in multi-model ensemble simulations

Directory of Open Access Journals (Sweden)

A. J. Pitman

2012-11-01

Full Text Available The impact of historical land use induced land cover change (LULCC on regional-scale climate extremes is examined using four climate models within the Land Use and Climate, IDentification of robust impacts project. To assess those impacts, multiple indices based on daily maximum and minimum temperatures and daily precipitation were used. We contrast the impact of LULCC on extremes with the impact of an increase in atmospheric CO₂ from 280 ppmv to 375 ppmv. In general, consistent changes in both high and low temperature extremes are similar to the simulated change in mean temperature caused by LULCC and are restricted to regions of intense modification. The impact of LULCC on both means and on most temperature extremes is statistically significant. While the magnitude of the LULCC-induced change in the extremes can be of similar magnitude to the response to the change in CO₂, the impacts of LULCC are much more geographically isolated. For most models, the impacts of LULCC oppose the impact of the increase in CO₂ except for one model where the CO₂-caused changes in the extremes are amplified. While we find some evidence that individual models respond consistently to LULCC in the simulation of changes in rainfall and rainfall extremes, LULCC's role in affecting rainfall is much less clear and less commonly statistically significant, with the exception of a consistent impact over South East Asia. Since the simulated response of mean and extreme temperatures to LULCC is relatively large, we conclude that unless this forcing is included, we risk erroneous conclusions regarding the drivers of temperature changes over regions of intense LULCC.

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...

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.

Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring

Energy Technology Data Exchange (ETDEWEB)

Mountassif, Driss; Fabre, Lucien [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Zaid, Younes [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Current address: Laboratory of Thrombosis and Hemostasis, Montreal Heart Institute, Montreal, Quebec (Canada); Halawani, Dalia [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Current address: Department of Cell Biology, Lerner Research Institute, 9500 Euclid Avenue NC10, Cleveland, OH 44195 (United States); Rouiller, Isabelle, E-mail: isabelle.rouiller@mcgill.ca [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada)

2015-12-25

Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. - Highlights: • p97{sub R155P} and p97{sub A232E} decrease the ability of p97 to bind to its co-factor Npl4. • p97{sub R155P} has a different isoelectric point than that of p97{sub R95G}, p97{sub A232E} and p97{sub WT}. • Mutation R155P changes principally the conformation of the D2 ring. • Mutation R155P modifies the interface between two protomers within the D2 ring.

Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring

International Nuclear Information System (INIS)

Mountassif, Driss; Fabre, Lucien; Zaid, Younes; Halawani, Dalia; Rouiller, Isabelle

2015-01-01

Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. - Highlights: • p97 R155P and p97 A232E decrease the ability of p97 to bind to its co-factor Npl4. • p97 R155P has a different isoelectric point than that of p97 R95G , p97 A232E and p97 WT . • Mutation R155P changes principally the conformation of the D2 ring. • Mutation R155P modifies the interface between two protomers within the D2 ring.

Microscopic insight into thermodynamics of conformational changes of SAP-SLAM complex in signal transduction cascade

Science.gov (United States)

Samanta, Sudipta; Mukherjee, Sanchita

2017-04-01

The signalling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, associate with SLAM-associated protein (SAP)-related molecules, composed of single SH2 domain architecture. SAP activates Src-family kinase Fyn after SLAM ligation, resulting in a SLAM-SAP-Fyn complex, where, SAP binds the Fyn SH3 domain that does not involve canonical SH3 or SH2 interactions. This demands insight into this SAP mediated signalling cascade. Thermodynamics of the conformational changes are extracted from the histograms of dihedral angles obtained from the all-atom molecular dynamics simulations of this structurally well characterized SAP-SLAM complex. The results incorporate the binding induced thermodynamic changes of individual amino acid as well as the secondary structural elements of the protein and the solvent. Stabilization of the peptide partially comes through a strong hydrogen bonding network with the protein, while hydrophobic interactions also play a significant role where the peptide inserts itself into a hydrophobic cavity of the protein. SLAM binding widens SAP's second binding site for Fyn, which is the next step in the signal transduction cascade. The higher stabilization and less fluctuation of specific residues of SAP in the Fyn binding site, induced by SAP-SLAM complexation, emerge as the key structural elements to trigger the recognition of SAP by the SH3 domain of Fyn. The thermodynamic quantification of the protein due to complexation not only throws deeper understanding in the established mode of SAP-SLAM interaction but also assists in the recognition of the relevant residues of the protein responsible for alterations in its activity.

Conformational fluctuation dynamics of domain I of human serum albumin in the course of chemically and thermally induced unfolding using fluorescence correlation spectroscopy.

Science.gov (United States)

Yadav, Rajeev; Sengupta, Bhaswati; Sen, Pratik

2014-05-22

The present study elucidates the involvement of conformational fluctuation dynamics during chemically and thermally induced unfolding of human serum albumin (HSA) by fluorescence correlation spectroscopic (FCS) study, time-resolved fluorescence measurements, and circular dichroism (CD) spectroscopic methods. Two fluorescent probes, tetramethylrhodamine-5-maleimide (TMR) and N-(7-dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA) were used to selectively label the domain I of HSA through the reaction with cys-34 for these studies. The guanidine hydrochloride (GnHCl) induced global structural change of HSA is monitored through its hydrodynamic radius (r(H)) and CD response, which is found to be two step in nature. In FCS experiment, along with the diffusion time component we have observed an exponential relaxation time component (τ(R)) that has been ascribed to the concerted chain dynamics of HSA. Unlike in the global structural change, we found that the τ(R) value changes in a different manner in the course of the unfolding. The dependence of τ(R) on the concentration of GnHCl was best fitted with a four state model, indicating the involvement of two intermediate states during the unfolding process, which were not observed through the CD response and r(H) data. The fluorescence lifetime measurement also supports our observation of intermediate states during the unfolding of HSA. However, no such intermediate states were observed during thermally induced unfolding of HSA.

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

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.

Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature.

Science.gov (United States)

Chaloupkova, Radka; Prokop, Zbynek; Sato, Yukari; Nagata, Yuji; Damborsky, Jiri

2011-08-01

The effect of pH and temperature on structure, stability, activity and enantioselectivity of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110 was investigated in this study. Conformational changes have been assessed by circular dichroism spectroscopy, functional changes by kinetic analysis, while quaternary structure was studied by gel filtration chromatography. Our study shows that the DbjA enzyme is highly tolerant to pH changes. Its secondary and tertiary structure was not affected by pH in the ranges 5.3-10.3 and 6.2-10.1, respectively. Oligomerization of DbjA was strongly pH-dependent: monomer, dimer, tetramer and a high molecular weight cluster of the enzyme were distinguished in solution at different pH conditions. Moreover, different oligomeric states of DbjA possessed different thermal stabilities. The highest melting temperature (T(m) = 49.1 ± 0.2 °C) was observed at pH 6.5, at which the enzyme occurs in dimeric form. Maximal activity was detected at 50 °C and in the pH interval 7.7-10.4. While pH did not have any effect on enantiodiscriminination of DbjA, temperature significantly altered DbjA enantioselectivity. A decrease in temperature results in significantly enhanced enantioselectivity. The temperature dependence of DbjA enantioselectivity was analysed with 2-bromobutane, 2-bromopentane, methyl 2-bromopropionate and ethyl 2-bromobutyrate, and differential activation parameters Δ(R-S)ΔH and Δ(R-S)ΔS were determined. The thermodynamic analysis revealed that the resolution of β-bromoalkanes was driven by both enthalpic and entropic terms, while the resolution of α-bromoesters was driven mainly by an enthalpic term. Unique catalytic activity and structural stability of DbjA in a broad pH range, combined with high enantioselectivity with particular substrates, make this enzyme a very versatile biocatalyst. Enzyme EC3.8.1.5 haloalkane dehalogenase. © 2011 The Authors Journal compilation © 2011 FEBS.

Hot Conformal Gauge Theories

DEFF Research Database (Denmark)

Mojaza, Matin; Pica, Claudio; Sannino, Francesco

2010-01-01

of flavors. Surprisingly this number, if computed to the order g^2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i......We compute the nonzero temperature free energy up to the order g^6 \\ln(1/g) in the coupling constant for vector like SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged...... in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Due to large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors and matter representation. We...

SUSY Unparticle and Conformal Sequestering

Energy Technology Data Exchange (ETDEWEB)

Nakayama, Yu; Nakayama, Yu

2007-07-17

We investigate unparticle physics with supersymmetry (SUSY). The SUSY breaking effects due to the gravity mediation induce soft masses for the SUSY unparticles and hence break the conformal invariance. The unparticle physics observable in near future experiments is only consistent if the SUSY breakingeffects from the hidden sector to the standard model sector are dominated by the gauge mediation, or if the SUSY breaking effects to the unparticle sector are sufficiently sequestered. We argue that the natural realization of the latter possibility is the conformal sequestering scenario.

The role of PEG conformation in mixed layers: from protein corona substrate to steric stabilization avoiding protein adsorption

Directory of Open Access Journals (Sweden)

Joan Comenge

2015-03-01

Full Text Available Although nanoparticles (NPs have been traditionally modified with a single ligand layer, mixture of ligands might help to combine different functionalities and to further engineer the NP surface. A detailed study of the competition between an alkanethiol (11-mercaptoundecanoic acid and SH-PEG for the surface of AuNPs and the resultant behaviors of this model nanoconjugate is presented here. As a result, the physicochemical properties of these conjugates can be progressively tuned by controlling the composition and especially the conformation of the mixed monolayer. This has implications in the physiological stability. The controlled changes on the SH-PEG conformation rather than its concentration induce a change in the stabilization mechanism from electrostatic repulsion to steric hindrance, which changes the biological fate of NPs. Importantly, the adsorption of proteins on the conjugates can be tailored by tuning the composition and conformation of the mixed layer.

Evaluating temperature changes of brain tissue due to induced heating of cell phone waves

Directory of Open Access Journals (Sweden)

Farhad Forouharmajd

2018-01-01

Full Text Available Background: Worries have recently been increased in the absorption of radiofrequency waves and their destructing effects on human health by increasing use of cell phones (mobile phones. This study performed to determine the thermal changes due to mobile phone radio frequency waves in gray and white brain tissue. Methods: This study is an empirical study, where the thermal changes of electromagnetic waves resulted from cell phones (900 MHZ, specific absorption rate for head 1.18 w/kg on the 15 brain tissue of a cow were analyzed in a compartment with three different thickness of 2 mm, 12 mm, and 22 mm, for 15 min. The Lutron thermometer (model: MT-917 with 0.01°C precision was used for measuring the tissue temperature. For each thickness was measured three times. Data analysis is done by Lutron and MATLAB software packages. Results: In confronting of the tissue with the cell phone, the temperature was increased by 0.53°C in the 2 mm thickness that is the gray matter of the brain, increased by 0.99°C in the 12 mm thickness, and also increased by 0.92°C in the 22 mm thickness. Brain temperature showed higher rates than the base temperature after 15 min of confrontation with cell phone waves in all the three thicknesses. Conclusions: Cell phone radiated radio frequency waves were effective on increasing brain tissue temperature, and this temperature increase has cumulative effect on the tissue, being higher, for some time after the confrontation than the time with no confrontation.

Distribution of temperature changes and neurovascular coupling in rat brain following 3,4-methylenedioxymethamphetamine (MDMA, "ecstasy") exposure.

Science.gov (United States)

Coman, Daniel; Sanganahalli, Basavaraju G; Jiang, Lihong; Hyder, Fahmeed; Behar, Kevin L

2015-10-01

(+/-)3,4-methylenedioxymethamphetamine (MDMA, "ecstasy") is an abused psychostimulant that produces strong monoaminergic stimulation and whole-body hyperthermia. MDMA-induced thermogenesis involves activation of uncoupling proteins (UCPs), primarily a type specific to skeletal muscle (UCP-3) and absent from the brain, although other UCP types are expressed in the brain (e.g. thalamus) and might contribute to thermogenesis. Since neuroimaging of brain temperature could provide insights into MDMA action, we measured spatial distributions of systemically administered MDMA-induced temperature changes and dynamics in rat cortex and subcortex using a novel magnetic resonance method, Biosensor Imaging of Redundant Deviation in Shifts (BIRDS), with an exogenous temperature-sensitive probe (thulium ion and macrocyclic chelate 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetramethyl-1,4,7,10-tetraacetate (DOTMA(4-))). The MDMA-induced temperature rise was greater in the cortex than in the subcortex (1.6 ± 0.4 °C versus 1.3 ± 0.4 °C) and occurred more rapidly (2.0 ± 0.2 °C/h versus 1.5 ± 0.2 °C/h). MDMA-induced temperature changes and dynamics in the cortex and body were correlated, although the body temperature exceeded the cortex temperature before and after MDMA. Temperature, neuronal activity, and blood flow (CBF) were measured simultaneously in the cortex and subcortex (i.e. thalamus) to investigate possible differences of MDMA-induced warming across brain regions. MDMA-induced warming correlated with increases in neuronal activity and blood flow in the cortex, suggesting that the normal neurovascular response to increased neural activity was maintained. In contrast to the cortex, a biphasic relationship was seen in the subcortex (i.e. thalamus), with a decline in CBF as temperature and neural activity rose, transitioning to a rise in CBF for temperature above 37 °C, suggesting that MDMA affected CBF and neurovascular coupling differently in subcortical regions

Photo-induced valence change of the sulfur atom in an L-cysteine thin film grown on a silver metal substrate in a saliva-emulated aqueous solution

Energy Technology Data Exchange (ETDEWEB)

Tsujibayashi, Toru [Department of Physics, Osaka Dental University, 8-1 Kuzuha-hanazono, Hirakata, Osaka 573-1121 (Japan); Azuma, Junpei; Yamamoto, Isamu; Takahashi, Kazutoshi; Kamada, Masao [Synchrotron Light Application Center, Saga University, 1 Honjo, Saga, Saga 840-8502 (Japan)

2015-04-27

A thin film of L-cysteine (HSCH{sub 2}CH(NH{sub 2})COOH) is grown on a silver substrate in saliva-emulated aqueous solution. X-ray photoemission spectroscopic measurements have revealed that the sulfur atom shows valence change under IR laser irradiation at 825 nm. The valence change maintains for about a minute at room temperature and more than an hour between 110 and 250 K after stopping the laser irradiation. It is not observed at all at temperatures lower than 110 K. This temperature-dependent behavior indicates that the photo-excited electronic change should be accompanied by a conformational change in the L-cysteine molecule. It is strongly suggested that the reversible valence change of the sulfur atom is applicable to a memory used around room temperature.

Double-trace deformations of conformal correlations

Science.gov (United States)

Giombi, Simone; Kirilin, Vladimir; Perlmutter, Eric

2018-02-01

Large N conformal field theories often admit unitary renormalization group flows triggered by double-trace deformations. We compute the change in scalar four-point functions under double-trace flow, to leading order in 1/ N. This has a simple dual in AdS, where the flow is implemented by a change of boundary conditions, and provides a physical interpretation of single-valued conformal partial waves. We extract the change in the conformal dimensions and three-point coefficients of infinite families of double-trace composite operators. Some of these quantities are found to be sign-definite under double-trace flow. As an application, we derive anomalous dimensions of spinning double-trace operators comprised of non-singlet constituents in the O( N) vector model.

A network model to correlate conformational change and the impedance spectrum of single proteins

Energy Technology Data Exchange (ETDEWEB)

Alfinito, Eleonora; Pennetta, Cecilia; Reggiani, Lino [Dipartimento di Ingegneria dell' Innovazione, Universita del Salento, Via Arnesano, Lecce (Italy); Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM) (Italy)

2008-02-13

Integrated nanodevices based on proteins or biomolecules are attracting increasing interest in today's research. In fact, it has been shown that proteins such as azurin and bacteriorhodopsin manifest some electrical properties that are promising for the development of active components of molecular electronic devices. Here we focus on two relevant kinds of protein: bovine rhodopsin, prototype of G-protein-coupled-receptor (GPCR) proteins, and the enzyme acetylcholinesterase (AChE), whose inhibition is one of the most qualified treatments of Alzheimer's disease. Both these proteins exert their function starting with a conformational change of their native structure. Our guess is that such a change should be accompanied with a detectable variation of their electrical properties. To investigate this conjecture, we present an impedance network model of proteins, able to estimate the different impedance spectra associated with the different configurations. The distinct types of conformational change of rhodopsin and AChE agree with their dissimilar electrical responses. In particular, for rhodopsin the model predicts variations of the impedance spectra up to about 30%, while for AChE the same variations are limited to about 10%, which supports the existence of a dynamical equilibrium between its native and complexed states.

Localized conformational interrogation of antibody and antibody-drug conjugates by site-specific carboxyl group footprinting.

Science.gov (United States)

Pan, Lucy Yan; Salas-Solano, Oscar; Valliere-Douglass, John F

Establishing and maintaining conformational integrity of monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) during development and manufacturing is critical for ensuring their clinical efficacy. As presented here, we applied site-specific carboxyl group footprinting (CGF) for localized conformational interrogation of mAbs. The approach relies on covalent labeling that introduces glycine ethyl ester tags onto solvent-accessible side chains of protein carboxylates. Peptide mapping is used to monitor the labeling kinetics of carboxyl residues and the labeling kinetics reflects the conformation or solvent-accessibility of side chains. Our results for two case studies are shown here. The first study was aimed at defining the conformational changes of mAbs induced by deglycosylation. We found that two residues in C H 2 domain (D268 and E297) show significantly enhanced side chain accessibility upon deglycosylation. This site-specific result highlighted the advantage of monitoring the labeling kinetics at the amino acid level as opposed to the peptide level, which would result in averaging out of highly localized conformational differences. The second study was designed to assess conformational effects brought on by conjugation of mAbs with drug-linkers. All 59 monitored carboxyl residues displayed similar solvent-accessibility between the ADC and mAb under native conditions, which suggests the ADC and mAb share similar side chain conformation. The findings are well correlated and complementary with results from other assays. This work illustrated that site-specific CGF is capable of pinpointing local conformational changes in mAbs or ADCs that might arise during development and manufacturing. The methodology can be readily implemented within the industry to provide comprehensive conformational assessment of these molecules.

Measuring the mechanical properties of molecular conformers

Science.gov (United States)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

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.

Renormalization, conformal ward identities and the origin of a conformal anomaly pole

Science.gov (United States)

Corianò, Claudio; Maglio, Matteo Maria

2018-06-01

We investigate the emergence of a conformal anomaly pole in conformal field theories in the case of the TJJ correlator. We show how it comes to be generated in dimensional renormalization, using a basis of 13 form factors (the F-basis), where only one of them requires renormalization (F13), extending previous studies. We then combine recent results on the structure of the non-perturbative solutions of the conformal Ward identities (CWI's) for the TJJ in momentum space, expressed in terms of a minimal set of 4 form factors (A-basis), with the properties of the F-basis, and show how the singular behaviour of the corresponding form factors in both basis can be related. The result proves the centrality of such massless effective interactions induced by the anomaly, which have recently found realization in solid state, in the theory of topological insulators and of Weyl semimetals. This pattern is confirmed in massless abelian and nonabelian theories (QED and QCD) investigated at one-loop.

Studies on the optical absorption of copper-dopped myoglobin: conformational changes

International Nuclear Information System (INIS)

Lamy, M.T.M.

1976-03-01

Optical absorption changes in the visible and near U.V. spectrum of myoglobin molecules are observed when copper ions are added to the macromolecule. The heme optical transitions are investigated through a theoretical simulation of the optical absorption spectrum. A study of the absorption band in the region of 700 nm associated with the copper - myoglobin complexes indicated the existence of two kinds of metal-protein complexes: one associated with the six or eitht first added copper ions and the other related with the higher concentrations. Conformational changes caused by thermal treatment are studied in myoglobin water solutions and solutions containing copper ions. The phenomenon named pre-denaturation is observed through the optical absorption at 245 nm. It is shown that interactions between myoglobin molecules occur in the pre-denaturation phenomenon. (Author) [pt

Dissecting the role of conformational change and membrane binding by the bacterial cell division regulator MinE in the stimulation of MinD ATPase activity.

Science.gov (United States)

Ayed, Saud H; Cloutier, Adam D; McLeod, Laura J; Foo, Alexander C Y; Damry, Adam M; Goto, Natalie K

2017-12-15

The bacterial cell division regulators MinD and MinE together with the division inhibitor MinC localize to the membrane in concentrated zones undergoing coordinated pole-to-pole oscillation to help ensure that the cytokinetic division septum forms only at the mid-cell position. This dynamic localization is driven by MinD-catalyzed ATP hydrolysis, stimulated by interactions with MinE's anti-MinCD domain. This domain is buried in the 6-β-stranded MinE "closed" structure, but is liberated for interactions with MinD, giving rise to a 4-β-stranded "open" structure through an unknown mechanism. Here we show that MinE-membrane interactions induce a structural change into a state resembling the open conformation. However, MinE mutants lacking the MinE membrane-targeting sequence stimulated higher ATP hydrolysis rates than the full-length protein, indicating that binding to MinD is sufficient to trigger this conformational transition in MinE. In contrast, conformational change between the open and closed states did not affect stimulation of ATP hydrolysis rates in the absence of membrane binding, although the MinD-binding residue Ile-25 is critical for this conformational transition. We therefore propose an updated model where MinE is brought to the membrane through interactions with MinD. After stimulation of ATP hydrolysis, MinE remains bound to the membrane in a state that does not catalyze additional rounds of ATP hydrolysis. Although the molecular basis for this inhibited state is unknown, previous observations of higher-order MinE self-association may explain this inhibition. Overall, our findings have general implications for Min protein oscillation cycles, including those that regulate cell division in bacterial pathogens. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

[Influence of LDAO on the conformation and release of bacteriochlorophyll of peripheral light-harvesting complex (LH2) from Rhodobacter azotoformans].

Science.gov (United States)

Zhao, Gen-gui; Dong, Yan-min; Yang, Su-ping; Jiao, Nian-zhi; Qu, Yin-bo

2010-10-01

The aim of this study is to reveal the interaction relationships between lauryl dimethylamine N-oxide (LDAO) and peripheral light-harvesting complex (LH2) as well as the influence of LDAO on structure and function of LH2. In the present work, the effects of LDAO on the conformation and release processes of bacteriochlorophyll (BChl) of LH2 when incubated under different temperature and pH in the presence and absence of LDAO were investigated by spectroscopy. The results indicated that (1) the presence of LDAO resulted in alterations in the conformation, alpha-helix content, and spectra of Tyr and B850 band of LH2 at room temperature and pH 8.0. Moreover, energy transfer efficiency of LH2 was enhanced markedly in the presence of LDAO. (2) At 60 degrees C, both the B800 and B850 band of LH2 were released and transited into free BChl at pH 8.0. However, the release rates of bacteriochlorophylls of B800 and B850 band from LH2 were slowed down and the release processes were changed when incubated in the presence of LDAO. Hence, the stability of LH2 was improved in the presence of LDAO. (3) The accelerated release processes of bacteriochlorophylls of B800 and B850 band of LH2 were induced to transform into bacteriopheophytin (BPhe) and free BChl by LDAO in strong acid and strong alkalic solution at room temperature. However, the kinetic patterns of the B800 and B850 band were remarkably different. The release and self-assemble processes of B850 in LH2 were observed in strong acid solution without LDAO. Therefore, the different release behaviors of B800 and B850 of LH2 are induced by LDAO under different extreme environmental conditions.

Susceptibility of β1 Na+-K+ pump subunit to glutathionylation and oxidative inhibition depends on conformational state of pump.

Science.gov (United States)

Liu, Chia-Chi; Garcia, Alvaro; Mahmmoud, Yasser A; Hamilton, Elisha J; Galougahi, Keyvan Karimi; Fry, Natasha A S; Figtree, Gemma A; Cornelius, Flemming; Clarke, Ronald J; Rasmussen, Helge H

2012-04-06

Glutathionylation of cysteine 46 of the β1 subunit of the Na(+)-K(+) pump causes pump inhibition. However, the crystal structure, known in a state analogous to an E2·2K(+)·P(i) configuration, indicates that the side chain of cysteine 46 is exposed to the lipid bulk phase of the membrane and not expected to be accessible to the cytosolic glutathione. We have examined whether glutathionylation depends on the conformational changes in the Na(+)-K(+) pump cycle as described by the Albers-Post scheme. We measured β1 subunit glutathionylation and function of Na(+)-K(+)-ATPase in membrane fragments and in ventricular myocytes. Signals for glutathionylation in Na(+)-K(+)-ATPase-enriched membrane fragments suspended in solutions that preferentially induce E1ATP and E1Na(3) conformations were much larger than signals in solutions that induce the E2 conformation. Ouabain further reduced glutathionylation in E2 and eliminated an increase seen with exposure to the oxidant peroxynitrite (ONOO(-)). Inhibition of Na(+)-K(+)-ATPase activity after exposure to ONOO(-) was greater when the enzyme had been in the E1Na(3) than the E2 conformation. We exposed myocytes to different extracellular K(+) concentrations to vary the membrane potential and hence voltage-dependent conformational poise. K(+) concentrations expected to shift the poise toward E2 species reduced glutathionylation, and ouabain eliminated a ONOO(-)-induced increase. Angiotensin II-induced NADPH oxidase-dependent Na(+)-K(+) pump inhibition was eliminated by conditions expected to shift the poise toward the E2 species. We conclude that susceptibility of the β1 subunit to glutathionylation depends on the conformational poise of the Na(+)-K(+) pump.

Susceptibility of β1 Na+-K+ Pump Subunit to Glutathionylation and Oxidative Inhibition Depends on Conformational State of Pump*

Science.gov (United States)

Liu, Chia-Chi; Garcia, Alvaro; Mahmmoud, Yasser A.; Hamilton, Elisha J.; Galougahi, Keyvan Karimi; Fry, Natasha A. S.; Figtree, Gemma A.; Cornelius, Flemming; Clarke, Ronald J.; Rasmussen, Helge H.

2012-01-01

Glutathionylation of cysteine 46 of the β1 subunit of the Na+-K+ pump causes pump inhibition. However, the crystal structure, known in a state analogous to an E2·2K+·Pi configuration, indicates that the side chain of cysteine 46 is exposed to the lipid bulk phase of the membrane and not expected to be accessible to the cytosolic glutathione. We have examined whether glutathionylation depends on the conformational changes in the Na+-K+ pump cycle as described by the Albers-Post scheme. We measured β1 subunit glutathionylation and function of Na+-K+-ATPase in membrane fragments and in ventricular myocytes. Signals for glutathionylation in Na+-K+-ATPase-enriched membrane fragments suspended in solutions that preferentially induce E1ATP and E1Na3 conformations were much larger than signals in solutions that induce the E2 conformation. Ouabain further reduced glutathionylation in E2 and eliminated an increase seen with exposure to the oxidant peroxynitrite (ONOO−). Inhibition of Na+-K+-ATPase activity after exposure to ONOO− was greater when the enzyme had been in the E1Na3 than the E2 conformation. We exposed myocytes to different extracellular K+ concentrations to vary the membrane potential and hence voltage-dependent conformational poise. K+ concentrations expected to shift the poise toward E2 species reduced glutathionylation, and ouabain eliminated a ONOO−-induced increase. Angiotensin II-induced NADPH oxidase-dependent Na+-K+ pump inhibition was eliminated by conditions expected to shift the poise toward the E2 species. We conclude that susceptibility of the β1 subunit to glutathionylation depends on the conformational poise of the Na+-K+ pump. PMID:22354969

Probing Conformational Change of Bovine Serum Albumin–Dextran Conjugates under Controlled Dry Heating

Energy Technology Data Exchange (ETDEWEB)

Xia, Shuqin; Li, Yunqi; Zhao, Qin; Li, Ji; Xia, Qiuyang; Zhang, Xiaoming; Huang, Qingrong (Rutgers); (Chinese Aca. Sci.); (Jiangnan)

2015-04-29

The time-dependent conformational change of bovine serum album (BSA) during Maillard reaction with dextran under controlled dry heating has been studied by small-angle X-ray scattering, fluorescence spectroscopy, dynamic light scattering, and circular dichroism analysis. Through the research on the radii of gyration (R_g), intrinsic fluorescence, and secondary structure, conjugates with dextran coating were found to inhibit BSA aggregation and preserve the secondary structure of native BSA against long-time heat treatment during Maillard reaction. The results suggested that the hydrophilic dextran was conjugated to the compact protein surface and enclosed it and more dextran chains were attached to BSA with the increase of the heating time. The study presented here will be beneficial to the understanding of the conformational evolution of BSA molecules during the dry-heating Maillard reaction and to the control of the protein–polysaccharide conjugate structure.

The Rate of Seasonal Changes in Temperature Alters Acclimation of Performance under Climate Change.

Science.gov (United States)

Nilsson-Örtman, Viktor; Johansson, Frank

2017-12-01

How the ability to acclimate will impact individual performance and ecological interactions under climate change remains poorly understood. Theory predicts that the benefit an organism can gain from acclimating depends on the rate at which temperatures change relative to the time it takes to induce beneficial acclimation. Here, we present a conceptual model showing how slower seasonal changes under climate change can alter species' relative performance when they differ in acclimation rate and magnitude. To test predictions from theory, we performed a microcosm experiment where we reared a mid- and a high-latitude damselfly species alone or together under the rapid seasonality currently experienced at 62°N and the slower seasonality predicted for this latitude under climate change and measured larval growth and survival. To separate acclimation effects from fixed thermal responses, we simulated growth trajectories based on species' growth rates at constant temperatures and quantified how much and how fast species needed to acclimate to match the observed growth trajectories. Consistent with our predictions, the results showed that the midlatitude species had a greater capacity for acclimation than the high-latitude species. Furthermore, since acclimation occurred at a slower rate than seasonal temperature changes, the midlatitude species had a small growth advantage over the high-latitude species under the current seasonality but a greater growth advantage under the slower seasonality predicted for this latitude under climate change. In addition, the two species did not differ in survival under the current seasonality, but the midlatitude species had higher survival under the predicted climate change scenario, possibly because rates of cannibalism were lower when smaller heterospecifics were present. These findings highlight the need to incorporate acclimation rates in ecological models.

Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes

International Nuclear Information System (INIS)

Matei, Iulia; Ionescu, Sorana; Hillebrand, Mihaela

2011-01-01

The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 10 5 M -1 was evidenced. Foerster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes in the CD band of HSA indicate a decrease in the α-helix content upon binding. An induced CD signal for bound fisetin was observed and rationalized in terms of density functional theory calculations. - Highlights: → Fisetin-BSA system was studied by fluorescence spectroscopy. → Binding parameters, association constant and number of sites were estimated. → Binding site of fisetin was identified by competitive experiments. → Conformational changes in HSA and fisetin were evidenced by circular dichroism. → TDDFT calculated CD spectra supported the experimental data.

Conformational dynamics and role of the acidic pocket in ASIC pH-dependent gating.

Science.gov (United States)

Vullo, Sabrina; Bonifacio, Gaetano; Roy, Sophie; Johner, Niklaus; Bernèche, Simon; Kellenberger, Stephan

2017-04-04

Acid-sensing ion channels (ASICs) are proton-activated Na + channels expressed in the nervous system, where they are involved in learning, fear behaviors, neurodegeneration, and pain sensation. In this work, we study the role in pH sensing of two regions of the ectodomain enriched in acidic residues: the acidic pocket, which faces the outside of the protein and is the binding site of several animal toxins, and the palm, a central channel domain. Using voltage clamp fluorometry, we find that the acidic pocket undergoes conformational changes during both activation and desensitization. Concurrently, we find that, although proton sensing in the acidic pocket is not required for channel function, it does contribute to both activation and desensitization. Furthermore, protonation-mimicking mutations of acidic residues in the palm induce a dramatic acceleration of desensitization followed by the appearance of a sustained current. In summary, this work describes the roles of potential pH sensors in two extracellular domains, and it proposes a model of acidification-induced conformational changes occurring in the acidic pocket of ASIC1a.

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.

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.

Effect of External Electric Field Stress on Gliadin Protein Conformation

OpenAIRE

Singh, Ashutosh; Munshi, Shirin; Raghavan, Vijaya

2013-01-01

A molecular dynamic (MD) modeling approach was applied to evaluate the effect of external electric field on gliadin protein structure and surface properties. Static electric field strengths of 0.001 V/nm and 0.002 V/nm induced conformational changes in the protein but had no significant effect on its surface properties. The study of hydrogen bond evolution during the course of simulation revealed that the root mean square deviation, radius of gyration and secondary structure formation, all de...

Changes in properties of DNA caused by gamma and ultraviolet radiation. Dependence of conformational changes on the chemical nature of the damage

Energy Technology Data Exchange (ETDEWEB)

Vorlickova, M; Palacek, E [Ceskoslovenska Akademie Ved, Brno. Biofysikalni Ustav

1978-02-16

Changes in the pulse-polarographic behaviour and circular dichroism spectra of DNA were investigated after gamma and ultraviolet irradiations and after degradation by DNAase I. It was found that moderate doses of radiation cause local conformational changes in the double helix which are dependent on the chemical nature of the damage. Only the accumulation of structural changes after high doses of the radiations or after extensive enzymic treatment may cause formation of single-standed regions in DNA.

Effect of the atmospheric pressure nonequilibrium plasmas on the conformational changes of plasmid DNA

International Nuclear Information System (INIS)

Yan Xu; He Guangyuan; Shi Mengjun; Gao Xuan; Li Yin; Ma Fengyun; Yu Men; Wang Changdong; Wang Yuesheng; Yang Guangxiao; Zou Fei; Lu Xinpei; Xiong Qing; Xiong Zilan

2009-01-01

The cold atmospheric pressure plasma, which has been widely used for biomedical applications, may potentially affect the conformation of DNA. In this letter, an atmospheric pressure plasma plume is used to investigate its effects on the conformational changes of DNA of plasmid pAHC25. It is found that the plasma plume could cause plasmid DNA topology alteration, resulting in the percentage of the supercoiled plasmid DNA form decreased while that of the open circular and linearized form of plasmid DNA increased as detected by agrose gel electrophoresis. On the other hand, further investigation by using polymerase chain reaction method shows that the atmospheric pressure plasma jet treatments under proper conditions does not affect the genes of the plasmid DNA, which may have potential application in increasing the transformation frequency by genetic engineering.

Intraocular Pressure Induced Retinal Changes Identified Using Synchrotron Infrared Microscopy.

Directory of Open Access Journals (Sweden)

Hsin-Hui Shen

Full Text Available Infrared (IR spectroscopy has been used to quantify chemical and structural characteristics of a wide range of materials including biological tissues. In this study, we examined spatial changes in the chemical characteristics of rat retina in response to intraocular pressure (IOP elevation using synchrotron infrared microscopy (SIRM, a non-destructive imaging approach. IOP elevation was induced by placing a suture around the eye of anaesthetised rats. Retinal sections were collected onto transparent CaF2 slides 10 days following IOP elevation. Using combined SIRM spectra and chemical mapping approaches it was possible to quantify IOP induced changes in protein conformation and chemical distribution in various layers of the rat retina. We showed that 10 days following IOP elevation there was an increase in lipid and protein levels in the inner nuclear layer (INL and ganglion cell layer (GCL. IOP elevation also resulted in an increase in nucleic acids in the INL. Analysis of SIRM spectra revealed a shift in amide peaks to lower vibrational frequencies with a more prominent second shoulder, which is consistent with the presence of cell death in specific layers of the retina. These changes were more substantial in the INL and GCL layers compared with those occurring in the outer nuclear layer. These outcomes demonstrate the utility of SIRM to quantify the effect of IOP elevation on specific layers of the retina. Thus SIRM may be a useful tool for the study of localised tissue changes in glaucoma and other eye diseases.

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.

Various anti-motion sickness drugs and core body temperature changes.

Science.gov (United States)

Cheung, Bob; Nakashima, Ann M; Hofer, Kevin D

2011-04-01

Blood flow changes and inactivity associated with motion sickness appear to exacerbate the rate of core temperature decrease during subsequent body cooling. We investigated the effects of various classes of anti-motion sickness drugs on core temperature changes. There were 12 healthy male and female subjects (20-35 yr old) who were given selected classes of anti-motion sickness drugs prior to vestibular Coriolis cross coupling induced by graded yaw rotation and periodic pitch-forward head movements in the sagittal plane. All subjects were then immersed in water at 18 degrees C for a maximum of 90 min or until their core temperature reached 35 degrees C. Double-blind randomized trials were administered, including a placebo, a non-immersion control with no drug, and six anti-motion sickness drugs: meclizine, dimenhydrinate, chlorpheniramine, promethazine + dexamphetamine, promethazine + caffeine, and scopolamine + dexamphetamine. A 7-d washout period was observed between trials. Core temperature and the severity of sickness were monitored throughout each trial. A repeated measures design was performed on the severity of sickness and core temperature changes prior to motion provocation, immediately after the motion sickness end point, and throughout the period of cold-water immersion. The most effective anti-motion sickness drugs, promethazine + dexamphetamine (with a sickness score/duration of 0.65 +/- 0.17) and scopolamine + dexamphetamine (with a sickness score/duration of 0.79 +/- 0.17), significantly attenuated the decrease in core temperature. The effect of this attenuation was lower in less effective drugs. Our results suggest that the two most effective anti-motion sickness drugs are also the most effective in attenuating the rate of core temperature decrease.

Electron paramagnetic resonance study of conformational effects in alkyl-substituted 2-cyclohexanonyl radicals in an adamantane matrix

International Nuclear Information System (INIS)

Walter, H.F.

1975-01-01

Electron paramagnetic resonance spectra have been obtained for radicals produced by x-irradiation of cyclohexanone and various alkyl-substituted cyclohexanones trapped in an adamantane matrix. Temperature variation of these spectra permits determination of the enthalpy and entropy of activation for interconversion between the two half-chair conformations. In those cases where the two conformations have intrinsically different energies, the enthalpy and entropy differences between conformations are determined. For 2-cyclohexanonyl radical, the enthalpy of activation is 3.90 +- 0.07 kcal/mole and the entropy of activation is -2.3 +- 0.3 e.u. Methyl substitution on C 3 or C 5 gives a radical with activation parameters similar to the parent radical, indicating moderate realignment of atoms during the conformational change. Methyl substitution on C 4 gives a radical with lower activation parameters, which are interpreted to indicate conformational change mainly be a folding along the diagonal through the radical site. Larger groups attached to C 3 influence enthalpy and entropy differences between conformations much less than when they are attached to C 5 . Very large groups attached to C 5 apparently flatten the ring; it is not known whether or not this is a matrix effect. Deuteration seems to cause a slight reduction in the activation parameters for 2-cyclohexanonyl radical

Temperature dependence of the radiation induced change of depletion voltage in silicon PIN detectors

International Nuclear Information System (INIS)

Ziock, H.J.; Holzscheiter, K.; Morgan, A.; Palounek, A.P.T.; Ellison, J.; Heinson, A.P.; Mason, M.; Wimpenny, S.J.; Barberis, E.; Cartiglia, N.; Grillo, A.; O'Shaughnessy, K.; Rahn, J.; Rinaldi, P.; Rowe, W.A.; Sadrozinski, H.F.W.; Seiden, A.; Spencer, E.; Webster, A.; Wichmann, R.; Wilder, M.; Coupal, D.; Pal, T.

1993-01-01

The silicon microstrip detectors that will be used in the SDC experiment at the Superconducting Super Collider (SSC) will be exposed to very large fluences of charged particles, neutrons, and gammas. The authors present a study of how temperature affects the change in the depletion voltage of silicon PIN detectors damaged by radiation. They study the initial radiation damage and the short-term and long-term annealing of that damage as a function of temperature in the range from -10 degrees C to +50 degrees C, and as a function of 800 MeV proton fluence up to 1.5 x 10 14 p/cm 2 . They express the pronounced temperature dependencies in a simple model in terms of two annealing time constants which depend exponentially on the temperature

Involvement of prostaglandins and histamine in radiation-induced temperature responses in rats

International Nuclear Information System (INIS)

Kandasamy, S.B.; Hunt, W.A.

1990-01-01

Exposure of rats to 1-15 Gy of gamma radiation induced hyperthermia, whereas exposure to 20-150 Gy produced hypothermia. Since radiation exposure induced the release of prostaglandins (PGs) and histamine, the role of PGs and histamine in radiation-induced temperature changes was examined. Radiation-induced hyper- and hypothermia were antagonized by pretreatment with indomethacin, a cyclooxygenase inhibitor. Intracerebroventricular administration of PGE2 and PGD2 induced hyper- and hypothermia, respectively. Administration of SC-19220, a specific PGE2 antagonist, attenuated PGE2- and radiation-induced hyperthermia, but it did not antagonize PGD2- or radiation-induced hypothermia. Consistent with an apparent role of histamine in hypothermia, administration of disodium cromoglycate (a mast cell stabilizer), mepyramine (H1-receptor antagonist), or cimetidine (H2-receptor antagonist) attenuated PGD2- and radiation-induced hypothermia. These results suggest that radiation-induced hyperthermia is mediated via PGE2 and that radiation-induced hypothermia is mediated by another PG, possibly PGD2, via histamine

Effects of temperature and thermally-induced microstructure change on hydraulic conductivity of Boom Clay

Directory of Open Access Journals (Sweden)

W.Z. Chen

2017-06-01

Full Text Available Boom Clay is one of the potential host rocks for deep geological disposal of high-level radioactive nuclear waste in Belgium. In order to investigate the mechanism of hydraulic conductivity variation under complex thermo-mechanical coupling conditions and to better understand the thermo-hydro-mechanical (THM coupling behaviour of Boom Clay, a series of permeability tests using temperature-controlled triaxial cell has been carried out on the Boom Clay samples taken from Belgian underground research laboratory (URL HADES. Due to its sedimentary nature, Boom Clay presents across-anisotropy with respect to its sub-horizontal bedding plane. Direct measurements of the vertical (Kv and horizontal (Kh hydraulic conductivities show that the hydraulic conductivity at 80 °C is about 2.4 times larger than that at room temperature (23 °C, and the hydraulic conductivity variation with temperature is basically reversible during heating–cooling cycle. The anisotropic property of Boom Clay is studied by scanning electron microscope (SEM tests, which highlight the transversely isotropic characteristics of intact Boom Clay. It is shown that the sub-horizontal bedding feature accounts for the horizontal permeability higher than the vertical one. The measured increment in hydraulic conductivity with temperature is lower than the calculated one when merely considering the changes in water kinematic viscosity and density with temperature. The nuclear magnetic resonance (NMR tests have also been carried out to investigate the impact of microstructure variation on the THM properties of clay. The results show that heating under unconstrained boundary condition will produce larger size of pores and weaken the microstructure. The discrepancy between the hydraulic conductivity experimentally measured and predicted (considering water viscosity and density changes with temperature can be attributed to the microstructural weakening effect on the thermal volume change

Temperature and ontogenetic effects on color change in the larval salamander species Ambystoma barbouri and Ambystoma texanum

Energy Technology Data Exchange (ETDEWEB)

Garcia, T S; Straus, R; Sih, A [Univ. of Kentucky, Dept. of Biological Sciences, Lexington, Kentucky (United States)

2003-04-01

Temperature has been shown to affect body color in several species of amphibians. The interaction between color and temperature may also change over larval ontogeny, perhaps because of age-related or seasonal changes in selection pressures on color. We quantified the effects of temperature on the color of the salamander sister species Ambystoma barbouri and Ambystoma texanum over larval ontogeny. We found that early-stage larvae responded to cold temperatures with a dark color relative to that of the warm temperature response. Both species then exhibited an ontogenetic shift in larval color, with larvae becoming lighter with age. Interestingly, older larvae showed decreased plasticity in color change to temperature when compared with younger stages. Older A. texanum larvae exhibited a reversal in the direction of color change, with cold temperatures inducing a lighter color relative to warm temperatures. We suggest that the overall pattern of color change (a plastic color response to temperature for young larvae, a progressive lightening of larvae over development, and an apparent loss of color plasticity to temperature over ontogeny) can be plausibly explained by seasonal changes in environmental factors (temperature, ultraviolet radiation) selecting for body color. (author)

Temperature and ontogenetic effects on color change in the larval salamander species Ambystoma barbouri and Ambystoma texanum

International Nuclear Information System (INIS)

Garcia, T.S.; Straus, R.; Sih, A.

2003-01-01

Temperature has been shown to affect body color in several species of amphibians. The interaction between color and temperature may also change over larval ontogeny, perhaps because of age-related or seasonal changes in selection pressures on color. We quantified the effects of temperature on the color of the salamander sister species Ambystoma barbouri and Ambystoma texanum over larval ontogeny. We found that early-stage larvae responded to cold temperatures with a dark color relative to that of the warm temperature response. Both species then exhibited an ontogenetic shift in larval color, with larvae becoming lighter with age. Interestingly, older larvae showed decreased plasticity in color change to temperature when compared with younger stages. Older A. texanum larvae exhibited a reversal in the direction of color change, with cold temperatures inducing a lighter color relative to warm temperatures. We suggest that the overall pattern of color change (a plastic color response to temperature for young larvae, a progressive lightening of larvae over development, and an apparent loss of color plasticity to temperature over ontogeny) can be plausibly explained by seasonal changes in environmental factors (temperature, ultraviolet radiation) selecting for body color. (author)

Electromagnetically induced transparency in high-temperature magnetoactive plasma

International Nuclear Information System (INIS)

Kryachko, A.Yu.; Litvak, A.G.; Tokman, M.D.

2002-01-01

The classical analog of the presently popular in the quantum electronics effect of the electromagnetically induced transparency (EIT) is studied. The EIT effect is considered for the electron-cyclotron waves in the plasma with the finite temperature. The expression for the effective index of the electromagnetic wave refraction is identified and the dispersion law and this wave absorption under the EIT conditions are studied. It is shown, that accounting for the thermal motion, which radically changes the behavior of the signal wave dispersion curves in the EIT area, as compared with the cold plasma case [ru

NMR and modelling techniques in structural and conformation analysis

Energy Technology Data Exchange (ETDEWEB)

Abraham, R J [Liverpool Univ. (United Kingdom)

1994-12-31

The use of Lanthanide Induced Shifts (L.I.S.) and modelling techniques in conformational analysis is presented. The use of Co{sup III} porphyrins as shift reagents is discussed, with examples of their use in the conformational analysis of some heterocyclic amines. (author) 13 refs., 9 figs.

Flow equation, conformal symmetry, and anti-de Sitter geometry

Science.gov (United States)

Aoki, Sinya; Yokoyama, Shuichi

2018-03-01

We argue that the anti-de Sitter (AdS) geometry in d+1 dimensions naturally emerges from an arbitrary conformal field theory in d dimensions using the free flow equation. We first show that an induced metric defined from the flowed field generally corresponds to the quantum information metric, called the Bures or Helstrom metric, if the flowed field is normalized appropriately. We next verify that the induced metric computed explicitly with the free flow equation always becomes the AdS metric when the theory is conformal. We finally prove that the conformal symmetry in d dimensions converts to the AdS isometry in d+1 dimensions after d-dimensional quantum averaging. This guarantees the emergence of AdS geometry without explicit calculation.

Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation.

Directory of Open Access Journals (Sweden)

César Augusto F de Oliveira

2011-10-01

Full Text Available Chagas' disease, caused by the protozoan parasite Trypanosoma cruzi (T. cruzi, is a life-threatening illness affecting 11-18 million people. Currently available treatments are limited, with unacceptable efficacy and safety profiles. Recent studies have revealed an essential T. cruzi proline racemase enzyme (TcPR as an attractive candidate for improved chemotherapeutic intervention. Conformational changes associated with substrate binding to TcPR are believed to expose critical residues that elicit a host mitogenic B-cell response, a process contributing to parasite persistence and immune system evasion. Characterization of the conformational states of TcPR requires access to long-time-scale motions that are currently inaccessible by standard molecular dynamics simulations. Here we describe advanced accelerated molecular dynamics that extend the effective simulation time and capture large-scale motions of functional relevance. Conservation and fragment mapping analyses identified potential conformational epitopes located in the vicinity of newly identified transient binding pockets. The newly identified open TcPR conformations revealed by this study along with knowledge of the closed to open interconversion mechanism advances our understanding of TcPR function. The results and the strategy adopted in this work constitute an important step toward the rationalization of the molecular basis behind the mitogenic B-cell response of TcPR and provide new insights for future structure-based drug discovery.

Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function.

Directory of Open Access Journals (Sweden)

Michael A Jamros

Full Text Available Protein kinases use ATP as a phosphoryl donor for the posttranslational modification of signaling targets. It is generally thought that the binding of this nucleotide induces conformational changes leading to closed, more compact forms of the kinase domain that ideally orient active-site residues for efficient catalysis. The kinase domain is oftentimes flanked by additional ligand binding domains that up- or down-regulate catalytic function. C-terminal Src kinase (Csk is a multidomain tyrosine kinase that is up-regulated by N-terminal SH2 and SH3 domains. Although the X-ray structure of Csk suggests the enzyme is compact, X-ray scattering studies indicate that the enzyme possesses both compact and open conformational forms in solution. Here, we investigated whether interactions with the ATP analog AMP-PNP and ADP can shift the conformational ensemble of Csk in solution using a combination of small angle x-ray scattering and molecular dynamics simulations. We find that binding of AMP-PNP shifts the ensemble towards more extended rather than more compact conformations. Binding of ADP further shifts the ensemble towards extended conformations, including highly extended conformations not adopted by the apo protein, nor by the AMP-PNP bound protein. These ensembles indicate that any compaction of the kinase domain induced by nucleotide binding does not extend to the overall multi-domain architecture. Instead, assembly of an ATP-bound kinase domain generates further extended forms of Csk that may have relevance for kinase scaffolding and Src regulation in the cell.

Calcium binding promotes prion protein fragment 90-231 conformational change toward a membrane destabilizing and cytotoxic structure.

Directory of Open Access Journals (Sweden)

Sacha Sorrentino

Full Text Available The pathological form of prion protein (PrP(Sc, as other amyloidogenic proteins, causes a marked increase of membrane permeability. PrP(Sc extracted from infected Syrian hamster brains induces a considerable change in membrane ionic conductance, although the contribution of this interaction to the molecular mechanism of neurodegeneration process is still controversial. We previously showed that the human PrP fragment 90-231 (hPrP₉₀₋₂₃₁ increases ionic conductance across artificial lipid bilayer, in a calcium-dependent manner, producing an alteration similar to that observed for PrP(Sc. In the present study we demonstrate that hPrP₉₀₋₂₃₁, pre-incubated with 10 mM Ca⁺⁺ and then re-suspended in physiological external solution increases not only membrane conductance but neurotoxicity as well. Furthermore we show the existence of a direct link between these two effects as demonstrated by a highly statistically significant correlation in several experimental conditions. A similar correlation between increased membrane conductance and cell degeneration has been observed assaying hPrP₉₀₋₂₃₁ bearing pathogenic mutations (D202N and E200K. We also report that Ca⁺⁺ binding to hPrP₉₀₋₂₃₁ induces a conformational change based on an alteration of secondary structure characterized by loss of alpha-helix content causing hydrophobic amino acid exposure and proteinase K resistance. These features, either acquired after controlled thermal denaturation or induced by D202N and E200K mutations were previously identified as responsible for hPrP₉₀₋₂₃₁ cytotoxicity. Finally, by in silico structural analysis, we propose that Ca⁺⁺ binding to hPrP₉₀₋₂₃₁ modifies amino acid orientation, in the same way induced by E200K mutation, thus suggesting a pathway for the structural alterations responsible of PrP neurotoxicity.

Two-Dimensional Correlation Analysis of pH-induced Raman Spectral Changes of α-Lactalbumin

Energy Technology Data Exchange (ETDEWEB)

Park, Yeonju; Kim, Yeseul; Vikram, Kunwar; Jung, Young Mee [Kangwon National University, Chuncheon (Korea, Republic of); Czarnik-Matusewicz, Boguslawa [University of Wrocław, Wrocław (Poland)

2016-05-15

In this study, spectral changes in aromatic amino acid residues, such as tyrosine (Tyr) and tryptophan (Trp), in bovine holo-ALA were investigated at varying pH values by Raman spectroscopy. PCA and 2D correlation spectroscopy were applied to the pH-induced Raman spectra of bovine holo-ALA to obtain a deeper understanding of the conformational changes in the polypeptide backbone. We can confirm that the Tyr residues are buried inside the protein as the pH decreases. The secondary structure change primarily occurred in the N-state (pH 7-4), and the Tyr residues changed during the A-state (pH 3-1). We are currently investigating the overall correlation between the side chain and peptide backbone in the transition of ALA from the N-state to the A-states during pH variations; the results of these analyses will be reported elsewhere.

Conformational analysis of 9β,19-cyclopropyl sterols: Detection of the pseudoplanar conformer by nuclear Overhauser effects and its functional implications

International Nuclear Information System (INIS)

Nes, W.D.; Benson, M.; Lundin, R.E.; Le, P.H.

1988-01-01

Nuclear Overhauser difference spectroscopy and variable temperature studies of the 9β,19-cyclopropyl sterols 24,25-dehydropollinastanol (4,4-desmethyl-5α-cycloart-24-en-3β-ol) and cyclolaudenol [(24S)-24-methyl-5α-cycloart-25(27)-en-3β-ol] have shown the solution conformation of the B/C rings to be twist-chair/twist-boat rather than boat/chair as suggested in the literature. This is very similar to the known crystal structure conformation of 9β,19-cyclopropyl sterols. The effect of these conformations on the molecular shape is highly significant; the first conformation orients into a pseudoplanar or flat shape analogous to lanosterol, whereas the latter conformation exhibits a bent shape. The results are interpreted to imply that, for conformational reasons, cyclopropyl sterols can be expected to maintain the pseudoplanar shape in membrane bilayers

Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

Science.gov (United States)

Frank, Martin

2015-01-01

Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

Resistive switching characteristics of interfacial phase-change memory at elevated temperature

Science.gov (United States)

Mitrofanov, Kirill V.; Saito, Yuta; Miyata, Noriyuki; Fons, Paul; Kolobov, Alexander V.; Tominaga, Junji

2018-04-01

Interfacial phase-change memory (iPCM) devices were fabricated using W and TiN for the bottom and top contacts, respectively, and the effect of operation temperature on the resistive switching was examined over the range between room temperature and 200 °C. It was found that the high-resistance (RESET) state in an iPCM device drops sharply at around 150 °C to a low-resistance (SET) state, which differs by ˜400 Ω from the SET state obtained by electric-field-induced switching. The iPCM device SET state resistance recovered during the cooling process and remained at nearly the same value for the RESET state. These resistance characteristics greatly differ from those of the conventional Ge-Sb-Te (GST) alloy phase-change memory device, underscoring the fundamentally different switching nature of iPCM devices. From the thermal stability measurements of iPCM devices, their optimal temperature operation was concluded to be less than 100 °C.

The Detrimental Effects of Oxytocin-Induced Conformity on Dishonesty in Competition.

Science.gov (United States)

Aydogan, Gökhan; Jobst, Andrea; D'Ardenne, Kimberlee; Müller, Norbert; Kocher, Martin G

2017-06-01

Justifications may promote unethical behavior because they constitute a convenient loophole through which people can gain from immoral behavior and preserve a positive self-image at the same time. A justification that is widely used is rooted in conformity: Unethical choices become more permissible because one's peers are expected to make the same unethical choices. In the current study, we tested whether an exogenous alteration of conformity led to a lower inclination to adhere to a widely accepted norm (i.e., honesty) under the pressure of competition. We took advantage of the well-known effects of intranasally applied oxytocin on affiliation, in-group conformity, and in-group favoritism in humans. We found that conformity was enhanced by oxytocin, and this enhancement had a detrimental effect on honesty in a competitive environment but not in a noncompetitive environment. Our findings contribute to recent evidence showing that competition may lead to unethical behavior and erode moral values.

Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility.

Science.gov (United States)

Pancera, Marie; Majeed, Shahzad; Ban, Yih-En Andrew; Chen, Lei; Huang, Chih-chin; Kong, Leopold; Kwon, Young Do; Stuckey, Jonathan; Zhou, Tongqing; Robinson, James E; Schief, William R; Sodroski, Joseph; Wyatt, Richard; Kwong, Peter D

2010-01-19

The viral spike of HIV-1 is composed of three gp120 envelope glycoproteins attached noncovalently to three gp41 transmembrane molecules. Viral entry is initiated by binding to the CD4 receptor on the cell surface, which induces large conformational changes in gp120. These changes not only provide a model for receptor-triggered entry, but affect spike sensitivity to drug- and antibody-mediated neutralization. Although some of the details of the CD4-induced conformational change have been visualized by crystal structures and cryoelectron tomograms, the critical gp41-interactive region of gp120 was missing from previous atomic-level characterizations. Here we determine the crystal structure of an HIV-1 gp120 core with intact gp41-interactive region in its CD4-bound state, compare this structure to unliganded and antibody-bound forms to identify structurally invariant and plastic components, and use ligand-oriented cryoelectron tomograms to define component mobility in the viral spike context. Newly defined gp120 elements proximal to the gp41 interface complete a 7-stranded beta-sandwich, which appeared invariant in conformation. Loop excursions emanating from the sandwich form three topologically separate--and structurally plastic--layers, topped off by the highly glycosylated gp120 outer domain. Crystal structures, cryoelectron tomograms, and interlayer chemistry were consistent with a mechanism in which the layers act as a shape-changing spacer, facilitating movement between outer domain and gp41-associated beta-sandwich and providing for conformational diversity used in immune evasion. A "layered" gp120 architecture thus allows movement among alternative glycoprotein conformations required for virus entry and immune evasion, whereas a beta-sandwich clamp maintains gp120-gp41 interaction and regulates gp41 transitions.

Theories of inflation and conformal transformations

International Nuclear Information System (INIS)

Kalara, S.; Kaloper, N.; Olive, K.A.

1990-01-01

We show that several different theories of inflation including R 2 , Brans-Dicke, and induced-gravity inflation are all related to generalized or power-law inflation by means of conformal transformations. These theories all involve non-standard gravity, and the use of conformal transformations allows one to obtain standard inflationary predictions such as the expansion time-scale, reheating and density perturbations in each case very simply. We also discuss the possibilities of this method to be applied to string theory. (orig.)

Effects of temperature changes on maize production in Mozambique

Science.gov (United States)

Harrison, L.; Michaelsen, J.; Funk, Chris; Husak, G.

2011-01-01

We examined intraseasonal changes in maize phenology and heat stress exposure over the 1979-2008 period, using Mozambique meteorological station data and maize growth requirements in a growing degree-day model. Identifying historical effects of warming on maize growth is particularly important in Mozambique because national food security is highly dependent on domestic food production, most of which is grown in already warm to hot environments. Warming temperatures speed plant development, shortening the length of growth periods necessary for optimum plant and grain size. This faster phenological development also alters the timing of maximum plant water demand. In hot growing environments, temperature increases during maize pollination threaten to make midseason crop failure the norm. In addition to creating a harsher thermal environment, we find that early season temperature increases have caused the maize reproductive period to start earlier, increasing the risk of heat and water stress. Declines in time to maize maturation suggest that, independent of effects to water availability, yield potential is becoming increasingly limited by warming itself. Regional variations in effects are a function of the timing and magnitude of temperature increases and growing season characteristics. Continuation of current climatic trends could induce substantial yield losses in some locations. Farmers could avoid some losses through simple changes to planting dates and maize varietal types.

Titanium carbide nanocube core induced interfacial growth of crystalline polypyrrole/polyvinyl alcohol lamellar shell for wide-temperature range supercapacitors

Science.gov (United States)

Weng, Yu-Ting; Pan, Hsiao-An; Wu, Nae-Lih; Chen, Geroge Zheng

2015-01-01

This is the first investigation on electrically conducting polymers-based supercapacitor electrodes over a wide temperature range, from -18 °C to 60 °C. A high-performance supercapacitor electrode material consisting of TiC nanocube core and conformal crystalline polypyrrole (PPy)/poly-vinyl-alcohol (PVA) lamellar shell has been synthesized by heterogeneous nucleation-induced interfacial crystallization. PPy is induced to crystallize on the negatively charged TiC nanocube surfaces via strong interfacial interactions. In this organic-inorganic hybrid nanocomposite, the long chain PVA enables enhanced cycle life due to improved mechanical properties, and the TiC nanocube not only contributes to electron conduction, but also dictates the PPy morphology/crystallinity for maximizing the charging-discharging performance. The crystalline PPy/PAV layer on the TiC nanocube offers unprecedented high capacity (>350 F g-1-PPy at 300 mV s-1 with ΔV = 1.6 V) and cycling stability in a temperature range from -18 °C to 60 °C. The presented hybrid-filler and interfacial crystallization strategies can be applied to the exploration of new-generation high-power conducting polymer-based supercapacitor materials.

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.

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.

Working gas temperature and pressure changes for microscale thermal creep-driven flow caused by discontinuous wall temperatures

International Nuclear Information System (INIS)

Han, Yen-Lin

2010-01-01

Microscale temperature gradient-driven (thermal creep/transpiration) gas flows have attracted significant interest during the past decade. For free molecular and transitional conditions, applying temperature gradients to a flow channel's walls induces the thermal creep effect. This results in a working gas flowing through the channel from cold to hot, which is generally accompanied by a rising pressure from cold to hot in the channel. Working gas temperature and pressure distributions can vary significantly, depending on a flow channel's configuration and wall temperature distribution. Understanding working gas temperature excursions, both increases and decreases, is essential to ensure the effective use of thermal creep flows in microscale applications. In this study, the characterizations of working gas temperature variations, due to both temperature discontinuities and more gradual changes, on a variety of flow channel walls, were systematically investigated using the direct simulation Monte Carlo (DSMC) method. A micro/meso-scale pump, the Knudsen compressor, was chosen to illustrate the importance of controlling working gas temperature in thermal creep-driven flows. Gas pressure and temperature variations, through several Knudsen compressor stage configurations, were studied to determine the most advantageous flow phenomena for the efficient operation of Knudsen compressors.

Conformational Complexity in the LH2 Antenna of the Purple Sulfur Bacterium Allochromatium vinosum Revealed by Hole-Burning Spectroscopy.

Science.gov (United States)

Kell, Adam; Jassas, Mahboobe; Acharya, Khem; Hacking, Kirsty; Cogdell, Richard J; Jankowiak, Ryszard

2017-06-15

This work discusses the protein conformational complexity of the B800-850 LH2 complexes from the purple sulfur bacterium Allochromatium vinosum, focusing on the spectral characteristics of the B850 chromophores. Low-temperature B850 absorption and the split B800 band shift blue and red, respectively, at elevated temperatures, revealing isosbestic points. The latter indicates the presence of two (unresolved) conformations of B850 bacteriochlorophylls (BChls), referred to as conformations 1 and 2, and two conformations of B800 BChls, denoted as B800 R and B800 B . The energy differences between average site energies of conformations 1 and 2, and B800 R and B800 B are similar (∼200 cm -1 ), suggesting weak and strong hydrogen bonds linking two major subpopulations of BChls and the protein scaffolding. Although conformations 1 and 2 of the B850 chromophores, and B800 R and B800 B , exist in the ground state, selective excitation leads to 1 → 2 and B800 R → B800 B phototransformations. Different static inhomogeneous broadening is revealed for the lowest energy exciton states of B850 (fwhm ∼195 cm -1 ) and B800 R (fwhm ∼140 cm -1 ). To describe the 5 K absorption spectrum and the above-mentioned conformations, we employ an exciton model with dichotomous protein conformation disorder. We show that both experimental data and the modeling study support a two-site model with strongly and weakly hydrogen-bonded B850 and B800 BChls, which under illumination undergo conformational changes, most likely caused by proton dynamics.

Conformational changes in human serum albumin studied by fluorescence and absorption spectroscopy. Distance measurements as a function of pH and fatty acids

DEFF Research Database (Denmark)

Honoré, B; Pedersen, A O

1989-01-01

pH- and fatty acid-induced conformational changes in human serum albumin were investigated by fluorescence-energy transfer, determining the distance between Trp-214 and bound bilirubin at 25 degrees C. This distance changes significantly with the pH, being 2.52 +/- 0.01 nm at pH 6, 2.31 +/- 0.04 nm...... at pH 9, 2.13 +/- 0.07 nm at pH 11.0 and 2.77 nm at pH 11.9. The influence of different fatty acids on the distance was also determined. At pH 7.4 medium-chain fatty acids seem to increase this distance, whereas long-chain fatty acids, at low concentrations, decrease the distance between the two...... chromophores. The contraction of the protein carrying long-chain saturated fatty acids is even more pronounced at pH 9. Udgivelsesdato: 1989-Feb-15...

Characterizing DNA condensation and conformational changes in organic solvents.

Directory of Open Access Journals (Sweden)

Fuyou Ke

Full Text Available Organic solvents offer a new approach to formulate DNA into novel structures suitable for gene delivery. In this study, we examined the in situ behavior of DNA in N, N-dimethylformamide (DMF at low concentration via laser light scattering (LLS, TEM, UV absorbance and Zeta potential analysis. Results revealed that, in DMF, a 21bp oligonucleotide remained intact, while calf thymus DNA and supercoiled plasmid DNA were condensed and denatured. During condensation and denaturation, the size was decreased by a factor of 8-10, with calf thymus DNA forming spherical globules while plasmid DNA exhibited a toroid-like conformation. In the condensed state, DNA molecules were still able to release the counterions to be negatively charged, indicating that the condensation was mainly driven by the excluded volume interactions. The condensation induced by DMF was reversible for plasmid DNA but not for calf thymus DNA. When plasmid DNA was removed from DMF and resuspended in an aqueous solution, the DNA was quickly regained a double stranded configuration. These findings provide further insight into the behavior and condensation mechanism of DNA in an organic solvent and may aid in developing more efficient non-viral gene delivery systems.

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

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.

ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece

Czech Academy of Sciences Publication Activity Database

Gryčová, Lenka; Sklenovský, P.; Lánský, Zdeněk; Janovská, M.; Otyepka, M.; Amler, E.; Teisinger, Jan; Kubala, M.

2009-01-01

Roč. 1788, č. 5 (2009), s. 1081-1091 ISSN 0005-2736 R&D Projects: GA ČR(CZ) GA303/07/0915 Grant - others:GA ČR(CZ) GA203/07/0564; GA ČR(CZ) GD522/08/H003; GA MŠk(CZ) LC512 Program:GD; LC Institutional research plan: CEZ:AV0Z50110509 Keywords : Na+/K+ ATPase * tryptophan fluorescence * conformational changes Subject RIV: BO - Biophysics Impact factor: 3.998, year: 2009

Distribution of temperature changes and neurovascular coupling in rat brain following 3,4-methylenedioxymethamphetamine (MDMA,‘ecstasy’) exposure

Science.gov (United States)

Coman, Daniel; Sanganahalli, Basavaraju G.; Jiang, Lihong; Hyder, Fahmeed; Behar, Kevin L.

2015-01-01

(+/−)3,4-methylenedioxymethamphetamine (MDMA, ‘ecstasy’) is an abused psychostimulant producing strong monoaminergic stimulation and whole-body hyperthermia. MDMA-induced thermogenesis involves activation of uncoupling proteins (UCP), primarily a type specific to skeletal muscle (UCP-3) and which is absent in brain, although other UCP types are expressed in brain (e.g., thalamus) and might contribute to thermogenesis. Since neuroimaging of brain temperature could provide insights of MDMA action, we measured spatial distributions of systemically-administered MDMA-induced temperature changes and dynamics in rat cortex and subcortex using a novel magnetic resonance method, Biosensor Imaging of Redundant Deviation of Shifts (BIRDS), with an exogenous temperature-sensitive probe (thulium ion and macrocyclic chelate 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetramethyl-1,4,7,10-tetraacetate (DOTMA4−)). The MDMA-induced temperature rise in cortex was greater than in subcortex (1.6±0.4°C vs. 1.3±0.4°C) and occurred more rapidly (2.0±0.2°C/h vs. 1.5±0.2°C/h). MDMA-induced temperature changes and dynamics in cortex and body were correlated, although body temperature exceeded cortex before and after MDMA. Temperature, neuronal activity, and blood flow (CBF) were measured simultaneously in cortex and subcortex (i.e., thalamus) to investigate possible differences of MDMA-induced warming across brain regions. MDMA-induced warming correlated with increases in neuronal activity and blood flow in cortex, suggesting that the normal neurovascular response to increased neural activity was maintained. In contrast to cortex, a biphasic relationship was seen in subcortex (i.e., thalamus), with a decline in CBF as temperature and neural activity rose, transitioning to a rise in CBF for temperature >37°C, suggesting that MDMA affected CBF and neurovascular coupling differently in subcortical regions. Considering that MDMA effects on CBF and heat dissipation (as well as

Quantitative characterization of conformational-specific protein-DNA binding using a dual-spectral interferometric imaging biosensor

Science.gov (United States)

Zhang, Xirui; Daaboul, George G.; Spuhler, Philipp S.; Dröge, Peter; Ünlü, M. Selim

2016-03-01

DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are not fully understood. Recently, it was discovered that DNA-binding proteins recognize specific binding sites to carry out their functions through an indirect readout mechanism by recognizing and capturing DNA conformational flexibility and deformation. High-throughput DNA microarray-based methods that provide large-scale protein-DNA binding information have shown effective and comprehensive analysis of protein-DNA binding affinities, but do not provide information of DNA conformational changes in specific protein-DNA complexes. Building on the high-throughput capability of DNA microarrays, we demonstrate a quantitative approach that simultaneously measures the amount of protein binding to DNA and nanometer-scale DNA conformational change induced by protein binding in a microarray format. Both measurements rely on spectral interferometry on a layered substrate using a single optical instrument in two distinct modalities. In the first modality, we quantitate the amount of binding of protein to surface-immobilized DNA in each DNA spot using a label-free spectral reflectivity technique that accurately measures the surface densities of protein and DNA accumulated on the substrate. In the second modality, for each DNA spot, we simultaneously measure DNA conformational change using a fluorescence vertical sectioning technique that determines average axial height of fluorophores tagged to specific nucleotides of the surface-immobilized DNA. The approach presented in this paper, when combined with current high-throughput DNA microarray-based technologies, has the potential to serve as a rapid and simple method for quantitative and large-scale characterization of conformational specific protein-DNA interactions.DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are

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.

Dynamics and diffusive-conformational coupling in polymer bulk samples and surfaces: a molecular dynamics study

International Nuclear Information System (INIS)

Vree, C; Mayr, S G

2010-01-01

The impact of free surfaces on the mobility and conformational fluctuations of model polymer chains is investigated with the help of classical molecular dynamics simulations over a broad temperature range. Below a critical temperature, T*, similar to the critical temperature of the mode coupling theory, the center-of-mass displacements and temporal fluctuations of the radius of gyration of individual chains-as a fingerprint of structural reconfigurations-reveal a strong enhancement close to surfaces, while this effect diminishes with increasing temperature and observation time. Interpreting conformational fluctuations as a random walk in conformational space, identical activation enthalpies for structural reconfigurations and diffusion are obtained within the error bars in the bulk and at the surfaces, thus indicating a coupling of diffusive and conformational dynamics.

Sensitivity of photoelectron diffraction to conformational changes of adsorbed molecules: Tetra-tert-butyl-azobenzene/Au(111

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A. Schuler

2017-01-01

Full Text Available Electron diffraction is a standard tool to investigate the atomic structure of surfaces, interfaces, and adsorbate systems. In particular, photoelectron diffraction is a promising candidate for real-time studies of structural dynamics combining the ultimate time resolution of optical pulses and the high scattering cross-sections for electrons. In view of future time-resolved experiments from molecular layers, we studied the sensitivity of photoelectron diffraction to conformational changes of only a small fraction of molecules in a monolayer adsorbed on a metallic substrate. 3,3′,5,5′-tetra-tert-butyl-azobenzene served as test case. This molecule can be switched between two isomers, trans and cis, by absorption of ultraviolet light. X-ray photoelectron diffraction patterns were recorded from tetra-tert-butyl-azobenzene/Au(111 in thermal equilibrium at room temperature and compared to patterns taken in the photostationary state obtained by exposing the surface to radiation from a high-intensity helium discharge lamp. Difference patterns were simulated by means of multiple-scattering calculations, which allowed us to determine the fraction of molecules that underwent isomerization.

Structure of conjugated polyketone reductase from Candida parapsilosis IFO 0708 reveals conformational changes for substrate recognition upon NADPH binding.

Science.gov (United States)

Qin, Hui-Min; Yamamura, Akihiro; Miyakawa, Takuya; Kataoka, Michihiko; Nagai, Takahiro; Kitamura, Nahoko; Urano, Nobuyuki; Maruoka, Shintaro; Ohtsuka, Jun; Nagata, Koji; Shimizu, Sakayu; Tanokura, Masaru

2014-01-01

Conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708, identified as a nicotinamide adenine dinucleotide phosphate (NADPH)-dependent ketopantoyl lactone reductase, belongs to the aldo-keto reductase superfamily. This enzyme reduces ketopantoyl lactone to D-pantoyl lactone in a strictly stereospecific manner. To elucidate the structural basis of the substrate specificity, we determined the crystal structures of the apo CPR-C2 and CPR-C2/NADPH complex at 1.70 and 1.80 Å resolutions, respectively. CPR-C2 adopted a triose-phosphate isomerase barrel fold at the core of the structure. Binding with the cofactor NADPH induced conformational changes in which Thr27 and Lys28 moved 15 and 5.0 Å, respectively, in the close vicinity of the adenosine 2'-phosphate group of NADPH to form hydrogen bonds. Based on the comparison of the CPR-C2/NADPH structure with 3-α-hydroxysteroid dehydrogenase and mutation analyses, we constructed substrate binding models with ketopantoyl lactone, which provided insight into the substrate specificity by the cofactor-induced structure. The results will be useful for the rational design of CPR-C2 mutants targeted for use in the industrial manufacture of ketopantoyl lactone.

Dodecylphosphocholine Micelles Induce Amyloid Formation of the PrP(110-136 Peptide via an α-Helical Metastable Conformation.

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Simon Sauvé

Full Text Available A peptide encompassing the conserved hydrophobic region and the first β-strand of the prion protein (PrP(110-136 shown to interact with the surface of dodecylphosphocholine micelles adopts an α-helical conformation that is localized below the head-group layer. This surface-bound peptide has a half-life of one day, and readily initiates the formation of amyloid fibrils. The presence of the latter was confirmed using birefringence microscopy upon Congo red binding and thioflavin T-binding induced fluorescence. The observation of this metastable α-helical conformer provides a unique snapshot of the early steps of the inter-conversion pathway. These findings together with the body of evidence from the prion literature allowed us to propose a mechanism for the conversion of PrPC to amyloid material.

Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes.

Science.gov (United States)

Ruiz-Tórtola, Ángela; Prats-Quílez, Francisco; Gónzalez-Lucas, Daniel; Bañuls, María-José; Maquieira, Ángel; Wheeler, Guy; Dalmay, Tamas; Griol, Amadeu; Hurtado, Juan; Bohlmann, Helge; Götzen, Reiner; García-Rupérez, Jaime

2018-04-17

An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes -upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors- is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained towards the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure. Schematic diagram of the PBG sensing structure on which the streptavidin-labeled MB probes were immobilized. This article is protected by copyright. All rights reserved.

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.

Microscopic insights into the NMR relaxation based protein conformational entropy meter

Science.gov (United States)

Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua

2013-01-01

Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven pro! teins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy. PMID:24007504

New open conformation of SMYD3 implicates conformational selection and allostery

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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.

Conformational responses to changes in the state of ionization of titrable groups in proteins

Science.gov (United States)

Richman, Daniel Eric

Electrostatic energy links the structural properties of proteins with some of their important biological functions, including catalysis, energy transduction, and binding and recognition. Accurate calculation of electrostatic energy is essential for predicting and for analyzing function from structure. All proteins have many ionizable residues at the protein-water interface. These groups tend to have ionization equilibria (pK a values) shifted slightly relative to their values in water. In contrast, groups buried in the hydrophobic interior usually have highly anomalous p Ka values. These shifts are what structure-based calculations have to reproduce to allow examination of contributions from electrostatics to stability, solubility and interactions of proteins. Electrostatic energies are challenging to calculate accurately because proteins are heterogeneous dielectric materials. Any individual ionizable group can experience very different local environments with different dielectric properties. The studies in this thesis examine the hypothesis that proteins reorganize concomitant with changes in their state of ionization. It appears that the pKa value measured experimentally reflects the average of pKa values experienced in the different electrostatic environments corresponding to different conformational microstates. Current computational models fail to sample conformational reorganization of the backbone correctly. Staphyloccocal nuclease (SNase) was used as a model protein in nuclear magnetic resonance (NMR) spectroscopy studies to characterize the conformational rearrangements of the protein coupled to changes in the ionization state of titrable groups. One set of experiments tests the hypothesis that proton binding to surface Asp and Glu side chains drives local unfolding by stabilizing less-native, more water-solvated conformations in which the side chains have normalized pKa values. Increased backbone flexibility in the ps-ns timescale, hydrogen bond (H

Conformational basis for the Li(+)-induced leak current in the rat gamma-aminobutyric acid (GABA) transporter-1

DEFF Research Database (Denmark)

MacAulay, Nanna; Zeuthen, Thomas; Gether, Ulrik

2002-01-01

The rat gamma-aminobutyric acid transporter-1 (GAT-1) was expressed in Xenopus laevis oocytes and the substrate-independent Li(+)-induced leak current was examined using two-electrode voltage clamp. The leak current was not affected by the addition of GABA and was not due to H(+) permeation. The Li......(+)-bound conformation of the protein displayed a lower passive water permeability than that of the Na(+)- and choline (Ch(+))-bound conformations and the leak current did not saturate with increasing amounts of Li(+) in the test solution. The mechanism that gives rise to the leak current did not support active water...... transport in contrast to the mechanism responsible for GABA translocation (approximately 330 water molecules per charge). Altogether, these data support the distinct nature of the leak conductance in relation to the substrate translocation process. It was observed that the leak current was inhibited by low...

WORM memory devices based on conformation change of a PVK derivative with a rigid spacer in side chain

International Nuclear Information System (INIS)

Liu Yuanhua; Li Najun; Xia Xuewei; Xu Qingfeng; Ge Jianfeng; Lu Jianmei

2010-01-01

A nonvolatile write-once-read-many-times (WORM) memory device based on poly((4-vinylbenzyl)-9H-carbazole) (PVCz) was fabricated by a simple and conventional process. The as-fabricated device was found to be at its OFF state and could be programmed irreversibly to the ON state with a low transition voltage of -1.7 V. The device exhibits a high ON/OFF current ratio of up to 10 6 , high stability in retention time up to 8 h and number of read cycles up to 10 8 under a read voltage of -1.0 V in both ON and OFF states. The results of X-ray diffraction (XRD) and fluorescence emission spectra in different states of PVCz indicate that the electrical bistable phenomenon is caused by the voltage-induced conformation change of the pendant carbazole groups. With high performance, low power consumption and low production cost, the device fabricated with PVCz has a potential application for nonvolatile memory.

Manipulation of Origin of Life Molecules: Recognizing Single-Molecule Conformations in β-Carotene and Chlorophyll-a/β-Carotene Clusters

Energy Technology Data Exchange (ETDEWEB)

Ngo, Anh T.; Skeini, Timur [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States; Iancu, Violeta [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States; Redfern, Paul C.; Curtiss, Larry A.; Hla, Saw Wai [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States

2018-01-11

Carotenoids and chlorophyll are essential parts of plant leaves and are involved in photosynthesis, a vital biological process responsible for the origin of life on Earth. Here, we investigate how beta-carotene and chlorophyll-a form mixed molecular phases On a Au(111) surface using low-temperature scanning tunneling microscopy and molecular manipulation at the single-molecule level supported by density functional theory calculations. By isolating individual molecules from nanoscale molecular clusters with a scanning tunneling microscope tip, we are able to identify five beta-carotene conformations including a structure exhibiting a three-dimensional conformation. Furthermore, molecular resolution images enable direct visualization of beta-carotene/chlorophyll-a clsuters, with intimate structural details highlighting how they pair: beta-carotene preferentially positions next to chlorophyll-a and induces switching of chlorophyll-a from straight to several bent tail conformations in the molecular clusters.

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.

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

Real-time observation of conformational switching in single conjugated polymer chains.

Science.gov (United States)

Tenopala-Carmona, Francisco; Fronk, Stephanie; Bazan, Guillermo C; Samuel, Ifor D W; Penedo, J Carlos

2018-02-01

Conjugated polymers (CPs) are an important class of organic semiconductors that combine novel optoelectronic properties with simple processing from organic solvents. It is important to study CP conformation in solution to understand the physics of these materials and because it affects the properties of solution-processed films. Single-molecule techniques are unique in their ability to extract information on a chain-to-chain basis; however, in the context of CPs, technical challenges have limited their general application to host matrices or semiliquid environments that constrain the conformational dynamics of the polymer. We introduce a conceptually different methodology that enables measurements in organic solvents using the single-end anchoring of polymer chains to avoid diffusion while preserving polymer flexibility. We explore the effect of organic solvents and show that, in addition to chain-to-chain conformational heterogeneity, collapsed and extended polymer segments can coexist within the same chain. The technique enables real-time solvent-exchange measurements, which show that anchored CP chains respond to sudden changes in solvent conditions on a subsecond time scale. Our results give an unprecedented glimpse into the mechanism of solvent-induced reorganization of CPs and can be expected to lead to a new range of techniques to investigate and conformationally manipulate CPs.

Corneal surface temperature change as the mode of stimulation of the non-contact corneal aesthesiometer.

Science.gov (United States)

Murphy, P J; Morgan, P B; Patel, S; Marshall, J

1999-05-01

The non-contact corneal aesthesiometer (NCCA) assesses corneal sensitivity by using a controlled pulse of air, directed at the corneal surface. The purpose of this paper was to investigate whether corneal surface temperature change was a component in the mode of stimulation. Thermocouple experiment: A simple model corneal surface was developed that was composed of a moistened circle of filter paper placed on a thermocouple and mounted on a glass slide. The temperature change produced by different stimulus pressures was measured for five different ambient temperatures. Thermal camera experiment: Using a thermal camera, the corneal surface temperature change was measured in nine young, healthy subjects after exposure to different stimulus air pulses. Pulse duration was set at 0.9 s but was varied in pressure from 0.5 to 3.5 millibars. Thermocouple experiment: An immediate drop in temperature was detected by the thermocouple as soon as the air flow was incident on the filter paper. A greater temperature change was produced by increasing the pressure of the incident air flow. A relationship was found and a calibration curve plotted. Thermal camera experiment: For each subject, a drop in surface temperature was detected at each stimulus pressure. Furthermore, as the stimulus pressure increased, the induced reduction in temperature also increased. A relationship was found and a calibration curve plotted. The NCCA air-pulse stimulus was capable of producing a localized temperature change on the corneal surface. The principal mode of corneal nerve stimulation, by the NCCA air pulse, was the rate of temperature change of the corneal surface.

Phase change based cooling for high burst mode heat loads with temperature regulation above the phase change temperature

Science.gov (United States)

The United States of America as represented by the United States Department of Energy

2009-12-15

An apparatus and method for transferring thermal energy from a heat load is disclosed. In particular, use of a phase change material and specific flow designs enables cooling with temperature regulation well above the fusion temperature of the phase change material for medium and high heat loads from devices operated intermittently (in burst mode). Exemplary heat loads include burst mode lasers and laser diodes, flight avionics, and high power space instruments. Thermal energy is transferred from the heat load to liquid phase change material from a phase change material reservoir. The liquid phase change material is split into two flows. Thermal energy is transferred from the first flow via a phase change material heat sink. The second flow bypasses the phase change material heat sink and joins with liquid phase change material exiting from the phase change material heat sink. The combined liquid phase change material is returned to the liquid phase change material reservoir. The ratio of bypass flow to flow into the phase change material heat sink can be varied to adjust the temperature of the liquid phase change material returned to the liquid phase change material reservoir. Varying the flowrate and temperature of the liquid phase change material presented to the heat load determines the magnitude of thermal energy transferred from the heat load.

Strain-induced structural changes and chemical reactions. 1: Thermomechanical and kinetic models

International Nuclear Information System (INIS)

Levitas, V.I.; Nesterenko, V.F.; Meyers, M.A.

1998-01-01

Strain-induced chemical reactions were observed recently (Nesterenko et al) in experiments in the shear band in both Ti-Si and Nb-Si mixtures. Reactions can start in the solid state or after melting of at least one component. One of the aims is to find theoretically whether there are possible macroscopic mechanisms of mechanical intensification of the above and other chemical reactions due to plastic shear in the solid state. Continuum thermodynamical theory of structural changes with an athermal kinetics, which includes martensitic phase transformations, plastic strain-induced chemical reactions and polymorphic transformations, is developed at finite strains. The theory includes kinematics, criterion of structural change and extremum principle for determination of all unknown variable parameters for the case with neglected elastic strains. Thermodynamically consistent kinetic theory of thermally activated structural changes is suggested. The concept of the effective temperature is introduced which takes into account that temperature can vary significantly (on 1,000 K) during the chemical reactions under consideration. The theory will be applied in Part 2 of the paper for the description of chemical reactions in the shear band

Supplement data for conformation changes by some binding - ConfC | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ent data for conformation changes by some binding DOI 10.18908/lsdba.nbdc00400-002 Description of data contents The distance values...Bank) Data analysis method The distance values of φ and ψ between the superimposed protein structures of eac

Neural Basis of Two Kinds of Social Influence: Obedience and Conformity

Directory of Open Access Journals (Sweden)

Ying eXie

2016-02-01

Full Text Available Event-related potentials (ERPs were used in this study to explore the neural mechanism of obedience and conformity on the model of online book purchasing. Participants were asked to decide as quickly as possible whether to buy a book based on limited information including its title, keywords and number of positive and negative reviews. Obedience was induced by forcing participants to buy books which received mostly negative reviews. In contrast, conformity was aroused by majority influence (caused by positive and negative comments. P3 and N2, two kinds of ERP components related to social cognitive process, were measured and recorded with electroencephalogram (EEG test. The results show that compared with conformity decisions, obedience decisions induced greater cognitive conflicts. In ERP measurements, greater amplitudes of N2 component were observed in the context of obedience. However, consistency level did not make a difference on P3 peak latency for both conformity and obedience. This shows that classification process is implicit in both conformity and obedience decision-making. In addition, for both conformity and obedience decisions, augmented P3 was observed when the reviews consistency (either negative or positive was higher.

Neural Basis of Two Kinds of Social Influence: Obedience and Conformity.

Science.gov (United States)

Xie, Ying; Chen, Mingliang; Lai, Hongxia; Zhang, Wuke; Zhao, Zhen; Anwar, Ch Mahmood

2016-01-01

Event-related potentials (ERPs) were used in this study to explore the neural mechanism of obedience and conformity on the model of online book purchasing. Participants were asked to decide as quickly as possible whether to buy a book based on limited information including its title, keywords and number of positive and negative reviews. Obedience was induced by forcing participants to buy books which received mostly negative reviews. In contrast, conformity was aroused by majority influence (caused by positive and negative comments). P3 and N2, two kinds of ERP components related to social cognitive process, were measured and recorded with electroencephalogram (EEG) test. The results show that compared with conformity decisions, obedience decisions induced greater cognitive conflicts. In ERP measurements, greater amplitudes of N2 component were observed in the context of obedience. However, consistency level did not make a difference on P3 peak latency for both conformity and obedience. This shows that classification process is implicit in both conformity and obedience decision-making. In addition, for both conformity and obedience decisions, augmented P3 was observed when the reviews consistency (either negative or positive) was higher.

Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring.

Science.gov (United States)

Mountassif, Driss; Fabre, Lucien; Zaid, Younes; Halawani, Dalia; Rouiller, Isabelle

2015-12-25

Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. Copyright © 2015 Elsevier Inc. All rights reserved.

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...

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

Decomposing climate-induced temperature and water effects on the expansion and operation of the US electricity system

Science.gov (United States)

Sun, Y.; Eurek, K.; Macknick, J.; Steinberg, D. C.; Averyt, K.; Badger, A.; Livneh, B.

2017-12-01

Climate change has the potential to affect the supply and demands of the U.S. power sector. Rising air temperatures can affect the seasonal and total demand for electricity, alter the thermal efficiency of power plants, and lower the maximum capacity of electric transmission lines. Changes in hydrology can affect seasonal and total availability of water used for power plant operations. Prior studies have examined some climate impacts on the electricity sector, but there has been no systematic study quantifying and comparing the importance of these climate-induced effects in isolation and in combination. Here, we perform a systematic assessment using the Regional Energy Deployment System (ReEDS) electricity sector model in combination with downscaled climate results from four models in the CMIP5 archive that provide contrasting temperature and precipitation trends for key regions in the U.S. The ReEDS model captures dynamic climate and hydrological resource data .when choosing the cost optimal mix of generation resources necessary to balance supply and demand for electricity. We examine how different climate-induced changes in air temperature and water availability, considered in isolation and in combination, may affect energy and economic outcomes at a regional and national level from the present through 2050. Results indicate that temperature-induced impacts on electricity consumption show consistent trends nationwide across all climate scenarios. Hydrological impacts and variability differ by model and tend to have a minor effect on national electricity trends, but can be important determinants regionally. Taken together, this suggests that isolated climate change impacts on the electricity system depend on the geographic scale of interest - the effect of rising temperatures on demand, which is qualitatively robust to the choice of climate model, largely determines impacts on generation, capacity and cost at the national level, whereas other impact pathways may

Dynamic changes in ear temperature in relation to separation distress in dogs.