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Sample records for involving transmembrane helices

  1. A monodisperse transmembrane α-helical peptide barrel

    Science.gov (United States)

    Mahendran, Kozhinjampara R.; Niitsu, Ai; Kong, Lingbing; Thomson, Andrew R.; Sessions, Richard B.; Woolfson, Derek N.; Bayley, Hagan

    2017-05-01

    The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel. We also show that the peptide pore is functional and capable of conducting ions and binding blockers. Such α-helix barrels engineered from peptides could find applications in nanopore technologies such as single-molecule sensing and nucleic-acid sequencing.

  2. Approaches to ab initio molecular replacement of α-helical transmembrane proteins

    OpenAIRE

    Thomas, Jens M. H.; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J.

    2017-01-01

    α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effe...

  3. MemBrain: improving the accuracy of predicting transmembrane helices.

    Directory of Open Access Journals (Sweden)

    Hongbin Shen

    Full Text Available Prediction of transmembrane helices (TMH in alpha helical membrane proteins provides valuable information about the protein topology when the high resolution structures are not available. Many predictors have been developed based on either amino acid hydrophobicity scale or pure statistical approaches. While these predictors perform reasonably well in identifying the number of TMHs in a protein, they are generally inaccurate in predicting the ends of TMHs, or TMHs of unusual length. To improve the accuracy of TMH detection, we developed a machine-learning based predictor, MemBrain, which integrates a number of modern bioinformatics approaches including sequence representation by multiple sequence alignment matrix, the optimized evidence-theoretic K-nearest neighbor prediction algorithm, fusion of multiple prediction window sizes, and classification by dynamic threshold. MemBrain demonstrates an overall improvement of about 20% in prediction accuracy, particularly, in predicting the ends of TMHs and TMHs that are shorter than 15 residues. It also has the capability to detect N-terminal signal peptides. The MemBrain predictor is a useful sequence-based analysis tool for functional and structural characterization of helical membrane proteins; it is freely available at http://chou.med.harvard.edu/bioinf/MemBrain/.

  4. Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

    Science.gov (United States)

    Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

    2017-12-01

    α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

  5. The activation energy for insertion of transmembrane alpha-helices is dependent on membrane composition.

    Science.gov (United States)

    Meijberg, Wim; Booth, Paula J

    2002-06-07

    The physical mechanisms that govern the folding and assembly of integral membrane proteins are poorly understood. It appears that certain properties of the lipid bilayer affect membrane protein folding in vitro, either by modulating helix insertion or packing. In order to begin to understand the origin of this effect, we investigate the effect of lipid forces on the insertion of a transmembrane alpha-helix using a water-soluble, alanine-based peptide, KKAAAIAAAAAIAAWAAIAAAKKKK-amide. This peptide binds to preformed 1,2-dioleoyl-l-alpha-phosphatidylcholine (DOPC) vesicles at neutral pH, but spontaneous transmembrane helix insertion directly from the aqueous phase only occurs at high pH when the Lys residues are de-protonated. These results suggest that the translocation of charge is a major determinant of the activation energy for insertion. Time-resolved measurements of the insertion process at high pH indicate biphasic kinetics with time constants of ca 30 and 430 seconds. The slower phase seems to correlate with formation of a predominantly transmembrane alpha-helical conformation, as determined from the transfer of the tryptophan residue to the hydrocarbon region of the membrane. Temperature-dependent measurements showed that insertion can proceed only above a certain threshold temperature and that the Arrhenius activation energy is of the order of 90 kJ mol(-1). The kinetics, threshold temperature and the activation energy change with the mole fraction of 1,2-dioleoyl-l-alpha-phosphatidylethanolamine (DOPE) introduced into the DOPC membrane. The activation energy increases with increasing DOPE content, which could reflect the fact that this lipid drives the bilayer towards a non-bilayer transition and increases the lateral pressure in the lipid chain region. This suggests that folding events involving the insertion of helical segments across the bilayer can be controlled by lipid forces. (c) 2002 Elsevier Science Ltd.

  6. Transmembrane Helices Are an Overlooked Source of Major Histocompatibility Complex Class I Epitopes

    NARCIS (Netherlands)

    Bianchi, F.; Textor, J.C.; Bogaart, G. van den

    2017-01-01

    About a fourth of the human proteome is anchored by transmembrane helices (TMHs) to lipid membranes. TMHs require multiple hydrophobic residues for spanning membranes, and this shows a striking resemblance with the requirements for peptide binding to major histocompatibility complex (MHC) class I.

  7. Spin versus helicity in processes involving transversity

    CERN Document Server

    Mekhfi, Mustapha

    2011-01-01

    We construct the spin formalism in order to deal in a direct and natural way with processes involving transversity which are now of increasing popularity. The helicity formalism which is more appropriate for collision processes of definite helicity has been so far used also to manage processes with transversity, but at the price of computing numerous helicity amplitudes generally involving unnecessary kinematical variables.In a second step we work out the correspondence between both formalisms and retrieve in another way all results of the helicity formalism but in simpler forms.We then compute certain processes for comparison.A special process:the quark dipole magnetic moment is shown to be exclusively treated within the spin formalism as it is directly related to the transverse spin of the quark inside the baryon.

  8. Dissecting the functions of conserved prolines within transmembrane helices of the D2 dopamine receptor.

    Science.gov (United States)

    Van Arnam, Ethan B; Lester, Henry A; Dougherty, Dennis A

    2011-10-21

    G protein-coupled receptors (GPCRs) contain a number of conserved proline residues in their transmembrane helices, and it is generally assumed these play important functional and/or structural roles. Here we use unnatural amino acid mutagenesis, employing α-hydroxy acids and proline analogues, to examine the functional roles of five proline residues in the transmembrane helices of the D2 dopamine receptor. The well-known tendency of proline to disrupt helical structure is important at all sites, while we find no evidence for a functional role for backbone amide cis-trans isomerization, another feature associated with proline. At most proline sites, the loss of the backbone NH is sufficient to explain the role of the proline. However, at one site, P210(5.50), a substituent on the backbone N appears to be essential for proper function. Interestingly, the pattern in functional consequences that we see is mirrored in the pattern of structural distortions seen in recent GPCR crystal structures.

  9. HMM_RA: An Improved Method for Alpha-Helical Transmembrane Protein Topology Prediction

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    Changhui Yan

    2008-01-01

    Full Text Available α-helical transmembrane (TM proteins play important and diverse functional roles in cells. The ability to predict the topology of these proteins is important for identifying functional sites and inferring function of membrane proteins. This paper presents a Hidden Markov Model (referred to as HMM_RA that can predict the topology of α-helical transmembrane proteins with improved performance. HMM_RA adopts the same structure as the HMMTOP method, which has five modules: inside loop, inside helix tail, membrane helix, outside helix tail and outside loop. Each module consists of one or multiple states. HMM_RA allows using reduced alphabets to encode protein sequences. Thus, each state of HMM_RA is associated with n emission probabilities, where n is the size of the reduced alphabet set. Direct comparisons using two standard data sets show that HMM_RA consistently outperforms HMMTOP and TMHMM in topology prediction. Specifically, on a high-quality data set of 83 proteins, HMM_RA outperforms HMMTOP by up to 7.6% in topology accuracy and 6.4% in α-helices location accuracy. On the same data set, HMM_RA outperforms TMHMM by up to 6.4% in topology accuracy and 2.9% in location accuracy. Comparison also shows that HMM_RA achieves comparable performance as Phobius, a recently published method.

  10. Transmembrane Helices Are an Overlooked Source of Major Histocompatibility Complex Class I Epitopes

    Science.gov (United States)

    Bianchi, Frans; Textor, Johannes; van den Bogaart, Geert

    2017-01-01

    About a fourth of the human proteome is anchored by transmembrane helices (TMHs) to lipid membranes. TMHs require multiple hydrophobic residues for spanning membranes, and this shows a striking resemblance with the requirements for peptide binding to major histocompatibility complex (MHC) class I. It, therefore, comes as no surprise that bioinformatics analysis predicts an over-representation of TMHs among strong MHC class I (MHC-I) binders. Published peptide elution studies confirm that TMHs are indeed presented by MHC-I. This raises the question how membrane proteins are processed for MHC-I (cross-)presentation, with current research focusing on soluble antigens. The presentation of membrane-buried peptides is likely important in health and disease, as TMHs are considerably conserved and their presentation might prevent escape mutations by pathogens. Therefore, it could contribute to the disease correlations described for many human leukocyte antigen haplotypes. PMID:28959259

  11. Location of the β4 transmembrane helices in the BK potassium channel

    Science.gov (United States)

    Wu, Roland S.; Chudasama, Neelesh; Zakharov, Sergey I.; Doshi, Darshan; Motoike, Howard; Liu, Guoxia; Yao, Yongneng; Niu, Xiaowei; Deng, Shi-Xian; Landry, Donald W.; Karlin, Arthur; Marx, Steven O.

    2009-01-01

    Large-conductance, voltage- and Ca2+-gated potassium (BK) channels control excitability in a number of cell types. BK channels are composed of α subunits, which contain the voltage-sensor domains and the Ca2+- sensor domains, and form the pore, and often one of four types of β subunits, which modulate the channel in a cell-specific manner. β4 is expressed in neurons throughout the brain. Deletion of β4 in mice causes temporal lobe epilepsy. Compared to channels composed of α alone, channels composed of α and β4 activate and deactivate more slowly. We inferred the locations of the two β4 transmembrane (TM) helices, TM1 and TM2, relative to the seven αTM helices, S0-S6, from the extent of disulfide bond formation between cysteines substituted in the extracellular flanks of these TM helices. We found that β4 TM2 is close to α S0 and that β4 TM1 is close to both α S1 and S2. At least at their extracellular ends, TM1 and TM2 are not close to S3 through S6. In six of eight of the most highly crosslinked cysteine pairs, four crosslinks from TM2 to S0 and one each from TM1 to S1 and S2 had small effects on the V50 and on the rates of activation and deactivation. That disulfide crosslinking caused only small functional perturbations is consistent with the proximity of the extracellular ends of TM2 to S0 and of TM1 to S1 and to S2, in both the open and closed states. PMID:19571123

  12. Structural details (kinks and non-α conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors

    Science.gov (United States)

    Rigoutsos, Isidore; Riek, Peter; Graham, Robert M.; Novotny, Jiri

    2003-01-01

    One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular α-helical character (i.e. π-helices, 310-helices and kinks). A ‘search engine’ derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above ‘non-canonical’ helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from α-helicity are encoded locally in sequence patterns only about 7–9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure–function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html. PMID:12888523

  13. Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors.

    Science.gov (United States)

    Rigoutsos, Isidore; Riek, Peter; Graham, Robert M; Novotny, Jiri

    2003-08-01

    One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular alpha-helical character (i.e. pi-helices, 3(10)-helices and kinks). A 'search engine' derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above 'non-canonical' helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from alpha-helicity are encoded locally in sequence patterns only about 7-9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure-function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html.

  14. High-resolution modeling of transmembrane helical protein structures from distant homologues.

    Directory of Open Access Journals (Sweden)

    Kuang-Yui M Chen

    2014-05-01

    Full Text Available Eukaryotic transmembrane helical (TMH proteins perform a wide diversity of critical cellular functions, but remain structurally largely uncharacterized and their high-resolution structure prediction is currently hindered by the lack of close structural homologues. To address this problem, we present a novel and generic method for accurately modeling large TMH protein structures from distant homologues exhibiting distinct loop and TMH conformations. Models of the adenosine A2AR and chemokine CXCR4 receptors were first ranked in GPCR-DOCK blind prediction contests in the receptor structure accuracy category. In a benchmark of 50 TMH protein homolog pairs of diverse topology (from 5 to 12 TMHs, size (from 183 to 420 residues and sequence identity (from 15% to 70%, the method improves most starting templates, and achieves near-atomic accuracy prediction of membrane-embedded regions. Unlike starting templates, the models are of suitable quality for computer-based protein engineering: redesigned models and redesigned X-ray structures exhibit very similar native interactions. The method should prove useful for the atom-level modeling and design of a large fraction of structurally uncharacterized TMH proteins from a wide range of structural homologues.

  15. Assessing the Structure and Stability of Transmembrane Oligomeric Intermediates of an α-Helical Toxin.

    Science.gov (United States)

    Desikan, Rajat; Maiti, Prabal K; Ayappa, K Ganapathy

    2017-10-24

    Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane-assisted protein aggregation to oligomerization and folding. Pore-forming toxins (PFTs) are the primary vehicle for infection by several strains of bacteria. These proteins which are expressed in a water-soluble form (monomers) bind to the target membrane and conformationally transform (protomers) and self-assemble to form a multimer transmembrane pore complex through a process of oligomerization. On the basis of the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins. In contrast to β-PFTs, the paucity of available crystal structures coupled with the amphipathic nature of the transmembrane domains has hindered our understanding of α-PFT pore formation. In this article, we use molecular dynamics (MD) simulations to examine the process of pore formation of the bacterial α-PFT, cytolysin A from Escherichia coli (ClyA) in lipid bilayer membranes. Using atomistic MD simulations ranging from 50 to 500 ns, we show that transmembrane oligomeric intermediates or "arcs" form stable proteolipidic complexes consisting of protein arcs with toroidal lipids lining the free edges. By creating initial conditions where the lipids are contained within the arcs, we study the dynamics of spontaneous lipid evacuation and toroidal edge formation. This process occurs on the time scale of tens of nanoseconds, suggesting that once protomers oligomerize, transmembrane arcs are rapidly stabilized to form functional water channels capable of leakage. Using umbrella sampling with a coarse-grained molecular model, we obtain the free energy of insertion of a single protomer into the membrane. A single inserted protomer has a stabilization free energy of -52.9 ± 1.2 kJ/mol and forms a stable transmembrane water channel capable of leakage. Our simulations reveal that arcs are stable and viable intermediates that can occur during the pore

  16. Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy

    DEFF Research Database (Denmark)

    Bugge, Katrine Østergaard; Steinocher, Helena; Brooks, Andrew J.

    2015-01-01

    -labeled protein. In this work, we have exploited the hydrophobic nature of membrane proteins to develop a simple and efficient production scheme for isotope-labeled single-pass transmembrane domains (TMDs) with or without intrinsically disordered regions. We have evaluated the applicability and limitations...... of the strategy using seven membrane protein variants that differ in their overall hydrophobicity and length and show a recovery for suitable variants of >70%. The developed production scheme is cost-efficient and easy to implement and has the potential to facilitate an increase in the number of structures...

  17. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids.

    Science.gov (United States)

    Öjemalm, Karin; Higuchi, Takashi; Lara, Patricia; Lindahl, Erik; Suga, Hiroaki; von Heijne, Gunnar

    2016-09-20

    Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of "snorkeling" of charged amino acids toward the lipid-water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells.

  18. NMR studies of the fifth transmembrane segment of Na+,K+-ATPase reveals a non-helical ion-binding region

    DEFF Research Database (Denmark)

    Underhaug, Jarl; Jakobsen, Louise Odgaard; Esmann, Mikael

    2006-01-01

    The structure of a synthetic peptide corresponding to the fifth membrane-spanning segment (M5) in Na(+),K(+)-ATPase in sodium dodecyl sulfate (SDS) micelles was determined using liquid-state nuclear magnetic resonance (NMR) spectroscopy. The spectra reveal that this peptide is substantially less...... transmembrane element of the Ca(2+)-ATPase. Furthermore, this region spans the residues implicated in Na(+) and K(+) transport, where they are likely to offer the flexibility needed to coordinate Na(+) as well as K(+) during active transport....... alpha-helical than the corresponding M5 peptide of Ca(2+)-ATPase. A well-defined alpha-helix is shown in the C-terminal half of the peptide. Apart from a short helical stretch at the N-terminus, the N-terminal half contains a non-helical region with two proline residues and sequence similarity to a non-structured...

  19. A transmembrane polar interaction is involved in the functional regulation of integrin alpha L beta 2.

    Science.gov (United States)

    Vararattanavech, Ardcharaporn; Chng, Choon-Peng; Parthasarathy, Krupakar; Tang, Xiao-Yan; Torres, Jaume; Tan, Suet-Mien

    2010-05-14

    Integrins are heterodimeric transmembrane (TM) receptors formed by noncovalent associations of alpha and beta subunits. Each subunit contains a single alpha-helical TM domain. Inside-out activation of an integrin involves the separation of its cytoplasmic tails, leading to disruption of alphabeta TM packing. The leukocyte integrin alpha L beta 2 is required for leukocyte adhesion, migration, proliferation, cytotoxic function, and antigen presentation. In this study, we show by mutagenesis experiments that the packing of alpha L beta 2 TMs is consistent with that of the integrin alpha IIb beta 3 TMs. However, molecular dynamics simulations of alpha L beta 2 TMs in lipids predicted a polar interaction involving the side chains of alpha L Ser1071 and beta2 Thr686 in the outer-membrane association clasp (OMC). This is supported by carbonyl vibrational shifts observed in isotope-labeled alpha L beta 2 TM peptides that were incorporated into lipid bilayers. Molecular dynamics studies simulating the separation of alpha L beta 2 tails showed the presence of polar interaction during the initial perturbation of the inner-membrane association clasp. When the TMs underwent further separation, the polar interaction was disrupted. OMC polar interaction is important in regulating the functions of beta2 integrins because mutations that disrupt the OMC polar interaction generated constitutively activated alpha L beta 2, alpha M beta 2, and alpha X beta 2 in 293T transfectants. We also show that the expression of mutant beta2 Thr686Gly in beta2-deficient T cells rescued cell adhesion to intercellular adhesion molecule 1, but the cells showed overt elongated morphologies in response to chemokine stromal-cell-derived factor 1 alpha treatment as compared to wild-type beta2-expressing cells. These two TM polar residues are totally conserved in other members of the beta2 integrins in humans and across different species. Our results provide an example of the stabilizing effect of polar

  20. Tryptophan scanning mutagenesis reveals distortions in the helical structure of the δM4 transmembrane domain of the Torpedo californica nicotinic acetylcholine receptor.

    Science.gov (United States)

    Caballero-Rivera, Daniel; Cruz-Nieves, Omar A; Oyola-Cintrón, Jessica; Torres-Nunez, David A; Otero-Cruz, Jose D; Lasalde-Dominicci, José A

    2012-01-01

    The lipid-protein interface is an important domain of the nicotinic acetylcholine receptor (nAChR) that has recently garnered increased relevance. Several studies have made significant advances toward determining the structure and dynamics of the lipid-exposed domains of the nAChR. However, there is still a need to gain insight into the mechanism by which lipid-protein interactions regulate the function and conformational transitions of the nAChR. In this study, we extended the tryptophan scanning mutagenesis (TrpScanM) approach to dissect secondary structure and monitor the conformational changes experienced by the δM4 transmembrane domain (TMD) of the Torpedo californica nAChR, and to identify which positions on this domain are potentially linked to the regulation of ion channel kinetics. The difference in oscillation patterns between the closed- and open-channel states suggests a substantial conformational change along this domain as a consequence of channel activation. Furthermore, TrpScanM revealed distortions along the helical structure of this TMD that are not present on current models of the nAChR. Our results show that a Thr-Pro motif at positions 462-463 markedly bends the helical structure of the TMD, consistent with the recent crystallographic structure of the GluCl Cys-loop receptor which reveals a highly bent TMD4 in each subunit. This Thr-Pro motif acts as a molecular hinge that delineates two gating blocks in the δM4 TMD. These results suggest a model in which a hinge-bending motion that tilts the helical structure is combined with a spring-like motion during transition between the closed- and open-channel states of the δM4 TMD.

  1. Orientations and proximities of the extracellular ends of transmembrane helices S0 and S4 in open and closed BK potassium channels.

    Directory of Open Access Journals (Sweden)

    Xiaowei Niu

    Full Text Available The large-conductance potassium channel (BK α subunit contains a transmembrane (TM helix S0 preceding the canonical TM helices S1 through S6. S0 lies between S4 and the TM2 helix of the regulatory β1 subunit. Pairs of Cys were substituted in the first helical turns in the membrane of BK α S0 and S4 and in β1 TM2. One such pair, W22C in S0 and W203C in S4, was 95% crosslinked endogenously. Under voltage-clamp conditions in outside-out patches, this crosslink was reduced by DTT and reoxidized by a membrane-impermeant bis-quaternary ammonium derivative of diamide. The rate constants for this reoxidation were not significantly different in the open and closed states of the channel. Thus, these two residues are approximately equally close in the two states. In addition, 90% crosslinking of a second pair, R20C in S0 and W203C in S4, had no effect on the V50 for opening. Taken together, these findings indicate that separation between residues at the extracellular ends of S0 and S4 is not required for voltage-sensor activation. On the contrary, even though W22C and W203C were equally likely to form a disulfide in the activated and deactivated states, relative immobilization by crosslinking of these two residues favored the activated state. Furthermore, the efficiency of recrosslinking of W22C and W203C on the cell surface was greater in the presence of the β1 subunit than in its absence, consistent with β1 acting through S0 to stabilize its immobilization relative to α S4.

  2. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

    International Nuclear Information System (INIS)

    Nishizawa, Manami; Nishizawa, Kazuhisa

    2014-01-01

    Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT OPLS ). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT OPLS PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT CHARMM ) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT OPLS PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA) 3 peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret

  3. SCIMP, a transmembrane adaptor protein involved in major histocompatibility complex class II signaling

    Czech Academy of Sciences Publication Activity Database

    Dráber, Peter; Vonková, Ivana; Štěpánek, Ondřej; Hrdinka, Matouš; Kucová, Markéta; Skopcová, Tereza; Otáhal, Pavel; Angelisová, Pavla; Hořejší, Václav; Yeung, M.; Weiss, A.; Brdička, Tomáš

    2011-01-01

    Roč. 31, č. 22 (2011), s. 4550-4562 ISSN 0270-7306 R&D Projects: GA MŠk 1M0506; GA ČR GEMEM/09/E011 Institutional research plan: CEZ:AV0Z50520514 Keywords : SCIMP * transmembrane adaptor protein * MHC II Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.527, year: 2011

  4. NTAL (non-T cell activation linker):a transmembrane adaptor protein involved in immunoreceptor signaling

    Czech Academy of Sciences Publication Activity Database

    Brdička, Tomáš; Imrich, Martin; Angelisová, Pavla; Brdičková, Naděžda; Horváth, Ondřej; Špička, Jiří; Hilgert, Ivan; Lusková, Petra; Dráber, Petr; Novák, P.; Engels, N.; Wienands, J.; Simeoni, L.; Osterreicher, J.; Aguado, E.; Malissen, M.; Schraven, B.; Hořejší, Václav

    2002-01-01

    Roč. 196, č. 12 (2002), s. 16180-16185 ISSN 0022-1007 R&D Projects: GA MŠk LN00A026 Keywords : NTAL * transmembrane adaptor * immunoreceptor signaling Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 15.838, year: 2002

  5. The soluble loop BC region guides, but not dictates, the assembly of the transmembrane cytochrome b6.

    Directory of Open Access Journals (Sweden)

    Lydia Tome-Stangl

    Full Text Available Studying folding and assembly of naturally occurring α-helical transmembrane proteins can inspire the design of membrane proteins with defined functions. Thus far, most studies have focused on the role of membrane-integrated protein regions. However, to fully understand folding pathways and stabilization of α-helical membrane proteins, it is vital to also include the role of soluble loops. We have analyzed the impact of interhelical loops on folding, assembly and stability of the heme-containing four-helix bundle transmembrane protein cytochrome b6 that is involved in charge transfer across biomembranes. Cytochrome b6 consists of two transmembrane helical hairpins that sandwich two heme molecules. Our analyses strongly suggest that the loop connecting the helical hairpins is not crucial for positioning the two protein "halves" for proper folding and assembly of the holo-protein. Furthermore, proteolytic removal of any of the remaining two loops, which connect the two transmembrane helices of a hairpin structure, appears to also not crucially effect folding and assembly. Overall, the transmembrane four-helix bundle appears to be mainly stabilized via interhelical interactions in the transmembrane regions, while the soluble loop regions guide assembly and stabilize the holo-protein. The results of this study might steer future strategies aiming at designing heme-binding four-helix bundle structures, involved in transmembrane charge transfer reactions.

  6. Residues within the Transmembrane Domain of the Glucagon-Like Peptide-1 Receptor Involved in Ligand Binding and Receptor Activation: Modelling the Ligand-Bound Receptor

    Science.gov (United States)

    Coopman, K.; Wallis, R.; Robb, G.; Brown, A. J. H.; Wilkinson, G. F.; Timms, D.

    2011-01-01

    The C-terminal regions of glucagon-like peptide-1 (GLP-1) bind to the N terminus of the GLP-1 receptor (GLP-1R), facilitating interaction of the ligand N terminus with the receptor transmembrane domain. In contrast, the agonist exendin-4 relies less on the transmembrane domain, and truncated antagonist analogs (e.g. exendin 9–39) may interact solely with the receptor N terminus. Here we used mutagenesis to explore the role of residues highly conserved in the predicted transmembrane helices of mammalian GLP-1Rs and conserved in family B G protein coupled receptors in ligand binding and GLP-1R activation. By iteration using information from the mutagenesis, along with the available crystal structure of the receptor N terminus and a model of the active opsin transmembrane domain, we developed a structural receptor model with GLP-1 bound and used this to better understand consequences of mutations. Mutation at Y152 [transmembrane helix (TM) 1], R190 (TM2), Y235 (TM3), H363 (TM6), and E364 (TM6) produced similar reductions in affinity for GLP-1 and exendin 9–39. In contrast, other mutations either preferentially [K197 (TM2), Q234 (TM3), and W284 (extracellular loop 2)] or solely [D198 (TM2) and R310 (TM5)] reduced GLP-1 affinity. Reduced agonist affinity was always associated with reduced potency. However, reductions in potency exceeded reductions in agonist affinity for K197A, W284A, and R310A, while H363A was uncoupled from cAMP generation, highlighting critical roles of these residues in translating binding to activation. Data show important roles in ligand binding and receptor activation of conserved residues within the transmembrane domain of the GLP-1R. The receptor structural model provides insight into the roles of these residues. PMID:21868452

  7. Cystic fibrosis transmembrane conductance regulator is involved in polyphenol-induced swelling of the endothelial glycocalyx.

    Science.gov (United States)

    Peters, Wladimir; Kusche-Vihrog, Kristina; Oberleithner, Hans; Schillers, Hermann

    2015-08-01

    Previous studies show that polyphenol-rich compounds can induce a swelling of the endothelial glycocalyx (eGC). Our goal was to reveal the mechanism behind the eGC-swelling. As polyphenols are potent modulators of fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel, the hypothesis was tested whether polyphenol-induced increase in CFTR activity is responsible for the eGC-swelling. The impact of the polyphenols resveratrol, (-)-epicatechin, and quercetin on nanomechanics of living endothelial GM7373 cells was monitored by AFM-nanoindentation. The tested polyphenols lead to eGC-swelling with a simultaneous decrease in cortical stiffness. EGC-swelling, but not the change in cortical stiffness, was prevented by the inhibition of CFTR. Polyphenol-induced eGC-swelling could be mimicked by cytochalasin D, an actin-depolymerizing agent. Thus, in the vascular endothelium, polyphenols induce eGC-swelling by softening cortical actin and activating CFTR. Our findings imply that CFTR plays an important role in the maintenance of vascular homeostasis and may explain the vasoprotective properties of polyphenols. Many vascular problems clinically can be attributed to a dysregulation of endothelial glycocalyx (eGC). The underlying mechanism however remains unclear. In this article, the authors used nanoindentation and showed that polyphenols could swell the endothelial glycocalyx and alter its function. This investigative method can lead to further mechanistic studies of other molecular pathways. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Azorhizobium caulinodans Transmembrane Chemoreceptor TlpA1 Involved in Host Colonization and Nodulation on Roots and Stems

    Directory of Open Access Journals (Sweden)

    Wei Liu

    2017-07-01

    Full Text Available Azorhizobium caulinodans ORS571 is a motile soil bacterium that interacts symbiotically with legume host Sesbania rostrata, forming nitrogen-fixing root and stem nodules. Bacterial chemotaxis plays an important role in establishing this symbiotic relationship. To determine the contribution of chemotaxis to symbiosis in A. caulinodans ORS571-S. rostrata, we characterized the function of TlpA1 (transducer-like protein in A. caulinodans, a chemoreceptor predicted by SMART (Simple Modular Architecture Research Tool, containing two N-terminal transmembrane regions. The tlpA1 gene is located immediately upstream of the unique che gene cluster and is transcriptionally co-oriented. We found that a ΔtlpA1 mutant is severely impaired for chemotaxis to various organic acids, glycerol and proline. Furthermore, biofilm forming ability of the strain carrying the mutation is reduced under certain growth conditions. Interestingly, competitive colonization ability on S. rostrata root surfaces is impaired in the ΔtlpA1 mutant, suggesting that chemotaxis of the A. caulinodans ORS571 contributes to root colonization. We also found that TlpA1 promotes competitive nodulation not only on roots but also on stems of S. rostrata. Taken together, our data strongly suggest that TlpA1 is a transmembrane chemoreceptor involved in A. caulinodans-S. rostrata symbiosis.

  9. Computer simulations and modeling-assisted ToxR screening in deciphering 3D structures of transmembrane α-helical dimers: ephrin receptor A1

    International Nuclear Information System (INIS)

    Volynsky, P E; Mineeva, E A; Goncharuk, M V; Ermolyuk, Ya S; Arseniev, A S; Efremov, R G

    2010-01-01

    Membrane-spanning segments of numerous proteins (e.g. receptor tyrosine kinases) represent a novel class of pharmacologically important targets, whose activity can be modulated by specially designed artificial peptides, the so-called interceptors. Rational construction of such peptides requires understanding of the main factors driving peptide–peptide association in lipid membranes. Here we present a new method for rapid prediction of the spatial structure of transmembrane (TM) helix–helix complexes. It is based on computer simulations in membrane-like media and subsequent refinement/validation of the results using experimental studies of TM helix dimerization in a bacterial membrane by means of the ToxR system. The approach was applied to TM fragments of the ephrin receptor A1 (EphA1). A set of spatial structures of the dimer was proposed based on Monte Carlo simulations in an implicit membrane followed by molecular dynamics relaxation in an explicit lipid bilayer. The resulting models were employed for rational design of wild-type and mutant genetic constructions for ToxR assays. The computational and the experimental data are self-consistent and provide an unambiguous spatial model of the TM dimer of EphA1. The results of this work can be further used to develop new biologically active 'peptide interceptors' specifically targeting membrane domains of proteins

  10. Helical tomotherapy for extramedullary hematopoiesis involving the pericardium in a patient with chronic myeloid leukemia.

    Science.gov (United States)

    Toms, Daniel R; Cannick, Leander; Stuart, Robert K; Jenrette, Joseph M; Terwiliger, Lacy

    2010-07-01

    Extramedullary hematopoiesis (EMH) refers to the development of foci of hematopoiesis outside its normal location in the bone marrow. This occurs normally during fetal development but is abnormal postpartum. The most common sites of EMH are the spleen and liver. The phenomenon occurs in a number of disease states, notably in myelofibrosis, thalassemia, immune thrombocytopenic purpura, sickle cell anemia, polycythemia vera, and myelodysplastic syndrome. Affected patients often develop symptoms related to the location of the EMH. Reported treatments include red blood cell transfusions, surgical excision, decompressive laminectomy in cases of cord compression, chemotherapy, and irradiation. Radiation therapy is highly effective for treating hematopoietic tissue because such tissues are extremely radiosensitive. Megavoltage helical tomotherapy is a technical advance in the delivery of radiation therapy, allowing more conformal and precise treatments. The present case report describes a patient with the diagnosis of atypical chronic myeloid leukemia and myelofibrosis who subsequently developed EMH of the pericardium with effusion and tamponade. By utilizing tomotherapy we were able to treat the pericardium while sparing much of the myocardium. The patient tolerated treatment well without acute adverse effects. His symptoms were alleviated, but he died approximately 1 year later.

  11. Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses

    Directory of Open Access Journals (Sweden)

    Sandra M. Schmöckel

    2017-06-01

    Full Text Available Chenopodium quinoa (quinoa is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri, and 2 C. hircinum. We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation (CNV in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions.

  12. Identification of an Arabidopsis transmembrane bZIP transcription factor involved in the endoplasmic reticulum stress response

    International Nuclear Information System (INIS)

    Tajima, Hiromi; Iwata, Yuji; Iwano, Megumi; Takayama, Seiji; Koizumi, Nozomu

    2008-01-01

    Among 75 bZIP transcription factors identified in Arabidopsis, 3 (AtbZIP17, AtbZIP28, and AtbZIP49) possess a putative transmembrane domain (TMD) in addition to AtbZIP60, which was characterized previously. In the present study, cDNAs of AtbZIP17 and AtbZIP28 were isolated. Truncated forms of AtbZIP17 and AtbZIP28 lacking the C-terminal domain including TMD were examined as putative active forms. One of them, AtbZIP28ΔC, activated BiP1 and BiP3 promoters through the cis-elements P-UPRE and ERSE responsible for the ER stress response. Subsequently, a fusion protein of green fluorescent protein (GFP) and AtbZIP28 was expressed in Arabidopsis cultured cells. Under non-stress conditions, GFP fluorescence localization almost overlapped with an ER marker; however, tunicamycin and dithiothreitol treatment clearly increased GFP fluorescence in the nucleus suggesting that the N-terminal fragment of AtbZIP28 translocates to the nucleus in response to ER stress

  13. Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses

    KAUST Repository

    Schmöckel, Sandra M.

    2017-06-21

    Chenopodium quinoa (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri, and 2 C. hircinum). We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation (CNV) in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions.

  14. Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses

    Science.gov (United States)

    Schmöckel, Sandra M.; Lightfoot, Damien J.; Razali, Rozaimi; Tester, Mark; Jarvis, David E.

    2017-01-01

    Chenopodium quinoa (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri, and 2 C. hircinum). We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation (CNV) in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions. PMID:28680429

  15. Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses.

    Science.gov (United States)

    Schmöckel, Sandra M; Lightfoot, Damien J; Razali, Rozaimi; Tester, Mark; Jarvis, David E

    2017-01-01

    Chenopodium quinoa (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa , 5 C. berlandieri , and 2 C. hircinum ). We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation (CNV) in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions.

  16. Transmembrane protein topology prediction using support vector machines

    Directory of Open Access Journals (Sweden)

    Nugent Timothy

    2009-05-01

    Full Text Available Abstract Background Alpha-helical transmembrane (TM proteins are involved in a wide range of important biological processes such as cell signaling, transport of membrane-impermeable molecules, cell-cell communication, cell recognition and cell adhesion. Many are also prime drug targets, and it has been estimated that more than half of all drugs currently on the market target membrane proteins. However, due to the experimental difficulties involved in obtaining high quality crystals, this class of protein is severely under-represented in structural databases. In the absence of structural data, sequence-based prediction methods allow TM protein topology to be investigated. Results We present a support vector machine-based (SVM TM protein topology predictor that integrates both signal peptide and re-entrant helix prediction, benchmarked with full cross-validation on a novel data set of 131 sequences with known crystal structures. The method achieves topology prediction accuracy of 89%, while signal peptides and re-entrant helices are predicted with 93% and 44% accuracy respectively. An additional SVM trained to discriminate between globular and TM proteins detected zero false positives, with a low false negative rate of 0.4%. We present the results of applying these tools to a number of complete genomes. Source code, data sets and a web server are freely available from http://bioinf.cs.ucl.ac.uk/psipred/. Conclusion The high accuracy of TM topology prediction which includes detection of both signal peptides and re-entrant helices, combined with the ability to effectively discriminate between TM and globular proteins, make this method ideally suited to whole genome annotation of alpha-helical transmembrane proteins.

  17. Helicity scalings

    Energy Technology Data Exchange (ETDEWEB)

    Plunian, F [ISTerre, CNRS, Universite Joseph Fourier, Grenoble (France); Lessinnes, T; Carati, D [Physique Statistique et Plasmas, Universite Libre de Bruxelles (Belgium); Stepanov, R, E-mail: Franck.Plunian@ujf-grenoble.fr [Institute of Continuous Media Mechanics of the Russian Academy of Science, Perm (Russian Federation)

    2011-12-22

    Using a helical shell model of turbulence, Chen et al. (2003) showed that both helicity and energy dissipate at the Kolmogorov scale, independently from any helicity input. This is in contradiction with a previous paper by Ditlevsen and Giuliani (2001) in which, using a GOY shell model of turbulence, they found that helicity dissipates at a scale larger than the Kolmogorov scale, and does depend on the helicity input. In a recent paper by Lessinnes et al. (2011), we showed that this discrepancy is due to the fact that in the GOY shell model only one helical mode (+ or -) is present at each scale instead of both modes in the helical shell model. Then, using the GOY model, the near cancellation of the helicity flux between the + and - modes cannot occur at small scales, as it should be in true turbulence. We review the main results with a focus on the numerical procedure needed to obtain accurate statistics.

  18. Surface imaging, laser positioning or volumetric imaging for breast cancer with nodal involvement treated by helical TomoTherapy

    Science.gov (United States)

    Pasquier, David; Baczkiewic, Amandine; Doré, Julie; Bequet, Lena; Steux, Emeline; Gadroy, Anne; Bouillon, Jacqueline; Florence, Clement; Muszynski, Laurence; Lacour, Mathilde; Lartigau, Eric

    2016-01-01

    A surface imaging system, Catalyst (C‐Rad), was compared with laser‐based positioning and daily mega voltage computed tomography (MVCT) setup for breast patients with nodal involvement treated by helical TomoTherapy. Catalyst‐based positioning performed better than laser‐based positioning. The respective modalities resulted in a standard deviation (SD), 68% confidence interval (CI) of positioning of left–right, craniocaudal, anterior–posterior, roll: 2.4 mm, 2.7 mm, 2.4 mm, 0.9° for Catalyst positioning, and 6.1 mm, 3.8 mm, 4.9 mm, 1.1° for laser‐based positioning, respectively. MVCT‐based precision is a combination of the interoperator variability for MVCT fusion and the patient movement during the time it takes for MVCT and fusion. The MVCT fusion interoperator variability for breast patients was evaluated at one SD left–right, craniocaudal, ant–post, roll as: 1.4 mm, 1.8 mm, 1.3 mm, 1.0°. There was no statistically significant difference between the automatic MVCT registration result and the manual adjustment; the automatic fusion results were within the 95% CI of the mean result of 10 users, except for one specific case where the patient was positioned with large yaw. We found that users add variability to the roll correction as the automatic registration was more consistent. The patient position uncertainty confidence interval was evaluated as 1.9 mm, 2.2 mm, 1.6 mm, 0.9° after 4 min, and 2.3 mm, 2.8 mm, 2.2 mm, 1° after 10 min. The combination of this patient movement with MVCT fusion interoperator variability results in total standard deviations of patient position when treatment starts 4 or 10 min after initial positioning of, respectively: 2.3 mm, 2.8 mm, 2.0 mm, 1.3° and 2.7 mm, 3.3 mm, 2.6 mm, 1.4°. Surface based positioning arrives at the same precision when taking into account the time required for MVCT imaging and fusion. These results can be used on a patient‐per‐patient basis to decide which positioning system performs

  19. Detecting pore-lining regions in transmembrane protein sequences

    Directory of Open Access Journals (Sweden)

    Nugent Timothy

    2012-07-01

    Full Text Available Abstract Background Alpha-helical transmembrane channel and transporter proteins play vital roles in a diverse range of essential biological processes and are crucial in facilitating the passage of ions and molecules across the lipid bilayer. However, the experimental difficulties associated with obtaining high quality crystals has led to their significant under-representation in structural databases. Computational methods that can identify structural features from sequence alone are therefore of high importance. Results We present a method capable of automatically identifying pore-lining regions in transmembrane proteins from sequence information alone, which can then be used to determine the pore stoichiometry. By labelling pore-lining residues in crystal structures using geometric criteria, we have trained a support vector machine classifier to predict the likelihood of a transmembrane helix being involved in pore formation. Results from testing this approach under stringent cross-validation indicate that prediction accuracy of 72% is possible, while a support vector regression model is able to predict the number of subunits participating in the pore with 62% accuracy. Conclusion To our knowledge, this is the first tool capable of identifying pore-lining regions in proteins and we present the results of applying it to a data set of sequences with available crystal structures. Our method provides a way to characterise pores in transmembrane proteins and may even provide a starting point for discovering novel routes of therapeutic intervention in a number of important diseases. This software is freely available as source code from: http://bioinf.cs.ucl.ac.uk/downloads/memsat-svm/.

  20. Accurate computational design of multipass transmembrane proteins.

    Science.gov (United States)

    Lu, Peilong; Min, Duyoung; DiMaio, Frank; Wei, Kathy Y; Vahey, Michael D; Boyken, Scott E; Chen, Zibo; Fallas, Jorge A; Ueda, George; Sheffler, William; Mulligan, Vikram Khipple; Xu, Wenqing; Bowie, James U; Baker, David

    2018-03-02

    The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer-a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices-are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  1. PRR7 Is a transmembrane adaptor protein expressed in activated T cells involved in regulation of T cell receptor signaling and apoptosis

    Czech Academy of Sciences Publication Activity Database

    Hrdinka, Matouš; Dráber, Peter; Štěpánek, Ondřej; Ormsby, Tereza; Otáhal, Pavel; Angelisová, Pavla; Brdička, Tomáš; Pačes, Jan; Hořejší, Václav; Drbal, Karel

    2011-01-01

    Roč. 286, č. 22 (2011), s. 19617-19629 ISSN 0021-9258 R&D Projects: GA MŠk 1M0506 Grant - others:GAČR(CZ) MEM/09/E011 Institutional research plan: CEZ:AV0Z50520514 Keywords : PRR7 * transmembrane adaptor protein * apoptosis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.773, year: 2011

  2. Modeling the structure of SARS 3a transmembrane protein using a ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 12. Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach. S Ramakrishna ... Keywords. Membrane protein modeling; ion channel; transmembrane helices; viroporin; molecular dynamics; SARS 3a.

  3. Aromatic Residues in the Fourth Transmembrane-Spanning Helix M4 Are Important for GABAρ Receptor Function.

    Science.gov (United States)

    Cory-Wright, James; Alqazzaz, Mona; Wroe, Francesca; Jeffreys, Jenny; Zhou, Lu; Lummis, Sarah C R

    2018-02-21

    GABAρ receptors are a subfamily of the GABA A receptor family of pentameric ligand-gated ion channels (pLGICs). Each of the five subunits has four transmembrane α-helices (M1-M4), with M4 most distant from the central pore. Aromatic residues in this M4 helix are important for receptor assembly in pLGICs and also may interact with adjacent lipids and/or residues in neighboring α-helices and the extracellular domain to modify or enable channel gating. This study examines the role of M4 receptor aromatic residues in the GABAρ receptor transmembrane domain using site-directed mutagenesis and subsequent expression in HEK293 cells, probing functional parameters using a fluorescent membrane-potential-sensitive dye. The data indicate that many of the aromatic residues in M4 play a role in receptor function, as substitution with other residues can ablate and/or modify functional parameters. Modeling showed that these residues likely interact with residues in the adjacent M1 and M3 α-helices and/or residues in the Cys-loop in the extracellular domain. We suggest that many of these aromatic interactions contribute to an "aromatic zipper", which allows interactions between M4 and the rest of the receptor that are essential for function. Thus, the data support other studies showing that M4 does not play a passive role in "protecting" the other transmembrane helices from the lipid bilayer but is actively involved in the function of the protein.

  4. Possible involvement of membrane lipids peroxidation and oxidation of catalytically essential thiols of the cerebral transmembrane sodium pump as component mechanisms of iron-mediated oxidative stress-linked dysfunction of the pump's activity.

    Science.gov (United States)

    Omotayo, T I; Akinyemi, G S; Omololu, P A; Ajayi, B O; Akindahunsi, A A; Rocha, J B T; Kade, I J

    2015-01-01

    The precise molecular events defining the complex role of oxidative stress in the inactivation of the cerebral sodium pump in radical-induced neurodegenerative diseases is yet to be fully clarified and thus still open. Herein we investigated the modulation of the activity of the cerebral transmembrane electrogenic enzyme in Fe(2+)-mediated in vitro oxidative stress model. The results show that Fe(2+) inhibited the transmembrane enzyme in a concentration dependent manner and this effect was accompanied by a biphasic generation of aldehydic product of lipid peroxidation. While dithiothreitol prevented both Fe(2+) inhibitory effect on the pump and lipid peroxidation, vitamin E prevented only lipid peroxidation but not inhibition of the pump. Besides, malondialdehyde (MDA) inhibited the pump by a mechanism not related to oxidation of its critical thiols. Apparently, the low activity of the pump in degenerative diseases mediated by Fe(2+) may involve complex multi-component mechanisms which may partly involve an initial oxidation of the critical thiols of the enzyme directly mediated by Fe(2+) and during severe progression of such diseases; aldehydic products of lipid peroxidation such as MDA may further exacerbate this inhibitory effect by a mechanism that is likely not related to the oxidation of the catalytically essential thiols of the ouabain-sensitive cerebral electrogenic pump. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  5. Possible involvement of membrane lipids peroxidation and oxidation of catalytically essential thiols of the cerebral transmembrane sodium pump as component mechanisms of iron-mediated oxidative stress-linked dysfunction of the pump's activity

    Directory of Open Access Journals (Sweden)

    T.I. Omotayo

    2015-04-01

    Full Text Available The precise molecular events defining the complex role of oxidative stress in the inactivation of the cerebral sodium pump in radical-induced neurodegenerative diseases is yet to be fully clarified and thus still open. Herein we investigated the modulation of the activity of the cerebral transmembrane electrogenic enzyme in Fe2+-mediated in vitro oxidative stress model. The results show that Fe2+ inhibited the transmembrane enzyme in a concentration dependent manner and this effect was accompanied by a biphasic generation of aldehydic product of lipid peroxidation. While dithiothreitol prevented both Fe2+ inhibitory effect on the pump and lipid peroxidation, vitamin E prevented only lipid peroxidation but not inhibition of the pump. Besides, malondialdehyde (MDA inhibited the pump by a mechanism not related to oxidation of its critical thiols. Apparently, the low activity of the pump in degenerative diseases mediated by Fe2+ may involve complex multi-component mechanisms which may partly involve an initial oxidation of the critical thiols of the enzyme directly mediated by Fe2+ and during severe progression of such diseases; aldehydic products of lipid peroxidation such as MDA may further exacerbate this inhibitory effect by a mechanism that is likely not related to the oxidation of the catalytically essential thiols of the ouabain-sensitive cerebral electrogenic pump.

  6. PDBTM: Protein Data Bank of transmembrane proteins after 8 years.

    Science.gov (United States)

    Kozma, Dániel; Simon, István; Tusnády, Gábor E

    2013-01-01

    The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ∼400 to 1700 entries but also new structural elements have been identified, in addition to the well-known α-helical bundle and β-barrel structures. Numerous 'exotic' transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community.

  7. Transmembrane helices : insertion and assembly into biological membranes

    OpenAIRE

    Bañó Polo, Manuel

    2013-01-01

    Todas las células, ya sean eubacterias, arqueas o eucariotas, están delimitadas por membranas, cuyo componente estructural básico es una fina capa de moléculas anfipáticas organizadas en dos monocapas lipídicas enfrentadas, en las que residen multitud de proteínas íntimamente asociadas a esta la bicapa de múltiples maneras. La membrana juega un papel fundamental para la supervivencia de las células, define sus límites estableciendo una barrera físico-química para moléculas polares a la vez qu...

  8. A hidden Markov model for prediction transmembrane helices in proteinsequences

    DEFF Research Database (Denmark)

    Sonnhammer, Erik L.L.; von Heijne, Gunnar; Krogh, Anders Stærmose

    1998-01-01

    , helix caps on either side, loop on the cytoplasmic side, two loops for the non-cytoplasmic side, and a globular domain state in the middle of each loop. The two loop paths on the non-cytoplasmic side are used to model short and long loops separately, which corresponds biologically to the two known...

  9. The Origins of Transmembrane Ion Channels

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Even though membrane proteins that mediate transport of ions and small molecules across cell walls are among the largest and least understood biopolymers in contemporary cells, it is still possible to shed light on their origins and early evolution. The central observation is that transmembrane portions of most ion channels are simply bundles of -helices. By combining results of experimental and computer simulation studies on synthetic models and natural channels, mostly of non-genomic origin, we show that the emergence of -helical channels was protobiologically plausible, and did not require highly specific amino acid sequences. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. Specifically, we explain how the antiamoebin channels, which are made of identical helices, 16 amino acids in length, achieve efficiency comparable to that of highly evolved channels. We further show that antiamoebin channels are extremely flexible, compared to modern, genetically coded channels. On the basis of our results, we propose that channels evolved further towards high structural complexity because they needed to acquire stable rigid structures and mechanisms for precise regulation rather than improve efficiency. In general, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.

  10. Identification of MarvelD3 as a tight junction-associated transmembrane protein of the occludin family

    Directory of Open Access Journals (Sweden)

    Balda Maria S

    2009-12-01

    Full Text Available Abstract Background Tight junctions are an intercellular adhesion complex of epithelial and endothelial cells, and form a paracellular barrier that restricts the diffusion of solutes on the basis of size and charge. Tight junctions are formed by multiprotein complexes containing cytosolic and transmembrane proteins. How these components work together to form functional tight junctions is still not well understood and will require a complete understanding of the molecular composition of the junction. Results Here we identify a new transmembrane component of tight junctions: MarvelD3, a four-span transmembrane protein. Its predicted transmembrane helices form a Marvel (MAL and related proteins for vesicle traffic and membrane link domain, a structural motif originally discovered in proteins involved in membrane apposition and fusion events, such as the tight junction proteins occludin and tricellulin. In mammals, MarvelD3 is expressed as two alternatively spliced isoforms. Both isoforms exhibit a broad tissue distribution and are expressed by different types of epithelial as well as endothelial cells. MarvelD3 co-localises with occludin at tight junctions in intestinal and corneal epithelial cells. RNA interference experiments in Caco-2 cells indicate that normal MarvelD3 expression is not required for the formation of functional tight junctions but depletion results in monolayers with increased transepithelial electrical resistance. Conclusions Our data indicate that MarvelD3 is a third member of the tight junction-associated occludin family of transmembrane proteins. Similar to occludin, normal expression of MarvelD3 is not essential for the formation of functional tight junctions. However, MarvelD3 functions as a determinant of epithelial paracellular permeability properties.

  11. Transmembrane Signaling Proteoglycans

    DEFF Research Database (Denmark)

    Couchman, John R

    2010-01-01

    and their glycosaminoglycan chains is matched by diverse functions. However, all assume roles as coreceptors, often working alongside high-affinity growth factor receptors or adhesion receptors such as integrins. Other common themes are an ability to signal through their cytoplasmic domains, often to the actin cytoskeleton......, and linkage to PDZ protein networks. Many transmembrane proteoglycans associate on the cell surface with metzincin proteases and can be shed by them. Work with model systems in vivo and in vitro reveal roles in growth, adhesion, migration, and metabolism. Furthermore, a wide range of phenotypes for the core...

  12. The Antibodies against the Computationally Designed Mimic of the Glycoprotein Hormone Receptor Transmembrane Domain Provide Insights into Receptor Activation and Suppress the Constitutively Activated Receptor Mutants*

    Science.gov (United States)

    Majumdar, Ritankar; Railkar, Reema; Dighe, Rajan R.

    2012-01-01

    The exoloops of glycoprotein hormone receptors (GpHRs) transduce the signal generated by the ligand-ectodomain interactions to the transmembrane helices either through direct hormonal contact and/or by modulating the interdomain interactions between the hinge region (HinR) and the transmembrane domain (TMD). The ligand-induced conformational alterations in the HinRs and the interhelical loops of luteinizing hormone receptor/follicle stimulating hormone receptor/thyroid stimulating hormone receptor were mapped using exoloop-specific antibodies generated against a mini-TMD protein designed to mimic the native exoloop conformations that were created by joining the thyroid stimulating hormone receptor exoloops constrained through helical tethers and library-derived linkers. The antibody against the mini-TMD specifically recognized all three GpHRs and inhibited the basal and hormone-stimulated cAMP production without affecting hormone binding. Interestingly, binding of the antibody to all three receptors was abolished by prior incubation of the receptors with the respective hormones, suggesting that the exoloops are buried in the hormone-receptor complexes. The antibody also suppressed the high basal activities of gain-of-function mutations in the HinRs, exoloops, and TMDs such as those involved in precocious puberty and thyroid toxic adenomas. Using the antibody and point/deletion/chimeric receptor mutants, we demonstrate that changes in the HinR-exoloop interactions play an important role in receptor activation. Computational analysis suggests that the mini-TMD antibodies act by conformationally locking the transmembrane helices by means of restraining the exoloops and the juxta-membrane regions. Using GpHRs as a model, we describe a novel computational approach of generating soluble TMD mimics that can be used to explain the role of exoloops during receptor activation and their interplay with TMDs. PMID:22904318

  13. Helicity content and tokamak applications of helicity

    International Nuclear Information System (INIS)

    Boozer, A.H.

    1986-05-01

    Magnetic helicity is approximately conserved by the turbulence associated with resistive instabilities of plasmas. To generalize the application of the concept of helicity, the helicity content of an arbitrary bounded region of space will be defined. The definition has the virtues that both the helicity content and its time derivative have simple expressions in terms of the poloidal and toroidal magnetic fluxes, the average toroidal loop voltage and the electric potential on the bounding surface, and the volume integral of E-B. The application of the helicity concept to tokamak plasmas is illustrated by a discussion of so-called MHD current drive, an example of a stable tokamak q profile with q less than one in the center, and a discussion of the possibility of a natural steady-state tokamak due to the bootstrap current coupling to tearing instabilities

  14. Helical type vacuum container

    International Nuclear Information System (INIS)

    Owada, Kimio.

    1989-01-01

    Helical type vacuum containers in the prior art lack in considerations for thermal expansion stresses to helical coils, and there is a possibility of coil ruptures. The object of the present invention is to avoid the rupture of helical coils wound around the outer surface of a vacuum container against heat expansion if any. That is, bellows or heat expansion absorbing means are disposed to a cross section of a helical type vacuum container. With such a constitution, thermal expansion of helical coils per se due to temperature elevation of the coils during electric supply can be absorbed by expansion of the bellows or absorption of the heat expansion absorbing means. Further, this can be attained by arranging shear pins in the direction perpendicular to the bellows axis so that the bellows are not distorted when the helical coils are wound around the helical type vacuum container. (I.S.)

  15. Hidden markov model for the prediction of transmembrane proteins using MATLAB.

    Science.gov (United States)

    Chaturvedi, Navaneet; Shanker, Sudhanshu; Singh, Vinay Kumar; Sinha, Dhiraj; Pandey, Paras Nath

    2011-01-01

    Since membranous proteins play a key role in drug targeting therefore transmembrane proteins prediction is active and challenging area of biological sciences. Location based prediction of transmembrane proteins are significant for functional annotation of protein sequences. Hidden markov model based method was widely applied for transmembrane topology prediction. Here we have presented a revised and a better understanding model than an existing one for transmembrane protein prediction. Scripting on MATLAB was built and compiled for parameter estimation of model and applied this model on amino acid sequence to know the transmembrane and its adjacent locations. Estimated model of transmembrane topology was based on TMHMM model architecture. Only 7 super states are defined in the given dataset, which were converted to 96 states on the basis of their length in sequence. Accuracy of the prediction of model was observed about 74 %, is a good enough in the area of transmembrane topology prediction. Therefore we have concluded the hidden markov model plays crucial role in transmembrane helices prediction on MATLAB platform and it could also be useful for drug discovery strategy. The database is available for free at bioinfonavneet@gmail.comvinaysingh@bhu.ac.in.

  16. Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor.

    Directory of Open Access Journals (Sweden)

    Vanessa Chantreau

    Full Text Available The thyrotropin receptor (TSHR is a G protein-coupled receptor (GPCR that is member of the leucine-rich repeat subfamily (LGR. In the absence of crystal structure, the success of rational design of ligands targeting the receptor internal cavity depends on the quality of the TSHR models built. In this subfamily, transmembrane helices (TM 2 and 5 are characterized by the absence of proline compared to most receptors, raising the question of the structural conformation of these helices. To gain insight into the structural properties of these helices, we carried out bioinformatics and experimental studies. Evolutionary analysis of the LGR family revealed a deletion in TM5 but provided no information on TM2. Wild type residues at positions 2.58, 2.59 or 2.60 in TM2 and/or at position 5.50 in TM5 were substituted to proline. Depending on the position of the proline substitution, different effects were observed on membrane expression, glycosylation, constitutive cAMP activity and responses to thyrotropin. Only proline substitution at position 2.59 maintained complex glycosylation and high membrane expression, supporting occurrence of a bulged TM2. The TSHR transmembrane domain was modeled by homology with the orexin 2 receptor, using a protocol that forced the deletion of one residue in the TM5 bulge of the template. The stability of the model was assessed by molecular dynamics simulations. TM5 straightened during the equilibration phase and was stable for the remainder of the simulations. Our data support a structural model of the TSHR transmembrane domain with a bulged TM2 and a straight TM5 that is specific of glycoprotein hormone receptors.

  17. NMR-based approach to measure the free energy of transmembrane helix-helix interactions.

    Science.gov (United States)

    Mineev, Konstantin S; Lesovoy, Dmitry M; Usmanova, Dinara R; Goncharuk, Sergey A; Shulepko, Mikhail A; Lyukmanova, Ekaterina N; Kirpichnikov, Mikhail P; Bocharov, Eduard V; Arseniev, Alexander S

    2014-01-01

    Knowledge of the energetic parameters of transmembrane helix-helix interactions is necessary for the establishment of a structure-energy relationship for α-helical membrane domains. A number of techniques have been developed to measure the free energies of dimerization and oligomerization of transmembrane α-helices, and all of these have their advantages and drawbacks. In this study we propose a methodology to determine the magnitudes of the free energy of interactions between transmembrane helices in detergent micelles. The suggested approach employs solution nuclear magnetic resonance (NMR) spectroscopy to determine the population of the oligomeric states of the transmembrane domains and introduces a new formalism to describe the oligomerization equilibrium, which is based on the assumption that both the dimerization of the transmembrane domains and the dissociation of the dimer can occur only upon the collision of detergent micelles. The technique has three major advantages compared with other existing approaches: it may be used to analyze both weak and relatively strong dimerization/oligomerization processes, it works well for the analysis of complex equilibria, e.g. when monomer, dimer and high-order oligomer populations are simultaneously present in the solution, and it can simultaneously yield both structural and energetic characteristics of the helix-helix interaction under study. The proposed methodology was applied to investigate the oligomerization process of transmembrane domains of fibroblast growth factor receptor 3 (FGFR3) and vascular endothelium growth factor receptor 2 (VEGFR2), and allowed the measurement of the free energy of dimerization of both of these objects. In addition the proposed method was able to describe the multi-state oligomerization process of the VEGFR2 transmembrane domain. © 2013 Elsevier B.V. All rights reserved.

  18. Polymorphic transformation of helical flagella of bacteria

    Science.gov (United States)

    Lim, Sookkyung; Howard Berg Collaboration; William Ko Collaboration; Yongsam Kim Collaboration; Wanho Lee Collaboration; Charles Peskin Collaboration

    2016-11-01

    Bacteria such as E. coli swim in an aqueous environment by utilizing the rotation of flagellar motors and alternate two modes of motility, runs and tumbles. Runs are steady forward swimming driven by bundles of flagellar filaments whose motors are turning CCW; tumbles involve a reorientation of the direction of swimming triggered by motor reversals. During tumbling, the helical flagellum undergoes polymorphic transformations, which is a local change in helical pitch, helical radius, and handedness. In this work, we investigate the underlying mechanism of structural conformation and how this polymorphic transition plays a role in bacterial swimming. National Science Foundation.

  19. Stimuli-Driven Control of the Helical Axis of Self-Organized Soft Helical Superstructures.

    Science.gov (United States)

    Bisoyi, Hari Krishna; Bunning, Timothy J; Li, Quan

    2018-03-30

    Supramolecular and macromolecular functional helical superstructures are ubiquitous in nature and display an impressive catalog of intriguing and elegant properties and performances. In materials science, self-organized soft helical superstructures, i.e., cholesteric liquid crystals (CLCs), serve as model systems toward the understanding of morphology- and orientation-dependent properties of supramolecular dynamic helical architectures and their potential for technological applications. Moreover, most of the fascinating device applications of CLCs are primarily determined by different orientations of the helical axis. Here, the control of the helical axis orientation of CLCs and its dynamic switching in two and three dimensions using different external stimuli are summarized. Electric-field-, magnetic-field-, and light-irradiation-driven orientation control and reorientation of the helical axis of CLCs are described and highlighted. Different techniques and strategies developed to achieve a uniform lying helix structure are explored. Helical axis control in recently developed heliconical cholesteric systems is examined. The control of the helical axis orientation in spherical geometries such as microdroplets and microshells fabricated from these enticing photonic fluids is also explored. Future challenges and opportunities in this exciting area involving anisotropic chiral liquids are then discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Molecular Dynamics Simulation of Membranes and a Transmembrane Helix

    Science.gov (United States)

    Duong, Tap Ha; Mehler, Ernest L.; Weinstein, Harel

    1999-05-01

    Three molecular dynamics (MD) simulations of 1.5-ns length were carried out on fully hydrated patches of dimyristoyl phosphatidylcholine (DMPC) bilayers in the liquid-crystalline phase. The simulations were performed using different ensembles and electrostatic conditions: a microcanonical ensemble or constant pressure-temperature ensemble, with or without truncated electrostatic interactions. Calculated properties of the membrane patches from the three different protocols were compared to available data from experiments. These data include the resulting overall geometrical dimensions, the order characteristics of the lipid hydrocarbon chains, as well as various measures of the conformations of the polar head groups. The comparisons indicate that the simulation carried out within the microcanonical ensemble with truncated electrostatic interactions yielded results closest to the experimental data, provided that the initial equilibration phase preceding the production run was sufficiently long. The effects of embedding a non-ideal helical protein domain in the membrane patch were studied with the same MD protocols. This simulation was carried out for 2.5 ns. The protein domain corresponds to the seventh transmembrane segment (TMS7) of the human serotonin 5HT 2Areceptor. The peptide is composed of two α-helical segments linked by a hinge domain around a perturbing Asn-Pro motif that produces at the end of the simulation a kink angle of nearly 80° between the two helices. Several aspects of the TMS7 structure, such as the bending angle, backbone Φ and Ψ torsion angles, the intramolecular hydrogen bonds, and the overall conformation, were found to be very similar to those determined by NMR for the corresponding transmembrane segment of the tachykinin NK-1 receptor. In general, the simulations were found to yield structural and dynamic characteristics that are in good agreement with experiment. These findings support the application of simulation methods to the study

  1. Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR

    Energy Technology Data Exchange (ETDEWEB)

    Zou Chao [University of Zurich, Institute of Organic Chemistry (Switzerland); Naider, Fred [College of Staten Island, CUNY, Department of Chemistry (United States); Zerbe, Oliver [University of Zurich, Institute of Organic Chemistry (Switzerland)], E-mail: oliver.zerbe@oci.uzh.ch

    2008-12-15

    The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His){sub 6} tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.

  2. Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR.

    Science.gov (United States)

    Zou, Chao; Naider, Fred; Zerbe, Oliver

    2008-12-01

    The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His)(6) tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.

  3. Metal ion site engineering indicates a global toggle switch model for seven-transmembrane receptor activation

    DEFF Research Database (Denmark)

    Elling, Christian E; Frimurer, Thomas M; Gerlach, Lars-Ole

    2006-01-01

    Much evidence indicates that, during activation of seven-transmembrane (7TM) receptors, the intracellular segments of the transmembrane helices (TMs) move apart with large amplitude, rigid body movements of especially TM-VI and TM-VII. In this study, AspIII:08 (Asp113), the anchor point...... in sites constructed between positions III:08 (Asp or His), VI:16 (preferentially Cys), and/or VII:06 (preferentially Cys). In molecular models built over the backbone conformation of the inactive rhodopsin structure, the heavy atoms that coordinate the metal ion were located too far away from each other...... ion sites, we propose a global toggle switch mechanism for 7TM receptor activation in which inward movement of the extracellular segments of especially TM-VI and, to some extent, TM-VII is coupled to the well established outward movement of the intracellular segments of these helices. We suggest...

  4. Transmembrane topology of FRO2, a ferric chelate reductase from Arabidopsis thaliana.

    Science.gov (United States)

    Schagerlöf, Ulrika; Wilson, Greer; Hebert, Hans; Al-Karadaghi, Salam; Hägerhäll, Cecilia

    2006-09-01

    Iron uptake in Arabidopsis thaliana is mediated by ferric chelate reductase FRO2, a transmembrane protein belonging to the flavocytochrome b family. There is no high resolution structural information available for any member of this family. We have determined the transmembrane topology of FRO2 experimentally using the alkaline phosphatase fusion method. The resulting topology is different from that obtained by theoretical predictions and contains 8 transmembrane helices, 4 of which build up the highly conserved core of the protein. This core is present in the entire flavocytochrome b family. The large water soluble domain of FRO2, which contains NADPH, FAD and oxidoreductase sequence motifs, was located on the inside of the membrane.

  5. Helical plasma thruster

    Energy Technology Data Exchange (ETDEWEB)

    Beklemishev, A. D., E-mail: bekl@bk.ru [Budker Institute of Nuclear Physics SB RAS, Novosibirsk (Russian Federation)

    2015-10-15

    A new scheme of plasma thruster is proposed. It is based on axial acceleration of rotating magnetized plasmas in magnetic field with helical corrugation. The idea is that the propellant ionization zone can be placed into the local magnetic well, so that initially the ions are trapped. The E × B rotation is provided by an applied radial electric field that makes the setup similar to a magnetron discharge. Then, from the rotating plasma viewpoint, the magnetic wells of the helically corrugated field look like axially moving mirror traps. Specific shaping of the corrugation can allow continuous acceleration of trapped plasma ions along the magnetic field by diamagnetic forces. The accelerated propellant is expelled through the expanding field of magnetic nozzle. By features of the acceleration principle, the helical plasma thruster may operate at high energy densities but requires a rather high axial magnetic field, which places it in the same class as the VASIMR{sup ®} rocket engine.

  6. Helical-D pinch

    International Nuclear Information System (INIS)

    Schaffer, M.J.

    1997-08-01

    A stabilized pinch configuration is described, consisting of a D-shaped plasma cross section wrapped tightly around a guiding axis. The open-quotes helical-Dclose quotes geometry produces a very large axial (toroidal) transform of magnetic line direction that reverses the pitch of the magnetic lines without the need of azimuthal (poloidal) plasma current. Thus, there is no need of a open-quotes dynamoclose quotes process and its associated fluctuations. The resulting configuration has the high magnetic shear and pitch reversal of the reversed field pinch (RFP). (Pitch = P = qR, where R = major radius). A helical-D pinch might demonstrate good confinement at q << 1

  7. Helical thermoelectrics and refrigeration.

    Science.gov (United States)

    Mani, Arjun; Benjamin, Colin

    2018-02-01

    The thermoelectric properties of a three-terminal quantum spin Hall (QSH) sample are examined. The inherent helicity of the QSH sample helps to generate a large charge power efficiently. Along with charge the system can be designed to work as a highly efficient spin heat engine too. The advantage of a helical over a chiral sample is that, while a multiterminal quantum Hall sample can only work as a quantum heat engine due to broken time reversal (TR) symmetry, a multiterminal QSH system can work effectively as both a charge or spin heat engine and as a charge or spin refrigerator as the TR symmetry is preserved.

  8. Helical thermoelectrics and refrigeration

    Science.gov (United States)

    Mani, Arjun; Benjamin, Colin

    2018-02-01

    The thermoelectric properties of a three-terminal quantum spin Hall (QSH) sample are examined. The inherent helicity of the QSH sample helps to generate a large charge power efficiently. Along with charge the system can be designed to work as a highly efficient spin heat engine too. The advantage of a helical over a chiral sample is that, while a multiterminal quantum Hall sample can only work as a quantum heat engine due to broken time reversal (TR) symmetry, a multiterminal QSH system can work effectively as both a charge or spin heat engine and as a charge or spin refrigerator as the TR symmetry is preserved.

  9. JOINT INVERSE CASCADE OF MAGNETIC ENERGY AND MAGNETIC HELICITY IN MHD TURBULENCE

    International Nuclear Information System (INIS)

    Stepanov, R.; Frick, P.; Mizeva, I.

    2015-01-01

    We show that oppositely directed fluxes of energy and magnetic helicity coexist in the inertial range in fully developed magnetohydrodynamic (MHD) turbulence with small-scale sources of magnetic helicity. Using a helical shell model of MHD turbulence, we study the high Reynolds number MHD turbulence for helicity injection at a scale that is much smaller than the scale of energy injection. In a short range of scales larger than the forcing scale of magnetic helicity, a bottleneck-like effect appears, which results in a local reduction of the spectral slope. The slope changes in a domain with a high level of relative magnetic helicity, which determines that part of the magnetic energy is related to the helical modes at a given scale. If the relative helicity approaches unity, the spectral slope tends to –3/2. We show that this energy pileup is caused by an inverse cascade of magnetic energy associated with the magnetic helicity. This negative energy flux is the contribution of the pure magnetic-to-magnetic energy transfer, which vanishes in the non-helical limit. In the context of astrophysical dynamos, our results indicate that a large-scale dynamo can be affected by the magnetic helicity generated at small scales. The kinetic helicity, in particular, is not involved in the process at all. An interesting finding is that an inverse cascade of magnetic energy can be provided by a small-scale source of magnetic helicity fluctuations without a mean injection of magnetic helicity

  10. Review of the helicity formalism

    International Nuclear Information System (INIS)

    Barreiro, F.; Cerrada, M.; Fernandez, E.

    1972-01-01

    Our purpose in these notes has been to present a brief and general review of the helicity formalism. We begin by discussing Lorentz invariance, spin and helicity ideas, in section 1 . In section 2 we deal with the construction of relativistic states and scattering amplitudes in the helicity basis and we study their transformation properties under discrete symmetries. Finally we present some more sophisticated topics like kinematical singularities of helicity amplitudes, kinematical constraints and crossing relations 3, 4, 5 respectively. (Author) 8 refs

  11. Helicity of the Neutrino

    Indian Academy of Sciences (India)

    IAS Admin

    Measurement of the helicity of the neutrino was crucial in identifying the nature of weak interac- tion. The measurement is an example of great ingenuity in choosing, (i) the right nucleus with a specific type of decay, (ii) the technique of res- onant fluorescence scattering for determining di- rection of neutrino and (iii) ...

  12. Toroidal helical fields

    International Nuclear Information System (INIS)

    Kucinski, M.Y.; Caldas, I.L.

    1986-08-01

    Using the conventional toroidal coordinate system Laplace's equation for the magnetic scalar potential due to toroidal helical currents is solved. The potential is written as a sum of an infinite series of functions. Each partial sum represents the potential within some accuracy. The effect of the winding law is analysed in the case of small curvature. (Author) [pt

  13. Helicity of the Neutrino

    Indian Academy of Sciences (India)

    IAS Admin

    attention as soon as we focus our gaze on it. The ex- periment on the determination of helicity of the neutrino falls in a similar category among experiments in the field of modern physics. The experiments on the discovery of parity violation in 1957 [1] had established that the vi- olation parity was maximal in beta decay and ...

  14. Specificity of transmembrane protein palmitoylation in yeast.

    Directory of Open Access Journals (Sweden)

    Ayelén González Montoro

    Full Text Available Many proteins are modified after their synthesis, by the addition of a lipid molecule to one or more cysteine residues, through a thioester bond. This modification is called S-acylation, and more commonly palmitoylation. This reaction is carried out by a family of enzymes, called palmitoyltransferases (PATs, characterized by the presence of a conserved 50- aminoacids domain called "Asp-His-His-Cys- Cysteine Rich Domain" (DHHC-CRD. There are 7 members of this family in the yeast Saccharomyces cerevisiae, and each of these proteins is thought to be responsible for the palmitoylation of a subset of substrates. Substrate specificity of PATs, however, is not yet fully understood. Several yeast PATs seem to have overlapping specificity, and it has been proposed that the machinery responsible for palmitoylating peripheral membrane proteins in mammalian cells, lacks specificity altogether.Here we investigate the specificity of transmembrane protein palmitoylation in S. cerevisiae, which is carried out predominantly by two PATs, Swf1 and Pfa4. We show that palmitoylation of transmembrane substrates requires dedicated PATs, since other yeast PATs are mostly unable to perform Swf1 or Pfa4 functions, even when overexpressed. Furthermore, we find that Swf1 is highly specific for its substrates, as it is unable to substitute for other PATs. To identify where Swf1 specificity lies, we carried out a bioinformatics survey to identify amino acids responsible for the determination of specificity or Specificity Determination Positions (SDPs and showed experimentally, that mutation of the two best SDP candidates, A145 and K148, results in complete and partial loss of function, respectively. These residues are located within the conserved catalytic DHHC domain suggesting that it could also be involved in the determination of specificity. Finally, we show that modifying the position of the cysteines in Tlg1, a Swf1 substrate, results in lack of palmitoylation, as

  15. From single helical relaxed states to helical equilibria

    Science.gov (United States)

    Paccagnella, Roberto

    2018-02-01

    This paper analyzes the relationship between the Single Helical relaxed states studied by R. Paccagnella [Phys. Plasmas 23, 092512 (2016)] and the so-called "helical ohmic equilibria," i.e., plasma states that are solutions of the helical Grad Shafranov equation and that satisfy the constraint imposed by the Ohm law. The existence of marginally stable helical equilibria is clearly demonstrated, while the ohmic constraint is not exactly satisfied within the proposed first order perturbation theory. The model predictions are however satisfactorily compared with experimental trends.

  16. Biophysical Aspects of Transmembrane Signaling

    CERN Document Server

    Damjanovich, Sandor

    2005-01-01

    Transmembrane signaling is one of the most significant cell biological events in the life and death of cells in general and lymphocytes in particular. Until recently biochemists and biophysicists were not accustomed to thinking of these processes from the side of a high number of complex biochemical events and an equally high number of physical changes at molecular and cellular levels at the same time. Both types of researchers were convinced that their findings are the most decisive, having higher importance than the findings of the other scientist population. Both casts were wrong. Life, even at cellular level, has a number of interacting physical and biochemical mechanisms, which finally build up the creation of an "excited" cell that will respond to particular signals from the outer or inner world. This book handles both aspects of the signalling events, and in some cases tries to unify our concepts and help understand the signals that govern the life and death of our cells. Not only the understanding, bu...

  17. MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

    Science.gov (United States)

    Xu, Yuanwei; Rodger, P. Mark

    2017-03-01

    We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A recently proposed Monte Carlo approach, which exploits the proven statistical optimality of the MBAR estimator in order to improve simulation efficiency, was used. The results show that with both two and four proteins present, the tendency to aggregate is strongly expedited by the presence of amphipathic helix (APH), whereas a transmembrane helix (TMH) slightly disfavours aggregation. When four protein molecules are present, partially aggregated states (dimers and trimers) were more common when the APH was present, compared with the cases where no helices or only the TMH is present.

  18. Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications

    Science.gov (United States)

    Cvicek, Vaclav; Goddard, William A.; Abrol, Ravinder

    2016-01-01

    The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs

  19. Helical CT for lumbosacral spinal

    Energy Technology Data Exchange (ETDEWEB)

    Tatsuno, Satoshi; Fukuda, Kunihiko [Jikei Univ., Tokyo (Japan). School of Medicine

    1996-10-01

    The aim of this study was to investigate the efficacy of helical CT for lumbosacral pathology. We performed helical CT with multiplanar reconstruction, including the formation of oblique transaxial and coronal images, in 62 patients with various lumboscral disorders, including 32 non-enhanced CT and 36 CT after myelography. We correlated the appearance of the stenotic spinal canal and neoplastic disease with the findings on MRI obtained at nearly the same time. We obtained helical CT images in all cases in about 30 seconds. The diagnostic ability of helical CT was roughly equal to that of MRI in patients with spondylosis deformans, spondylolisthesis and herniated nucleus pulposus. There was no significant difference in diagnostic value for degenerative lumbosacral disease with canal and foraminal stenosis between non-enhanced and post-myelography helical CT. However, non-enhanced helical CT could not clearly demonstrate neoplastic disease because of the poor contrast resolution. Helical CT was useful in evaluating degenerative disorder and its diagnostic value was nearly equal to that of MRI. We considered that helical CT may be suitable for the assessment of patients with severe lumbago owing to the markedly shortened examination time. However, if helical CT is used as a screening method for lumbosacral disease, one must be careful of its limitations, for example, poor detectability of neoplastic disease, vascular anomalies and so on. (author)

  20. Buried lysine, but not arginine, titrates and alters transmembrane helix tilt.

    Science.gov (United States)

    Gleason, Nicholas J; Vostrikov, Vitaly V; Greathouse, Denise V; Koeppe, Roger E

    2013-01-29

    The ionization states of individual amino acid residues of membrane proteins are difficult to decipher or assign directly in the lipid-bilayer membrane environment. We address this issue for lysines and arginines in designed transmembrane helices. For lysines (but not arginines) at two locations within dioleoyl-phosphatidylcholine bilayer membranes, we measure pK(a) values below 7.0. We find that buried charged lysine, in fashion similar to arginine, will modulate helix orientation to maximize its own access to the aqueous interface or, if occluded by aromatic rings, may cause a transmembrane helix to exit the lipid bilayer. Interestingly, the influence of neutral lysine (vis-à-vis leucine) upon helix orientation also depends upon its aqueous access. Our results suggest that changes in the ionization states of particular residues will regulate membrane protein function and furthermore illustrate the subtle complexity of ionization behavior with respect to the detailed lipid and protein environment.

  1. TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

    Science.gov (United States)

    Cao, Han; Ng, Marcus C. K.; Jusoh, Siti Azma; Tai, Hio Kuan; Siu, Shirley W. I.

    2017-09-01

    α-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577-585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD MySQL and Apache, with all major browsers supported.

  2. Examining the Conservation of Kinks in Alpha Helices.

    Directory of Open Access Journals (Sweden)

    Eleanor C Law

    Full Text Available Kinks are a structural feature of alpha-helices and many are known to have functional roles. Kinks have previously tended to be defined in a binary fashion. In this paper we have deliberately moved towards defining them on a continuum, which given the unimodal distribution of kink angles is a better description. From this perspective, we examine the conservation of kinks in proteins. We find that kink angles are not generally a conserved property of homologs, pointing either to their not being functionally critical or to their function being related to conformational flexibility. In the latter case, the different structures of homologs are providing snapshots of different conformations. Sequence identity between homologous helices is informative in terms of kink conservation, but almost equally so is the sequence identity of residues in spatial proximity to the kink. In the specific case of proline, which is known to be prevalent in kinked helices, loss of a proline from a kinked helix often also results in the loss of a kink or reduction in its kink angle. We carried out a study of the seven transmembrane helices in the GPCR family and found that changes in kinks could be related both to subfamilies of GPCRs and also, in a particular subfamily, to the binding of agonists or antagonists. These results suggest conformational change upon receptor activation within the GPCR family. We also found correlation between kink angles in different helices, and the possibility of concerted motion could be investigated further by applying our method to molecular dynamics simulations. These observations reinforce the belief that helix kinks are key, functional, flexible points in structures.

  3. Employing Helicity Amplitudes for Resummation

    NARCIS (Netherlands)

    Moult, I.; Stewart, I.W.; Tackmann, F.J.; Waalewijn, W.J.

    2015-01-01

    Many state-of-the-art QCD calculations for multileg processes use helicity amplitudes as their fundamental ingredients. We construct a simple and easy-to-use helicity operator basis in soft-collinear effective theory (SCET), for which the hard Wilson coefficients from matching QCD onto SCET are

  4. Coordinated movement of cytoplasmic and transmembrane domains of RyR1 upon gating.

    Directory of Open Access Journals (Sweden)

    Montserrat Samsó

    2009-04-01

    Full Text Available Ryanodine receptor type 1 (RyR1 produces spatially and temporally defined Ca2+ signals in several cell types. How signals received in the cytoplasmic domain are transmitted to the ion gate and how the channel gates are unknown. We used EGTA or neuroactive PCB 95 to stabilize the full closed or open states of RyR1. Single-channel measurements in the presence of FKBP12 indicate that PCB 95 inverts the thermodynamic stability of RyR1 and locks it in a long-lived open state whose unitary current is indistinguishable from the native open state. We analyzed two datasets of 15,625 and 18,527 frozen-hydrated RyR1-FKBP12 particles in the closed and open conformations, respectively, by cryo-electron microscopy. Their corresponding three-dimensional structures at 10.2 A resolution refine the structure surrounding the ion pathway previously identified in the closed conformation: two right-handed bundles emerging from the putative ion gate (the cytoplasmic "inner branches" and the transmembrane "inner helices". Furthermore, six of the identifiable transmembrane segments of RyR1 have similar organization to those of the mammalian Kv1.2 potassium channel. Upon gating, the distal cytoplasmic domains move towards the transmembrane domain while the central cytoplasmic domains move away from it, and also away from the 4-fold axis. Along the ion pathway, precise relocation of the inner helices and inner branches results in an approximately 4 A diameter increase of the ion gate. Whereas the inner helices of the K+ channels and of the RyR1 channel cross-correlate best with their corresponding open/closed states, the cytoplasmic inner branches, which are not observed in the K+ channels, appear to have at least as important a role as the inner helices for RyR1 gating. We propose a theoretical model whereby the inner helices, the inner branches, and the h1 densities together create an efficient novel gating mechanism for channel opening by relaxing two right

  5. Magnetic design constraints of helical solenoids

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, M. L. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Krave, S. T. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Tompkins, J. C. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Yonehara, K. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Flanagan, G. [Muons Inc., Batavia, IL (United States); Kahn, S. A. [Muons Inc., Batavia, IL (United States); Melconian, K. [Texas A & M Univ., College Station, TX (United States)

    2015-01-30

    Helical solenoids have been proposed as an option for a Helical Cooling Channel for muons in a proposed Muon Collider. Helical solenoids can provide the required three main field components: solenoidal, helical dipole, and a helical gradient. In general terms, the last two are a function of many geometric parameters: coil aperture, coil radial and longitudinal dimensions, helix period and orbit radius. In this paper, we present design studies of a Helical Solenoid, addressing the geometric tunability limits and auxiliary correction system.

  6. LHD helical divertor

    International Nuclear Information System (INIS)

    Ohyabu, N.; Watanabe, T.; Ji Hantao

    1993-07-01

    The Large Helical Device (LHD) now under construction is a heliotron/torsatron device with a closed divertor system. The edge LHD magnetic structure has been studied in detail. A peculiar feature of the configuration is existence of edge surface layers, a complicated three dimensional magnetic structure which does not, however, seem to hamper the expected divertor functions. Two divertor operational modes are being considered for the LHD experiment, high density, cold radiative divertor operation as a safe heat removal scheme and high temperature divertor plasma operation. In the latter operation, a divertor plasma with temperature of a few kev, generated by efficient pumping, expects to lead to significant improvement in core plasma confinement. Conceptual designs of the LHD divertor components are under way. (author)

  7. Helical vortices: linear stability analysis and nonlinear dynamics

    Science.gov (United States)

    Selçuk, C.; Delbende, I.; Rossi, M.

    2018-02-01

    We numerically investigate, within the context of helical symmetry, the dynamics of a regular array of two or three helical vortices with or without a straight central hub vortex. The Navier–Stokes equations are linearised to study the instabilities of such basic states. For vortices with low pitches, an unstable mode is extracted which corresponds to a displacement mode and growth rates are found to compare well with results valid for an infinite row of point vortices or an infinite alley of vortex rings. For larger pitches, the system is stable with respect to helically symmetric perturbations. In the nonlinear regime, we follow the time-evolution of the above basic states when initially perturbed by the dominant instability mode. For two vortices, sequences of overtaking events, leapfrogging and eventually merging are observed. The transition between such behaviours occurs at a critical ratio involving the core size and the vortex-separation distance. Cases with three helical vortices are also presented.

  8. Nanomechanical properties of MscL α helices: A steered molecular dynamics study.

    Science.gov (United States)

    Bavi, N; Bavi, O; Vossoughi, M; Naghdabadi, R; Hill, A P; Martinac, B; Jamali, Y

    2017-05-04

    Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during stretching and high dependency of the elastic properties on the pulling rate. We estimated Young's moduli of the α-helices of MscL to vary between 0.2 and 12.5 GPa with TM2 helix being the stiffest. We also studied the effect of water on the properties of the pore-lining TM1 helix. In the absence of water, this helix exhibited a much stiffer response. By monitoring the number of hydrogen bonds, it appears that water acts like a 'lubricant' (softener) during TM1 helix elongation. These data shed light on another physical aspect underlying hydrophobic gating of MS channels, in particular MscL.

  9. A Novel Type III Endosome Transmembrane Protein, TEMP

    Directory of Open Access Journals (Sweden)

    Rohan D. Teasdale

    2012-11-01

    Full Text Available As part of a high-throughput subcellular localisation project, the protein encoded by the RIKEN mouse cDNA 2610528J11 was expressed and identified to be associated with both endosomes and the plasma membrane. Based on this, we have assigned the name TEMP for Type III Endosome Membrane Protein. TEMP encodes a short protein of 111 amino acids with a single, alpha-helical transmembrane domain. Experimental analysis of its membrane topology demonstrated it is a Type III membrane protein with the amino-terminus in the lumenal, or extracellular region, and the carboxy-terminus in the cytoplasm. In addition to the plasma membrane TEMP was localized to Rab5 positive early endosomes, Rab5/Rab11 positive recycling endosomes but not Rab7 positive late endosomes. Video microscopy in living cells confirmed TEMP's plasma membrane localization and identified the intracellular endosome compartments to be tubulovesicular. Overexpression of TEMP resulted in the early/recycling endosomes clustering at the cell periphery that was dependent on the presence of intact microtubules. The cellular function of TEMP cannot be inferred based on bioinformatics comparison, but its cellular distribution between early/recycling endosomes and the plasma membrane suggests a role in membrane transport.

  10. Godbillon Vey Helicity and Magnetic Helicity in Magnetohydrodynamics

    Science.gov (United States)

    Webb, G. M.; Hu, Q.; Anco, S.; Zank, G. P.

    2017-12-01

    The Godbillon-Vey invariant arises in homology theory, and algebraic topology, where conditions for a layered family of 2D surfaces forms a 3D manifold were elucidated. The magnetic Godbillon-Vey helicity invariant in magnetohydrodynamics (MHD) is a helicity invariant that occurs for flows, in which the magnetic helicity density hm= A\\cdotB=0 where A is the magnetic vector potential and B is the magnetic induction. Our purpose is to elucidate the evolution of the magnetic Godbillon-Vey field η =A×B/|A|2 and the Godbillon-Vey helicity hgv}= η \\cdot∇ × η in general MHD flows in which the magnetic helicity hm≠q 0. It is shown that hm acts as a source term in the Godbillon-Vey helicity transport equation, in which hm is coupled to hgv via the shear tensor of the background flow. The transport equation for hgv depends on the electric field potential ψ , which is related to the gauge for A, which takes its simplest form for the advected A gauge in which ψ =A\\cdot u where u is the fluid velocity.

  11. Transmembrane signal transduction by peptide hormones via family B G protein-coupled receptors.

    Science.gov (United States)

    Culhane, Kelly J; Liu, Yuting; Cai, Yingying; Yan, Elsa C Y

    2015-01-01

    Although family B G protein-coupled receptors (GPCRs) contain only 15 members, they play key roles in transmembrane signal transduction of hormones. Family B GPCRs are drug targets for developing therapeutics for diseases ranging from metabolic to neurological disorders. Despite their importance, the molecular mechanism of activation of family B GPCRs remains largely unexplored due to the challenges in expression and purification of functional receptors to the quantity for biophysical characterization. Currently, there is no crystal structure available of a full-length family B GPCR. However, structures of key domains, including the extracellular ligand binding regions and seven-helical transmembrane regions, have been solved by X-ray crystallography and NMR, providing insights into the mechanisms of ligand recognition and selectivity, and helical arrangements within the cell membrane. Moreover, biophysical and biochemical methods have been used to explore functions, key residues for signaling, and the kinetics and dynamics of signaling processes. This review summarizes the current knowledge of the signal transduction mechanism of family B GPCRs at the molecular level and comments on the challenges and outlook for mechanistic studies of family B GPCRs.

  12. Transmembrane signal transduction by peptide hormones via family B G protein-coupled receptors

    Directory of Open Access Journals (Sweden)

    Kelly J Culhane

    2015-11-01

    Full Text Available Although family B G protein-coupled receptors (GPCRs contain only 15 members, they play key roles in transmembrane signal transduction of hormones. Family B GPCRs are drug targets for developing therapeutics for diseases ranging from metabolic to neurological disorders. Despite their importance, the molecular mechanism of activation of family B GPCRs remains largely unexplored due to the challenges in expression and purification of functional receptors to the quantity for biophysical characterization. Currently, there is no crystal structure available of a full-length family B GPCR. However, structures of key domains, including the extracellular ligand binding regions and seven-helical transmembrane regions, have been solved by X-ray crystallography and NMR, providing insights into the mechanisms of ligand recognition and selectivity, and helical arrangements within the cell membrane. Moreover, biophysical and biochemical methods have been used to explore functions, key residues for signaling, and the kinetics and dynamics of signaling processes. This review summarizes the current knowledge of the signal transduction mechanism of family B GPCRs at the molecular level and comments on the challenges and outlook for mechanistic studies of family B GPCRs.

  13. Helicity multiplexed broadband metasurface holograms

    Science.gov (United States)

    Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Yue Bun Pun, Edwin; Zhang, Shuang; Chen, Xianzhong

    2015-09-01

    Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices.

  14. Employing helicity amplitudes for resummation

    International Nuclear Information System (INIS)

    Moult, Ian; Stewart, Iain W.; Tackmann, Frank J.; Waalewijn, Wouter J.; Amsterdam Univ.

    2015-08-01

    Many state-of-the-art QCD calculations for multileg processes use helicity amplitudes as their fundamental ingredients. We construct a simple and easy-to-use helicity operator basis in soft-collinear effective theory (SCET), for which the hard Wilson coefficients from matching QCD onto SCET are directly given in terms of color-ordered helicity amplitudes. Using this basis allows one to seamlessly combine fixed-order helicity amplitudes at any order they are known with a resummation of higher-order logarithmic corrections. In particular, the virtual loop amplitudes can be employed in factorization theorems to make predictions for exclusive jet cross sections without the use of numerical subtraction schemes to handle real-virtual infrared cancellations. We also discuss matching onto SCET in renormalization schemes with helicities in 4- and d-dimensions. To demonstrate that our helicity operator basis is easy to use, we provide an explicit construction of the operator basis, as well as results for the hard matching coefficients, for pp → H+0,1,2 jets, pp → W/Z/γ+0,1,2 jets, and pp → 2,3 jets. These operator bases are completely crossing symmetric, so the results can easily be applied to processes with e + e - and e - p collisions.

  15. Molecular pharmacology of promiscuous seven transmembrane receptors sensing organic nutrients

    DEFF Research Database (Denmark)

    Wellendorph, Petrine; Johansen, Lars Dan; Bräuner-Osborne, Hans

    2009-01-01

    A number of highly promiscuous seven transmembrane (7TM) receptors have been cloned and characterized within the last few years. It is noteworthy that many of these receptors are activated broadly by amino acids, proteolytic degradation products, carbohydrates, or free fatty acids and are expressed...... receptors FFA1, FFA2, FFA3, GPR84, and GPR120. The involvement of the individual receptors in sensing of food intake has been validated to different degrees because of limited availability of specific pharmacological tools and/or receptor knockout mice. However, as a group, the receptors represent potential...

  16. PDBTM: Protein Data Bank of transmembrane proteins after 8 years

    OpenAIRE

    Kozma, D?niel; Simon, Istv?n; Tusn?dy, G?bor E.

    2012-01-01

    The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the la...

  17. Attenuation of Phosphorylation-dependent Activation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Disease-causing Mutations at the Transmission Interface*

    OpenAIRE

    Chin, Stephanie; Yang, Donghe; Miles, Andrew J.; Eckford, Paul D. W.; Molinski, Steven; Wallace, B. A.; Bear, Christine E.

    2016-01-01

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein that functions as a phosphorylation-regulated anion channel. The interface between its two cytosolic nucleotide binding domains and coupling helices conferred by intracellular loops extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory domain of CFTR by protein...

  18. Energetics and Structure Prediction of the Network of Homo- and Hetero-Oligomers Formed by the Transmembrane Domains of the ErbReceptor Family of Proteins

    Science.gov (United States)

    2006-06-01

    higher-order oligomer) can bind to the cholera toxin promoter and activate transcription of a reporter gene. Using this assay, Lemmon and colleagues...identical to the transmembrane sequences of the chicken Klg and Hydra Lemon orthologues (9), and a pattern of residues with helical periodicity is...Steele, R. E. (2000) Lemon encodes an unusual receptor protein-tyrosine kinase expressed during gametogenesis in Hydra , DeV. Biol. 224, 286-298. 10

  19. Toroidal helical quartz forming machine

    International Nuclear Information System (INIS)

    Hanks, K.W.; Cole, T.R.

    1977-01-01

    The Scyllac fusion experimental machine used 10 cm diameter smooth bore discharge tubes formed into a simple toroidal shape prior to 1974. At about that time, it was discovered that a discharge tube was required to follow the convoluted shape of the load coil. A machine was designed and built to form a fused quartz tube with a toroidal shape. The machine will accommodate quartz tubes from 5 cm to 20 cm diameter forming it into a 4 m toroidal radius with a 1 to 5 cm helical displacement. The machine will also generate a helical shape on a linear tube. Two sets of tubes with different helical radii and wavelengths have been successfully fabricated. The problems encountered with the design and fabrication of this machine are discussed

  20. Generalized helicity and Beltrami fields

    International Nuclear Information System (INIS)

    Buniy, Roman V.; Kephart, Thomas W.

    2014-01-01

    We propose covariant and non-abelian generalizations of the magnetic helicity and Beltrami equation. The gauge invariance, variational principle, conserved current, energy–momentum tensor and choice of boundary conditions elucidate the subject. In particular, we prove that any extremal of the Yang–Mills action functional 1/4 ∫ Ω trF μν F μν d 4 x subject to the local constraint ε μναβ trF μν F αβ =0 satisfies the covariant non-abelian Beltrami equation. -- Highlights: •We introduce the covariant non-abelian helicity and Beltrami equation. •The Yang–Mills action and instanton term constraint lead to the Beltrami equation. •Solutions of the Beltrami equation conserve helicity

  1. Generalized helicity and Beltrami fields

    Energy Technology Data Exchange (ETDEWEB)

    Buniy, Roman V., E-mail: roman.buniy@gmail.com [Schmid College of Science, Chapman University, Orange, CA 92866 (United States); Isaac Newton Institute, University of Cambridge, Cambridge, CB3 0EH (United Kingdom); Kephart, Thomas W., E-mail: tom.kephart@gmail.com [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States); Isaac Newton Institute, University of Cambridge, Cambridge, CB3 0EH (United Kingdom)

    2014-05-15

    We propose covariant and non-abelian generalizations of the magnetic helicity and Beltrami equation. The gauge invariance, variational principle, conserved current, energy–momentum tensor and choice of boundary conditions elucidate the subject. In particular, we prove that any extremal of the Yang–Mills action functional 1/4 ∫{sub Ω}trF{sub μν}F{sup μν}d{sup 4}x subject to the local constraint ε{sup μναβ}trF{sub μν}F{sub αβ}=0 satisfies the covariant non-abelian Beltrami equation. -- Highlights: •We introduce the covariant non-abelian helicity and Beltrami equation. •The Yang–Mills action and instanton term constraint lead to the Beltrami equation. •Solutions of the Beltrami equation conserve helicity.

  2. Helical muon beam cooling channel engineering design

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Rolland [Muons, Inc., Batavia, IL (United States)

    2015-08-07

    The Helical Cooling Channel (HCC) achieves effective ionization cooling of the six-dimensional (6d) phase space of a muon beam by means of a series of 21st century inventions. In the HCC, hydrogen-pressurized RF cavities enable high RF gradients in strong external magnetic fields. The theory of the HCC, which requires a magnetic field with solenoid, helical dipole, and helical quadrupole components, demonstrates that dispersion in the gaseous hydrogen energy absorber provides effective emittance exchange to enable longitudinal ionization cooling. The 10-year development of a practical implementation of a muon-beam cooling device has involved a series of technical innovations and experiments that imply that an HCC of less than 300 m length can cool the 6d emittance of a muon beam by six orders of magnitude. We describe the design and construction plans for a prototype HCC module based on oxygen-doped hydrogen-pressurized RF cavities that are loaded with dielectric, fed by magnetrons, and operate in a superconducting helical solenoid magnet. The first phase of this project saw the development of a conceptual design for the integration of 805 MHz RF cavities into a 10 T Nb3Sn-based HS test section. Two very novel ideas are required to realize the design. The first idea is the use of dielectric inserts in the RF cavities to make them smaller for a given frequency so that the cavities and associated plumbing easily fit inside the magnet cryostat. Calculations indicate that heat loads will be tolerable, while RF breakdown of the dielectric inserts will be suppressed by the pressurized hydrogen gas. The second new idea is the use of a multi-layer Nb3Sn helical solenoid. The technology demonstrations for the two aforementioned key components of a 10T, 805 MHz HCC were begun in this project. The work load in the Fermilab Technical Division made it difficult to test a multi-layer Nb3Sn solenoid as originally planned. Instead, a complementary

  3. Helical muon beam cooling channel engineering design

    International Nuclear Information System (INIS)

    Johnson, Rolland

    2015-01-01

    The Helical Cooling Channel (HCC) achieves effective ionization cooling of the six-dimensional (6d) phase space of a muon beam by means of a series of 21st century inventions. In the HCC, hydrogen-pressurized RF cavities enable high RF gradients in strong external magnetic fields. The theory of the HCC, which requires a magnetic field with solenoid, helical dipole, and helical quadrupole components, demonstrates that dispersion in the gaseous hydrogen energy absorber provides effective emittance exchange to enable longitudinal ionization cooling. The 10-year development of a practical implementation of a muon-beam cooling device has involved a series of technical innovations and experiments that imply that an HCC of less than 300 m length can cool the 6d emittance of a muon beam by six orders of magnitude. We describe the design and construction plans for a prototype HCC module based on oxygen-doped hydrogen-pressurized RF cavities that are loaded with dielectric, fed by magnetrons, and operate in a superconducting helical solenoid magnet. The first phase of this project saw the development of a conceptual design for the integration of 805 MHz RF cavities into a 10 T Nb 3 Sn-based HS test section. Two very novel ideas are required to realize the design. The first idea is the use of dielectric inserts in the RF cavities to make them smaller for a given frequency so that the cavities and associated plumbing easily fit inside the magnet cryostat. Calculations indicate that heat loads will be tolerable, while RF breakdown of the dielectric inserts will be suppressed by the pressurized hydrogen gas. The second new idea is the use of a multi-layer Nb 3 Sn helical solenoid. The technology demonstrations for the two aforementioned key components of a 10T, 805 MHz HCC were begun in this project. The work load in the Fermilab Technical Division made it difficult to test a multi-layer Nb 3 Sn solenoid as originally planned. Instead, a complementary project was approved by the

  4. Resonant helical fields in tokamaks

    International Nuclear Information System (INIS)

    Okano, V.

    1990-01-01

    Poincare maps of magnetic field lines of a toroidal helical system were made. The magnetic field is a linear superposition of the magnetic fields produced by a toroidal plasma in equilibrium and by external helical currents. Analytical expression for the Poincare maps was no obtained since the magnetic field do not have symmetry. In order to obtain the maps, the equation minus derivative of l vector times B vector = 0 was numerically integrated. In the Poincare maps, the principal and the secondary magnetic island were observed. (author)

  5. Conserved allosteric hot spots in the transmembrane domains of cystic fibrosis transmembrane conductance regulator (CFTR) channels and multidrug resistance protein (MRP) pumps.

    Science.gov (United States)

    Wei, Shipeng; Roessler, Bryan C; Chauvet, Sylvain; Guo, Jingyu; Hartman, John L; Kirk, Kevin L

    2014-07-18

    ATP-binding cassette (ABC) transporters are an ancient family of transmembrane proteins that utilize ATPase activity to move substrates across cell membranes. The ABCC subfamily of the ABC transporters includes active drug exporters (the multidrug resistance proteins (MRPs)) and a unique ATP-gated ion channel (cystic fibrosis transmembrane conductance regulator (CFTR)). The CFTR channel shares gating principles with conventional ligand-gated ion channels, but the allosteric network that couples ATP binding at its nucleotide binding domains (NBDs) with conformational changes in its transmembrane helices (TMs) is poorly defined. It is also unclear whether the mechanisms that govern CFTR gating are conserved with the thermodynamically distinct MRPs. Here we report a new class of gain of function (GOF) mutation of a conserved proline at the base of the pore-lining TM6. Multiple substitutions of this proline promoted ATP-free CFTR activity and activation by the weak agonist, 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP). TM6 proline mutations exhibited additive GOF effects when combined with a previously reported GOF mutation located in an outer collar of TMs that surrounds the pore-lining TMs. Each TM substitution allosterically rescued the ATP sensitivity of CFTR gating when introduced into an NBD mutant with defective ATP binding. Both classes of GOF mutations also rescued defective drug export by a yeast MRP (Yor1p) with ATP binding defects in its NBDs. We conclude that the conserved TM6 proline helps set the energy barrier to both CFTR channel opening and MRP-mediated drug efflux and that CFTR channels and MRP pumps utilize similar allosteric mechanisms for coupling conformational changes in their translocation pathways to ATP binding at their NBDs. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Field-theoretic calculation of kinetic helicity flux

    Indian Academy of Sciences (India)

    Given all these practical aspects, kinetic helicity is an important quantity to study in fluid turbulence. Turbulence involves millions of interacting modes. It is very difficult to analyze these modes theoretically as well as numerically. In recent times, a new numeri- cal procedure called 'large eddy simulations' (LES) has become ...

  7. Helically symmetric equilibria with pressure anisotropy and incompressible plasma flow

    Science.gov (United States)

    Evangelias, A.; Kuiroukidis, A.; Throumoulopoulos, G. N.

    2018-02-01

    We derive a generalized Grad-Shafranov equation governing helically symmetric equilibria with pressure anisotropy and incompressible flow of arbitrary direction. Through the most general linearizing ansatz for the various free surface functions involved therein, we construct equilibrium solutions and study their properties. It turns out that pressure anisotropy can act either paramegnetically or diamagnetically, the parallel flow has a paramagnetic effect, while the non-parallel component of the flow associated with the electric field has a diamagnetic one. Also, pressure anisotropy and flow affect noticeably the helical current density.

  8. Applications of 2D helical vortex dynamics

    DEFF Research Database (Denmark)

    Okulov, Valery; Sørensen, Jens Nørkær

    2010-01-01

    In the paper, we show how the assumption of helical symmetry in the context of 2D helical vortices can be exploited to analyse and to model various cases of rotating flows. From theory, examples of three basic applications of 2D dynamics of helical vortices embedded in flows with helical symmetry...... of the vorticity field are addressed. These included some of the problems related to vortex breakdown, instability of far wakes behind rotors and vortex theory of ideal rotors....

  9. Parameterization and measurements of helical magnetic fields

    International Nuclear Information System (INIS)

    Fischer, W.; Okamura, M.

    1997-01-01

    Magnetic fields with helical symmetry can be parameterized using multipole coefficients (a n , b n ). We present a parameterization that gives the familiar multipole coefficients (a n , b n ) for straight magnets when the helical wavelength tends to infinity. To measure helical fields all methods used for straight magnets can be employed. We show how to convert the results of those measurements to obtain the desired helical multipole coefficients (a n , b n )

  10. ICRF heating on helical devices

    International Nuclear Information System (INIS)

    Rasmussen, D.A.; Lyon, J.F.; Hoffman, D.J.; Murakami, M.; England, A.C.; Wilgen, J.B.

    1995-01-01

    Ion cyclotron range of frequency (ICRF) heating is currently in use on CHS and W7-AS and is a major element of the heating planned for steady state helical devices. In helical devices, the lack of a toroidal current eliminates both disruptions and the need for ICFR current drive, simplifying the design of antenna structures as compared to tokamak applications. However the survivability of plasma facing components and steady state cooling issues are directly applicable to tokamak devices. Results from LHD steady state experiments should be available on a time scale to strongly influence the next generation of steady state tokamak experiments. the helical plasma geometry provides challenges not faced with tokamak ICRF heating, including the potential for enhanced fast ion losses, impurity accumulation, limited access for antenna structures, and open magnetic field lines in the plasma edge. The present results and near term plans provide the basis for steady state ICRF heating of larger helical devices. An approach which includes direct electron, mode conversion, ion minority and ion Bernstein wave heating addresses these issues. 12 refs

  11. Helicity Within and Among Macromolecules

    Science.gov (United States)

    Green, Mark M.

    2004-03-01

    There are several classes of helical polymers and supramolecular arrays in which the left and right helical senses are of equal probability and as well in dynamic equilibrium. One example of this class of materials is a polymer first created at Dupont as a commercial fiber candidate almost fifty years ago but which did not rise to the level necessary for commercial use. The polymer, nylon 1, widely known as a polyisocyanate, did become a focal point of research for polymer physics because of its stiff archetypical wormlike nature. An array of research tools was able to elucidate the conformational characteristics of this polymer and therefore reveal in quantitative detail both the source of its stiffness and the limit to this characteristic. Further effort explored the nature of the expected lyotropic liquid crystal properties with similar success. As part of these studies, chiral experiments, which were introduced to determine how to favor one helical sense, played a key role. Statistical physical analysis of these chiral experiments first by Shneior Lifson for uniform chiral fields and later by Jonathan Selinger for quenched random chiral fields gave insight into the cooperative characteristics by which the chiral information influenced the helical senses in these polymers. These kinds of experiments finding parallels to the behavior of sergeants and soldiers and to majority rule were later applied widely in the literature offering insight into the cooperative nature of helical polymers and arrays in general. Moreover, the interplay between the character of the single chains and the liquid crystals that arise in concentrated solutions from the polyisocyanates yielded new kinds of information about the cholesteric state formed by lyotropic liquid crystals in general and even led to new phenomena connecting liquid crystal behavior to temperature.

  12. Transmembrane Helix-helix Association: Relative Stabilities at Low pH†

    Science.gov (United States)

    Valluru, Neelima; Silva, Frances; Dhage, Manmath; Rodriguez, Gustavo; Alloor, Srinivas R.; Renthal, Robert

    2008-01-01

    We have previously studied the unfolding equilibrium of bacterio-opsin in a single phase solvent, using Förster mechanism fluorescence resonance energy transfer (FRET) as a probe, from tryptophan donors to a dansyl acceptor. We observed an apparent unfolding transition in bacterio-opsin perturbed by increasing ethanol concentrations [Nannepaga et al.(2004) Biochemistry 43, 50–59]. We have further investigated this transition and find the unfolding is pH-dependent. We have now measured the apparent pK of acid-induced unfolding of bacterio-opsin in 90% ethanol. When the acceptor is on helix B (Lys 41), the apparent pK for unfolding is 4.75; on the EF connecting loop (Cys 163), 5.15; and on helix G (Cys 222), 5.75. Five-helix proteolytic fragments are less stable. The apparent unfolding pKs are, for residues 72-248 (Cys 163), 5.46; and 1-166 (Lys 41), 7.36. When interpreted in terms of a simple equilibrium model for unfolding, the apparent pKs give relative free energies of unfolding, in the range of −0.54 to −3.5 kcal/mol. The results suggest that the C-terminal helix of bacterio-opsin is less stably folded than the N-terminal helices. We analyzed the pair-wise helix-helix interaction surfaces of bacteriorhodopsin and three other 7-transmembrane helix proteins, based on crystal structures. The results show that the interaction surfaces are smoother and the helix axis separations are closer in the amino-terminal two-thirds of the proteins compared with the carboxyl terminal one-third. However, the F helix is important in stabilizing the folded structure, as shown by the instability of the 1-166 fragment. Considering the high resolution crystal structure of bacteriorhodopsin, there are no obvious helix-helix interactions involving protein side chains which would be destabilized by protonation at the estimated pH of the unfolding transitions. However, a number of helix-bridging water molecules could become protonated, thereby weakening the helix

  13. Transmembrane helix-helix association: relative stabilities at low pH.

    Science.gov (United States)

    Valluru, Neelima; Silva, Frances; Dhage, Manmath; Rodriguez, Gustavo; Alloor, Srinivas R; Renthal, Robert

    2006-04-11

    We have previously studied the unfolding equilibrium of bacterioopsin in a single phase solvent, using Förster mechanism fluorescence resonance energy transfer (FRET) as a probe, from tryptophan donors to a dansyl acceptor. We observed an apparent unfolding transition in bacterioopsin perturbed by increasing ethanol concentrations [Nannepaga et al. (2004) Biochemistry 43, 50-59]. We have further investigated this transition and find that the unfolding is pH-dependent. We have now measured the apparent pK of acid-induced unfolding of bacterioopsin in 90% ethanol. When the acceptor is on helix B (Lys 41), the apparent pK for unfolding is 4.75; on the EF connecting loop (Cys 163), 5.15; and on helix G (Cys 222), 5.75. Five-helix proteolytic fragments are less stable. The apparent unfolding pKs are 5.46 for residues 72-248 (Cys 163) and 7.36 for residues 1-166 (Lys 41). When interpreted in terms of a simple equilibrium model for unfolding, the apparent pKs give relative free energies of unfolding in the range of -0.54 to -3.5 kcal/mol. The results suggest that the C-terminal helix of bacterioopsin is less stably folded than the N-terminal helices. We analyzed the pairwise helix-helix interaction surfaces of bacteriorhodopsin and three other seven-transmembrane-helix proteins on the basis of crystal structures. The results show that the interaction surfaces are smoother and the helix axis separations are closer in the amino-terminal two-thirds of the proteins compared with the carboxyl-terminal one-third. However, the F helix is important in stabilizing the folded structure, as shown by the instability of the 1-166 fragment. Considering the high-resolution crystal structure of bacteriorhodopsin, there are no obvious helix-helix interactions involving protein side chains which would be destabilized by protonation at the estimated pH of the unfolding transitions. However, a number of helix-bridging water molecules could become protonated, thereby weakening the helix

  14. The role of transmembrane segment II in 7TM receptor activation

    DEFF Research Database (Denmark)

    Benned-Jensen, Tau; Rosenkilde, M M

    2009-01-01

    During the two past decades tremendous effort has been put into uncovering the activation mechanism of 7TM receptors. The majority of such studies have focused on the major binding pocket, comprised of transmembrane segments (TM) -III through -VII, as most non-peptide and peptide ligands......, in addition to biogenic amines and retinal a.m.o. bind to residues in this region. Consequently the major helical movements occur here during activation, as described recently in the Global Toggle Switch Model for Family A (also known as rhodopsin-like) members of the 7TM receptors. As a result, the minor......, accumulating evidence emphasize that this is not the case. In this review, we focus on TM-II with an emphasis on position II:20/2.60, and present data from structure-activity studies on a range of Family A 7TM receptors including chemokine, ghrelin and melanocortin receptors in addition to the orphan EBI2...

  15. Generalized helicity and its time derivative

    International Nuclear Information System (INIS)

    Jarboe, T.R.; Marklin, G.J.

    1985-01-01

    Spheromaks can be sustained against resistive decay by helicity injection because they tend to obey the minimum energy principle. This principle states that a plasma-laden magnetic configuration will relax to a state of minimum energy subject to the constraint that the magnetic helicity is conserved. Use of helicity as a constraint on the minimization of energy was first proposed by Woltjer in connection with astrophysical phenomena. Helicity does decay on the resistive diffusion time. However, if helicity is created and made to flow continuoiusly into a confinement geometry, these additional linked fluxes can relax and sustain the configuration indefinitely against the resistive decay. In this paper we will present an extension of the definition of helicity to include systems where B vector can penetrate the boundary and the penetration can be varying in time. We then discuss the sustainment of RFPs and spheromaks in terms of helicity injection

  16. The transmembrane channel-like protein family and human papillomaviruses

    Science.gov (United States)

    Horton, Jaime S; Stokes, Alexander J

    2014-01-01

    Epidermodysplasia verruciformis (EV) is a rare genodermatosis characterized by increased sensitivity to infection by the β-subtype of human papillomaviruses (β-HPVs), causing persistent, tinea versicolor-like dermal lesions. In a majority of affected individuals, these macular lesions progress to invasive cutaneous squamous cell carcinoma (CSCC) in sun-exposed areas. While mutations in transmembrane channel-like 6 (TMC6 / EVER1) and 8 (TMC8 / EVER2) have been causally linked to EV, their molecular functions are unclear. It is likely that their protective effects involve regulation of the β-HPV life cycle, host keratinocyte apoptosis vs. survival balance and/or T-cell interaction with infected host cells. PMID:24800179

  17. A helical scintillating fiber hodoscope

    CERN Document Server

    Altmeier, M; Bisplinghoff, J; Bissel, T; Bollmann, R; Busch, M; Büsser, K; Colberg, T; Demiroers, L; Diehl, O; Dohrmann, F; Engelhardt, H P; Eversheim, P D; Felden, O; Gebel, R; Glende, M; Greiff, J; Gross, A; Gross-Hardt, R; Hinterberger, F; Jahn, R; Jeske, M; Jonas, E; Krause, H; Lahr, U; Langkau, R; Lindemann, T; Lindlein, J; Maier, R; Maschuw, R; Mayer-Kuckuck, T; Meinerzhagen, A; Naehle, O; Pfuff, M; Prasuhn, D; Rohdjess, H; Rosendaal, D; Von Rossen, P; Sanz, B; Schirm, N; Schulz-Rojahn, M; Schwarz, V; Scobel, W; Thomas, S; Trelle, H J; Weise, E; Wellinghausen, A; Wiedmann, W; Woller, K; Ziegler, R

    1999-01-01

    A novel scintillating fiber hodoscope in helically cylindric geometry has been developed for detection of low multiplicity events of fast protons and other light charged particles in the internal target experiment EDDA at the Cooler Synchrotron COSY. The hodoscope consists of 640 scintillating fibers (2.5 mm diameter), arranged in four layers surrounding the COSY beam pipe. The fibers are helically wound in opposing directions and read out individually using 16-channel photomultipliers connected to a modified commercial encoding system. The detector covers an angular range of 9 deg. <= THETA<=72 deg. and 0 deg. <=phi (cursive,open) Greek<=360 deg. in the lab frame. The detector length is 590 mm, the inner diameter 161 mm. Geometry and granularity of the hodoscope afford a position resolution of about 1.3 mm. The detector design took into consideration a maximum of reliability and a minimum of maintenance. An LED array may be used for monitoring purposes. (author)

  18. Baryon helicity in B decay

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Mahiko [Department of Physics and Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720 (United States)

    2005-07-01

    The unexpectedly large transverse polarization measured in the decay B {yields} {phi}K* poses the question whether it is accounted for as a strong interaction effect or possibly points to a hidden nonstandard weak interaction. We extend here the perturbative argument to the helicity structure of the two-body baryonic decay and discuss qualitatively on how the baryonic B decay modes might help us in understanding the issue raised by B {yields} {phi}K*. We find among others that the helicity +1/2 amplitude dominates the leading order in the B(b-barq) decay and that unlike the B {yields} VV decay the dominant amplitude is sensitive to the right-handed b {yields} s current, if any, in the penguin interaction.

  19. Helical screw expander evaluation project

    Science.gov (United States)

    McKay, R.

    1982-03-01

    A one MW helical rotary screw expander power system for electric power generation from geothermal brine was evaluated. The technology explored in the testing is simple, potentially very efficient, and ideally suited to wellhead installations in moderate to high enthalpy, liquid dominated field. A functional one MW geothermal electric power plant that featured a helical screw expander was produced and then tested with a demonstrated average performance of approximately 45% machine efficiency over a wide range of test conditions in noncondensing, operation on two-phase geothermal fluids. The Project also produced a computer equipped data system, an instrumentation and control van, and a 1000 kW variable load bank, all integrated into a test array designed for operation at a variety of remote test sites. Data are presented for the Utah testing and for the noncondensing phases of the testing in Mexico. Test time logged was 437 hours during the Utah tests and 1101 hours during the Mexico tests.

  20. An experimental superconducting helical undulator

    Energy Technology Data Exchange (ETDEWEB)

    Caspi, S.; Taylor, C. [Lawrence Berkeley Lab., CA (United States)

    1995-12-31

    Improvements in the technology of superconducting magnets for high energy physics and recent advancements in SC materials with the artificial pinning centers (APC){sup 2}, have made a bifilar helical SC device an attractive candidate for a single-pass free electron laser (FEL){sup 3}. Initial studies have suggested that a 6.5 mm inner diameter helical device, with a 27 mm period, can generate a central field of 2-2.5 Tesla. Additional studies have also suggested that with a stored energy of 300 J/m, such a device can be made self-protecting in the event of a quench. However, since the most critical area associated with high current density SC magnets is connected with quenching and training, a short experimental device will have to be built and tested. In this paper we discuss technical issues relevant to the construction of such a device, including a conceptual design, fields, and forces.

  1. Helical Antimicrobial Sulfono- {gamma} -AApeptides

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yaqiong; Wu, Haifan; Teng, Peng; Bai, Ge; Lin, Xiaoyang; Zuo, Xiaobing; Cao, Chuanhai; Cai, Jianfeng

    2015-06-11

    Host-defense peptides (HDPs) such as magainin 2 have emerged as potential therapeutic agents combating antibiotic resistance. Inspired by their structures and mechanism of action, herein we report the fi rst example of antimicrobial helical sulfono- γ - AApeptide foldamers. The lead molecule displays broad-spectrum and potent antimicrobial activity against multi-drug-resistant Gram- positive and Gram-negative bacterial pathogens. Time-kill studies and fl uorescence microscopy suggest that sulfono- γ -AApeptides eradicate bacteria by taking a mode of action analogous to that of HDPs. Clear structure - function relationships exist in the studied sequences. Longer sequences, presumably adopting more-de fi ned helical structures, are more potent than shorter ones. Interestingly, the sequence with less helical propensity in solution could be more selective than the stronger helix-forming sequences. Moreover, this class of antimicrobial agents are resistant to proteolytic degradation. These results may lead to the development of a new class of antimicrobial foldamers combating emerging antibiotic-resistant pathogens.

  2. Evolution of vertebrate interferon inducible transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Hickford Danielle

    2012-04-01

    Full Text Available Abstract Background Interferon inducible transmembrane proteins (IFITMs have diverse roles, including the control of cell proliferation, promotion of homotypic cell adhesion, protection against viral infection, promotion of bone matrix maturation and mineralisation, and mediating germ cell development. Most IFITMs have been well characterised in human and mouse but little published data exists for other animals. This study characterised IFITMs in two distantly related marsupial species, the Australian tammar wallaby and the South American grey short-tailed opossum, and analysed the phylogeny of the IFITM family in vertebrates. Results Five IFITM paralogues were identified in both the tammar and opossum. As in eutherians, most marsupial IFITM genes exist within a cluster, contain two exons and encode proteins with two transmembrane domains. Only two IFITM genes, IFITM5 and IFITM10, have orthologues in both marsupials and eutherians. IFITM5 arose in bony fish and IFITM10 in tetrapods. The bone-specific expression of IFITM5 appears to be restricted to therian mammals, suggesting that its specialised role in bone production is a recent adaptation specific to mammals. IFITM10 is the most highly conserved IFITM, sharing at least 85% amino acid identity between birds, reptiles and mammals and suggesting an important role for this presently uncharacterised protein. Conclusions Like eutherians, marsupials also have multiple IFITM genes that exist in a gene cluster. The differing expression patterns for many of the paralogues, together with poor sequence conservation between species, suggests that IFITM genes have acquired many different roles during vertebrate evolution.

  3. 12/10-Helical β-Peptide with Dynamic Folding Propensity: Coexistence of Right- and Left-Handed Helices in an Enantiomeric Foldamer.

    Science.gov (United States)

    Shin, Seonho; Lee, Mihye; Guzei, Ilia A; Kang, Young Kee; Choi, Soo Hyuk

    2016-10-12

    We present the first examples of atomic-resolution crystal data for the β-peptide 12/10-helix from oligomers of cis-2-aminocyclohexane carboxylic acid (cis-ACHC) with alternating chirality. The local conformations of two enantiomeric cis-ACHC dimer units suggested that a chiral β-peptide may adopt both right-handed and left-handed helical conformations in solution. To probe the conformational behavior of 12/10-helical β-peptides, the two reference helices with a single handedness were synthesized with a more rigidified cis-ACHC derivative. Comparison with these reference helices at low temperature revealed that a chiral cis-ACHC oligomer with alternating chirality indeed displays 12/10-helical conformations with both handedness that equilibrate rapidly in solution. This is a very rare example of chiral oligomers with helix inversion ability. The 12/10-helical backbone should be a valuable addition to potential scaffolds for applications involving helices with dynamic folding propensity.

  4. Probing the interaction mechanisms between transmembrane peptides and the chaperonin GroEL with fluorescence anisotropy

    Science.gov (United States)

    Wang, Xiaoqiang; Chen, Han; Lu, Xinwei; Chi, Haixia; Li, Shixin; Huang, Fang

    2018-04-01

    Proper translocation, membrane insertion and folding are crucial biophysical steps in the biogenesis of functional transmembrane peptides/proteins (TMPs). ATP-dependent chaperonins are able to regulate each of these processes, but the underlying mechanisms remain unclear. In this work, interaction between the bacterial chaperonin GroEL and a synthetic fluorescent transmembrane peptide was investigated by fluorescence anisotropy. Binding of the peptide with GroEL resulted in increased fluorescence anisotropy and intensity. The dissociation constant and binding stoichiometry, as assessed by titration of the peptide with GroEL, were estimated to be 0.6 ± 0.2 μM and 2.96 ± 0.35, respectively. Complementary study with the single-ring version of GroEL confirmed the high-affinity peptide binding, and indicates that the two GroEL rings may function alternatively in binding the peptides. The co-chaperonin GroES was found to be effective at releasing the peptides initially bound to GroEL with the help of ATP. Moreover, our observation with the single-ring GroEL mutant demonstrated that during the encapsulation of GroEL by GroES, the bound peptides may either be confined in the cage thus formed, or escape outside. Competitive binding experiments indicated that the peptides studied interact with GroEL through the paired helices H and I on its apical domain. Our spectroscopic studies revealed some basic mechanisms of interaction between transmembrane peptides and GroEL, which would be instrumental for deciphering the chaperonin-mediated TMP biogenesis.

  5. Magnetic helicity and active filament configuration

    Science.gov (United States)

    Romano, P.; Zuccarello, F.; Poedts, S.; Soenen, A.; Zuccarello, F. P.

    2009-11-01

    Context: The role of magnetic helicity in active filament formation and destabilization is still under debate. Aims: Although active filaments usually show a sigmoid shape and a twisted configuration before and during their eruption, it is unclear which mechanism leads to these topologies. In order to provide an observational contribution to clarify these issues, we describe a filament evolution whose characteristics seem to be directly linked to the magnetic helicity transport in corona. Methods: We applied different methods to determine the helicity sign and the chirality of the filament magnetic field. We also computed the magnetic helicity transport rate at the filament footpoints. Results: All the observational signatures provided information on the positive helicity and sinistral chirality of the flux rope containing the filament material: its forward S shape, the orientation of its barbs, the bright and dark threads at 195 Å. Moreover, the magnetic helicity transport rate at the filament footpoints showed a clear accumulation of positive helicity. Conclusions: The study of this event showed a correspondence between several signatures of the sinistral chirality of the filament and several evidences of the positive magnetic helicity of the filament magnetic field. We also found that the magnetic helicity transported along the filament footpoints showed an increase just before the change of the filament shape observed in Hα images. We argued that the photospheric regions where the filament was rooted might be the preferential ways where the magnetic helicity was injected along the filament itself and where the conditions to trigger the eruption were yielded.

  6. MemBrain: An Easy-to-Use Online Webserver for Transmembrane Protein Structure Prediction

    Science.gov (United States)

    Yin, Xi; Yang, Jing; Xiao, Feng; Yang, Yang; Shen, Hong-Bin

    2018-03-01

    Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels, transporters, receptors. Because it is difficult to determinate the membrane protein's structure by wet-lab experiments, accurate and fast amino acid sequence-based computational methods are highly desired. In this paper, we report an online prediction tool called MemBrain, whose input is the amino acid sequence. MemBrain consists of specialized modules for predicting transmembrane helices, residue-residue contacts and relative accessible surface area of α-helical membrane proteins. MemBrain achieves a prediction accuracy of 97.9% of A TMH, 87.1% of A P, 3.2 ± 3.0 of N-score, 3.1 ± 2.8 of C-score. MemBrain-Contact obtains 62%/64.1% prediction accuracy on training and independent dataset on top L/5 contact prediction, respectively. And MemBrain-Rasa achieves Pearson correlation coefficient of 0.733 and its mean absolute error of 13.593. These prediction results provide valuable hints for revealing the structure and function of membrane proteins. MemBrain web server is free for academic use and available at www.csbio.sjtu.edu.cn/bioinf/MemBrain/. [Figure not available: see fulltext.

  7. The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinity.

    Science.gov (United States)

    Johnson, Rachel M; Rath, Arianna; Deber, Charles M

    2006-12-01

    Although the intrinsic low solubility of membrane proteins presents challenges to their high-resolution structure determination, insight into the amino acid sequence features and forces that stabilize their folds has been provided through study of sequence-dependent helix-helix interactions between single transmembrane (TM) helices. While the stability of helix-helix partnerships mediated by the Gly-xxx-Gly (GG4) motif is known to be generally modulated by distal interfacial residues, it has not been established whether the position of this motif, with respect to the ends of a given TM segment, affects dimer affinity. Here we examine the relationship between motif position and affinity in the homodimers of 2 single-spanning membrane protein TM sequences: glycophorin A (GpA) and bacteriophage M13 coat protein (MCP). Using the TOXCAT assay for dimer affinity on a series of GpA and MCP TM segments that have been modified with either 4 Leu residues at each end or with 8 Leu residues at the N-terminal end, we show that in each protein, centrally located GG4 motifs are capable of stronger helix-helix interactions than those proximal to TM helix ends, even when surrounding interfacial residues are maintained. The relative importance of GG4 motifs in stabilizing helix-helix interactions therefore must be considered not only in its specific residue context but also in terms of the location of the interactive surface relative to the N and C termini of alpha-helical TM segments.

  8. Membrane-bound state of the colicin E1 channel domain as an extended two-dimensional helical array.

    Science.gov (United States)

    Zakharov, S D; Lindeberg, M; Griko, Y; Salamon, Z; Tollin, G; Prendergast, F G; Cramer, W A

    1998-04-14

    Atomic level structures have been determined for the soluble forms of several colicins and toxins, but the structural changes that occur after membrane binding have not been well characterized. Changes occurring in the transition from the soluble to membrane-bound state of the C-terminal 190-residue channel polypeptide of colicin E1 (P190) bound to anionic membranes are described. In the membrane-bound state, the alpha-helical content increases from 60-64% to 80-90%, with a concomitant increase in the average length of the helical segments from 12 to 16 or 17 residues, close to the length required to span the membrane bilayer in the open channel state. The average distance between helical segments is increased and interhelix interactions are weakened, as shown by a major loss of tertiary structure interactions, decreased efficiency of fluorescence resonance energy transfer from an energy donor on helix V of P190 to an acceptor on helix IX, and decreased resonance energy transfer at higher temperatures, not observed in soluble P190, implying freedom of motion of helical segments. Weaker interactions are also shown by a calorimetric thermal transition of low cooperativity, and the extended nature of the helical array is shown by a 3- to 4-fold increase in the average area subtended per molecule to 4,200 A2 on the membrane surface. The latter, with analysis of the heat capacity changes, implies the absence of a developed hydrophobic core in the membrane-bound P190. The membrane interfacial layer thus serves to promote formation of a highly helical extended two-dimensional flexible net. The properties of the membrane-bound state of the colicin channel domain (i.e., hydrophobic anchor, lengthened and loosely coupled alpha-helices, and close association with the membrane interfacial layer) are plausible structural features for the state that is a prerequisite for voltage gating, formation of transmembrane helices, and channel opening.

  9. New formulae for magnetic relative helicity and field line helicity

    Science.gov (United States)

    Aly, Jean-Jacques

    2018-01-01

    We consider a magnetic field {B} occupying the simply connected domain D and having all its field lines tied to the boundary S of D. We assume here that {B} has a simple topology, i.e., the mapping {M} from positive to negative polarity areas of S associating to each other the two footpoints of any magnetic line, is continuous. We first present new formulae for the helicity H of {B} relative to a reference field {{B}}r having the same normal component {B}n on S, and for its field line helicity h relative to a reference vector potential {{C}}r of {{B}}r. These formulae make immediately apparent the well known invariance of these quantities under all the ideal MHD deformations that preserve the positions of the footpoints on S. They express indeed h and H either in terms of {M} and {B}n, or in terms of the values on S of a pair of Euler potentials of {B}. We next show that, for a specific choice of {{C}}r, the field line helicity h of {B} fully characterizes the magnetic mapping {M} and then the topology of the lines. Finally, we give a formula that describes the rate of change of h in a situation where the plasma moves on the perfectly conducting boundary S without changing {B}n and/or non-ideal processes, described by an unspecified term {N} in Ohm’s law, are at work in some parts of D.

  10. Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix.

    Science.gov (United States)

    Hsin, Jen; LaPointe, Loren M; Kazy, Alla; Chipot, Christophe; Senes, Alessandro; Schulten, Klaus

    2011-09-07

    In the Rhodobacter (Rba.) species of photosynthetic purple bacteria, a single transmembrane α-helix, PufX, is found within the core complex, an essential photosynthetic macromolecular assembly that performs the absorption and the initial processing of light energy. Despite its structural simplicity, many unresolved questions surround PufX, the most important of which is its location within the photosynthetic core complex. One proposed placement of PufX is at the center of a core complex dimer, where two PufX helices associate in the membrane and form a homodimer. Inability for PufX of certain Rba. species to form a homodimer is thought to lead to monomeric core complexes. In the present study, we employ a combination of computational and experimental techniques to test the hypothesized homodimerization of PufX. We carry out a systematic investigation to measure the dimerization affinity of PufX from four Rba. species, Rba. blasticus , Rba. capsulatus , Rba. sphaeroides , and Rba. veldkampii , using a molecular dynamics-based free-energy method, as well as experimental TOXCAT assays. We found that the four PufX helices have substantially different dimerization affinities. Both computational and experimental techniques demonstrate that species with dimeric core complexes have PufX that can potentially form a homodimer, whereas the one species with monomeric core complexes has a PufX with little to no dimerization propensity. Our analysis of the helix-helix interface revealed a number of positions that may be important for PufX dimerization and the formation of a hydrogen-bond network between these GxxxG-containing helices. Our results suggest that the different oligomerization states of core complexes in various Rba. species can be attributed, among other factors, to the different propensity of its PufX helix to homodimerize.

  11. Employing helicity amplitudes for resummation in SCET

    International Nuclear Information System (INIS)

    Moult, Ian; Stewart, Iain W.; Tackmann, Frank J.; Waalewijn, Wouter J.; Nikhef, Amsterdam

    2016-05-01

    Helicity amplitudes are the fundamental ingredients of many QCD calculations for multi-leg processes. We describe how these can seamlessly be combined with resummation in Soft-Collinear Effective Theory (SCET), by constructing a helicity operator basis for which the Wilson coefficients are directly given in terms of color-ordered helicity amplitudes. This basis is crossing symmetric and has simple transformation properties under discrete symmetries.

  12. MHD stability analysis of helical system plasmas

    International Nuclear Information System (INIS)

    Nakamura, Yuji

    2000-01-01

    Several topics of the MHD stability studies in helical system plasmas are reviewed with respect to the linear and ideal modes mainly. Difference of the method of the MHD stability analysis in helical system plasmas from that in tokamak plasmas is emphasized. Lack of the cyclic (symmetric) coordinate makes an analysis more difficult. Recent topic about TAE modes in a helical system is also described briefly. (author)

  13. Tubular Unimolecular Transmembrane Channels: Construction Strategy and Transport Activities.

    Science.gov (United States)

    Si, Wen; Xin, Pengyang; Li, Zhan-Ting; Hou, Jun-Li

    2015-06-16

    Lipid bilayer membranes separate living cells from their environment. Membrane proteins are responsible for the processing of ion and molecular inputs and exports, sensing stimuli and signals across the bilayers, which may operate in a channel or carrier mechanism. Inspired by these wide-ranging functions of membrane proteins, chemists have made great efforts in constructing synthetic mimics in order to understand the transport mechanisms, create materials for separation, and develop therapeutic agents. Since the report of an alkylated cyclodextrin for transporting Cu(2+) and Co(2+) by Tabushi and co-workers in 1982, chemists have constructed a variety of artificial transmembrane channels by making use of either the multimolecular self-assembly or unimolecular strategy. In the context of the design of unimolecular channels, important advances have been made, including, among others, the tethering of natural gramicidin A or alamethicin and the modification of various macrocycles such as crown ethers, cyclodextrins, calixarenes, and cucurbiturils. Many of these unimolecular channels exhibit high transport ability for metal ions, particularly K(+) and Na(+). Concerning the development of artificial channels based on macrocyclic frameworks, one straightforward and efficient approach is to introduce discrete chains to reinforce their capability to insert into bilayers. Currently, this approach has found the widest applications in the systems of crown ethers and calixarenes. We envisioned that for macrocycle-based unimolecular channels, control of the arrangement of the appended chains in the upward and/or downward direction would favor the insertion of the molecular systems into bilayers, while the introduction of additional interactions among the chains would further stabilize a tubular conformation. Both factors should be helpful for the formation of new efficient channels. In this Account, we discuss our efforts in designing new unimolecular artificial channels from

  14. Transmembrane protein sorting driven by membrane curvature

    Science.gov (United States)

    Strahl, H.; Ronneau, S.; González, B. Solana; Klutsch, D.; Schaffner-Barbero, C.; Hamoen, L. W.

    2015-11-01

    The intricate structure of prokaryotic and eukaryotic cells depends on the ability to target proteins to specific cellular locations. In most cases, we have a poor understanding of the underlying mechanisms. A typical example is the assembly of bacterial chemoreceptors at cell poles. Here we show that the classical chemoreceptor TlpA of Bacillus subtilis does not localize according to the consensus stochastic nucleation mechanism but accumulates at strongly curved membrane areas generated during cell division. This preference was confirmed by accumulation at non-septal curved membranes. Localization appears to be an intrinsic property of the protein complex and does not rely on chemoreceptor clustering, as was previously shown for Escherichia coli. By constructing specific amino-acid substitutions, we demonstrate that the preference for strongly curved membranes arises from the curved shape of chemoreceptor trimer of dimers. These findings demonstrate that the intrinsic shape of transmembrane proteins can determine their cellular localization.

  15. Virus-Encoded 7 Transmembrane Receptors

    DEFF Research Database (Denmark)

    Mølleskov-Jensen, Ann-Sofie; Oliveira, MarthaTrindade; Farrell, Helen Elizabeth

    2015-01-01

    have acquired a range of distinctive characteristics. This chapter reviews key features of the v7TMRs which are likely to impact upon their functional roles: trafficking properties, ligand specificity, and signaling capacity. Rapid, constitutive endocytosis, reminiscent of cellular “scavenger......Herpesviruses are an ancient group which have exploited gene capture of multiple cellular modulators of the immune response. Viral homologues of 7 transmembrane receptors (v7TMRs) are a consistent feature of beta- and gammaherpesviruses; the majority of the v7TMRs are homologous to cellular...... chemokine receptors (CKRs). Conserved families of v7TMRs distinguish between beta- versus gammaherpesviruses; furthermore, significant divisions within these subfamilies, such as between genera of the gammaherpesviruses or between the primate and rodent cytomegaloviruses, coincide with specific v7TMR gene...

  16. Molecular mechanisms for generating transmembrane proton gradients

    Science.gov (United States)

    Gunner, M.R.; Amin, Muhamed; Zhu, Xuyu; Lu, Jianxun

    2013-01-01

    Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side. PMID:23507617

  17. Phases in holographic helical superconductor

    Science.gov (United States)

    Mukhopadhyay, Subir; Paul, Chandrima

    2017-05-01

    We study SU(2)×U(1) gauge theory with Chern-Simons term, coupled to scalar field in adjoint, in a probe approximation by ignoring back reaction on metric. Considering a simple ansatz for non-Abelian gauge field with helical structure, we find it admits s-wave and p-wave phases along with their coexistence. We study free energies for different phases along with those for p-wave phases for different values of pitch and frequency dependence of optical conductivities below critical temperature.

  18. Role of Side-Chain Conformational Entropy in Transmembrane Helix Dimerization of Glycophorin A

    Science.gov (United States)

    Liu, Wei; Crocker, Evan; Siminovitch, David J.; Smith, Steven O.

    2003-01-01

    Dimerization of the transmembrane domain of glycophorin A is mediated by a seven residue motif LIxxGVxxGVxxT through a combination of van der Waals and hydrogen bonding interactions. One of the unusual features of the motif is the large number of β-branched amino acids that may limit the entropic cost of dimerization by restricting side-chain motion in the monomeric transmembrane helix. Deuterium NMR spectroscopy is used to characterize the dynamics of fully deuterated Val80 and Val84, two essential amino acids of the dimerization motif. Deuterium spectra of the glycophorin A transmembrane dimer were obtained using synthetic peptides corresponding to the transmembrane sequence containing either perdeuterated Val80 or Val84. These data were compared with spectra of monomeric glycophorin A peptides deuterated at Val84. In all cases, the deuterium line shapes are characterized by fast methyl group rotation with virtually no motion about the Cα-Cβ bond. This is consistent with restriction of the side chain in both the monomer and dimer due to intrahelical packing interactions involving the β-methyl groups, and indicates that there is no energy cost associated with dimerization due to loss of conformational entropy. In contrast, deuterium NMR spectra of Met81 and Val82, in the lipid interface, reflected greater motional averaging and fast exchange between different side-chain conformers. PMID:12547806

  19. Structural insights into triglyceride storage mediated by fat storage-inducing transmembrane (FIT protein 2.

    Directory of Open Access Journals (Sweden)

    David A Gross

    2010-05-01

    Full Text Available Fat storage-Inducing Transmembrane proteins 1 & 2 (FIT1/FITM1 and FIT2/FITM2 belong to a unique family of evolutionarily conserved proteins localized to the endoplasmic reticulum that are involved in triglyceride lipid droplet formation. FIT proteins have been shown to mediate the partitioning of cellular triglyceride into lipid droplets, but not triglyceride biosynthesis. FIT proteins do not share primary sequence homology with known proteins and no structural information is available to inform on the mechanism by which FIT proteins function. Here, we present the experimentally-solved topological models for FIT1 and FIT2 using N-glycosylation site mapping and indirect immunofluorescence techniques. These methods indicate that both proteins have six-transmembrane-domains with both N- and C-termini localized to the cytosol. Utilizing this model for structure-function analysis, we identified and characterized a gain-of-function mutant of FIT2 (FLL(157-9AAA in transmembrane domain 4 that markedly augmented the total number and mean size of lipid droplets. Using limited-trypsin proteolysis we determined that the FLL(157-9AAA mutant has enhanced trypsin cleavage at K86 relative to wild-type FIT2, indicating a conformational change. Taken together, these studies indicate that FIT2 is a 6 transmembrane domain-containing protein whose conformation likely regulates its activity in mediating lipid droplet formation.

  20. Field-theoretic calculation of kinetic helicity flux

    Indian Academy of Sciences (India)

    In the inertial range the kinetic helicity flux is found to be constant and forward. The universal constant KH appearing in the spectrum of kinetic helicity was found to be. 2.47. Keywords. Kinetic helicity; helical turbulence. PACS Nos 47.27.Ak; 47.27.Gs. Kinetic helicity plays an important role in the dynamics of turbulence.

  1. Helicity amplitudes for massive gravitinos in { N }=1 supergravity

    Science.gov (United States)

    Diaz-Cruz, J. Lorenzo; Larios, Bryan O.

    2018-01-01

    We develop the formal tools needed to construct helicity amplitudes for massive gravitinos in { N }=1 supergravity. We start by considering the helicity states for massive spin-3/2 particles, which involve the solutions of the Rarita-Schwinger equation. These solutions are written using the modern spinor bra-ket notation and are then used to derive the interactions of gravitinos with matter and gauge supermultiplets within { N }=1 supergravity. The corresponding interactions of goldstinos are discussed too, with the help of the goldstino-gravitino equivalence theorem. The methods are then applied to calculate the production and decays involving the gravitino, namely for: {e}+{e}-\\to \\tilde{G}\\tilde{G},{\\tilde{{{\\Psi }}}}μ {\\tilde{χ }}0 and {\\tilde{χ }}0\\to {\\tilde{{{\\Psi }}}}μ +γ . The neutralino decay is then used to compare the precision of the equivalence goldstino approximation.

  2. The free-boundary equilibrium problem for helically symmetric plasmas

    International Nuclear Information System (INIS)

    Gardner, H.J.; Dewar, R.L.; Sy, W.N-C.

    1987-05-01

    An iterative technique for solving the ideal MHD equilibrium equations for a helically symmetric plasma with a free boundary is described. The method involves an application of Green's theorem and has been formulated for the geometry of a heliac. It is used to determine a stability diagram for the SHEILA heliac as a function of the plasma pressure and the current in one of the external coils

  3. Trefoil knot timescales for reconnection and helicity

    Science.gov (United States)

    Kerr, Robert M.

    2018-02-01

    Three-dimensional images of evolving numerical trefoil vortex knots are used to study the growth and decay of the enstrophy and helicity. Negative helicity density (hhydrofoil models is used to correct the published experimental circulations Γ that use only the flat-plate approximation.

  4. Generalized helicity and its time derivative

    International Nuclear Information System (INIS)

    Jarboe, T.R.; Marklin, G.J.

    1986-01-01

    Spheromaks can be sustained against resistive decay by helicity injection because they tend to obey the minimum energy principle. This principle states that a plasma-laden magnetic configuration will relax to a state of minimum energy subject to the constraint that the magnetic helicity is conserved. Use of helicity as a constraint on the minimization of energy was first proposed by Woltjer in connection with astrophysical phenomena. Use of the helicity constraint was first applied to the spheromak by Wells and Norwood. The principle was later applied to the reversed-field pinch (RFP) by Taylor, who was most responsible for the eventual acceptance and recognition of the principle as being important for RFP-type confinement devices. Of course, helicity does decay on the resistive diffusion time. However, if helicity is created and made to flow continuously into a confinement geometry, these additional linked fluxes can relax and sustain the configuration indefinitely against the resistive decay. In this paper an extension of the definition of helicity to include systems where B can penetrate the boundary and the penetration can be varying in time is presented. The sustainment of RFPs and spheromaks in terms of helicity injection is discussed

  5. Guided Transport of a Transmembrane Nanochannel

    Science.gov (United States)

    Dutt, Meenakshi; Kuksenok, Olga; Balazs, Anna

    2011-03-01

    Via the Dissipative Particle Dynamics approach, we design a system that allows transport of a nanochannel to a desired location by applying an external force. Each nanochannel encompasses an ABA architecture, with a hydrophobic shaft (B) with two hydrophilic ends (A). One of the hydrophilic ends of the nanochannel is functionalized with hydrophilic functional groups, or hairs. The hydrophilic hairs serve a dual role: (1) control transport across the membrane barrier when the channel diffuses freely in the membrane, and (2) enable the channel relocation to a specific membrane site. Our system comprises a transmembrane hairy nanochannel with the hairs extending into solution. In our earlier work, we demonstrated the spontaneous insertion of such a hairy nanochannel into a lipid bilayer (Nanoscale DOI: 10.1039/C0NR00578A). First, we hold a suitably functionalized pipette stationary above the membrane while the nanochannel freely diffuses within the membrane. For an optimal range of parameters, we demonstrate that the hairs find the pipette and spontaneously anchor onto it. We then show that by moving the pipette for a range of velocities, we can effectively transport the channel to any location within the membrane. This prototype system can provide guidelines for designing a number of biomimetic applications.

  6. Asymptotic Helicity Conservation in SUSY

    CERN Document Server

    Gounaris, G J; Renard, F M

    2010-01-01

    We summarize the extensive work started in ref.1, according to which total helicity is conserved for any two-to-two process, at sqrt{s} larger than M_{SUSY} and fixed angles, in any SUSY extension of SM. Asymptotically the theorem is exact. But it may also have important implications at lower energies sqrt{s} close to M_{SUSY}. Up to now, these have been investigated to 1loop electroweak (EW) order for the processes ug to d W+, sd_L chi+; as well as the 17 gg to HH', and the 9 gg to VH processes, where H,H' denote Higgs or Goldstone bosons, and V=Z, W.

  7. Topology of helical fluid flow

    DEFF Research Database (Denmark)

    Andersen, Morten; Brøns, Morten

    2014-01-01

    Phys. Fluids 25, 1949–1952) contains an infinite sum of modified Bessel functions. Using the approach by Okulov (Okulov, V. L. 1995 Russ. J. Eng. Thermophys. 5, 63–75) we obtain a closed-form approximation which is considerably easier to analyse. Critical points of the stream function can be found from...... function for the topology of the streamline pattern in incompressible flows. On this basis, we perform a comprehensive study of the topology of the flow field generated by a helical vortex filament in an ideal fluid. The classical expression for the stream function obtained by Hardin (Hardin, J. C. 1982...... the zeroes of a single real function of one variable, and we show that three different flow topologies can occur, depending on a single dimensionless parameter. By including the self-induced velocity on the vortex filament by a localised induction approximation, the stream function is slightly modified...

  8. On the diffusion of alpha-helical proteins in solvents

    Science.gov (United States)

    Barredo, Wilson I.; Bornales, Jinky B.; Bernido, Christopher C.; Aringa, Henry P.

    2015-01-01

    The winding probability function for a biopolymer diffusing in a crowded cell is obtained with the drift coefficient f(s) involving Bessel functions of general form f(s) = kJ2p+1 (νs). The variable s is the length along the chain and ν is a constant which can be used to simulate the frequency of appearance of a certain type of amino acid. Application of a particular case p = 3 to protein chains is carried out for different alpha helical proteins found in the Protein Data Bank (PDB). Analysis of our results leads us to an empirical formula that can be used to conveniently predict k/D and ν, where D is the diffusion coefficient of various α-helical proteins in solvents.

  9. Alternative function for the mitochondrial SAM complex in biogenesis of alpha-helical TOM proteins.

    Science.gov (United States)

    Stojanovski, Diana; Guiard, Bernard; Kozjak-Pavlovic, Vera; Pfanner, Nikolaus; Meisinger, Chris

    2007-12-03

    The mitochondrial outer membrane contains two preprotein translocases: the general translocase of outer membrane (TOM) and the beta-barrel-specific sorting and assembly machinery (SAM). TOM functions as the central entry gate for nuclear-encoded proteins. The channel-forming Tom40 is a beta-barrel protein, whereas all Tom receptors and small Tom proteins are membrane anchored by a transmembrane alpha-helical segment in their N- or C-terminal portion. Synthesis of Tom precursors takes place in the cytosol, and their import occurs via preexisting TOM complexes. The precursor of Tom40 is then transferred to SAM for membrane insertion and assembly. Unexpectedly, we find that the biogenesis of alpha-helical Tom proteins with a membrane anchor in the C-terminal portion is SAM dependent. Each SAM protein is necessary for efficient membrane integration of the receptor Tom22, whereas assembly of the small Tom proteins depends on Sam37. Thus, the substrate specificity of SAM is not restricted to beta-barrel proteins but also includes the majority of alpha-helical Tom proteins.

  10. Evidence for Mixed Helicity in Erupting Filaments

    Science.gov (United States)

    Muglach, K.; Wang, Y.-M.; Kliem, B.

    2009-09-01

    Erupting filaments are sometimes observed to undergo a rotation about the vertical direction as they rise. This rotation of the filament axis is generally interpreted as a conversion of twist into writhe in a kink-unstable magnetic flux rope. Consistent with this interpretation, the rotation is usually found to be clockwise (as viewed from above) if the post-eruption arcade has right-handed helicity, but counterclockwise if it has left-handed helicity. Here, we describe two non-active-region filament events recorded with the Extreme-Ultraviolet Imaging Telescope on the Solar and Heliospheric Observatory in which the sense of rotation appears to be opposite to that expected from the helicity of the post-event arcade. Based on these observations, we suggest that the rotation of the filament axis is, in general, determined by the net helicity of the erupting system, and that the axially aligned core of the filament can have the opposite helicity sign to the surrounding field. In most cases, the surrounding field provides the main contribution to the net helicity. In the events reported here, however, the helicity associated with the filament "barbs" is opposite in sign to and dominates that of the overlying arcade.

  11. A Dimeric Bis(melamine)-Substituted Bispidine for Efficient Transmembrane H+/Cl-Cotransport.

    Science.gov (United States)

    Shinde, Sopan Valiba; Talukdar, Pinaki

    2017-04-03

    A 3,7-diazabicyclo[3.3.1]nonane linking to two melamines is a unique transmembrane H + /Cl - carrier. In the solid state, the V-shaped compound forms a HCl-bound zig-zag network through cooperative protonation and hydrogen bond interactions. In the lipid membrane, the receptor forms a dimeric self-assembly involving multiple H + and Cl - leading to the efficient transport of the acid. The pH-dependent Cl - efflux observed for the compound was rationalized based on a gradual protonation model that confers an active transmembrane carrier at physiological pH. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. [Research advances in CKLF-like MARVEL transmembrane domain containing member 5].

    Science.gov (United States)

    Yuan, Ye-qing; Xiao, Yun-bei; Liu, Zhen-hua; Zhang, Xiao-wei; Xu, Tao; Wang, Xiao-feng

    2012-12-01

    CKLF-like MARVEL transmembrane domain containing member(CMTM)is a novel generic family firstly reported by Peking University Center for Human Disease Genomics. CMTM5 belongs to this family and has exhibited tumor-inhibiting activities. It can encode proteins approaching to the transmembrane 4 superfamily(TM4SF). CMTM5 is broadly expressed in normal adult and fetal human tissues, but is undetectable or down-regulated in most carcinoma cell lines and tissues. Restoration of CMTM5 may inhibit the proliferation, migration, and invasion of carcinoma cells. Although the exact mechanism of its anti-tumor activity remains unclear, CMTM5 may be involved in various signaling pathways governing the occurrence and development of tumors. CMTM5 may be a new target in the gene therapies for tumors, while further studies on CMTM5 and its anti-tumor mechanisms are warranted.

  13. Modeling Transmembrane Domain Dimers/Trimers of Plexin Receptors: Implications for Mechanisms of Signal Transmission across the Membrane

    Science.gov (United States)

    Zhang, Liqun; Polyansky, Anton; Buck, Matthias

    2015-01-01

    Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and –B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, –A3, -A4, -C1 and –D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 – trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures

  14. Helical magnetized wiggler for synchrotron radiation laser

    CERN Document Server

    Wang Mei; Hirshfield, J L

    1999-01-01

    A helical magnetized iron wiggler has been built for a novel infrared synchrotron radiation laser (SRL) experiment. The wiggler consists of four periods of helical iron structure immersed in a solenoid field. This wiggler is to impart transverse velocity to a prebunched 6 MeV electron beam, and thus to obtain a desired high orbit pitch ratio for the SRL. Field tapering at beam entrance is considered and tested on a similar wiggler. Analytic and simulated characteristics of wigglers of this type are discussed and the performance of the fabricated wigglers is demonstrated experimentally. A 4.7 kG peak field was measured for a 6.4 mm air gap and a 5.4 cm wiggler period at a 20 kG solenoid field. The measured helical fields compare favorably with the analytical solution. This type of helical iron wigglers has the potential to be scaled to small periods with strong field amplitude.

  15. Helical magnetized wiggler for synchrotron radiation laser

    International Nuclear Information System (INIS)

    Wang Mei; Park, S.Y.; Hirshfield, J.L.

    1999-01-01

    A helical magnetized iron wiggler has been built for a novel infrared synchrotron radiation laser (SRL) experiment. The wiggler consists of four periods of helical iron structure immersed in a solenoid field. This wiggler is to impart transverse velocity to a prebunched 6 MeV electron beam, and thus to obtain a desired high orbit pitch ratio for the SRL. Field tapering at beam entrance is considered and tested on a similar wiggler. Analytic and simulated characteristics of wigglers of this type are discussed and the performance of the fabricated wigglers is demonstrated experimentally. A 4.7 kG peak field was measured for a 6.4 mm air gap and a 5.4 cm wiggler period at a 20 kG solenoid field. The measured helical fields compare favorably with the analytical solution. This type of helical iron wigglers has the potential to be scaled to small periods with strong field amplitude

  16. Helicity and Filament Channels? The Straight Twist!

    Science.gov (United States)

    Antiochos, Spiro K.

    2010-01-01

    One of the most important and most puzzling features of the coronal magnetic field is that it appears to have smooth magnetic structure with little evidence for non-potentiality except at special locations, photospheric polarity inversions lines where the non-potentiality is observed as a filament channel. This characteristic feature of the closed-field corona is highly unexpected given that photospheric motions continuously tangle its magnetic field. Although reconnection can eliminate some of the injected structure, it cannot destroy the helicity, which should build up to produce observable complexity. We propose that an inverse cascade process transports the injected helicity from the interior of closed flux regions to their boundaries, polarity inversion lines, creating filament channels. We describe how the helicity is injected and transported and calculate the relevant rates. We argue that one process, helicity transport, can explain both the observed lack and presence of structure in the coronal magnetic field.

  17. Flow-induced vibration of helical coil compression springs

    International Nuclear Information System (INIS)

    Stokes, F.E.; King, R.A.

    1983-01-01

    Helical coil compression springs are used in some nuclear fuel assembly designs to maintain holddown and to accommodate thermal expansion. In the reactor environment, the springs are exposed to flowing water, elevated temperatures and pressures, and irradiation. Flow parallel to the longitudinal axis of the spring may excite the spring coils and cause vibration. The purpose of this investigation was to determine the flow-induced vibration (FIV) response characteristics of the helical coil compression springs. Experimental tests indicate that a helical coil spring responds like a single circular cylinder in cross-flow. Two FIV excitation mechanisms control spring vibration. Namely: 1) Turbulent Buffeting causes small amplitude vibration which increases as a function of velocity squared. 2) Vortex Shedding causes large amplitude vibration when the spring natural frequency and Strouhal frequency coincide. Several methods can be used to reduce or to prevent vortex shedding large amplitude vibrations. One method is compressing the spring to a coil pitch-to-diameter ratio of 2 thereby suppressing the vibration amplitude. Another involves modifying the spring geometry to alter its stiffness and frequency characteristics. These changes result in separation of the natural and Strouhal frequencies. With an understanding of how springs respond in the flowing water environment, the spring physical parameters can be designed to avoid large amplitude vibration. (orig.)

  18. Predicting helical topologies in RNA junctions as tree graphs.

    Directory of Open Access Journals (Sweden)

    Christian Laing

    Full Text Available RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires knowledge of their tertiary structures. Though computational RNA folding approaches exist, they often require manual manipulation and expert intuition; predicting global long-range tertiary contacts remains challenging. Here we develop a computational approach and associated program module (RNAJAG to predict helical arrangements/topologies in RNA junctions. Our method has two components: junction topology prediction and graph modeling. First, junction topologies are determined by a data mining approach from a given secondary structure of the target RNAs; second, the predicted topology is used to construct a tree graph consistent with geometric preferences analyzed from solved RNAs. The predicted graphs, which model the helical arrangements of RNA junctions for a large set of 200 junctions using a cross validation procedure, yield fairly good representations compared to the helical configurations in native RNAs, and can be further used to develop all-atom models as we show for two examples. Because junctions are among the most complex structural elements in RNA, this work advances folding structure prediction methods of large RNAs. The RNAJAG module is available to academic users upon request.

  19. Predicting helical topologies in RNA junctions as tree graphs.

    Science.gov (United States)

    Laing, Christian; Jung, Segun; Kim, Namhee; Elmetwaly, Shereef; Zahran, Mai; Schlick, Tamar

    2013-01-01

    RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires knowledge of their tertiary structures. Though computational RNA folding approaches exist, they often require manual manipulation and expert intuition; predicting global long-range tertiary contacts remains challenging. Here we develop a computational approach and associated program module (RNAJAG) to predict helical arrangements/topologies in RNA junctions. Our method has two components: junction topology prediction and graph modeling. First, junction topologies are determined by a data mining approach from a given secondary structure of the target RNAs; second, the predicted topology is used to construct a tree graph consistent with geometric preferences analyzed from solved RNAs. The predicted graphs, which model the helical arrangements of RNA junctions for a large set of 200 junctions using a cross validation procedure, yield fairly good representations compared to the helical configurations in native RNAs, and can be further used to develop all-atom models as we show for two examples. Because junctions are among the most complex structural elements in RNA, this work advances folding structure prediction methods of large RNAs. The RNAJAG module is available to academic users upon request.

  20. From plasma crystals and helical structures towards inorganic living matter

    International Nuclear Information System (INIS)

    Tsytovich, V N; Morfill, G E; Fortov, V E; Gusein-Zade, N G; Klumov, B A; Vladimirov, S V

    2007-01-01

    Complex plasmas may naturally self-organize themselves into stable interacting helical structures that exhibit features normally attributed to organic living matter. The self-organization is based on non-trivial physical mechanisms of plasma interactions involving over-screening of plasma polarization. As a result, each helical string composed of solid microparticles is topologically and dynamically controlled by plasma fluxes leading to particle charging and over-screening, the latter providing attraction even among helical strings of the same charge sign. These interacting complex structures exhibit thermodynamic and evolutionary features thought to be peculiar only to living matter such as bifurcations that serve as 'memory marks', self-duplication, metabolic rates in a thermodynamically open system, and non-Hamiltonian dynamics. We examine the salient features of this new complex 'state of soft matter' in light of the autonomy, evolution, progenity and autopoiesis principles used to define life. It is concluded that complex self-organized plasma structures exhibit all the necessary properties to qualify them as candidates for inorganic living matter that may exist in space provided certain conditions allow them to evolve naturally

  1. Predicting Helical Topologies in RNA Junctions as Tree Graphs

    Science.gov (United States)

    Kim, Namhee; Elmetwaly, Shereef; Zahran, Mai; Schlick, Tamar

    2013-01-01

    RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires knowledge of their tertiary structures. Though computational RNA folding approaches exist, they often require manual manipulation and expert intuition; predicting global long-range tertiary contacts remains challenging. Here we develop a computational approach and associated program module (RNAJAG) to predict helical arrangements/topologies in RNA junctions. Our method has two components: junction topology prediction and graph modeling. First, junction topologies are determined by a data mining approach from a given secondary structure of the target RNAs; second, the predicted topology is used to construct a tree graph consistent with geometric preferences analyzed from solved RNAs. The predicted graphs, which model the helical arrangements of RNA junctions for a large set of 200 junctions using a cross validation procedure, yield fairly good representations compared to the helical configurations in native RNAs, and can be further used to develop all-atom models as we show for two examples. Because junctions are among the most complex structural elements in RNA, this work advances folding structure prediction methods of large RNAs. The RNAJAG module is available to academic users upon request. PMID:23991010

  2. Helicity evolution at small x

    International Nuclear Information System (INIS)

    Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

    2016-01-01

    We construct small-x evolution equations which can be used to calculate quark and anti-quark helicity TMDs and PDFs, along with the g 1 structure function. These evolution equations resum powers of α s ln 2  (1/x) in the polarization-dependent evolution along with the powers of α s ln (1/x) in the unpolarized evolution which includes saturation effects. The equations are written in an operator form in terms of polarization-dependent Wilson line-like operators. While the equations do not close in general, they become closed and self-contained systems of non-linear equations in the large-N c and large-N c   N f limits. As a cross-check, in the ladder approximation, our equations map onto the same ladder limit of the infrared evolution equations for the g 1 structure function derived previously by Bartels, Ermolaev and Ryskin http://dx.doi.org/10.1007/s002880050285.

  3. Multiple helical modes of vortex breakdown

    DEFF Research Database (Denmark)

    Sørensen, Jens Nørkær; Naumov, I. V.; Okulov, Valery

    2011-01-01

    Experimental observations of vortex breakdown in a rotating lid-driven cavity are presented. The results show that vortex breakdown for cavities with high aspect ratios is associated with the appearance of stable helical vortex multiplets. By using results from stability theory generalizing Kelvin......’s problem on vortex polygon stability, and systematically exploring the cavity flow, we succeeded in identifying two new stable vortex breakdown states consisting of triple and quadruple helical multiplets....

  4. Dynamics of helicity transport and Taylor relaxation

    International Nuclear Information System (INIS)

    Diamond, P.H.; Malkov, M.

    2003-01-01

    A simple model of the dynamics of Taylor relaxation is derived using symmetry principles alone. No statistical closure approximations are invoked or detailed plasma model properties assumed. Notably, the model predicts several classes of nondiffusive helicity transport phenomena, including traveling nonlinear waves and superdiffusive turbulent pulses. A universal expression for the scaling of the effective magnetic Reynolds number of a system undergoing Taylor relaxation is derived. Some basic properties of intermittency in helicity transport are examined

  5. Lumineszierende zweikernig dreisträngige Helicate

    OpenAIRE

    Schmid, Sören

    2005-01-01

    Luminescent triple-stranded dinuclear helicates The building of systems showing a special function or a property that makes them suitable for the preparation of functional materials will become more and more important in the next years. Based on the "bottom-up approach" supramolecular chemistry can play an important part on this field. This work deals with the building and examination of triple-stranded dinuclear helicates. By using special ligand systems and metals, it its possible to give t...

  6. The helical flow pump with a hydrodynamic levitation impeller.

    Science.gov (United States)

    Abe, Yusuke; Ishii, Kohei; Isoyama, Takashi; Saito, Itsuro; Inoue, Yusuke; Ono, Toshiya; Nakagawa, Hidemoto; Nakano, Emiko; Fukazawa, Kyoko; Ishihara, Kazuhiko; Fukunaga, Kazuyoshi; Ono, Minoru; Imachi, Kou

    2012-12-01

    The helical flow pump (HFP) is a novel rotary blood pump invented for developing a total artificial heart (TAH). The HFP with a hydrodynamic levitation impeller, which consists of a multi-vane impeller involving rotor magnets, stator coils at the core position, and double helical-volute pump housing, was developed. Between the stator and impeller, a hydrodynamic bearing is formed. Since the helical volutes are formed at both sides of the impeller, blood flows with a helical flow pattern inside the pump. The developed HFP showed maximum output of 19 l/min against 100 mmHg of pressure head and 11 % maximum efficiency. The profile of the H-Q (pressure head vs. flow) curve was similar to that of the undulation pump. Hydrodynamic levitation of the impeller was possible with higher than 1,000 rpm rotation speed. The normalized index of the hemolysis ratio of the HFP to centrifugal pump (BPX-80) was from 2.61 to 8.07 depending on the design of the bearing. The HFP was implanted in two goats with a left ventricular bypass method. After surgery, hemolysis occurred in both goats. The hemolysis ceased on postoperative days 14 and 9, respectively. In the first experiment, no thrombus was found in the pump after 203 days of pumping. In the second experiment, a white thrombus was found in the pump after 23 days of pumping. While further research and development are necessary, we are expecting to develop an excellent TAH with the HFP.

  7. Intrahepatic arterioportal shunt: helical CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Quiroga, S.; Sebastia, M.C.; Moreiras, M.; Pallisa, E.; Rius, J.M.; Alvarez-Castells, A. [I. D. I. Hospital General i Universitari Vall d`Hebron, Barcelona (Spain). Servei de Radiodiagnostic

    1999-08-01

    The purpose of this study was to characterize the appearance of intrahepatic arterioportal shunts (APS) on two-phase helical CT, with emphasis on the importance of the hepatic arterial-dominant phase (HAP) to demonstrate perfusion disorders. We review eight cases of APS diagnosed by helical CT in our institution from January 1996 to March 1997 and describe the CT findings that established diagnosis. Five of them were confirmed by angiography. In seven (87.5 %) cases of APS we found early enhancement of the peripheral portal branches during the HAP of helical CT, whereas the superior mesenteric and splenic veins remained unenhanced. In five (62.5 %) cases of APS, transient, peripheral, triangular parenchymal enhancement was depicted during the HAP of helical CT; in four of these cases there was associated early enhancement of the portal branches. Helical CT can show perfusion alterations that might remain undiagnosed with conventional CT. An understanding of the hemodynamic changes that occur in APS can help in the interpretation of focal transient hepatic parenchymal enhancement and to differentiate APS from hypervascular tumors. We believe that the helical CT findings described herein are characteristic enough to suggest the diagnosis of APS. (orig.) With 3 figs., 1 tab., 16 refs.

  8. Activation of the bacterial thermosensor DesK involves a serine zipper dimerization motif that is modulated by bilayer thickness.

    Science.gov (United States)

    Cybulski, Larisa Estefanía; Ballering, Joost; Moussatova, Anastassiia; Inda, Maria Eugenia; Vazquez, Daniela B; Wassenaar, Tsjerk A; de Mendoza, Diego; Tieleman, D Peter; Killian, J Antoinette

    2015-05-19

    DesK is a bacterial thermosensor protein involved in maintaining membrane fluidity in response to changes in environmental temperature. Most likely, the protein is activated by changes in membrane thickness, but the molecular mechanism of sensing and signaling is still poorly understood. Here we aimed to elucidate the mode of action of DesK by studying the so-called "minimal sensor DesK" (MS-DesK), in which sensing and signaling are captured in a single transmembrane segment. This simplified version of the sensor allows investigation of membrane thickness-dependent protein-lipid interactions simply by using synthetic peptides, corresponding to the membrane-spanning parts of functional and nonfunctional mutants of MS-DesK incorporated in lipid bilayers with varying thicknesses. The lipid-dependent behavior of the peptides was investigated by circular dichroism, tryptophan fluorescence, and molecular modeling. These experiments were complemented with in vivo functional studies on MS-DesK mutants. Based on the results, we constructed a model that suggests a new mechanism for sensing in which the protein is present as a dimer and responds to an increase in bilayer thickness by membrane incorporation of a C-terminal hydrophilic motif. This results in exposure of three serines on the same side of the transmembrane helices of MS-DesK, triggering a switching of the dimerization interface to allow the formation of a serine zipper. The final result is activation of the kinase state of MS-DesK.

  9. Pentameric ligand-gated ion channels exhibit distinct transmembrane domain archetypes for folding/expression and function.

    Science.gov (United States)

    Therien, J P Daniel; Baenziger, John E

    2017-03-27

    Although transmembrane helix-helix interactions must be strong enough to drive folding, they must still permit the inter-helix movements associated with conformational change. Interactions between the outermost M4 and adjacent M1 and M3 α-helices of pentameric ligand-gated ion channels have been implicated in folding and function. Here, we evaluate the role of different physical interactions at this interface in the function of two prokaryotic homologs, GLIC and ELIC. Strikingly, disruption of most interactions in GLIC lead to either a reduction or a complete loss of expression and/or function, while analogous disruptions in ELIC often lead to gains in function. Structural comparisons suggest that GLIC and ELIC represent distinct transmembrane domain archetypes. One archetype, exemplified by GLIC, the glycine and GABA receptors and the glutamate activated chloride channel, has extensive aromatic contacts that govern M4-M1/M3 interactions and that are essential for expression and function. The other archetype, exemplified by ELIC and both the nicotinic acetylcholine and serotonin receptors, has relatively few aromatic contacts that are detrimental to function. These archetypes likely have evolved different mechanisms to balance the need for strong M4 "binding" to M1/M3 to promote folding/expression, and the need for weaker interactions that allow for greater conformational flexibility.

  10. Assessment of the transmembrane domain structures in GPCR Dock 2013 models.

    Science.gov (United States)

    Wang, Ting; Liu, Haiguang; Duan, Yong

    2018-03-01

    The community-wide blind prediction of G-protein coupled receptor (GPCR) structures and ligand docking has been conducted three times and the quality of the models was primarily assessed by the accuracy of ligand binding modes. The seven transmembrane (TM) helices of the receptors were taken as a whole; thus the model quality within the 7TM domains has not been evaluated. Here we evaluate the 7TM domain structures in the models submitted for the last round of prediction - GPCR Dock 2013. Applying the 7 × 7 RMSD matrix analysis described in our prior work, we show that the models vary widely in prediction accuracy of the 7TM structures, exhibiting diverse structural differences from the targets. For the prediction of the 5-hydroxytryptamine receptors, the top 7TM models are rather close to the targets, which however are not ranked top by ligand-docking. On the other hand, notable deviations of the TMs are found in in the previously identified top docking models that closely resemble other receptors. We further reveal reasons of success and failure in ligand docking for the models. This current assessment not only complements the previous assessment, but also provides important insights into the current status of GPCR modeling and ligand docking. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. The MARVEL transmembrane motif of occludin mediates oligomerization and targeting to the basolateral surface in epithelia.

    Science.gov (United States)

    Yaffe, Yakey; Shepshelovitch, Jeanne; Nevo-Yassaf, Inbar; Yeheskel, Adva; Shmerling, Hedva; Kwiatek, Joanna M; Gaus, Katharina; Pasmanik-Chor, Metsada; Hirschberg, Koret

    2012-08-01

    Occludin (Ocln), a MARVEL-motif-containing protein, is found in all tight junctions. MARVEL motifs are comprised of four transmembrane helices associated with the localization to or formation of diverse membrane subdomains by interacting with the proximal lipid environment. The functions of the Ocln MARVEL motif are unknown. Bioinformatics sequence- and structure-based analyses demonstrated that the MARVEL domain of Ocln family proteins has distinct evolutionarily conserved sequence features that are consistent with its basolateral membrane localization. Live-cell microscopy, fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC) were used to analyze the intracellular distribution and self-association of fluorescent-protein-tagged full-length human Ocln or the Ocln MARVEL motif excluding the cytosolic C- and N-termini (amino acids 60-269, FP-MARVEL-Ocln). FP-MARVEL-Ocln efficiently arrived at the plasma membrane (PM) and was sorted to the basolateral PM in filter-grown polarized MDCK cells. A series of conserved aromatic amino acids within the MARVEL domain were found to be associated with Ocln dimerization using BiFC. FP-MARVEL-Ocln inhibited membrane pore growth during Triton-X-100-induced solubilization and was shown to increase the membrane-ordered state using Laurdan, a lipid dye. These data demonstrate that the Ocln MARVEL domain mediates self-association and correct sorting to the basolateral membrane.

  12. Fabrication and experimentation of FRP helical spring

    Science.gov (United States)

    Ekanthappa, J.; Shiva Shankar, G. S.; Amith, B. M.; Gagan, M.

    2016-09-01

    In present scenario, the automobile industry sector is showing increased interest in reducing the unsprung weight of the automobile & hence increasing the fuel Efficiency. One of the feasible sub systems of a vehicle where weight reduction may be attempted is vehicle- suspension system. Usage of composite material is a proven way to lower the component weight without any compromise in strength. The composite materials are having high specific strength, more elastic strain energy storage capacity in comparison with those of steel. Therefore, helical coil spring made of steel is replaceable by composite cylindrical helical coil spring. This research aims at preparing a re-usable mandrel (mould) of Mild steel, developing a setup for fabrication, fabrication of FRP helical spring using continuous glass fibers and Epoxy Resin (Polymer). Experimentation has been conducted on fabricated FRP helical spring to determine its strength parameters & for failure analysis. It is found that spring stiffness (K) of Glass/Epoxy helical-spring is greater than steel-coil spring with reduced weight.

  13. Site mutations disrupt inter-helical H-bonds (alpha14W-alpha67T and beta15W-beta72S) involved in kinetic steps in the hemoglobin R-->T transition without altering the free energies of oxygenation.

    Science.gov (United States)

    Tsai, Ching-Hsuan; Simplaceanu, Virgil; Ho, Nancy T; Shen, Tong-Jian; Wang, Daojing; Spiro, Thomas G; Ho, Chien

    2003-01-01

    Three recombinant mutant hemoglobins (rHbs) of human normal adult hemoglobin (Hb A), rHb (alphaT67V), rHb (betaS72A), and rHb (alphaT67V, betaS72A), have been constructed to test the role of the tertiary intra-subunit H-bonds between alpha67T and alpha14W and between beta72S and beta15W in the cooperative oxygenation of Hb A. Oxygen-binding studies in 0.1 M sodium phosphate buffer at 29 degrees C show that rHb (alphaT67V), rHb (betaS72A), and rHb (alphaT67V, betaS72A) exhibit oxygen-binding properties similar to those of Hb A. The binding of oxygen to these rHbs is highly cooperative, with a Hill coefficient of approximately 2.8, compared to approximately 3.1 for Hb A. Proton nuclear magnetic resonance (NMR) studies show that rHb (alphaT67V), rHb (betaS72A), rHb (alphaT67V, betaS72A), and Hb A have similar quaternary structures in the alpha(1)beta(2) subunit interfaces. In particular, the inter-subunit H-bonds between alpha42Tyr and beta99Asp and between beta37Trp and alpha94Asp are maintained in the mutants in the deoxy form. There are slight perturbations in the distal heme pocket region of the alpha- and beta-chains in the mutants. A comparison of the exchangeable 1H resonances of Hb A with those of these three rHbs suggests that alpha67T and beta72S are H-bonded to alpha14W and beta15W, respectively, in the CO and deoxy forms of Hb A. The absence of significant free energy changes for the oxygenation process of these three rHbs compared to those of Hb A, even though the inter-helical H-bonds are abolished, indicates that these two sets of H-bonds are of comparable strength in the ligated and unligated forms of Hb A. Thus, the mutations at alphaT67V and betaS72A do not affect the overall energetics of the oxygenation process. The preserved cooperativity in the binding of oxygen to these three mutants also implies that there are multiple interactions involved in the oxygenation process of Hb A.

  14. Metallofoldamers supramolecular architectures from helicates to biomimetics

    CERN Document Server

    Maayan, Galia

    2013-01-01

    Metallofoldamers are oligomers that fold into three-dimensional structures in a controlled manner upon coordination with metal ions. Molecules in this class have shown an impressive ability to form single-handed helical structures and other three-dimensional architectures. Several metallofoldamers have been applied as sensors due to their selective folding when binding to a specific metal ion, while others show promise for applications as responsive materials on the basis of their ability to fold and unfold upon changes in the oxidation state of the coordinated metal ion, and as novel catalysts. Metallofoldamers: From Helicates to Biomimetic Architectures describes the variety of interactions between oligomers and metal species, with a focus on non-natural synthetic molecules. Topics covered include: the major classes of foldamers and their folding driving force metalloproteins and metalloenzymes helicates: self-assembly, structure and applications abiotic metallo-DNA metallo-PNA and iDNA metallopeptides inte...

  15. Nondispersive optical activity of meshed helical metamaterials.

    Science.gov (United States)

    Park, Hyun Sung; Kim, Teun-Teun; Kim, Hyeon-Don; Kim, Kyungjin; Min, Bumki

    2014-11-17

    Extreme optical properties can be realized by the strong resonant response of metamaterials consisting of subwavelength-scale metallic resonators. However, highly dispersive optical properties resulting from strong resonances have impeded the broadband operation required for frequency-independent optical components or devices. Here we demonstrate that strong, flat broadband optical activity with high transparency can be obtained with meshed helical metamaterials in which metallic helical structures are networked and arranged to have fourfold rotational symmetry around the propagation axis. This nondispersive optical activity originates from the Drude-like response as well as the fourfold rotational symmetry of the meshed helical metamaterials. The theoretical concept is validated in a microwave experiment in which flat broadband optical activity with a designed magnitude of 45° per layer of metamaterial is measured. The broadband capabilities of chiral metamaterials may provide opportunities in the design of various broadband optical systems and applications.

  16. Helicity antenna showers for hadron colliders

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Nadine; Skands, Peter [Monash University, School of Physics and Astronomy, Clayton, VIC (Australia); Lifson, Andrew [Monash University, School of Physics and Astronomy, Clayton, VIC (Australia); ETH Zuerich, Zurich (Switzerland)

    2017-10-15

    We present a complete set of helicity-dependent 2 → 3 antenna functions for QCD initial- and final-state radiation. The functions are implemented in the Vincia shower Monte Carlo framework and are used to generate showers for hadron-collider processes in which helicities are explicitly sampled (and conserved) at each step of the evolution. Although not capturing the full effects of spin correlations, the explicit helicity sampling does permit a significantly faster evaluation of fixed-order matrix-element corrections. A further speed increase is achieved via the implementation of a new fast library of analytical MHV amplitudes, while matrix elements from Madgraph are used for non-MHV configurations. A few examples of applications to QCD 2 → 2 processes are given, comparing the newly released Vincia 2.200 to Pythia 8.226. (orig.)

  17. Helicity antenna showers for hadron colliders

    Science.gov (United States)

    Fischer, Nadine; Lifson, Andrew; Skands, Peter

    2017-10-01

    We present a complete set of helicity-dependent 2→ 3 antenna functions for QCD initial- and final-state radiation. The functions are implemented in the Vincia shower Monte Carlo framework and are used to generate showers for hadron-collider processes in which helicities are explicitly sampled (and conserved) at each step of the evolution. Although not capturing the full effects of spin correlations, the explicit helicity sampling does permit a significantly faster evaluation of fixed-order matrix-element corrections. A further speed increase is achieved via the implementation of a new fast library of analytical MHV amplitudes, while matrix elements from Madgraph are used for non-MHV configurations. A few examples of applications to QCD 2→ 2 processes are given, comparing the newly released Vincia 2.200 to Pythia 8.226.

  18. Clinical application of helical CT colonography

    International Nuclear Information System (INIS)

    Zeng Huiliang; Zhu Xinjin; Liang Rujian; Liang Jianhao; Ou Weiqian; Wen Haomao

    2009-01-01

    Objective: To investigate the clinical value of 16-slice helical CT colonography in the diagnosis of colon tumor and polypus. Methods: 16-slice helical CT volumetric scanning was performed in 18 patients with colonic disease, including colonic tumor (n=16) and colonic polypus (n=2). 3D images, virtual endoscopy and multiplanar reformation were obtained in the AW4.1 workstation. CT appearances were compared with operation and fiberoptic colonoscopy. Results: Satisfied results were achieved from 18 patients, no difference found in results between CT colonography and operation in 16 patients with colonic tumor. Conclusion: 16-slice helical CT colonography is of great value in preoperative staging of colonic tumor and have a high value in clinical application. (authors)

  19. Single-superfield helical-phase inflation

    Energy Technology Data Exchange (ETDEWEB)

    Ketov, Sergei V., E-mail: ketov@tmu.ac.jp [Department of Physics, Tokyo Metropolitan University, Minami-ohsawa 1-1, Hachioji-shi, Tokyo 192-0397 (Japan); Kavli Institute for the Physics and Mathematics of the Universe (IPMU), The University of Tokyo, Chiba 277-8568 (Japan); Institute of Physics and Technology, Tomsk Polytechnic University, 30 Lenin Ave., Tomsk 634050 (Russian Federation); Terada, Takahiro, E-mail: takahiro@hep-th.phys.s.u-tokyo.ac.jp [Department of Physics, The University of Tokyo, Tokyo 113-0033 (Japan); Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg (Germany)

    2016-01-10

    Large-field inflation in supergravity requires the approximate global symmetry needed to protect flatness of the scalar potential. In helical-phase inflation, the U(1) symmetry of the Kähler potential is assumed, the phase part of the complex scalar of a chiral superfield plays the role of inflaton, and the radial part is strongly stabilized. The original model of helical phase inflation, proposed by Li, Li and Nanopoulos (LLN), employs an extra (stabilizer) superfield. We propose a more economical new class of the helical phase inflationary models without a stabilizer superfield. As the specific examples, the quadratic, the natural, and the Starobinsky-type inflationary models are studied in our approach.

  20. Neutrino's helicity in a gravitational field

    International Nuclear Information System (INIS)

    Pansart, J.P.

    1996-01-01

    By using approximated solutions of Dirac's equation, we show that there is no helicity reversal for light neutrinos in the Schwarzschild metric nor in an expanding universe. The actual coupling between a particle spin and the angular momentum of a heavy rotating body induces a possible helicity reversal but with an unobservable probability proportional to m 2 p / E 2 , where m p is the particle mass and E its energy. In these calculations, the helicity is defined through the spin orientation with respect to the current and not with respect to the linear momentum. This definition gives simple expressions and is equal to the usual definition in the case of a flat space. (N.T.)

  1. Helical post stellarator. Part 1: Vacuum configuration

    International Nuclear Information System (INIS)

    Moroz, P.E.

    1997-08-01

    Results on a novel type of stellarator configuration, the Helical Post Stellarator (HPS), are presented. This configuration is different significantly from all previously known stellarators due to its unique geometrical characteristics and unique physical properties. Among those are: the magnetic field has only one toroidal period (M = 1), the plasma has an extremely low aspect ratio, A ∼ 1, and the variation of the magnetic field, B, along field lines features a helical ripple on the inside of the torus. Among the main advantages of a HPS for a fusion program are extremely compact, modular, and simple design compatible with significant rotational transform, large plasma volume, and improved particle transport characteristics

  2. Helicity and nuclear β decay correlations

    Science.gov (United States)

    Hong, Ran; Sternberg, Matthew G.; Garcia, Alejandro

    2017-01-01

    We present simple derivations of nuclear β-decay correlations with an emphasis on the special role of helicity. This topic provides a good opportunity to teach students about helicity and chirality in particle physics with exercises that use simple aspects of quantum mechanics. In addition, this paper serves as an introduction to nuclear β-decay correlations from both a theoretical and experimental perspective. This article can be used to introduce students to ongoing experiments searching for hints of new physics in the low-energy precision frontier.

  3. Helicity injection experiment in the SINP tokamak

    International Nuclear Information System (INIS)

    Bhattacharyya, Krishnendu; Ray, Nihar Ranjan

    2000-01-01

    The current drive or sustainment in magnetized toroidal resistive plasmas can be though of as a 'balance' between helicity injection and dissipation. In the present work, the mechanisms of the 'balance' in the fluctuating magnetized resistive plasmas of the SINP tokamak, have been studied experimentally. The result shows that the oscillatory vertical magnetic field and oscillatory plasmas' velocity in a definite phase relationship causes the balancing effect between helicity injection and dissipation and thus sustainment of plasma current for a longer period of time has been observed in the resistive plasmas of the SINP tokamak. (author)

  4. PI-line-based image reconstruction in helical cone-beam computed tomography with a variable pitch

    International Nuclear Information System (INIS)

    Zou Yu; Pan Xiaochuan; Xia Dan; Wang Ge

    2005-01-01

    Current applications of helical cone-beam computed tomography (CT) involve primarily a constant pitch where the translating speed of the table and the rotation speed of the source-detector remain constant. However, situations do exist where it may be more desirable to use a helical scan with a variable translating speed of the table, leading a variable pitch. One of such applications could arise in helical cone-beam CT fluoroscopy for the determination of vascular structures through real-time imaging of contrast bolus arrival. Most of the existing reconstruction algorithms have been developed only for helical cone-beam CT with constant pitch, including the backprojection-filtration (BPF) and filtered-backprojection (FBP) algorithms that we proposed previously. It is possible to generalize some of these algorithms to reconstruct images exactly for helical cone-beam CT with a variable pitch. In this work, we generalize our BPF and FBP algorithms to reconstruct images directly from data acquired in helical cone-beam CT with a variable pitch. We have also performed a preliminary numerical study to demonstrate and verify the generalization of the two algorithms. The results of the study confirm that our generalized BPF and FBP algorithms can yield exact reconstruction in helical cone-beam CT with a variable pitch. It should be pointed out that our generalized BPF algorithm is the only algorithm that is capable of reconstructing exactly region-of-interest image from data containing transverse truncations

  5. Contributions of H G Khorana to Understanding Transmembrane ...

    Indian Academy of Sciences (India)

    IAS Admin

    GENERAL | ARTICLE. Contributions of H G Khorana to Understanding. Transmembrane Signal Transduction. David L Farrens and Thomas P Sakmar. Heptahelical G protein-coupled receptors (GPCRs) are lo- cated in the cell's plasma membrane and are responsible for transmitting chemical signals across the lipid bilayer.

  6. Modelling of a transmembrane evaporation module for desalination of seawater

    NARCIS (Netherlands)

    Guijt, C.M.; Racz, I.G.; van Heuven, Jan Willem; Reith, T.; de Haan, A.B.

    1999-01-01

    Transmembrane evaporation (often called membrane distillation) carried out in a countercurrent flow module, in which incoming cold seawater is heated by the condensing product water flow, is a promising technology for low-cost seawater desalination. This paper presents a model for preliminary design

  7. Solitons and helices: the search for a math-physics bridge

    OpenAIRE

    Zaslow, Eric

    1996-01-01

    We present evidence for an undiscovered link between N=2 supersymmetric quantum field theories and the mathematical theory of helices of coherent sheaves. We give a thorough review for nonspecialists of both the mathematics and physics involved, and invite the reader to take up the search for this elusive connection.

  8. Nucleotide dependent packing differences in helical crystals of the ABC transporter MsbA.

    Science.gov (United States)

    Ward, Andrew; Mulligan, Sheila; Carragher, Bridget; Chang, Geoffrey; Milligan, Ronald A

    2009-03-01

    Bacterial ATP binding cassette (ABC) exporters fulfill a wide variety of transmembrane transport roles and are homologous to the human multidrug resistance P-glycoprotein. Recent X-ray structures of the exporters MsbA and Sav1866 have begun to describe the conformational changes that accompany the ABC transport cycle. Here we present cryo-electron microscopy structures of MsbA reconstituted into a lipid bilayer. Using ATPase inhibitors, we captured three nucleotide transition states of the transporter that were subsequently reconstituted into helical arrays. The enzyme-substrate complex (trapped by ADP-aluminum fluoride or AMPPNP) crystallized in a different helical lattice than the enzyme-product complex (trapped by ADP-vanadate). Approximately 20A resolution maps were calculated for each state and revealed MsbA to be a dimer with a large channel between the membrane spanning domains, similar to the outward facing crystal structures of MsbA and Sav1866. This suggests that while there are likely structural differences between the nucleotide transition states, membrane embedded MsbA remains in an outward facing conformation while nucleotide is bound.

  9. Review of the helicity formalism; Revision del formalismo de helicidad

    Energy Technology Data Exchange (ETDEWEB)

    Barreiro, F.; Cerrada, M.; Fernandez, E.

    1972-07-01

    Our purpose in these notes has been to present a brief and general review of the helicity formalism. We begin by discussing Lorentz invariance, spin and helicity ideas, in section 1 . In section 2 we deal with the construction of relativistic states and scattering amplitudes in the helicity basis and we study their transformation properties under discrete symmetries. Finally we present some more sophisticated topics like kinematical singularities of helicity amplitudes, kinematical constraints and crossing relations 3, 4, 5 respectively. (Author) 8 refs.

  10. Dynamics and deformability of α-, 310- and π-helices

    Directory of Open Access Journals (Sweden)

    Narwani Tarun Jairaj

    2018-01-01

    Full Text Available Protein structures are often represented as seen in crystals as (i rigid macromolecules (ii with helices, sheets and coils. However, both definitions are partial because (i proteins are highly dynamic macromolecules and (ii the description of protein structures could be more precise. With regard to these two points, we analyzed and quantified the stability of helices by considering α-helices as well as 310- and π-helices. Molecular dynamic (MD simulations were performed on a large set of 169 representative protein domains. The local protein conformations were followed during each simulation and analyzed. The classical flexibility index (B-factor was confronted with the MD root mean square flexibility (RMSF index. Helical regions were classified according to their level of helicity from high to none. For the first time, a precise quantification showed the percentage of rigid and flexible helices that underlie unexpected behaviors. Only 76.4% of the residues associated with α-helices retain the conformation, while this tendency drops to 40.5% for 310-helices and is never observed for π-helices. α-helix residues that do not remain as an α-helix have a higher tendency to assume β-turn conformations than 310- or π-helices. The 310-helices that switch to the α-helix conformation have a higher B-factor and RMSF values than the average 310-helix but are associated with a lower accessibility. Rare π-helices assume a β-turn, bend and coil conformations, but not α- or 310-helices. The view on π-helices drastically changes with the new DSSP (Dictionary of Secondary Structure of Proteins assignment approach, leading to behavior similar to 310-helices, thus underlining the importance of secondary structure assignment methods.

  11. A Prospective Evaluation of Helical Tomotherapy

    International Nuclear Information System (INIS)

    Bauman, Glenn; Yartsev, Slav; Rodrigues, George; Lewis, Craig; Venkatesan, Varagur M.; Yu, Edward; Hammond, Alex; Perera, Francisco; Ash, Robert; Dar, A. Rashid; Lock, Michael; Baily, Laura; Coad, Terry C; Trenka, Kris C.; Warr, Barbara; Kron, Tomas; Battista, Jerry; Van Dyk, Jake

    2007-01-01

    Purpose: To report results from two clinical trials evaluating helical tomotherapy (HT). Methods and Materials: Patients were enrolled in one of two prospective trials of HT (one for palliative and one for radical treatment). Both an HT plan and a companion three-dimensional conformal radiotherapy (3D-CRT) plan were generated. Pretreatment megavoltage computed tomography was used for daily image guidance. Results: From September 2004 to January 2006, a total of 61 sites in 60 patients were treated. In all but one case, a clinically acceptable tomotherapy plan for treatment was generated. Helical tomotherapy plans were subjectively equivalent or superior to 3D-CRT in 95% of plans. Helical tomotherapy was deemed equivalent or superior in two thirds of dose-volume point comparisons. In cases of inferiority, differences were either clinically insignificant and/or reflected deliberate tradeoffs to optimize the HT plan. Overall imaging and treatment time (median) was 27 min (range, 16-91 min). According to a patient questionnaire, 78% of patients were satisfied to very satisfied with the treatment process. Conclusions: Helical tomotherapy demonstrated clear advantages over conventional 3D-CRT in this diverse patient group. The prospective trials were helpful in deploying this technology in a busy clinical setting

  12. On statistical equilibrium in helical fluid flows

    Directory of Open Access Journals (Sweden)

    M. V. Kurgansky

    2006-01-01

    Full Text Available The statistical mechanics of 3-D helical flows is re-examined for a continuum truncated at a top wavenumber. Based on the principle of equipartition of the flow enstrophy between helical modes, the emerging (i energy spectrum law '–2' and (ii formal mathematical analogy between the helicity and the thermodynamic entropy are discussed. It is noted that the '–2' scaling law is consistent with both spectral equilibrium and spectral cascade paradigms. In an attempt to apply the obtained results to a turbulent flow regime within the Earth's outer liquid core, where the net helicity of a turbulent flow component is presumably explained by Earth's rotation, it has been noticed that it is the energy spectral law '–1', but not '–2', which is likely realized there and within the logarithmic accuracy corresponds to the case of the velocity structure function [u(l]2 independency on the spatial scale l, the latter is consistent with observations. It is argued that the '–1' scaling law can also be interpreted in terms of the spectral equilibrium and it is emphasized that the causes of the likely dominance of the spectral law '–1' over the spectral law '–2' in this geophysical application deserve further investigation and clarification.

  13. Helical chirality induction of expanded porphyrin analogues

    Indian Academy of Sciences (India)

    2,2 -Bipyridine was readily obtained from 6,6 - dibromo-2,2 -bipyridine and then used for synthesizing cyclotetrapyrroletetrapyridine O3.18. 3. Helical chirality induction. 3.1 Chirality sensing of carboxylic acids by O1. Facile methods for the determination of molecular chi- rality are of increasing interest in view of the role of.

  14. Topological characteristics of helical repeat proteins

    NARCIS (Netherlands)

    Groves, M R; Barford, D

    The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

  15. Amphipathic helices from aromatic amino acid oligomers.

    Science.gov (United States)

    Gillies, Elizabeth R; Dolain, Christel; Léger, Jean-Michel; Huc, Ivan

    2006-10-13

    Synthetic helical foldamers are of significant interest for mimicking the conformations of naturally occurring molecules while at the same time introducing new structures and properties. In particular, oligoamides of aromatic amino acids are attractive targets, as their folding is highly predictable and stable. Here the design and synthesis of new amphipathic helical oligoamides based on quinoline-derived amino acids having either hydrophobic or cationic side chains are described. Their structures were characterized in the solid state by single-crystal X-ray diffraction and in solution by NMR. Results of these studies suggest that an oligomer as short as a pentamer folds into a stable helical conformation in protic solvents, including MeOH and H(2)O. The introduction of polar proteinogenic side chains to these foldamers, as described here for the first time, promises to provide possibilities for the biological applications of these molecules. In particular, amphipathic helices are versatile targets to explore due to their importance in a variety of biological processes, and the unique structure and properties of the quinoline-derived oligoamides may allow new structure-activity relationships to be developed.

  16. Electron image reconstruction of helical protein assemblies

    International Nuclear Information System (INIS)

    Cremers, A.F.M.

    1980-01-01

    The analysis of projections of large ordered biological systems obtained by electron microscopy of negatively stained specimens is described. The biological structures amenable to this approach are constructed from a large number of identical protein molecules, which are arranged according to helical symmetry. Electron images of these structures generally contain sufficient information in order to calculate a three-dimensional density map. (Auth.)

  17. Helical CT without contrast in choledocholithiasis diagnosis

    International Nuclear Information System (INIS)

    Jimenez Cuenca, I.; Perez Homs, M.; Olmo Martinez, L. del

    2001-01-01

    The goal of this study was to determine the diagnostic value of the helical CT without contrast in suspected cases of choledocholithiasis, comparing this test with endoscopic retrograde cholangiopancreatography (ERCP). Forty patients with possible choledocholithiasis were studied prospectively. There were 23 women and 17 men, ranging in age from 24 to 91 years. Helical CT was performed immediately before ERCP (time interval between the two procedures was less than 1 h). A biliary area previously selected was studied with a technique of pitch 1 and slice thickness of 3.2 mm. Average time was 30 s. Reconstruction with different increments and windows were made. Stone presence was evaluated in bile duct and Vater's ampulla. Biliary dilation was evaluated too. Endoscopic retrograde cholangiopancreatography found stones in 19 patients and absence of stones in 20. One case was failed, but stones in bile duct were demonstrated during intraoperative cholangiography. Helical CT demonstrated stones in 15 of the 19 patients with positive ERCP. There were no false positives with CT. Patients without stones in ERCP were also negative in CT. The patient having the failed ERCP was considered positive in CT. The CT sensitivity was 80 % and specificity was 100 %, with an accuracy of 90 %. Helical CT without contrast has sensitivity and specificity good enough to be used as a screening technique in patients with suspected choledocholithiasis. (orig.)

  18. Helical CT without contrast in choledocholithiasis diagnosis

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez Cuenca, I.; Perez Homs, M. [Radiodiagnostic Service, Hospital Universitario, Valladolid (Spain); Olmo Martinez, L. del [Digestive Service, Hospital Universitario, Valladolid (Spain)

    2001-02-01

    The goal of this study was to determine the diagnostic value of the helical CT without contrast in suspected cases of choledocholithiasis, comparing this test with endoscopic retrograde cholangiopancreatography (ERCP). Forty patients with possible choledocholithiasis were studied prospectively. There were 23 women and 17 men, ranging in age from 24 to 91 years. Helical CT was performed immediately before ERCP (time interval between the two procedures was less than 1 h). A biliary area previously selected was studied with a technique of pitch 1 and slice thickness of 3.2 mm. Average time was 30 s. Reconstruction with different increments and windows were made. Stone presence was evaluated in bile duct and Vater's ampulla. Biliary dilation was evaluated too. Endoscopic retrograde cholangiopancreatography found stones in 19 patients and absence of stones in 20. One case was failed, but stones in bile duct were demonstrated during intraoperative cholangiography. Helical CT demonstrated stones in 15 of the 19 patients with positive ERCP. There were no false positives with CT. Patients without stones in ERCP were also negative in CT. The patient having the failed ERCP was considered positive in CT. The CT sensitivity was 80 % and specificity was 100 %, with an accuracy of 90 %. Helical CT without contrast has sensitivity and specificity good enough to be used as a screening technique in patients with suspected choledocholithiasis. (orig.)

  19. Modeling of high gain helical antenna for improved performance ...

    African Journals Online (AJOL)

    The modeling of High Gain Helical Antenna structure is subdivided into three sections : introduction of helical structures ,Numerical analysis, modeling and simulation based on the parameters of helical antenna. The basic foundation software for the research paper is Matlab technical computing software, the modeling were ...

  20. Field-theoretic calculation of kinetic helicity flux

    Indian Academy of Sciences (India)

    In this paper we apply perturbative field-theoretic technique to helical turbulence. In the inertial range the kinetic helicity flux is found to be constant and forward. The universal constant H appearing in the spectrum of kinetic helicity was found to be 2.47.

  1. Distinct Roles for the Hsp40 and Hsp90 Molecular Chaperones during Cystic Fibrosis Transmembrane Conductance Regulator Degradation in Yeast

    OpenAIRE

    Youker, Robert T.; Walsh, Peter; Beilharz, Traude; Lithgow, Trevor; Brodsky, Jeffrey L.

    2004-01-01

    Aberrant secreted proteins can be destroyed by ER-associated protein degradation (ERAD), and a prominent, medically relevant ERAD substrate is the cystic fibrosis transmembrane conductance regulator (CFTR). To better define the chaperone requirements during CFTR maturation, the protein was expressed in yeast. Because Hsp70 function impacts CFTR biogenesis in yeast and mammals, we first sought ER-associated Hsp40 cochaperones involved in CFTR maturation. Ydj1p and Hlj1p enhanced Hsp70 ATP hydr...

  2. Pyrolysis of Helical Coordination Polymers for Metal-Sulfide-Based Helices with Broadband Chiroptical Activity.

    Science.gov (United States)

    Hirai, Kenji; Yeom, Bongjun; Sada, Kazuki

    2017-06-27

    Fabrication of chiroptical materials with broadband response in the visible light region is vital to fully realize their potential applications. One way to achieve broadband chiroptical activity is to fabricate chiral nanostructures from materials that exhibit broadband absorption in the visible light region. However, the compounds used for chiroptical materials have predominantly been limited to materials with narrowband spectral response. Here, we synthesize Ag 2 S-based nanohelices derived from helical coordination polymers. The right- and left-handed coordination helices used as precursors are prepared from l- and d-glutathione with Ag + and a small amount of Cu 2+ . The pyrolysis of the coordination helices yields right- and left-handed helices of Cu 0.12 Ag 1.94 S/C, which exhibit chiroptical activity spanning the entire visible light region. Finite element method simulations substantiate that the broadband chiroptical activity is attributed to synergistic broadband light absorption and light scattering. Furthermore, another series of Cu 0.10 Ag 1.90 S/C nanohelices are synthesized by choosing the l- or d-Glu-Cys as starting materials. The pitch length of nanohelicies is controlled by changing the peptides, which alters their chiroptical properties. The pyrolysis of coordination helices enables one to fabricate helical Ag 2 S-based materials that enable broadband chiroptical activity but have not been explored owing to the lack of synthetic routes.

  3. Bearing capacity of helical pile foundation in peat soil from different, diameter and spacing of helical plates

    Science.gov (United States)

    Fatnanta, F.; Satibi, S.; Muhardi

    2018-03-01

    In an area dominated by thick peat soil layers, driven piles foundation is often used. These piles are generally skin friction piles where the pile tips do not reach hard stratum. Since the bearing capacity of the piles rely on the resistance of their smooth skin, the bearing capacity of the piles are generally low. One way to increase the bearing capacity of the piles is by installing helical plates around the pile tips. Many research has been performed on helical pile foundation. However, literature on the use of helical pile foundation on peat soil is still hardly found. This research focus on the study of axial bearing capacity of helical pile foundation in peat soil, especially in Riau Province. These full-scale tests on helical pile foundation were performed in a rectangular box partially embedded into the ground. The box is filled with peat soil, which was taken from Rimbo Panjang area in the district of Kampar, Riau Province. Several helical piles with different number, diameter and spacing of the helical plates have been tested and analysed. The tests result show that helical pile with three helical plates of uniform diameter has better bearing capacity compared to other helical piles with varying diameter and different number of helical plates. The bearing capacity of helical pile foundation is affected by the spacing between helical plates. It is found that the effective helical plates spacing for helical pile foundation with diameter of 15cm to 35cm is between 20cm to 30cm. This behaviour may be considered to apply to other type of helical pile foundations in peat soil.

  4. Regulation of Exocytotic Fusion Pores by SNARE Protein Transmembrane Domains

    Directory of Open Access Journals (Sweden)

    Zhenyong Wu

    2017-10-01

    Full Text Available Calcium-triggered exocytotic release of neurotransmitters and hormones from neurons and neuroendocrine cells underlies neuronal communication, motor activity and endocrine functions. The core of the neuronal exocytotic machinery is composed of soluble N-ethyl maleimide sensitive factor attachment protein receptors (SNAREs. Formation of complexes between vesicle-attached v- and plasma-membrane anchored t-SNAREs in a highly regulated fashion brings the membranes into close apposition. Small, soluble proteins called Complexins (Cpx and calcium-sensing Synaptotagmins cooperate to block fusion at low resting calcium concentrations, but trigger release upon calcium increase. A growing body of evidence suggests that the transmembrane domains (TMDs of SNARE proteins play important roles in regulating the processes of fusion and release, but the mechanisms involved are only starting to be uncovered. Here we review recent evidence that SNARE TMDs exert influence by regulating the dynamics of the fusion pore, the initial aqueous connection between the vesicular lumen and the extracellular space. Even after the fusion pore is established, hormone release by neuroendocrine cells is tightly controlled, and the same may be true of neurotransmitter release by neurons. The dynamics of the fusion pore can regulate the kinetics of cargo release and the net amount released, and can determine the mode of vesicle recycling. Manipulations of SNARE TMDs were found to affect fusion pore properties profoundly, both during exocytosis and in biochemical reconstitutions. To explain these effects, TMD flexibility, and interactions among TMDs or between TMDs and lipids have been invoked. Exocytosis has provided the best setting in which to unravel the underlying mechanisms, being unique among membrane fusion reactions in that single fusion pores can be probed using high-resolution methods. An important role will likely be played by methods that can probe single fusion pores

  5. Aortic non communicating dissections. A study with helical CT

    International Nuclear Information System (INIS)

    Midiri, M.; Strada, A.; Stabile Ianora, A.A.; Rotondo, A.; Angelelli, G.; D'Agostino, D.; De Luca Tupputi Schinosa, L.

    2000-01-01

    The evaluate the signs of aortic intramural hematoma with helical CT and the diagnostic role of this technique in patients with this condition. It was reviewed the CT findings of 396 patients submitted to emergency examinations for suspected aortic dissection from 1995 to 1999. Only 18 patients (6 women and 12 men) had CT signs of aortic intramural hematoma. Helical CT studies were carried out with the following parameters: slice thickness 10 mm, reconstruction index 10, feed 1.5 mm, conventional algorithm with minimum values of 130 kV and 125mA. All patients were examined with dynamic contrast-enhanced CT, before and after a power injection of 130 mL ionic contrast material. It was studied: hematoma localization and longitudinal extension; thickness and density of aortic wall; presence and location of intimal calcifications; integrity of intimal wall; hemo mediastinum and/or hemo thorax. Aortic wall thickening appeared as a high density crescent-shaped area at baseline CT and had low density on enhanced images in all patients. Thickening was eccentric in 14/18 patients and concentric in 4/18 only; it always exceeded 4 mm. It was found some intimal calcifications in 8 patients and hemo thorax and/or hemo mediastinum in 9 patients. A patient with type A hematoma died of cardiac tamponade a few hours after CT diagnosis. Six patients (5 type B and 1 type A) underwent anti-hypertensive treatment and radiological follow-up. Eleven patients (6 type A and 5 type B) underwent prosthesis replacement and 5 of them (3 type A and 2 type B) died of postoperative complications. In the 5 type B patients surgery was performed because of treatment-resistant pain and of the onset of ischemic complications to abdominal organs caused by involvement of the main collateral branches of the aorta. One patient with type A hematoma was submitted to drug treatment because it was judged unresectable. Intramural hematoma of the aorta is a distinct pathological entity, which should not be

  6. Attempt of helical CT densitometry for assessing regional pulmonary ventilation

    International Nuclear Information System (INIS)

    Kume, Norihiko; Suga, Kazuyoshi; Nishigauchi, Kazuya; Takano, Katsuyuki; Koike, Shinji; Matsumoto, Tsuneo; Matsunaga, Naofumi

    1996-01-01

    Pulmonary dynamic CT densitometry during steady-state breathing was recorded and analyzed using helical CT scan in 14 patients with obstructive disorders involving small and large airways, and 2 with restrictive lung disease. The data set of 7-second, continuous helical scan at constant table position were reconstructed as 35 one-second temporarily overlapping images at 0.2-second intervals over 2-3 respiratory cycles, and regional CT densitometry was displayed. Normal lungs (5 volunteers) showed a regular sinusoidal curve, and maximal lung density change (LDC) was greater independent lungs than in independent lungs, with an average difference of 29.5 HU, indicating the gravitational effect. In contrast, a regular sinusoidal curve was not shown in obstructive disorders, and a significant reduction in maximal LDC (33.7±22.6 HU) compared with the normal lungs (60.8±25.9 HU) (p<0.001) was indicated. In contrast, no marked reduction in maximal LDC (53.7±28.6 HU) was shown in restrictive disorders. This method is fast and easy, and appears useful for the detection of ventilation abnormalities in obstructive lung disorders. (author)

  7. The ER membrane protein complex is a transmembrane domain insertase

    Science.gov (United States)

    Guna, Alina; Volkmar, Norbert; Christianson, John C.; Hegde, Ramanujan S.

    2018-01-01

    Insertion of proteins into membranes is an essential cellular process. The extensive biophysical and topological diversity of membrane proteins necessitates multiple insertion pathways that remain incompletely defined. Here, we found that known membrane insertion pathways fail to effectively engage tail-anchored membrane proteins with moderately hydrophobic transmembrane domains. These proteins are instead shielded in the cytosol by calmodulin. Dynamic release from calmodulin allowed sampling of the endoplasmic reticulum (ER), where the conserved ER membrane protein complex (EMC) was shown to be essential for efficient insertion in vitro and in cells. Purified EMC in synthetic liposomes catalyzed insertion of its substrates in a reconstituted system. Thus, EMC is a transmembrane domain insertase, a function that may explain its widely pleiotropic membrane-associated phenotypes across organisms. PMID:29242231

  8. Transmembrane electron transport and the neutral theory of evolution.

    Science.gov (United States)

    Scherer, S

    1984-01-01

    Based on the concept of "pairs of basic functional states" the evolution of the first chemiosmotic mechanism of energy conversion is discussed in terms of point mutations, gene duplications and of the neutral theory of evolution. A model for estimating the overall probability of the evolutionary step in question is presented, both for the "selectionist" and "neutralist" position. It is concluded that, concerning the present stage of knowledge, the evolution of transmembrane electron transport is an unsolved problem in evolutionary biology.

  9. Delivering Transmembrane Peptide Complexes to the Gas Phase Using Nanodiscs and Electrospray Ionization

    Science.gov (United States)

    Li, Jun; Richards, Michele R.; Kitova, Elena N.; Klassen, John S.

    2017-10-01

    The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)2+ ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å2 (conformation 1, C1), 708 Å2 (C2), and 737 Å2 (C3). The addition of NH4CH3CO2 produced (2GA + 2Na)2+ and (2GA + H + Na)2+ ions, with Ω similar to those of C1, C2, and C3, as well as (2GA + 2H)2+, (2GA + 2NH4)2+, and (2GA + H + NH4)2+ ions, which adopt a single conformation with a Ω similar to that of C2. These results suggest that the nature of the charging agents, imparted by the ESI process, can influence dimer conformation in the gas phase. Notably, the POPC NDs produced exclusively (2GA + 2NH4)2+ dimer ions; the DMPC NDs produced both (2GA + 2H)2+ and (2GA + 2NH4)2+ dimer ions. While the Ω of (2GA + 2H)2+ is similar to that of C2, the (2GA + 2NH4)2+ ions from NDs adopt a more compact structure, with a Ω of 656 Å2. It is proposed that this compact structure corresponds to the ion conducting single stranded head-to-head helical GA dimer. These findings highlight the potential of NDs, combined with ESI, for transferring transmembrane peptide complexes directly from lipid bilayers to the gas phase. [Figure not available: see fulltext.

  10. SUPERCONDUCTING HELICAL SNAKE MAGNETS: CONSTRUCTION AND MEASUREMENTS

    International Nuclear Information System (INIS)

    Mackay, W.W.; Anerella, M.; Courant, E.

    1999-01-01

    In order to collide polarized protons, the RHIC project will have two snakes in each ring and four rotators around each of two interaction regions. Two snakes on opposite sides of each ring can minimize depolarization during acceleration by keeping the spin tune at a half. Since the spin direction is normally along the vertical direction in a flat ring, spin rotators must be used around an interaction point to have longitudinal polarization in a collider experiment. Each snake or rotator will be composed of four helical dipoles to provide the required rotation of spin with minimal transverse orbit excursions in a compact length of 10m. The basic helical dipole is a superconducting magnet producing a transverse dipole field which is twisted about the magnet axis through 360 o in a length of 2.4 m. The design and construction of the magnets is described in this paper

  11. Statistical mechanics of helical wormlike chain model

    Science.gov (United States)

    Liu, Ya; Pérez, Toni; Li, Wei; Gunton, J. D.; Green, Amanda

    2011-02-01

    We investigate the statistical mechanics of polymers with bending and torsional elasticity described by the helical wormlike model. Noticing that the energy function is factorizable, we provide a numerical method to solve the model using a transfer matrix formulation. The tangent-tangent and binormal-binormal correlation functions have been calculated and displayed rich profiles which are sensitive to the combination of the temperature and the equilibrium torsion. Their behaviors indicate that there is no finite temperature Lifshitz point between the disordered and helical phases. The asymptotic behavior at low temperature has been investigated theoretically and the predictions fit the numerical results very well. Our analysis could be used to understand the statics of dsDNA and other chiral polymers.

  12. Helical CT of congenital ossicular anomalies

    International Nuclear Information System (INIS)

    Osada, Hisato; Machida, Kikuo; Honda, Norinari

    2001-01-01

    Since January 1996 to December 2000, 26 cases of congenital ossicular anomaly could be diagnosed with helical CT. All cases were unilateral. In 8 patients with malformation of the external ear, CT showed malleoincudal fixation (n=5), malleoincudal fixation and deformed incuts long process (n=1), deformed incus long process (n=1), and partial fusion of malleus neck and incus long process (n=1). In 18 patients with normal external ear, CT showed defect of the incus long process (n=5), defect of both the incus long process and stapes superstructure (n=8, 2 patients with congenital cholesteatoma, 1 with hypoplastic oval window), defect of the stapes superstructure (n=2, 1 patient with oval window absence), defect of the malleus manubrium (n=1), ossification of the stampede's tendon (n=1), and monopod stapes (n=1). Helical CT can evaluate the auditory ossicular chain in detail and is useful for diagnosing congenital ossicular anomaly. (author)

  13. Vacuum systems for the ILC helical undulator

    CERN Document Server

    Malyshev, O B; Clarke, J A; Bailey, I R; Dainton, J B; Malysheva, L I; Barber, D P; Cooke, P; Baynham, E; Bradshaw, T; Brummitt, A; Carr, S; Ivanyushenkov, Y; Rochford, J; Moortgat-Pick, G A

    2007-01-01

    The International Linear Collider (ILC) positron source uses a helical undulator to generate polarized photons of ∼10MeV∼10MeV at the first harmonic. Unlike many undulators used in synchrotron radiation sources, the ILC helical undulator vacuum chamber will be bombarded by photons, generated by the undulator, with energies mostly below that of the first harmonic. Achieving the vacuum specification of ∼100nTorr∼100nTorr in a narrow chamber of 4–6mm4–6mm inner diameter, with a long length of 100–200m100–200m, makes the design of the vacuum system challenging. This article describes the vacuum specifications and calculations of the flux and energy of photons irradiating the undulator vacuum chamber and considers possible vacuum system design solutions for two cases: cryogenic and room temperature.

  14. Recent progress in Large Helical Device experiments

    Energy Technology Data Exchange (ETDEWEB)

    Komori, A.; Morisaki, T.; Mutoh, T.; Sakakibara, S.; Takeiri, Y.; Kumazawa, R.; Kubo, S.; Ida, K.; Morita, S.; Narihara, K.; Shimozuma, T.; Tanaka, K.; Watanabe, K. Y.; Yamada, H.; Yoshinuma, M.; Akiyama, T.; Ashikawa, N.; Beidler, C. D.; Emoto, M.; Fujita, T.

    2005-07-01

    In order to realize the thermonuclear fusion reactor some critical issues to be solved are underlying in our path. The steady state operation with high confinement performance is known to be essential for the purpose. From the view point of economic feasibility, the high beta operation is favorable for the reduction of the construction cost. However compatibility between good confinement and high beta plasma is an important issue for the helical devices. When the plasma shifts outward with an increasing in beta, confinement degradation takes place because orbit of helically trapped particles drifts from the magnetic flux surfaces [1,2]. The restrict of the plasma shift is possible and valid for high-beta plasma production, to be sure, while it is important to investigate the beta-limit determined by the magnetohydrodynamics (MHD) equilibrium and stability, which is an essential subject to repress the confinement degradation due to other causes. (Author)

  15. Design studies on three-dimensional issues for liquid blanket systems in helical reactor FFHR

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, T., E-mail: teru@nifs.ac.jp [National Institute for Fusion Science, Toki, Gifu (Japan); Sagara, A.; Goto, T.; Yanagi, N.; Tamura, H.; Hirooka, Y.; Miyazawa, J.; Muroga, T. [National Institute for Fusion Science, Toki, Gifu (Japan)

    2012-08-15

    Highlights: Black-Right-Pointing-Pointer Three-dimensional blanket design issues have been studied for helical DEMO FFHR-d1. Black-Right-Pointing-Pointer (1) A minimum blanket space required for decision of the reactor parameter. Black-Right-Pointing-Pointer (2) A supporting method for a helical blanket system. Black-Right-Pointing-Pointer (3) Size of blanket module and effect of magnetic field on liquid coolants. - Abstract: A new design activity is under way for a helical type DEMO reactor FFHR-d1. The first stage of the activity involves the fundamental issues related to three-dimensional blanket design: (1) the minimum blanket space required for reactor parameter decisions, (2) the support method for the helical blanket system, and (3) the blanket module design. Investigations have been performed with neutronics and mechanical finite-element method calculations. Neutronics investigations indicate that a tungsten carbide radiation shield could reduce the minimum blanket space requirement by {approx}30 cm at the inboard region of FFHR-d1 compared with the blanket space of {approx}100 cm in the previous FFHR2 design. The investigations also showed that main shielding materials, ferritic steel and B{sub 4}C, could be used separately in a two-layered shielding configuration. The ferritic steel layer of the radiation shield is considered suitable to support the helical blanket system instead of relying on a thin vacuum vessel of the helical reactor. A size of a blanket module for a replacement process and the preferable cooling channel direction under a magnetic field are also discussed.

  16. Molecular Dynamics with Helical Periodic Boundary Conditions

    Czech Academy of Sciences Publication Activity Database

    Kessler, Jiří; Bouř, Petr

    2014-01-01

    Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014

  17. Winding light beams along elliptical helical trajectories

    OpenAIRE

    Wen, Yuanhui; Chen, Yujie; Zhang, Yanfeng; Chen, Hui; Yu, Siyuan

    2016-01-01

    Conventional caustic methods in real or Fourier space produced accelerating optical beams only with convex trajectories. We develop a superposition caustic method capable of winding light beams along non-convex trajectories. We ascertain this method by constructing a one-dimensional (1D) accelerating beam moving along a sinusoidal trajectory, and subsequently extending to two-dimensional (2D) accelerating beams along arbitrarily elliptical helical trajectories. We experimentally implement the...

  18. Inter-ethnic differences in genetic variants within the transmembrane protease, serine 6 (TMPRSS6) gene associated with iron status indicators: a systematic review with meta-analyses

    NARCIS (Netherlands)

    Gichohi-Wainaina, W.N.; Towers, G.W.; Swinkels, D.W.; Zimmermann, M.B.; Feskens, E.J.M.; Melse-Boonstra, A.

    2015-01-01

    Transmembrane protease, serine 6 (TMPRSS6), is likely to be involved in iron metabolism through its pleiotropic effect on hepcidin concentrations. Recently, genome-wide association studies have identified common variants in the TMPRSS6 gene to be linked to anaemia and low iron status. To get a more

  19. Transmembrane START domain proteins: in silico identification, characterization and expression analysis under stress conditions in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Satheesh, Viswanathan; Chidambaranathan, Parameswaran; Jagannadham, Prasanth Tejkumar; Kumar, Vajinder; Jain, Pradeep K; Chinnusamy, Viswanathan; Bhat, Shripad R; Srinivasan, R

    2016-01-01

    Steroidogenic acute regulatory related transfer (StART) proteins that are involved in transport of lipid molecules, play a myriad of functions in insects, mammals and plants. These proteins consist of a modular START domain of approximately 200 amino acids which binds and transfers the lipids. In the present study we have performed a genome-wide search for all START domain proteins in chickpea. The search identified 36 chickpea genes belonging to the START domain family. Through a phylogenetic tree reconstructed with Arabidopsis, rice, chickpea, and soybean START proteins, we were able to identify four transmembrane START (TM-START) proteins in chickpea. These four proteins are homologous to the highly conserved mammalian phosphatidylcholine transfer proteins. Multiple sequence alignment of all the transmembrane containing START proteins from Arabidopsis, rice, chickpea, and soybean revealed that the amino acid residues to which phosphatidylcholine binds in mammals, is also conserved in all these plant species, implying an important functional role and a very similar mode of action of all these proteins across dicots and monocots. This study characterizes a few of the not so well studied transmembrane START superfamily genes that may be involved in stress signaling. Expression analysis in various tissues showed that these genes are predominantly expressed in flowers and roots of chickpea. Three of the chickpea TM-START genes showed induced expression in response to drought, salt, wound and heat stress, suggesting their role in stress response.

  20. Superconducting Helical Snake Magnet for the AGS

    CERN Document Server

    Willen, Erich; Escallier, John; Ganetis, George; Ghosh, Arup; Gupta, Ramesh C; Harrison, Michael; Jain, Animesh K; Luccio, Alfredo U; MacKay, William W; Marone, Andrew; Muratore, Joseph F; Okamura, Masahiro; Plate, Stephen R; Roser, Thomas; Tsoupas, Nicholaos; Wanderer, Peter

    2005-01-01

    A superconducting helical magnet has been built for polarized proton acceleration in the Brookhaven AGS. This "partial Snake" magnet will help to reduce the loss of polarization of the beam due to machine resonances. It is a 3 T magnet some 1940 mm in magnetic length in which the dipole field rotates with a pitch of 0.2053 degrees/mm for 1154 mm in the center and a pitch of 0.3920 degrees/mm for 393 mm in each end. The coil cross-section is made of two slotted cylinders containing superconductor. In order to minimize residual offsets and deflections of the beam on its orbit through the Snake, a careful balancing of the coil parameters was necessary. In addition to the main helical coils, a solenoid winding was built on the cold bore tube inside the main coils to compensate for the axial component of the field that is experienced by the beam when it is off-axis in this helical magnet. Also, two dipole corrector magnets were placed on the same tube with the solenoid. A low heat leak cryostat was built so that t...

  1. THE EFFECTS OF SPATIAL SMOOTHING ON SOLAR MAGNETIC HELICITY PARAMETERS AND THE HEMISPHERIC HELICITY SIGN RULE

    Energy Technology Data Exchange (ETDEWEB)

    Ocker, Stella Koch [Department of Physics, Oberlin College, Oberlin, OH 44074 (United States); Petrie, Gordon, E-mail: socker@oberlin.edu, E-mail: gpetrie@nso.edu [National Solar Observatory, Boulder, CO 80303 (United States)

    2016-12-01

    The hemispheric preference for negative/positive helicity to occur in the northern/southern solar hemisphere provides clues to the causes of twisted, flaring magnetic fields. Previous studies on the hemisphere rule may have been affected by seeing from atmospheric turbulence. Using Hinode /SOT-SP data spanning 2006–2013, we studied the effects of two spatial smoothing tests that imitate atmospheric seeing: noise reduction by ignoring pixel values weaker than the estimated noise threshold, and Gaussian spatial smoothing. We studied in detail the effects of atmospheric seeing on the helicity distributions across various field strengths for active regions (ARs) NOAA 11158 and NOAA 11243, in addition to studying the average helicities of 179 ARs with and without smoothing. We found that, rather than changing trends in the helicity distributions, spatial smoothing modified existing trends by reducing random noise and by regressing outliers toward the mean, or removing them altogether. Furthermore, the average helicity parameter values of the 179 ARs did not conform to the hemisphere rule: independent of smoothing, the weak-vertical-field values tended to be negative in both hemispheres, and the strong-vertical-field values tended to be positive, especially in the south. We conclude that spatial smoothing does not significantly affect the overall statistics for space-based data, and thus seeing from atmospheric turbulence seems not to have significantly affected previous studies’ ground-based results on the hemisphere rule.

  2. Transmembrane amyloid-related proteins in CSF as potential biomarkers for Alzheimer’s disease

    Directory of Open Access Journals (Sweden)

    Inmaculada eLopez-Font

    2015-06-01

    Full Text Available In the continuing search for new cerebrospinal fluid (CSF biomarkers for Alzheimer’s disease (AD, reasonable candidates are the secretase enzymes involved in the processing of the amyloid precursor protein (APP, as well as the large proteolytic cleavage fragments sAPPα and sAPPβ. The enzymatic activities of some of these secretases, such as BACE1 and TACE, have been investigated as potential AD biomarkers, and it has been assumed that these activities present in human CSF result from the soluble truncated forms of the membrane-bound enzymes. However, we and others recently identified soluble forms of BACE1 and APP in CSF containing the intracellular domains, as well as the multi-pass transmembrane presenilin-1 (PS1 and other subunits of γ-secretase. We also review recent findings that suggest that most of these soluble transmembrane proteins could display self-association properties based on hydrophobic and/or ionic interactions leading to the formation of heteromeric complexes. The oligomerization state of these potential new biomarkers needs to be taken into consideration for assessing their real potential as CSF biomarkers for AD by adequate molecular tools.

  3. Hydrodynamic studies of CNT nanofluids in helical coil heat exchanger

    Science.gov (United States)

    Babita; Sharma, S. K.; Mital Gupta, Shipra; Kumar, Arinjay

    2017-12-01

    Helical coils are extensively used in several industrial processes such as refrigeration systems, chemical reactors, recovery processes etc to accommodate a large heat transfer area within a smaller space. Nanofluids are getting great attention due to their enhanced heat transfer capability. In heat transfer equipments, pressure drop is one of the major factors of consideration for pumping power calculations. So, the present work is aimed to study hydrodynamics of CNT nanofluids in helical coils. In this study, pressure drop characteristics of CNT nanofluid flowing inside horizontal helical coils are investigated experimentally. The helical coil to tube diameter was varied from 11.71 to 27.34 keeping pitch of the helical coil constant. Double distilled water was used as basefluid. SDBS and GA surfactants were added to stablilize CNT nanofluids. The volumetric fraction of CNT nanofluid was varied from 0.003 vol% to 0.051 vol%. From the experimental data, it was analyzed that the friction factor in helical coils is greater than that of straight tubes. Concentration of CNT in nanofluids also has a significant influence on the pressure drop/friction factor of helical coils. At a constant concentration of CNT, decreasing helical coil to tube diameter from 27.24 to 11.71, fanning friction factor of helical coil; f c increases for a constant value of p/d t. This increase in the value of fanning friction factor can be attributed to the secondary flow of CNT nanofluid in helical coils.

  4. Locomotion of helical bodies in viscoelastic fluids: enhanced swimming at large helical amplitudes.

    Science.gov (United States)

    Spagnolie, Saverio E; Liu, Bin; Powers, Thomas R

    2013-08-09

    The motion of a rotating helical body in a viscoelastic fluid is considered. In the case of force-free swimming, the introduction of viscoelasticity can either enhance or retard the swimming speed and locomotive efficiency, depending on the body geometry, fluid properties, and the body rotation rate. Numerical solutions of the Oldroyd-B equations show how previous theoretical predictions break down with increasing helical radius or with decreasing filament thickness. Helices of large pitch angle show an increase in swimming speed to a local maximum at a Deborah number of order unity. The numerical results show how the small-amplitude theoretical calculations connect smoothly to the large-amplitude experimental measurements.

  5. Helical polymer carrying helical grafts from peptide-based acetylene macromonomers: synthesis.

    Science.gov (United States)

    Sanda, Fumio; Gao, Guangzheng; Masuda, Toshio

    2004-06-25

    N-Propargylamide-terminated peptide-based macromonomers with a degree of polymerization ranging from 4 to 40 were synthesized by the polymerization of gamma-benzyl and gamma-stearyl-L-glutamate-N-carboxy anhydrides initiated with propargylamine. The macromonomers took an alpha-helical structure, which was confirmed by signals at 208 and 220 nm in CD spectra. The macromonomers were subjected to polymerization and copolymerization with an alanine-derived N-propargylamide [N-(tert-butoxycarbonyl)-L-alanine-N'-propargylamide] catalyzed with (2,5-norbornadiene)Rh+[eta6-C6H5B- (C6H5)3]. It was confirmed through a CD spectroscopic study that the copolymer obtained from the copolymerization of the gamma-stearyl-L-glutamate-based macromonomer with the alanine-derived N-propargylamide had a helical polyacetylene main chain and helical polypeptide side chains.

  6. Coordination chemistry strategies for dynamic helicates: time-programmable chirality switching with labile and inert metal helicates.

    Science.gov (United States)

    Miyake, Hiroyuki; Tsukube, Hiroshi

    2012-11-07

    'Chirality switching' is one of the most important chemical processes controlling many biological systems. DNAs and proteins often work as time-programmed functional helices, in which specific external stimuli alter the helical direction and tune the time scale of subsequent events. Although a variety of organic foldamers and their hybrids with natural helices have been developed, we highlight coordination chemistry strategies for development of structurally and functionally defined metal helicates. These metal helicates have characteristic coordination geometries, redox reactivities and spectroscopic/magnetic properties as well as complex chiralities. Several kinds of inert metal helicates maintain rigid helical structures and their stereoisomers are separable by optical resolution techniques, while labile metal helicates offer dynamic inversion of their helical structures via non-covalent interactions with external chemical signals. The latter particularly have dynamically ordered helical structures, which are controlled by the combinations of metal centres and chiral ligands. They further function as time-programmable switches of chirality-derived dynamic rotations, translations, stretching and shape flipping, which are useful applications in nanoscience and related technology.

  7. System assessment of helical reactors in comparison with tokamaks

    International Nuclear Information System (INIS)

    Yamazaki, K.; Imagawa, S.; Muroga, T.; Sagara, A.; Okamura, S.

    2002-01-01

    A comparative assessment of tokamak and helical reactors has been performed using equivalent physics/engineering model and common costing model. Higher-temperature plasma operation is required in tokamak reactors to increase bootstrap current fraction and to reduce current-drive (CD) power. In helical systems, lower-temperature operation is feasible and desirable to reduce helical ripple transport. The capital cost of helical reactor is rather high, however, the cost of electricity (COE) is almost same as that of tokamak reactor because of smaller re-circulation power (no CD power) and less-frequent blanket replacement (lower neutron wall loading). The standard LHD-type helical reactor with 5% beta value is economically equivalent to the standard tokamak with 3% beta. The COE of lower-aspect ratio helical reactor is on the same level of high-β N tokamak reactors. (author)

  8. Design Studies of Magnet Systems for Muon Helical Cooling Channels

    Energy Technology Data Exchange (ETDEWEB)

    Kashikhin, V.; Kashikhin, V.S.; Lamm, M.J.; Lopes, M.L.; Zlobin, A.V.; /Fermilab; Alsharo' a, M.; Johnson, R.P.; Kahn, Stephen A.; /MUONS Inc., Batavia

    2008-06-25

    Helical cooling channels with superimposed solenoid and helical dipole and quadrupole coils, and a pressurized gas absorber in the aperture offer high efficiency of 6D muon beam cooling. In this paper, we continue design studies and comparison of two basic concepts of magnet system proposed for a helical cooling channel focusing on the high field sections. The results of magnetic analysis and Lorentz force calculations as well as the superconductor choice are presented and discussed.

  9. Performance studies of oil lubricated helical groove journal bearing

    OpenAIRE

    Khan, Muhammad Zubair

    1992-01-01

    This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University. The provision of helical grooves on the surface of a plain journal bearing can improve the stability of a rotor-bearing system. However, the improvement depends on the arrangement of the grooves along the axial length of the bearing. In order to verify this improved stability three types of helical groove bearing and a reference plain journal bearing were investigated. The helical groove jour...

  10. Role of protein dynamics in transmembrane receptor signalling

    DEFF Research Database (Denmark)

    Wang, Yong; Bugge, Katrine Østergaard; Kragelund, Birthe Brandt

    2018-01-01

    Cells are dependent on transmembrane receptors to communicate and transform chemical and physical signals into intracellular responses. Because receptors transport 'information', conformational changes and protein dynamics play a key mechanistic role. We here review examples where experiment...... and computation have been used to study receptor dynamics. Recent studies on three distinct classes of receptors (G-protein coupled receptors, ligand-gated ion-channels and single-pass receptors) are highlighted to show that conformational changes across a range of time-scales and length-scales are central...

  11. Structure of the transmembrane domain of HIV-1 envelope glycoprotein.

    Science.gov (United States)

    Chen, Bing; Chou, James J

    2017-04-01

    HIV-1 envelope spike (Env) is a heavily glycosylated, type I membrane protein that mediates fusion of viral and cell membranes to initiate infection. It is also a primary target of neutralizing antibodies and thus an important candidate for vaccine development. We have recently reported a nuclear magnetic resonance structure of the transmembrane (TM) domain of HIV-1 Env reconstituted in a membrane-like environment. Taking HIV-1 as an example, we discuss here how a TM domain can anchor, stabilize, and modulate a viral envelope spike and how its high-resolution structure can contribute to understanding viral membrane fusion and to immunogen design. © 2016 Federation of European Biochemical Societies.

  12. Promiscuous Seven Transmembrane Receptors Sensing L-α-amino Acids

    DEFF Research Database (Denmark)

    Smajilovic, Sanela; Wellendorph, Petrine; Bräuner-Osborne, Hans

    2014-01-01

    A number of nutrient sensing seven trans-membrane (7TM) receptors have been identified and characterized over the past few years. While the sensing mechanisms to carbohydrates and free fatty acids are well understood, the molecular basis of amino acid sensing has recently come to the limelight. T....... The present review describes the current status of promiscuous L-α-amino acid sensors, the calcium sensing receptor (CaSR), the GPRC6A receptor, the T1R1/T1R3 receptor and also their molecular pharmacology, expression pattern and physiological significance....

  13. The nectin-1α transmembrane domain, but not the cytoplasmic tail, influences cell fusion induced by HSV-1 glycoproteins

    International Nuclear Information System (INIS)

    Subramanian, Ravi P.; Dunn, Jennifer E.; Geraghty, Robert J.

    2005-01-01

    Nectin-1 is a receptor for herpes simplex virus (HSV), a member of the immunoglobulin superfamily, and a cellular adhesion molecule. To study domains of nectin-1α involved in cell fusion, we measured the ability of nectin-1α/nectin-2α chimeras, nectin-1α/CD4 chimeras, and transmembrane domain and cytoplasmic tail mutants of nectin-1α to promote cell fusion induced by HSV-1 glycoproteins. Our results demonstrate that only chimeras and mutants containing the entire V-like domain and a link to the plasma membrane conferred cell-fusion activity. The transmembrane domain and cytoplasmic tail of nectin-1 were not required for any viral receptor or cell adhesion function tested. Cellular cytoplasmic factors that bind to the nectin-1α cytoplasmic tail, therefore, did not influence virus entry or cell fusion. Interestingly, the efficiency of cell fusion was reduced when membrane-spanning domains of nectin-1α and gD were replaced by glycosylphosphatidylinositol tethers, indicating that transmembrane domains may play a modulatory role in the gD/nectin-1α interaction in fusion

  14. Alteration of helical vortex core without change in flow topology

    DEFF Research Database (Denmark)

    Velte, Clara Marika; Okulov, Valery; Hansen, Martin Otto Laver

    2011-01-01

    The abrupt expansion of the slender vortex core with changes in flow topology is commonly known as vortex breakdown. We present new experimental observations of an alteration of the helical vortex core in wall bounded turbulent flow with abrupt growth in core size, but without change in flow...... topology. The helical symmetry as such is preserved, although the characteristic parameters of helical symmetry of the vortex core transfer from a smooth linear variation to a different trend under the influence of a non-uniform pressure gradient, causing an increase in helical pitch without changing its...

  15. Superposition of helical beams by using a Michelson interferometer.

    Science.gov (United States)

    Gao, Chunqing; Qi, Xiaoqing; Liu, Yidong; Weber, Horst

    2010-01-04

    Orbital angular momentum (OAM) of a helical beam is of great interests in the high density optical communication due to its infinite number of eigen-states. In this paper, an experimental setup is realized to the information encoding and decoding on the OAM eigen-states. A hologram designed by the iterative method is used to generate the helical beams, and a Michelson interferometer with two Porro prisms is used for the superposition of two helical beams. The experimental results of the collinear superposition of helical beams and their OAM eigen-states detection are presented.

  16. Rotation influence on the plasma helical instability

    International Nuclear Information System (INIS)

    Gutkin, T.I.; Tsypin, V.S.; Boleslavskaya, G.I.

    1980-01-01

    The influence of the rotation on helical instability of a plasma with the fixed boundaries (HIFB) is investigated taking into account the compressibility. A case of infinitely long cylinder with distributed current is considered. Cases when a rotating plasma is confined by current magnetic field are analytically considered. It is shown that in the case of the fixed boundary taking into account the compressibility in the HIFB increment increases and the picture of the rotation influence on HIFB considerably changes. Besides, it is shown that in the case of high plasma pressures HIFB can stabilize as a result of the rotation

  17. Holographic Metals and Insulators with Helical Symmetry

    CERN Document Server

    Donos, Aristomenis; Kiritsis, Elias

    2014-01-01

    Homogeneous, zero temperature scaling solutions with Bianchi VII spatial geometry are constructed in Einstein-Maxwell-Dilaton theory. They correspond to quantum critical saddle points with helical symmetry at finite density. Assuming $AdS_{5}$ UV asymptotics, the small frequency/(temperature) dependence of the AC/(DC) electric conductivity along the director of the helix are computed. A large class of insulating and conducting anisotropic phases is found, as well as isotropic, metallic phases. Conduction can be dominated by dissipation due to weak breaking of translation symmetry or by a quantum critical current.

  18. Insertion of helical Siberian snakes in RHIC

    International Nuclear Information System (INIS)

    Luccio, A.; Pilat, F.

    1995-01-01

    Spin rotators and Siberian snakes for RHIC can be built using 4 helical magnets obtained, by twisting, from the cosine dipoles. The authors found that the fringe fields are important. In the calculations they have used a plausible model for the fringe. However, only magnetic measurements on the prototypes presently being built will allow a final optimization. The linear coupling at injection, ΔQ min -2 , is well within the range of the RHIC decoupling system. At storage, the coupling introduced by the devices (ΔQ min -4 ) is negligible

  19. Vitamin A transport and the transmembrane pore in the cell-surface receptor for plasma retinol binding protein.

    Directory of Open Access Journals (Sweden)

    Ming Zhong

    Full Text Available Vitamin A and its derivatives (retinoids play diverse and crucial functions from embryogenesis to adulthood and are used as therapeutic agents in human medicine for eye and skin diseases, infections and cancer. Plasma retinol binding protein (RBP is the principal and specific vitamin A carrier in the blood and binds vitamin A at 1:1 ratio. STRA6 is the high-affinity membrane receptor for RBP and mediates cellular vitamin A uptake. STRA6 null mice have severely depleted vitamin A reserves for vision and consequently have vision loss, even under vitamin A sufficient conditions. STRA6 null humans have a wide range of severe pathological phenotypes in many organs including the eye, brain, heart and lung. Known membrane transport mechanisms involve transmembrane pores that regulate the transport of the substrate (e.g., the gating of ion channels. STRA6 represents a new type of membrane receptor. How this receptor interacts with its transport substrate vitamin A and the functions of its nine transmembrane domains are still completely unknown. These questions are critical to understanding the molecular basis of STRA6's activities and its regulation. We employ acute chemical modification to introduce chemical side chains to STRA6 in a site-specific manner. We found that modifications with specific chemicals at specific positions in or near the transmembrane domains of this receptor can almost completely suppress its vitamin A transport activity. These experiments provide the first evidence for the existence of a transmembrane pore, analogous to the pore of ion channels, for this new type of cell-surface receptor.

  20. What Helicity Can Tell Us about Solar Magnetic Fields Alexei A ...

    Indian Academy of Sciences (India)

    damental properties as hemispheric helicity rule, and role of helicity in magnetic reconnection and ... however, might not be always practical especially if one has no physical access to an object. Alternatively, one .... magnetic helicity), it has the same sign as Hm. Two different helicity proxies based on current helicity were ...

  1. Structure and function of transmembrane segment XII in osmosensor and osmoprotectant transporter ProP of Escherichia coli.

    Science.gov (United States)

    Liu, Feng; Culham, Doreen E; Vernikovska, Yaroslava I; Keates, Robert A B; Boggs, Joan M; Wood, Janet M

    2007-05-15

    Escherichia coli transporter ProP acts as both an osmosensor and an osmoregulator. As medium osmolality rises, ProP is activated and mediates H+-coupled uptake of osmolytes like proline. A homology model of ProP with 12-transmembrane (TM) helices and cytoplasmic termini was created, and the protein's topology was substantiated experimentally. Residues 468-497, at the end of the C-terminal domain and linked to TM XII, form an intermolecular, homodimeric alpha-helical coiled-coil that tunes the transporter's response to osmolality. We aim to further define the structure and function of ProP residues Q415-E440, predicted to include TM XII. Each residue was replaced with cysteine (Cys) in a histidine-tagged, Cys-less ProP variant (ProP*). Cys at positions 415-418 and 438-440 were most reactive with Oregon Green Maleimide (OGM), suggesting that residues 419 through 437 are in the membrane. Except for V429-I433, reactivity of those Cys varied with helical periodicity. Cys predicted to face the interior of ProP were more reactive than Cys predicted to face the lipid. The former may be exposed to hydrated polar residues in the protein interior, particularly on the periplasmic side. Intermolecular cross-links formed when ProP* variants with Cys at positions 419, 420, 422, and 439 were treated with DTME. Thus TM XII can participate, along its entire length, in the dimer interface of ProP. Cys substitution E440C rendered ProP* inactive. All other variants retained more than 30% of the proline uptake activity of ProP* at high osmolality. Most variants with Cys substitutions in the periplasmic half of TM XII activated at lower osmolalities than ProP*. Variants with Cys substitutions on one face of the cytoplasmic half of TM XII required a higher osmolality to activate. They included elements of a GXXXG motif that are predicted to form the interface of TM XII with TM VII. These studies define the position of ProP TM XII within the membrane, further support the predicted

  2. Electronic transport in single-helical protein molecules: Effects of multiple charge conduction pathways and helical symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Kundu, Sourav, E-mail: sourav.kunduphy@gmail.com; Karmakar, S.N.

    2016-07-15

    We propose a tight-binding model to investigate electronic transport properties of single helical protein molecules incorporating both the helical symmetry and the possibility of multiple charge transfer pathways. Our study reveals that due to existence of both the multiple charge transfer pathways and helical symmetry, the transport properties are quite rigid under influence of environmental fluctuations which indicates that these biomolecules can serve as better alternatives in nanoelectronic devices than its other biological counterparts e.g., single-stranded DNA.

  3. Metastatic tumor of the pancreas: helical CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Soon Jin; Lee, Won Jae; Lim, Hyo Keun; Kim, Seung Hoon; Kim, Kyeong Ah; Choi, Sang Hee; Jang, Hyun Jung; Lee, Ji Yeon [Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul (Korea, Republic of)

    2000-04-01

    To analyze the helical computed tomographic (CT) findings of distant metastatic tumors to the pancreas and to determine the differential points between these and primary pamcreatic carcinomas. We sruveyed 22 patients with metastatic tumor of the pancreas, proven on the basis of clinical and pathological findings. Seventeen patients were men, and five were women, and their ages ranged between 36 and 83 years. Their primary conditions were lung cancer (n=3D15), rectal cancer (n=3D2), melanoma of the foot, chondrosarcoma of the sacrum, cervical cancer, leiomyosarcoma of the uterus, and extragonadal choriocarcinoma of the mediastinum. We retrospectively reviewed the abdominal helical CT findings, analysing the number, location, size and attenuation of masses, as well as secondary change, which included dilatation of the pancreatic and biliary ducts and invasion of peripancreatic tissue or vessels. We also evaluated the differential findings of primary pancreatic cancer. Sixteen patients had a solitary focal mass, while in five, two masses were present. Among the 22 patients, low-density nodular masses were present in 21; in the other, in whom multiple metastasis from chondrosarcoma had occurred, there was dense calcification. The size of metastatic masses varied, ranging from 0.6 to 6 cm in diameter. The pancreatic duct proximal to the mass was dilated in ten cases, while the bile duct was dilated in six. The metastatic masses masses demonstrated no peripancreatic or vascular invasion, though they showed a discrete margin and contour bulging. Single metastasis to the pancreas was most common, and metastatic masses had a discrete margin, with contour bulging. There was no peripancreatic or vascular invasion. If the metastasis involved a single low-attenuated mass, however, with pancreatic or biliary dilatation, it was difficult to differentiate this from primary pancreatic cancer. (author)

  4. Stability analysis of the inverse transmembrane potential problem in electrocardiography

    Science.gov (United States)

    Burger, Martin; Mardal, Kent-André; Nielsen, Bjørn Fredrik

    2010-10-01

    In this paper we study some mathematical properties of an inverse problem arising in connection with electrocardiograms (ECGs). More specifically, we analyze the possibility for recovering the transmembrane potential in the heart from ECG recordings, a challenge currently investigated by a growing number of groups. Our approach is based on the bidomain model for the electrical activity in the myocardium, and leads to a parameter identification problem for elliptic partial differential equations (PDEs). It turns out that this challenge can be split into two subproblems: the task of recovering the potential at the heart surface from body surface recordings; the problem of computing the transmembrane potential inside the heart from the potential determined at the heart surface. Problem (1), which can be formulated as the Cauchy problem for an elliptic PDE, has been extensively studied and is well known to be severely ill-posed. The main purpose of this paper is to prove that problem (2) is stable and well posed if a suitable prior is available. Moreover, our theoretical findings are illuminated by a series of numerical experiments. Finally, we discuss some aspects of uniqueness related to the anisotropy in the heart.

  5. Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore

    Science.gov (United States)

    Song, Langzhou; Hobaugh, Michael R.; Shustak, Christopher; Cheley, Stephen; Bayley, Hagan; Gouaux, J. Eric

    1996-12-01

    The structure of the Staphylococcus aureus α-hemolysin pore has been determined to 1.9 overset{circ}{mathrm A} resolution. Contained within the mushroom-shaped homo-oligomeric heptamer is a solvent-filled channel, 100 overset{circ}{mathrm A} in length, that runs along the sevenfold axis and ranges from 14 overset{circ}{mathrm A} to 46 overset{circ}{mathrm A} in diameter. The lytic, transmembrane domain comprises the lower half of a 14-strand antiparallel β barrel, to which each protomer contributes two β strands, each 65 overset{circ}{mathrm A} long. The interior of the β barrel is primarily hydrophilic, and the exterior has a hydrophobic belt 28 overset{circ}{mathrm A} wide. The structure proves the heptameric subunit stoichiometry of the α-hemolysin oligomer, shows that a glycine-rich and solvent-exposed region of a water-soluble protein can self-assemble to form a transmembrane pore of defined structure, and provides insight into the principles of membrane interaction and transport activity of β barrel pore-forming toxins.

  6. Structure and function of the cystic fibrosis transmembrane conductance regulator

    Directory of Open Access Journals (Sweden)

    M.M. Morales

    1999-08-01

    Full Text Available Cystic fibrosis (CF is a lethal autosomal recessive genetic disease caused by mutations in the CF transmembrane conductance regulator (CFTR. Mutations in the CFTR gene may result in a defective processing of its protein and alter the function and regulation of this channel. Mutations are associated with different symptoms, including pancreatic insufficiency, bile duct obstruction, infertility in males, high sweat Cl-, intestinal obstruction, nasal polyp formation, chronic sinusitis, mucus dehydration, and chronic Pseudomonas aeruginosa and Staphylococcus aureus lung infection, responsible for 90% of the mortality of CF patients. The gene responsible for the cellular defect in CF was cloned in 1989 and its protein product CFTR is activated by an increase of intracellular cAMP. The CFTR contains two membrane domains, each with six transmembrane domain segments, two nucleotide-binding domains (NBDs, and a cytoplasmic domain. In this review we discuss the studies that have correlated the role of each CFTR domain in the protein function as a chloride channel and as a regulator of the outwardly rectifying Cl- channels (ORCCs.

  7. Tryptophan Scanning Reveals Dense Packing of Connexin Transmembrane Domains in Gap Junction Channels Composed of Connexin32*

    Science.gov (United States)

    Brennan, Matthew J.; Karcz, Jennifer; Vaughn, Nicholas R.; Woolwine-Cunningham, Yvonne; DePriest, Adam D.; Escalona, Yerko; Perez-Acle, Tomas; Skerrett, I. Martha

    2015-01-01

    Tryptophan was substituted for residues in all four transmembrane domains of connexin32. Function was assayed using dual cell two-electrode voltage clamp after expression in Xenopus oocytes. Tryptophan substitution was poorly tolerated in all domains, with the greatest impact in TM1 and TM4. For instance, in TM1, 15 substitutions were made, six abolished coupling and five others significantly reduced function. Only TM2 and TM3 included a distinct helical face that lacked sensitivity to tryptophan substitution. Results were visualized on a comparative model of Cx32 hemichannel. In this model, a region midway through the membrane appears highly sensitive to tryptophan substitution and includes residues Arg-32, Ile-33, Met-34, and Val-35. In the modeled channel, pore-facing regions of TM1 and TM2 were highly sensitive to tryptophan substitution, whereas the lipid-facing regions of TM3 and TM4 were variably tolerant. Residues facing a putative intracellular water pocket (the IC pocket) were also highly sensitive to tryptophan substitution. Although future studies will be required to separate trafficking-defective mutants from those that alter channel function, a subset of interactions important for voltage gating was identified. Interactions important for voltage gating occurred mainly in the mid-region of the channel and focused on TM1. To determine whether results could be extrapolated to other connexins, TM1 of Cx43 was scanned revealing similar but not identical sensitivity to TM1 of Cx32. PMID:25969535

  8. A nicotinic acetylcholine receptor transmembrane point mutation (G275E) associated with resistance to spinosad in Frankliniella occidentalis.

    Science.gov (United States)

    Puinean, Alin M; Lansdell, Stuart J; Collins, Toby; Bielza, Pablo; Millar, Neil S

    2013-03-01

    High levels of resistance to spinosad, a macrocyclic lactone insecticide, have been reported previously in western flower thrips, Frankliniella occidentalis, an economically important insect pest of vegetables, fruit and ornamental crops. We have cloned the nicotinic acetylcholine receptor (nAChR) α6 subunit from F. occidentalis (Foα6) and compared the nucleotide sequence of Foα6 from susceptible and spinosad-resistant insect populations (MLFOM and R1S respectively). A single nucleotide change has been identified in Foα6, resulting in the replacement of a glycine (G) residue in susceptible insects with a glutamic acid (E) in resistant insects. The resistance-associated mutation (G275E) is predicted to lie at the top of the third α-helical transmembrane domain of Foα6. Although there is no direct evidence identifying the location of the spinosad binding site, the analogous amino acid in the C. elegans glutamate-gated chloride channel lies in close proximity (4.4 Å) to the known binding site of ivermectin, another macrocyclic lactone pesticide. The functional consequences of the resistance-associated mutation have been examined in the human nAChR α7 subunit. Introduction of an analogous (A272E) mutation in α7 abolishes the modulatory effects of spinosad whilst having no significant effect upon activation by acetylcholine, consistent with spinosad having an allosteric mechanism of action. © 2012 International Society for Neurochemistry.

  9. Neutrino helicity reversal and fundamental symmetries

    International Nuclear Information System (INIS)

    Jentschura, U D; Wundt, B J

    2014-01-01

    A rather elusive helicity reversal occurs in a gedanken experiment in which a massive left-handed Dirac neutrino, traveling at a velocity u < c, is overtaken on a highway by a speeding vehicle (traveling at velocity v with u < v < c). Namely, after passing the neutrino, looking back, one would see a right-handed neutrino (which has never been observed in nature). The Lorentz-invariant mass of the right-handed neutrino is still the same as before the passing. The gedanken experiment thus implies the existence of right-handed, light neutrinos, which are not completely sterile. Furthermore, overtaking a bunch of massive right-handed Dirac neutrinos leads to gradual de-sterilization. We discuss the helicity reversal and the concomitant sterilization and de-sterilization mechanisms by way of an illustrative example calculation, with a special emphasis on massive Dirac and Majorana neutrinos. We contrast the formalism with a modified Dirac neutrino described by a Dirac equation with a pseudoscalar mass term proportional to the fifth current. (paper)

  10. Determining How Magnetic Helicity Injection Really Works

    International Nuclear Information System (INIS)

    Paul M Bellan

    2001-01-01

    OAK-B135 The goal of the Caltech program is to determine how helicity injection works by investigating the actual dynamics and topological evolution associated with magnetic relaxation. A new coaxial helicity injection source has been constructed and brought into operation. The key feature of this source is that it has maximum geometric simplicity. Besides being important for fusion research, this work also has astrophysical implications. Photos obtained using high-speed cameras show a clear sequence of events in the formation process. In particular, they show initial merging/reconnection processes, jet-like expansion, kinking, and separation of the plasma from the source. Various diagnostics have been developed, including laser induced fluorescence and soft x-ray detection using high speed diodes. Gas valves have been improved and a patent disclosure relating to puffed gas valves has been filed. Presentations on this work have been given in the form of invited talks at several university physics departments that were previously unfamiliar with laboratory plasma experiments

  11. Perspectives on confinement in helical systems

    International Nuclear Information System (INIS)

    Itoh, Kimitaka; Itoh, Sanae

    1989-01-01

    A review on recent experimental results and theoretical models on anomalous transport and density limit in toroidal helical devices is presented. Importance of transport problems is discussed. Experiments on Heliotron-E, Wendelstein-VIIA and new devices, i.e., ATF, Wendelstein-VIIAS and CHS, are reviewed and an overview on confinement property is given. From recent experimental results one sees that there are anomalous transport, which increases with temperature, and density limit, and that they limit the energy confinement time as well as the attainable beta value. The confinement characteristics of the scrape off layer plasma and loss cone loss are discussed, and perspectives on the high temperature plasma are given. These anomalous transport and density limit will be difficult obstacles in realizing a reactor grade plasma in helical systems. It is an urgent task to draw a realistic picture of the confinement based on the present data base. The relevant knowledge now would be critically essential for the successful development of the research in 1990's. (author) 102 refs

  12. Helical type thermonuclear device and control method

    International Nuclear Information System (INIS)

    Ishigaki, Yukio.

    1990-01-01

    In a conventional helical type thermonuclear device, electric current flows in the toroidal direction under magnetic fields of helical coils and vertical magnetic coils, by which a circulating electric field is caused. Therefore, there is a problem that electrons as a seed are generated by cosmic rays, etc., the electrons are confined in a magnetic field boundary, are accelerated by the circulating electric field, to reach a high energy level, collide against structures in a vacuum vessel and emit a great amount of X-rays. Then, compensation coils for offsetting the magnetic fields generated upon energization and deenergization of the vertical magnetic coils and the power source therefor are disposed at the positions opposing to each other on both sides of the vertical magnetic coils for controlling the variation coefficient rate of electric current upon energization and deenergization of the vertical magnetic coils. Since the compensation coils also offset the magnetic field generated upon energization and deenergization of the vertical magnetic field coils by this control, the circulating magnetic field is not caused in the vacuum vessel to reduce the X-ray radiation by electrons at high energy level. (N.H.)

  13. Internal Transport Barrier Physics in Helical Systems

    International Nuclear Information System (INIS)

    Yokoyama, M.; Maassberg, H.; Ida, K.; Estrada, T.; Castejon, F.; Minami, T.; Fujisawa, A.; Yamagishi, O.; Shats, M. G.; Dinklage, A.; Tribaldos, V.; Beidler, C. D.; Shimozuma, T.; Takeiri, Y.; Herranz, J.; Murakami, S.; Yamada, H.

    2005-01-01

    The characteristics of electron internal transport barriers (eITBs) in helical systems are reviewed. The common features are highly peaked Te profile with strongly positive Er in the core region. The transition nature of Er based on neoclassical (NC) ambipolarity, with the clear threshold feature such as ECH power and Ohmic current, is the common mechanism for the eITB formation. The electron heat confinement improvement has been revealed within the eITB region. The ECH power threshold can be lowered in the presence of ripple-trapped electrons-induced convective flux, and rational surfaces at the core region. The gyrokinetic calculations, for example eITB in LHD, have shown that the ETG mode is unstable in eITB region due to the large Te gradient. A larger zonal flow amplitude has been observed in eITB phase in CHS. The geodesic transfer of energy from stationary zonal flow to oscillatory modes (GAMs) recognized in H-1 implies that the stationary zonal flows can be maintained at a higher level by reducing the geodesic curvature in helical systems. This is the first report of the eITB branch in the framework of the International Stellarator Profile DataBase (ISPDB). (Author)

  14. Quality assurance of a helical tomotherapy machine

    International Nuclear Information System (INIS)

    Fenwick, J D; Tome, W A; Jaradat, H A; Hui, S K; James, J A; Balog, J P; DeSouza, C N; Lucas, D B; Olivera, G H; Mackie, T R; Paliwal, B R

    2004-01-01

    Helical tomotherapy has been developed at the University of Wisconsin, and 'Hi-Art II' clinical machines are now commercially manufactured. At the core of each machine lies a ring-gantry-mounted short linear accelerator which generates x-rays that are collimated into a fan beam of intensity-modulated radiation by a binary multileaf, the modulation being variable with gantry angle. Patients are treated lying on a couch which is translated continuously through the bore of the machine as the gantry rotates. Highly conformal dose-distributions can be delivered using this technique, which is the therapy equivalent of spiral computed tomography. The approach requires synchrony of gantry rotation, couch translation, accelerator pulsing and the opening and closing of the leaves of the binary multileaf collimator used to modulate the radiation beam. In the course of clinically implementing helical tomotherapy, we have developed a quality assurance (QA) system for our machine. The system is analogous to that recommended for conventional clinical linear accelerator QA by AAPM Task Group 40 but contains some novel components, reflecting differences between the Hi-Art devices and conventional clinical accelerators. Here the design and dosimetric characteristics of Hi-Art machines are summarized and the QA system is set out along with experimental details of its implementation. Connections between this machine-based QA work, pre-treatment patient-specific delivery QA and fraction-by-fraction dose verification are discussed

  15. Kinetic assembly of block copolymers in solution helical cylindrical micelles and patchy nanoparticles

    Science.gov (United States)

    Zhong, Sheng

    uniform structural parameters, including the width of the micelles, width of the helix, and the pitch distance. There is no preference to the handedness, and both handednesses are observed, which is understandable since there are no chiral molecules or specific binding effects applied during the assembly. The helical structure is a product of kinetic process. Cryogenic transmission electron microscopy has been employed to monitor the morphological transformation. The study indicates there are two complicated but reproducible kinetic pathways to form the helices. One pathway involves the stacks of bended cylinders at early stages and the subsequent interconnection of these bended cylinders. Spherical micelles bud off of the interconnected nanostructure as the final step towards a defect-free helix. Another kinetic pathway shows very short helices are formed at first and aligned via head-to-tail style in the solution, and the subsequent sequential addition of these short helices results in prolonged mature helices. By using a ninhydrin-staining technique, amine molecules within the micellar corona are visualized and confirmed to preferentially locate in the inner side of the helical turns. The aggregation of amine molecules provides a strong attraction force due to electrostatic association between oppositely charged amine and acid groups and accumulation of hydrogen bonding among amine molecules to coil the cylindrical micelles into helical twisting features which are stabilized by the repulsion forces due to the chain packing frustration within the hydrophobic core, steric hindrance of amine molecules as well as the Coulomb repulsion of the excess charged amine groups. The formation mechanism of the helix offers the feasibility to manipulate the helical pitch distance and formation kinetics. The helical pitch distance can be enlarged or shrunk by varying the type and amount of amine molecules used in assembly, introducing inorganic salts, and changing pH. Luckily, the

  16. Fourier transform coupled tryptophan scanning mutagenesis identifies a bending point on the lipid-exposed δM3 transmembrane domain of the Torpedo californica nicotinic acetylcholine receptor.

    Science.gov (United States)

    Caballero-Rivera, Daniel; Cruz-Nieves, Omar A; Oyola-Cintrón, Jessica; Torres-Núñez, David A; Otero-Cruz, Jose D; Lasalde-Dominicci, José A

    2011-01-01

    The nicotinic acetylcholine receptor (nAChR) is a member of a family of ligand-gated ion channels that mediate diverse physiological functions, including fast synaptic transmission along the peripheral and central nervous systems. Several studies have made significant advances toward determining the structure and dynamics of the lipid-exposed domains of the nAChR. However, a high-resolution atomic structure of the nAChR still remains elusive. In this study, we extended the Fourier transform coupled tryptophan scanning mutagenesis (FT-TrpScanM) approach to gain insight into the secondary structure of the δM3 transmembrane domain of the Torpedo californica nAChR, to monitor conformational changes experienced by this domain during channel gating, and to identify which lipid-exposed positions are linked to the regulation of ion channel kinetics. The perturbations produced by periodic tryptophan substitutions along the δM3 transmembrane domain were characterized by two-electrode voltage clamp and (125)I-labeled α-bungarotoxin binding assays. The periodicity profiles and Fourier transform spectra of this domain revealed similar helical structures for the closed- and open-channel states. However, changes in the oscillation patterns observed between positions Val-299 and Val-304 during transition between the closed- and open-channel states can be explained by the structural effects caused by the presence of a bending point introduced by a Thr-Gly motif at positions 300-301. The changes in periodicity and localization of residues between the closed-and open-channel states could indicate a structural transition between helix types in this segment of the domain. Overall, the data further demonstrate a functional link between the lipid-exposed transmembrane domain and the nAChR gating machinery.

  17. Fourier transform coupled tryptophan scanning mutagenesis identifies a bending point on the lipid-exposed δM3 transmembrane domain of the Torpedo californica nicotinic acetylcholine receptor

    Science.gov (United States)

    Caballero-Rivera, Daniel; Cruz-Nieves, Omar A; Oyola-Cintrón, Jessica; Torres-Núñez, David A; Otero-Cruz, José D

    2011-01-01

    The nicotinic acetylcholine receptor (nAChR) is a member of a family of ligand-gated ion channels that mediate diverse physiological functions, including fast synaptic transmission along the peripheral and central nervous systems. Several studies have made significant advances toward determining the structure and dynamics of the lipid-exposed domains of the nAChR. However, a high-resolution atomic structure of the nAChR still remains elusive. In this study, we extended the Fourier transform coupled tryptophan scanning mutagenesis (FT-TrpScanM) approach to gain insight into the secondary structure of the δM3 transmembrane domain of the Torpedo californica nAChR, to monitor conformational changes experienced by this domain during channel gating, and to identify which lipid-exposed positions are linked to the regulation of ion channel kinetics. The perturbations produced by periodic tryptophan substitutions along the δM3 transmembrane domain were characterized by two-electrode voltage clamp and 125I-labeled α-bungarotoxin binding assays. The periodicity profiles and Fourier transform spectra of this domain revealed similar helical structures for the closed- and open-channel states. However, changes in the oscillation patterns observed between positions Val-299 and Val-304 during transition between the closed- and open-channel states can be explained by the structural effects caused by the presence of a bending point introduced by a Thr-Gly motif at positions 300–301. The changes in periodicity and localization of residues between the closed-and open-channel states could indicate a structural transition between helix types in this segment of the domain. Overall, the data further demonstrate a functional link between the lipid-exposed transmembrane domain and the nAChR gating machinery. PMID:21785268

  18. Solution Structure of LC4 Transmembrane Segment of CCR5

    OpenAIRE

    Miyamoto, Kazuhide; Togiya, Kayo

    2011-01-01

    CC-chemokine receptor 5 (CCR5) is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1). The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescdence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 ...

  19. Computational fluid dynamics analysis of the pump parameters in the helical flow pump.

    Science.gov (United States)

    Hosoda, Kyohei; Ishii, Kohei; Isoyama, Takashi; Saito, Itsuro; Inoue, Yusuke; Ariyoshi, Kouki; Ono, Toshiya; Nakagawa, Hidemoto; Imachi, Kou; Kumagai, Hiroshi; Abe, Yusuke

    2014-03-01

    The helical flow pump (HFP) was invented to develop a total artificial heart at the University of Tokyo in 2005. The HFP consists of the multi-vane impeller involving rotor magnets, a motor stator and pump housing having double-helical volutes. To investigate the characteristics of the HFP, computational fluid dynamics analysis was performed. Validation of the computational model was performed with the data of the actual pump. A control computational model in which the vane area corresponded approximately to that of the actual pump was designed for the parametric study. The parametric study was performed varying the vane height, vane width and helical volute pitch. When the vane height was varied from 0.5 to 1.5 times that of the control computational model, the H-Q (pressure head vs. flow) and efficiency curves were translated in parallel with the vane height. When the vane height was two and three times that of the control computational model, the profile of these curves changed. From the results, the best proportion for the vane was considered to be a vane height between 1.5 and 2 times the vane width. The effect of vane width was not very strong compared to that of the vane height. A similar tendency in vane height was observed by varying the helical volute pitch. The best helical volute-pitch size is considered to be between 1.5 and 2 times the vane width. Although further study is necessary to determine the best values for these parameters, the characteristics of the pump parameters in the HFP could be approximately clarified.

  20. Attenuation of Phosphorylation-dependent Activation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Disease-causing Mutations at the Transmission Interface.

    Science.gov (United States)

    Chin, Stephanie; Yang, Donghe; Miles, Andrew J; Eckford, Paul D W; Molinski, Steven; Wallace, B A; Bear, Christine E

    2017-02-03

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein that functions as a phosphorylation-regulated anion channel. The interface between its two cytosolic nucleotide binding domains and coupling helices conferred by intracellular loops extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory domain of CFTR by protein kinase A (PKA) is required for its channel activity. However, it was unclear if phosphorylation modifies the transmission interface. Here, we studied purified full-length CFTR protein using spectroscopic techniques to determine the consequences of PKA-mediated phosphorylation. Synchrotron radiation circular dichroism spectroscopy confirmed that purified full-length wild-type CFTR is folded and structurally responsive to phosphorylation. Intrinsic tryptophan fluorescence studies of CFTR showed that phosphorylation reduced iodide-mediated quenching, consistent with an effect of phosphorylation in burying tryptophans at the transmission interface. Importantly, the rate of phosphorylation-dependent channel activation was compromised by the introduction of disease-causing mutations in either of the two coupling helices predicted to interact with nucleotide binding domain 1 at the interface. Together, these results suggest that phosphorylation modifies the interface between the catalytic and pore domains of CFTR and that this modification facilitates CFTR channel activation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Fermion helicity flip in higher-derivative electromagnetism

    Energy Technology Data Exchange (ETDEWEB)

    Accioly, A.J. [Instituto de Fisica Teorica (IFT), Sao Paulo, SP (Brazil); Mukai, H. [Universidade Estadual de Maringa, PR (Brazil). Dept. de Fisica

    1996-10-01

    It is shown that massive fermions have their helicity flipped on account of their interaction with an electromagnetic field described by Podolsky`s generalized electrodynamics. Massless fermions, in turn, seem to be unaffected by the electromagnetic field as far as their helicity is concerned. (author).

  2. Low-energy properties of fractional helical Luttinger liquids

    NARCIS (Netherlands)

    Meng, T.; Fritz, L.|info:eu-repo/dai/nl/371569559; Schuricht, D.|info:eu-repo/dai/nl/369284690; Loss, D.

    2014-01-01

    We investigate the low-energy properties of (quasi) helical and fractional helical Luttinger liquids. In particular, we calculate the Drude peak of the optical conductivity, the density of states, as well as charge transport properties of the interacting system with and without attached Fermi liquid

  3. Experimental investigation of solar powered diaphragm and helical pumps

    Science.gov (United States)

    For several years, many types of solar powered water pumping systems were evaluated, and in this paper, diaphragm and helical solar photovoltaic (PV) powered water pumping systems are discussed. Data were collected on diaphragm and helical pumps which were powered by different solar PV arrays at mul...

  4. A helical naphthopyran dopant for photoresponsive cholesteric liquid crystals

    OpenAIRE

    Kim, Yuna; Frigoli, Michel; Vanthuyne, Nicolas; Tamaoki, Nobuyuki

    2017-01-01

    The first photoresponsive cholesteric liquid crystal comprising a photoisomerizable helical naphthopyran derivative dopant and a nematic liquid crystal is reported. An unprecedented helical twisting power switching ratio of over 90% allowed us to demonstrate multi-cycle rotational motion of micro-objects by UV light irradiation.

  5. Two new twisted helical nickel (II) and cobalt (III) octahedral ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 6. Two new twisted helical nickel(II) and cobalt(III) octahedral monomer complexes: Synthesis and structural characterization. Malay Dolai ... Keywords. Coordination chemistry; nickel(II); cobalt(III); Schiff base; twisted helicity; supramolecular interactions.

  6. Helical dipole magnets for polarized protons in RHIC

    International Nuclear Information System (INIS)

    Syphers, M.; Courant, E.; Fischer, W.

    1997-01-01

    Superconducting helical dipole magnets will be used in the Brookhaven Relativistic Heavy Ion Collider (RHIC) to maintain polarization of proton beams and to perform localized spin rotations at the two major experimental detector regions. Requirements for the helical dipole system are discussed, and magnet prototype work is reported

  7. Interaction of 18-residue peptides derived from amphipathic helical ...

    Indian Academy of Sciences (India)

    We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from –1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical ...

  8. Coronary artery angioplasty with a helical autoperfusion balloon catheter

    NARCIS (Netherlands)

    Gurbel, PA; Anderson, RD; vanBoven, AJ; denHeijer, P

    The initial in-hospital and long-term clinical experience with a helical autoperfusion balloon catheter in the treatment of coronary artery disease is reported, This new catheter design allows blood to flow passively around the inflated balloon through a protected helical channel molded into the

  9. Alpha-Effect, Current and Kinetic Helicities for Magnetically Driven ...

    Indian Academy of Sciences (India)

    tribpo

    Key words. Sun—dynamo, helicity, turbulent convection. Extended abstract. Recent numerical simulations lead to the result that turbulence is much more mag- netically driven than believed. ... positive (and negative in the northern hemisphere), this being just opposite to what occurs for the current helicity which is negative ...

  10. Nucleonic helicity distributions revisited with an emphasis on their ...

    Indian Academy of Sciences (India)

    ... on various distribution functions describing nucleonic helicity structure and calculate a complete set of splitting functions relevant for their quantum chromodynamics (QCD) evolutions using light-front Hamiltonian perturbation theory in light front gauge + = 0. Twist-two structures of the helicity distributions are self-evident ...

  11. Space vehicle electromechanical system and helical antenna winding fixture

    Science.gov (United States)

    Judd, Stephen; Dallmann, Nicholas; Guenther, David; Enemark, Donald; Seitz, Daniel; Martinez, John; Storms, Steven

    2017-12-26

    A space vehicle electromechanical system may employ an architecture that enables convenient and practical testing, reset, and retesting of solar panel and antenna deployment on the ground. A helical antenna winding fixture may facilitate winding and binding of the helical antenna.

  12. Energy fluxes in helical magnetohydrodynamics and dynamo action

    Indian Academy of Sciences (India)

    Renormalized viscosity, renormalized resistivity, and various energy fluxes are calculated for helical magnetohydrodynamics using perturbative field theory. The calculation is of first-order in perturbation. Kinetic and magnetic helicities do not affect the renormalized parameters, but they induce an inverse cascade of ...

  13. Energy fluxes in helical magnetohydrodynamics and dynamo action

    Indian Academy of Sciences (India)

    Abstract. Renormalized viscosity, renormalized resistivity, and various energy fluxes are calcu- lated for helical magnetohydrodynamics using perturbative field theory. The calculation is of first- order in perturbation. Kinetic and magnetic helicities do not affect the renormalized parameters, but they induce an inverse cascade ...

  14. Micro helical polymeric structures produced by variable voltage direct electrospinning

    NARCIS (Netherlands)

    Shariatpanahi, S.P.; Iraji zad, A.; Abdollahzadeh, I.; Shirsavar, R.; Bonn, D.; Ejtehadi, R.

    2011-01-01

    Direct near field electrospinning is used to produce very long helical polystyrene microfibers in water. The pitch length of helices can be controlled by changing the applied voltage, allowing the production of both microsprings and microchannels. Using a novel high frequency variable voltage

  15. Stimuli-Directed Helical Chirality Inversion and Bio-Applications

    Directory of Open Access Journals (Sweden)

    Ziyu Lv

    2016-08-01

    Full Text Available Helical structure is a sophisticated ubiquitous motif found in nature, in artificial polymers, and in supramolecular assemblies from microscopic to macroscopic points of view. Significant progress has been made in the synthesis and structural elucidation of helical polymers, nevertheless, a new direction for helical polymeric materials, is how to design smart systems with controllable helical chirality, and further use them to develop chiral functional materials and promote their applications in biology, biochemistry, medicine, and nanotechnology fields. This review summarizes the recent progress in the development of high-performance systems with tunable helical chirality on receiving external stimuli and discusses advances in their applications as drug delivery vesicles, sensors, molecular switches, and liquid crystals. Challenges and opportunities in this emerging area are also presented in the conclusion.

  16. Helicity conservation and twisted Seifert surfaces for superfluid vortices.

    Science.gov (United States)

    Salman, Hayder

    2017-04-01

    Starting from the continuum definition of helicity, we derive from first principles its different contributions for superfluid vortices. Our analysis shows that an internal twist contribution emerges naturally from the mathematical derivation. This reveals that the spanwise vector that is used to characterize the twist contribution must point in the direction of a surface of constant velocity potential. An immediate consequence of the Seifert framing is that the continuum definition of helicity for a superfluid is trivially zero at all times. It follows that the Gauss-linking number is a more appropriate definition of helicity for superfluids. Despite this, we explain how a quasi-classical limit can arise in a superfluid in which the continuum definition for helicity can be used. This provides a clear connection between a microscopic and a macroscopic description of a superfluid as provided by the Hall-Vinen-Bekarevich-Khalatnikov equations. This leads to consistency with the definition of helicity used for classical vortices.

  17. Patterns of uterine enhancement with helical CT

    International Nuclear Information System (INIS)

    Kaur, H.; Loyer, E.M.; Charnsangavej, C.; Minami, M.

    1998-01-01

    Objective: The purpose of this study was to evaluate the enhancement characteristics of the normal uterine body and cervix using dynamic contrast-enhanced helical CT. Methods: Thirty-eight women scheduled for pelvic CT for non-gynecologic malignancies underwent dynamic contrast-enhanced helical CT of the pelvis. Data acquisition was during the arterial phase (30-45 s after the start of injection), the parenchymal phase (90-120 s after the start of injection), and delayed phase (3-9 min after the start of injection). The images were evaluated by four radiologists for the pattern of myometrial and cervical enhancement. Correlation was made with the age and menstrual status of the patients. Results: In the uterine body, three types of enhancement were observed. Type 1 enhancement, seen in 16 patients (42%), was characterized by the visualization of a subendometrial zone of enhancement, 30-120 s after the start of injection. Eight of these patients also showed an enhancing zone in the outer myometrium. Both zones were transitory, and in all cases, the uterus became homogeneous in the delayed phase. This pattern was seen predominantly in premenopausal women with a mean age of 34 years. Type 2 enhancement, seen in 17 cases (45%), was defined by the absence of subendometrial enhancement in the early phase. Enhancement was either diffuse from the outset or originated in the outer myometrium. This pattern was seen nearly equally in premenopausal and postmenopausal women with a mean age of 40 years. Type 3 enhancement was seen in five postmenopausal patients (13%) with a mean age of 53 years and was characterized by faint diffuse enhancement. In the cervix, a zonal pattern of enhancement defining inner and outer stroma was seen in 23 patients (61%). Fifteen patients were premenopausal and eight were postmenopausal. Conclusion: In this study, we have shown a transitory zonal distribution of the contrast in the myometrium and cervix using dynamic contrast-enhanced helical CT

  18. Comparative analysis of the orientation of transmembrane peptides using solid-state (2)H- and (15)N-NMR: mobility matters.

    Science.gov (United States)

    Grage, Stephan L; Strandberg, Erik; Wadhwani, Parvesh; Esteban-Martín, Santiago; Salgado, Jesús; Ulrich, Anne S

    2012-05-01

    Many solid-state nuclear magnetic resonance (NMR) approaches for membrane proteins rely on orientation-dependent parameters, from which the alignment of peptide segments in the lipid bilayer can be calculated. Molecules embedded in liquid-crystalline membranes, such as monomeric helices, are highly mobile, leading to partial averaging of the measured NMR parameters. These dynamic effects need to be taken into account to avoid misinterpretation of NMR data. Here, we compare two common NMR approaches: (2)H-NMR quadrupolar waves, and separated local field (15)N-(1)H polarization inversion spin exchange at magic angle (PISEMA) spectra, in order to identify their strengths and drawbacks for correctly determining the orientation and mobility of α-helical transmembrane peptides. We first analyzed the model peptide WLP23 in oriented dimyristoylphosphatidylcholine (DMPC) membranes and then contrasted it with published data on GWALP23 in dilauroylphosphatidylcholine (DLPC). We only obtained consistent tilt angles from the two methods when taking dynamics into account. Interestingly, the two related peptides differ fundamentally in their mobility. Although both helices adopt the same tilt in their respective bilayers (~20°), WLP23 undergoes extensive fluctuations in its azimuthal rotation angle, whereas GWALP23 is much less dynamic. Both alternative NMR methods are suitable for characterizing orientation and dynamics, yet they can be optimally used to address different aspects. PISEMA spectra immediately reveal the presence of large-amplitude rotational fluctuations, which are not directly seen by (2)H-NMR. On the other hand, PISEMA was unable to define the azimuthal rotation angle in the case of the highly dynamic WLP23, though the helix tilt could still be determined, irrespective of any dynamics parameters.

  19. Solid-State Nuclear Magnetic Resonance Investigation of the Structural Topology and Lipid Interactions of a Viral Fusion Protein Chimera Containing the Fusion Peptide and Transmembrane Domain.

    Science.gov (United States)

    Yao, Hongwei; Lee, Myungwoon; Liao, Shu-Yu; Hong, Mei

    2016-12-13

    The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of parainfluenza virus 5 (PIV5) fusion protein F using solid-state nuclear magnetic resonance. These studies provide structural information about the two domains when they are spatially well separated in the fusion process. To investigate how these two domains are structured relative to each other in the postfusion state, when the ectodomain forms a six-helix bundle that is thought to force the FP and TMD together in the membrane, we have now expressed and purified a chimera of the FP and TMD, connected by a Gly-Lys linker, and measured the chemical shifts and interdomain contacts of the protein in several lipid membranes. The FP-TMD chimera exhibits α-helical chemical shifts in all the membranes examined and does not cause strong curvature of lamellar membranes or membranes with negative spontaneous curvature. These properties differ qualitatively from those of the separate peptides, indicating that the FP and TMD interact with each other in the lipid membrane. However, no 13 C- 13 C cross peaks are observed in two-dimensional correlation spectra, suggesting that the two helices are not tightly associated. These results suggest that the ectodomain six-helix bundle does not propagate into the membrane to the two hydrophobic termini. However, the loosely associated FP and TMD helices are found to generate significant negative Gaussian curvature to membranes that possess spontaneous positive curvature, consistent with the notion that the FP-TMD assembly may

  20. Glycosylation and the cystic fibrosis transmembrane conductance regulator

    Science.gov (United States)

    Scanlin, Thomas F; Glick, Mary Catherine

    2001-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) has been known for the past 11 years to be a membrane glycoprotein with chloride channel activity. Only recently has the glycosylation of CFTR been examined in detail, by O'Riordan et al in Glycobiology. Using cells that overexpress wild-type (wt)CFTR, the presence of polylactosamine was noted on the fully glycosylated form of CFTR. In the present commentary the results of that work are discussed in relation to the glycosylation phenotype of cystic fibrosis (CF), and the cellular localization and processing of ΔF508 CFTR. The significance of the glycosylation will be known when endogenous CFTR from primary human tissue is examined. PMID:11686896

  1. Glycosylation and the cystic fibrosis transmembrane conductance regulator

    Directory of Open Access Journals (Sweden)

    Glick Mary Catherine

    2001-08-01

    Full Text Available Abstract The cystic fibrosis transmembrane conductance regulator (CFTR has been known for the past 11 years to be a membrane glycoprotein with chloride channel activity. Only recently has the glycosylation of CFTR been examined in detail, by O'Riordan et al in Glycobiology. Using cells that overexpress wild-type (wtCFTR, the presence of polylactosamine was noted on the fully glycosylated form of CFTR. In the present commentary the results of that work are discussed in relation to the glycosylation phenotype of cystic fibrosis (CF, and the cellular localization and processing of ΔF508 CFTR. The significance of the glycosylation will be known when endogenous CFTR from primary human tissue is examined.

  2. MutHTP: Mutations in Human Transmembrane Proteins.

    Science.gov (United States)

    A, Kulandaisamy; S, Binny Priya; R, Sakthivel; Tarnovskaya, Svetlana; Bizin, Ilya; Hönigschmid, Peter; Frishman, Dmitrij; Gromiha, M Michael

    2018-02-01

    We have developed a novel database, MutHTP, which contains information on 183395 disease-associated and 17827 neutral mutations in human transmembrane proteins. For each mutation site MutHTP provides a description of its location with respect to the membrane protein topology, structural environment (if available) and functional features. Comprehensive visualization, search, display and download options are available. The database is publicly available at http://www.iitm.ac.in/bioinfo/MutHTP/. The website is implemented using HTML, PHP and javascript and supports recent versions of all major browsers, such as Firefox, Chrome and Opera. gromiha@iitm.ac.in. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  3. Effect of ionizing radiation on transmembrane potential of Streptococcus

    International Nuclear Information System (INIS)

    Fomenko, B.S.; Akoev, I.G.

    1979-01-01

    Treatment of Streptococcus faecalis with ionizing radiation at doses of 5 to 100 krad is shown to reduce the energy-dependent accumulation of dibenzyldimethylammonium (DDA + ) by the cell. Since transmembrane potential is the moving force of DDA + transport across the membrane, the decrease in DDA + accumulation is suggested to be due to potential reduction. This radiation effect was not due to inactivation of the potential-generating mechanism; thus, the ATPase activity and glycolytic activity of the irradiated cells were higher than in the control. At the same time, the membranes exhibited an increased permeability for K + and protons, which is probably due to structural rearrangements in the membranes after irradiation. It is suggested that the potential reduction results from the increase in proton permeability of membranes

  4. Statistical Mechanics of Helical Wormlike Model

    Science.gov (United States)

    Liu, Ya; Perez, Toni; Li, Wei; Gunton, James; Green, Amanda

    2011-03-01

    The bending and torsional elasticities are crucial in determining the static and dynamic properties of ~biopolymers such as dsDNA and sickle hemoglobin. We investigate the statistical mechanics of stiff polymers ~described by the helical wormlike model. We provide a numerical method to solve the model using a transfer matrix formulation. The correlation functions have been calculated and display rich profiles which are sensitive to the combination of the temperature and the equilibrium torsion. The asymptotic behavior at low temperature has been investigated theoretically and the predictions fit the numerical results very well. Our analysis could be used to understand the statics of dsDNA and other chiral polymers. This work is supported by grants from the NSF and Mathers Foundation.

  5. Helical spin rotators and snakes for RHIC

    International Nuclear Information System (INIS)

    Ptitsin, V.I.; Shatunov, Yu.M.; Peggs, S.

    1995-01-01

    The RHIC collider, now under construction at BNL, will have the possibility of polarized proton-proton collisions up to a beam energy of 250 Gev. Polarized proton beams of such high energy can be only obtained with the use of siberian snakes, a special kind of spin rotator that rotates the particle spin by 180 degree around an axis lying in the horizontal plane. Siberian snakes help to preserve the beam polarization while numerous spin depolarizing resonances are crossed, during acceleration. In order to collide longitudinally polarized beams, it is also planned to install spin rotators around two interaction regions. This paper discusses snake and spin rotator designs based on sequences of four helical magnets. The schemes that were chosen to be applied at RHIC are presented

  6. Winding light beams along elliptical helical trajectories

    Science.gov (United States)

    Wen, Yuanhui; Chen, Yujie; Zhang, Yanfeng; Chen, Hui; Yu, Siyuan

    2016-07-01

    Conventional caustic methods in real or Fourier space produced accelerating optical beams only with convex trajectories. We developed a superposition caustic method capable of winding light beams along nonconvex trajectories. We ascertain this method by constructing a one-dimensional (1D) accelerating beam moving along a sinusoidal trajectory, and subsequently extending to two-dimensional (2D) accelerating beams along arbitrarily elliptical helical trajectories. We experimentally implemented the method with a compact and robust integrated optics approach by fabricating micro-optical structures on quartz glass plates to perform the spatial phase and amplitude modulation to the incident light, generating beam trajectories highly consistent with prediction. The theoretical and implementation methods can in principle be extended to the construction of accelerating beams with a wide variety of nonconvex trajectories, thereby opening up a route of manipulating light beams for fundamental research and practical applications.

  7. Conformational constraining of inactive and active States of a seven transmembrane receptor by metal ion site engineering in the extracellular end of transmembrane segment V

    DEFF Research Database (Denmark)

    Rosenkilde, Mette M; David, Ralf; Oerlecke, Ilka

    2006-01-01

    The extracellular part of transmembrane segment V (TM-V) is expected to be involved in the activation process of 7TM receptors, but its role is far from clear. Here, we study the highly constitutively active CXC-chemokine receptor encoded by human herpesvirus 8 (ORF74-HHV8), in which a metal ion......-fold). Zn(II) in activating concentrations (100 microM) acted as an allosteric enhancer as it increased the B(max) (7.1-fold), the potency (9.9-fold), the affinity (1.7- and 6.1-fold in competition against agonist and inverse agonist, respectively), and the efficacy (2.5-fold) of CXCL1/GROalpha....... The activating properties of Zn(II) were not due to a metal ion site between the ligand and the receptor because CXCL1/GROalpha analogs in which the putative metal-ion binding residues had been substituted-[H19A] and [H34A]-acted like wild-type CXCL1/GROalpha. Based on the complex action of Zn...

  8. Evolutionary Optimization of a Quadrifilar Helical Antenna

    Science.gov (United States)

    Lohn, Jason D.; Kraus, William F.; Linden, Derek S.; Clancy, Daniel (Technical Monitor)

    2002-01-01

    Automated antenna synthesis via evolutionary design has recently garnered much attention in the research literature. Evolutionary algorithms show promise because, among search algorithms, they are able to effectively search large, unknown design spaces. NASA's Mars Odyssey spacecraft is due to reach final Martian orbit insertion in January, 2002. Onboard the spacecraft is a quadrifilar helical antenna that provides telecommunications in the UHF band with landed assets, such as robotic rovers. Each helix is driven by the same signal which is phase-delayed in 90 deg increments. A small ground plane is provided at the base. It is designed to operate in the frequency band of 400-438 MHz. Based on encouraging previous results in automated antenna design using evolutionary search, we wanted to see whether such techniques could improve upon Mars Odyssey antenna design. Specifically, a co-evolutionary genetic algorithm is applied to optimize the gain and size of the quadrifilar helical antenna. The optimization was performed in-situ in the presence of a neighboring spacecraft structure. On the spacecraft, a large aluminum fuel tank is adjacent to the antenna. Since this fuel tank can dramatically affect the antenna's performance, we leave it to the evolutionary process to see if it can exploit the fuel tank's properties advantageously. Optimizing in the presence of surrounding structures would be quite difficult for human antenna designers, and thus the actual antenna was designed for free space (with a small ground plane). In fact, when flying on the spacecraft, surrounding structures that are moveable (e.g., solar panels) may be moved during the mission in order to improve the antenna's performance.

  9. Helical CT in the primary trauma evaluation of the cervical spine: an evidence-based approach

    Energy Technology Data Exchange (ETDEWEB)

    Blackmore, C.C. [Washington Univ., Seattle, WA (United States). Dept. of Radiology; Center for Cost and Outcomes Research, Univ. of Washington, Seattle (United States); Dept. of Radiology, Harborview Medical Center, Seattle, WA (United States); Mann, F.A. [Washington Univ., Seattle, WA (United States). Dept. of Radiology; Harborview Injury Prevention and Research Center, University of Washington, Seattle (United States); Wilson, A.J. [Washington Univ., Seattle, WA (United States). Dept. of Radiology

    2000-11-01

    This review provides a summary of the cost-effectiveness, clinical utility, performance, and interpretation of screening helical cervical spine CT for trauma patients. Recent evidence supports the use of helical CT as a cost-effective method for screening the cervical spine in high-risk trauma patients. Screening cervical spine CT can be performed at the time of head CT to lower the cost of the evaluation, and when all short- and long-term costs are considered, CT may actually save money when compared with traditional radiographic screening. In addition to having higher sensitivity and specificity for cervical spine injury, CT screening also allows more rapid radiological clearance of the cervical spine than radiography. Patients who are involved in high-energy trauma, who sustain head injury, or who have neurological deficits are candidates for CT screening. Screening with CT may enhance detection of other potentially important injuries of the cervical region. (orig.)

  10. Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

    Energy Technology Data Exchange (ETDEWEB)

    Koropatkin, Nicole M.; Martens, Eric C.; Gordon, Jeffrey I.; Smith, Thomas J. (WU); (Danforth)

    2009-01-12

    The human gut microbiota performs functions that are not encoded in our Homo sapiens genome, including the processing of otherwise undigestible dietary polysaccharides. Defining the structures of proteins involved in the import and degradation of specific glycans by saccharolytic bacteria complements genomic analysis of the nutrient-processing capabilities of gut communities. Here, we describe the atomic structure of one such protein, SusD, required for starch binding and utilization by Bacteroides thetaiotaomicron, a prominent adaptive forager of glycans in the distal human gut microbiota. The binding pocket of this unique {alpha}-helical protein contains an arc of aromatic residues that complements the natural helical structure of starch and imposes this conformation on bound maltoheptaose. Furthermore, SusD binds cyclic oligosaccharides with higher affinity than linear forms. The structures of several SusD/oligosaccharide complexes reveal an inherent ligand recognition plasticity dominated by the three-dimensional conformation of the oligosaccharides rather than specific interactions with the composite sugars.

  11. Barbs facilitate the helical penetration of honeybee (Apis mellifera ligustica stingers.

    Directory of Open Access Journals (Sweden)

    Jianing Wu

    Full Text Available The stinger is a very small and efficient device that allows honeybees to perform two main physiological activities: repelling enemies and laying eggs for reproduction. In this study, we explored the specific characteristics of stinger penetration, where we focused on its movements and the effects of it microstructure. The stingers of Italian honeybees (Apis mellifera ligustica were grouped and fixed onto four types of cubic substrates, before pressing into different substrates. The morphological characteristics of the stinger cross-sections were analyzed before and after penetration by microscopy. Our findings suggest that the honeybee stinger undergoes helical and clockwise rotation during penetration. We also found that the helical penetration of the stinger is associated directly with the spiral distribution of the barbs, thereby confirming that stinger penetration involves an advanced microstructure rather than a simple needle-like apparatus. These results provide new insights into the mechanism of honeybee stinger penetration.

  12. Barbs facilitate the helical penetration of honeybee (Apis mellifera ligustica) stingers.

    Science.gov (United States)

    Wu, Jianing; Yan, Shaoze; Zhao, Jieliang; Ye, Yuying

    2014-01-01

    The stinger is a very small and efficient device that allows honeybees to perform two main physiological activities: repelling enemies and laying eggs for reproduction. In this study, we explored the specific characteristics of stinger penetration, where we focused on its movements and the effects of it microstructure. The stingers of Italian honeybees (Apis mellifera ligustica) were grouped and fixed onto four types of cubic substrates, before pressing into different substrates. The morphological characteristics of the stinger cross-sections were analyzed before and after penetration by microscopy. Our findings suggest that the honeybee stinger undergoes helical and clockwise rotation during penetration. We also found that the helical penetration of the stinger is associated directly with the spiral distribution of the barbs, thereby confirming that stinger penetration involves an advanced microstructure rather than a simple needle-like apparatus. These results provide new insights into the mechanism of honeybee stinger penetration.

  13. 21 CFR 866.5900 - Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation detection system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cystic fibrosis transmembrane conductance... DEVICES Immunological Test Systems § 866.5900 Cystic fibrosis transmembrane conductance regulator (CFTR... intended as an aid in confirmatory diagnostic testing of individuals with suspected cystic fibrosis (CF...

  14. General architecture of the alpha-helical globule.

    Science.gov (United States)

    Murzin, A G; Finkelstein, A V

    1988-12-05

    A model is presented for the arrangement of alpha-helices in globular proteins. In the model, helices are placed on certain ribs of "quasi-spherical" polyhedra. The polyhedra are chosen so as to allow the close packing of helices around a hydrophobic core and to stress the collective interactions of the individual helices. The model predicts a small set of stable architectures for alpha-helices in globular proteins and describes the geometries of the helix packings. Some of the predicted helix arrangements have already been observed in known protein structures; others are new. An analysis of the three-dimensional structures of all proteins for which co-ordinates are available shows that the model closely approximates the arrangements and packing of helices actually observed. The average deviations of the real helix axes from those in the model polyhedra is +/- 20 degrees in orientation and +/- 2 A in position (1 A = 0.1 nm). We also show that for proteins that are not homologous, but whose helix arrangements are described by the same polyhedron, the root-mean-square difference in the position of the C alpha atoms in the helices is 1.6 to 3.0 A.

  15. Solution structure of LC4 transmembrane segment of CCR5.

    Directory of Open Access Journals (Sweden)

    Kazuhide Miyamoto

    Full Text Available CC-chemokine receptor 5 (CCR5 is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1. The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 binds to the HIV-1 inhibitory peptide LC5 were determined by docking calculations in addition to NMR data. The poses showed the importance of the hydrophobic interface of the assembled structures. The solution structure of LC4 elucidated in the present work provides a structural basis for further studies on the HIV-1 inhibitory function of the LC4 region.

  16. Solution structure of LC4 transmembrane segment of CCR5.

    Science.gov (United States)

    Miyamoto, Kazuhide; Togiya, Kayo

    2011-01-01

    CC-chemokine receptor 5 (CCR5) is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1). The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 binds to the HIV-1 inhibitory peptide LC5 were determined by docking calculations in addition to NMR data. The poses showed the importance of the hydrophobic interface of the assembled structures. The solution structure of LC4 elucidated in the present work provides a structural basis for further studies on the HIV-1 inhibitory function of the LC4 region.

  17. High-n helicity-induced shear Alfven eigenmodes

    International Nuclear Information System (INIS)

    Nakajima, N.; Cheng, C.Z.; Okamoto, M.

    1992-05-01

    The high-n Helicity-induced shear Alfven Eigenmodes (HAE) are considered both analytically and numerically for the straight helical magnetic system, where n is the toroidal mode number. The eigenmode equation for the high-n HAE modes is derived along the field line and with the aid of the averaging method is shown to reduce to the Mathieu equation asymptotically. The discrete HAE modes are shown to exist inside the continuum spectrum gaps. The continuous spectrum gaps appear around ω 2 = ω A 2 [N(lι-m)/2] 2 for N = 1,2,.., where ω A is the toroidal Alfven transit frequency, and l, m, and ι are the polarity of helical coils, the toroidal pitch number of helical coils, and the rotational transform, respectively. For the same ω A and ι, the frequency of the helical continuum gap is larger than that of the continuum gap in tokamak plasmas by |l-ι -1 m|. The polarity of helical coils l plays a crucial role in determining the spectrum gaps and the properties of the high-n HAE modes. The spectrum gaps near the magnetic axis are created by the helical ripple with circular flux surfaces for l = 1, and ≥ 3 helicals. For l = 2 helical systems, the spectrum gaps are created by the ellipticity of the flux surfaces. These analytical results for the continuum gaps and the existence of the high-n HAE modes in the continuum gaps are confirmed numerically for the l = 2 case, and we find that the HAE modes exist for mode structures with the even and the odd parities. (author)

  18. Multipinhole SPECT helical scan parameters and imaging volume.

    Science.gov (United States)

    Yao, Rutao; Deng, Xiao; Wei, Qingyang; Dai, Tiantian; Ma, Tianyu; Lecomte, Roger

    2015-11-01

    The authors developed SPECT imaging capability on an animal PET scanner using a multiple-pinhole collimator and step-and-shoot helical data acquisition protocols. The objective of this work was to determine the preferred helical scan parameters, i.e., the angular and axial step sizes, and the imaging volume, that provide optimal imaging performance. The authors studied nine helical scan protocols formed by permuting three rotational and three axial step sizes. These step sizes were chosen around the reference values analytically calculated from the estimated spatial resolution of the SPECT system and the Nyquist sampling theorem. The nine helical protocols were evaluated by two figures-of-merit: the sampling completeness percentage (SCP) and the root-mean-square (RMS) resolution. SCP was an analytically calculated numerical index based on projection sampling. RMS resolution was derived from the reconstructed images of a sphere-grid phantom. The RMS resolution results show that (1) the start and end pinhole planes of the helical scheme determine the axial extent of the effective field of view (EFOV), and (2) the diameter of the transverse EFOV is adequately calculated from the geometry of the pinhole opening, since the peripheral region beyond EFOV would introduce projection multiplexing and consequent effects. The RMS resolution results of the nine helical scan schemes show optimal resolution is achieved when the axial step size is the half, and the angular step size is about twice the corresponding values derived from the Nyquist theorem. The SCP results agree in general with that of RMS resolution but are less critical in assessing the effects of helical parameters and EFOV. The authors quantitatively validated the effective FOV of multiple pinhole helical scan protocols and proposed a simple method to calculate optimal helical scan parameters.

  19. Radiation Field of a Square, Helical Beam Antenna

    DEFF Research Database (Denmark)

    Knudsen, Hans Lottrup

    1952-01-01

    square helices are used. Further, in connection with corresponding rigorous formulas for the field from a circular, helical antenna with a uniformly progressing current wave of constant amplitude the present formulas may be used for an investigation of the magnitude of the error introduced in Kraus......' approximate calculation of the field from a circular, helical antenna by replacing this antenna with an ``equivalent'' square helix. This investigation is carried out by means of a numerical example. The investigation shows that Kraus' approximate method of calculation yields results in fair agreement...

  20. Experimental Evidence of Helical Flow in Porous Media

    DEFF Research Database (Denmark)

    Ye, Yu; Chiogna, Gabriele; Cirpka, Olaf A.

    2015-01-01

    . The resulting helical flow entails twisting streamlines which cause a significant increase in lateral mass exchange and thus a large enhancement of plume dilution (up to 235%) compared to transport in homogenous media. The setup may be used to effectively mix solutes in parallel streams similarly to static......Helical flow leads to deformation of solute plumes and enhances transverse mixing in porous media. We present experiments in which macroscopic helical flow is created by arranging different materials to obtain an anisotropic macroscopic permeability tensor with spatially variable orientation...... mixers, but in porous media....

  1. Experimental Evidence of Helical Flow in Porous Media

    Science.gov (United States)

    Ye, Yu; Chiogna, Gabriele; Cirpka, Olaf A.; Grathwohl, Peter; Rolle, Massimo

    2015-11-01

    Helical flow leads to deformation of solute plumes and enhances transverse mixing in porous media. We present experiments in which macroscopic helical flow is created by arranging different materials to obtain an anisotropic macroscopic permeability tensor with spatially variable orientation. The resulting helical flow entails twisting streamlines which cause a significant increase in lateral mass exchange and thus a large enhancement of plume dilution (up to 235%) compared to transport in homogenous media. The setup may be used to effectively mix solutes in parallel streams similarly to static mixers, but in porous media.

  2. Linear local stability of electrostatic drift modes in helical systems

    International Nuclear Information System (INIS)

    Yamagishi, O.; Nakajima, N.; Sugama, H.; Nakamura, Y.

    2003-01-01

    We investigate the stability of the drift wave in helical systems. For this purpose, we solve the linear local gyrokinetic-Poisson equation, in the electrostatic regime. As a model of helical plasmas, Large helical Device (LHD) is considered. The equation we apply is rather exact in the framework of linear gyrokinetic theory, where only the approximation is the ballooning representation. In this paper, we consider only collisionless cases. All the frequency regime can be naturally reated without any assumptions, and in such cases, ion temperature gradient modes (ITG), trapped electron modes (TEM), and electron temperature gradient modes (ETG) are expected to become unstable linearly independently. (orig.)

  3. Dynamic Behavior of Helical Structure in Ferroelectric Liquid Crystals

    Science.gov (United States)

    Katayama, Takashi; Uehara, Hiroyuki; Furue, Hirokazu; Hatano, Jun

    2004-09-01

    Ferroelectric liquid crystals (FLCs) take a helical structure which can be unwound by the application of an electric field. Although the static orientational process of FLC molecules is well known, the dynamic modification process of the helical structure is not clearly understood. We formulated equations for simulating the dynamic response in terms of the elastic free-energy density based on the continuum theory, and subsequently was solved the dynamic equations numerically. Furthermore, the conoscopic image was simulated by a 4× 4 matrix method. We investigated the effect of spontaneous polarization and dielectric anisotropy on the dynamic behavior of the helical structure in FLC.

  4. Alpha-effect dynamos with zero kinetic helicity.

    Science.gov (United States)

    Rädler, Karl-Heinz; Brandenburg, Axel

    2008-02-01

    A simple explicit example of a Roberts-type dynamo is given in which the alpha effect of mean-field electrodynamics exists in spite of pointwise vanishing kinetic helicity of the fluid flow. In this way, it is shown that alpha-effect dynamos do not necessarily require nonzero kinetic helicity. A mean-field theory of Roberts-type dynamos is established within the framework of the second-order correlation approximation. In addition, numerical solutions of the original dynamo equations are given that are independent of any approximation of that kind. Both theory and numerical results demonstrate the possibility of dynamo action in the absence of kinetic helicity.

  5. Magnetic Helical Micro- and Nanorobots: Toward Their Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Famin Qiu

    2015-03-01

    Full Text Available Magnetic helical micro- and nanorobots can perform 3D navigation in various liquids with a sub-micrometer precision under low-strength rotating magnetic fields (<10 mT. Since magnetic fields with low strengths are harmless to cells and tissues, magnetic helical micro/nanorobots are promising tools for biomedical applications, such as minimally invasive surgery, cell manipulation and analysis, and targeted therapy. This review provides general information on magnetic helical micro/nanorobots, including their fabrication, motion control, and further functionalization for biomedical applications.

  6. Combining fixed-order helicity amplitudes with resummation using SCET

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, Ian W. [Massachusetts Institute of Technology, Cambridge, MA (United States). Center for Theoretical Physics; Tackmann, Frank J. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Theory Group; Waalewijn, Wouter J. [California Univ., San Diego, La Jolla, CA (United States). Dept. of Physics

    2012-11-15

    We discuss how to construct a simple and easy-to-use helicity operator basis in Soft-Collinear Effective Theory (SCET), for which the hard Wilson coefficients from matching QCD onto SCET are directly given in terms of the color-ordered QCD helicity amplitudes. This provides an interface to seamlessly combine fixed-order helicity amplitudes, which are the basic building blocks of state-of-the-art next-to-leading order calculations for multileg processes, with a resummation of higher-order logarithmic corrections using SCET.

  7. Manipulating the membrane penetration mechanism of helical polypeptides via aromatic modification for efficient gene delivery.

    Science.gov (United States)

    Zheng, Nan; Song, Ziyuan; Yang, Jiandong; Liu, Yang; Li, Fangfang; Cheng, Jianjun; Yin, Lichen

    2017-08-01

    The delivery performance of non-viral gene vectors is greatly related to their intracellular kinetics. Cationic helical polypeptides with potent membrane penetration properties and gene transfection efficiencies have been recently developed by us. However, they suffer from severe drawbacks in terms of their membrane penetration mechanisms that mainly include endocytosis and pore formation. The endocytosis mechanism leads to endosomal entrapment of gene cargos, while the charge- and helicity-induced pore formation causes appreciable cytotoxicity at high concentrations. With the attempt to overcome such critical challenges, we incorporated aromatic motifs into the design of helical polypeptides to enhance their membrane activities and more importantly, to manipulate their membrane penetration mechanisms. The aromatically modified polypeptides exhibited higher cellular internalization level than the unmodified analogue by up to 2.5 folds. Such improvement is possibly because aromatic domains promoted the polypeptides to penetrate cell membranes via direct transduction, a non-endocytosis and non-pore formation mechanism. As such, gene cargos were more efficiently delivered into cells by bypassing endocytosis and subsequently avoiding endosomal entrapment, and the material toxicity associated with excessive pore formation was also reduced. The top-performing aromatic polypeptide containing naphthyl side chains at the incorporated content of 20mol% revealed notably higher transfection efficiencies than commercial reagents in melanoma cells in vitro (by 11.7 folds) and in vivo (by 9.1 folds), and thus found potential utilities toward topical gene delivery for cancer therapy. Cationic helical polypeptides, as efficient gene delivery materials, suffer from severe drawbacks in terms of their membrane penetration mechanisms. The main cell penetration mechanisms involved are endocytosis and pore formation. However, the endocytosis mechanism has the limitation of endosomal

  8. Investigations of peripheral dose for helical tomotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Lissner, Steffen; Schubert, Kai; Sterzing, Florian; Herfarth, Klaus; Sroka-Perez, Gabriele; Debus, Juergen [University Hospital Heidelberg (Germany). Dept. of Radiation Oncology; Wiezorek, Tilo [University Hospital Jena (Germany). Dept. of Radiotherapy

    2013-07-01

    Purpose: Whenever treating a patient with percutaneous radiotherapy, a certain amount of dose is inevitably delivered to healthy tissue. This is mainly due to beam's entry and exit in the region of the target volume. In regions distant from the target volume, dose is delivered by leakage from the MLC and head scatter from the accelerator head and phantom scatter from the target volume (peripheral dose). Helical tomotherapy is a form of radiation therapy with a uniquely designed machine and delivery pattern which influence the peripheral dose. The goal of this work was to investigate peripheral dose in helical tomotherapy. The experiments were used to establish a complex characterization of the peripheral dose. Materials and methods: A 30*30*60cm{sup 3} slab phantom and TLD-100 (Lithium fluoride) were used for the experiments. Treatment procedures were generated with the tomotherapy planning system (TPS). Additionally, procedures were created on the Operator Station of the tomotherapy system without a calculation of the dose distribution. The peripheral dose which was produced by a typical tomotherapy treatment plan was measured. Furthermore, these procedures were used to differentiate the parts of the peripheral dose in phantom scatter dose and head scatter and leakage dose. Additionally, the relation between peripheral dose and treatment time and between peripheral dose and delivered dose was investigated. Additionally, the peripheral dose was measured in an Alderson phantom. Results: Distances of 30cm or more resulted in a decrease of the peripheral dose to less than 0.1% of the target dose. The measured doses have an offset of approximately 1cGy in comparison to the calculated doses from the TPS. The separated head scatter and leakage dose was measured in the range of 1cGy for typical treatments. Furthermore, the investigations show a linear correlation between head scatter leakage dose and treatment time and between scatter dose parts and delivered dose. A

  9. Helical CT of the urinary organs

    Energy Technology Data Exchange (ETDEWEB)

    Schreyer, H.H.; Uggowitzer, M.M.; Ruppert-Kohlmayr, A. [Graz Univ. (Austria). Dept. of Radiology

    2002-03-01

    Despite of the diagnostic potential of conventional CT (CCT), limitations being inherent in this technology reduce its diagnostic confidence and limit clinical CT applications as 3D imaging. Helical CT (HCT) has far overcome the limitations of CCT and has become the standard CT technology. After a short overview on the technique of HCT and its advantages over CCT, the impact of HCT on the detection of disorders of the urinary organs is discussed. Due to the high quality of 3D reconstructions, vessels are visualized free of artefacts resulting in a dramatic improvement and acceptance of CT angiography, which has become a clinically important examination in the evaluation of obstructive renal artery disease. Fast HCT provides a precise assessment of the three phases of the nephrogram and it is a prerequisite for an improved depiction of abnormal vascular perfusion and impaired tubule transit of contrast material. Helical CT enables an improved characterization of cystic mass lesions reducing the diagnosis of indeterminate masses and thus facilitating a better therapeutic management. The diagnosis of renal cell carcinomas (RCC) has improved due to an increased sensitivity in detecting small RCCs, and an increased specificity in the diagnosis of neoplastic lesions. Improved staging of RCCs is the result of accurate assessment of venous tumour extension. When planning nephron-sparing surgery 3D display of the renal tumour helps to determine the resectability of the mass depicting its relation to major renal vessels and the renal collecting system. In the evaluation of renal trauma HCT provides shorter scanning time and thus fewer artefacts in the examination of traumatized patients who cannot cooperate adequately. Three-dimensional postprocessing modalities allow the assessment of the renal vascular pedicel by CT angiography and improve the demonstration of complex lacerations of the renal parenchyma. In the evaluation of the upper urinary tract unenhanced HCT has

  10. Structural models of the transmembrane region of voltage-gated and other K+ channels in open, closed, and inactivated conformations.

    Science.gov (United States)

    Durell, S R; Hao, Y; Guy, H R

    1998-01-01

    A large collaborative, multidisciplinary effort involving many research laboratories continues which uses indirect methods of molecular biology and membrane biophysics to analyze the three-dimensional structures and functional mechanisms of K+ channels. This work also extends to the distant relatives of these channels, including the voltage-gated Na+ and Ca2+ channels. The role that our group plays in this process is to combine the information gained from experimental studies with molecular modeling techniques to generate atomic-scale structural models of these proteins. The modeling process involves three stages which are summarized as: (I) prediction of the channel sequence transmembrane topology, including the functionality and secondary structure of the segments; (II) prediction of the relative positions of the transmembrane segments, and (III) filling in all atoms of the amino acid residues, with conformations for energetically stabilized interactions. Both physiochemical and evolutionary principles (including sequence homology analysis) are used to guide the development. In addition to testing the steric and energetic feasibilities of different structural hypotheses, the models provide guidance for the design of new experiments. Structural modeling also serves to "fill in the gaps" of experimental data, such as predicting additional residue interactions and conformational changes responsible for functional processes. The modeling process is currently at the stage that experimental studies have definitely confirmed most of our earlier predictions about the transmembrane topology and functionality of different segments. Additionally, this report describes the detailed, three-dimensional models we have developed for the entire transmembrane region and important functional sites of the voltage-gated Shaker K+ channel in the open, closed, and inactivated conformations (including the ion-selective pore and voltage-sensor regions). As part of this effort, we also

  11. Mice deficient in transmembrane prostatic acid phosphatase display increased GABAergic transmission and neurological alterations.

    Directory of Open Access Journals (Sweden)

    Heidi O Nousiainen

    Full Text Available Prostatic acid phosphatase (PAP, the first diagnostic marker and present therapeutic target for prostate cancer, modulates nociception at the dorsal root ganglia (DRG, but its function in the central nervous system has remained unknown. We studied expression and function of TMPAP (the transmembrane isoform of PAP in the brain by utilizing mice deficient in TMPAP (PAP-/- mice. Here we report that TMPAP is expressed in a subpopulation of cerebral GABAergic neurons, and mice deficient in TMPAP show multiple behavioral and neurochemical features linked to hyperdopaminergic dysregulation and altered GABAergic transmission. In addition to increased anxiety, disturbed prepulse inhibition, increased synthesis of striatal dopamine, and augmented response to amphetamine, PAP-deficient mice have enlarged lateral ventricles, reduced diazepam-induced loss of righting reflex, and increased GABAergic tone in the hippocampus. TMPAP in the mouse brain is localized presynaptically, and colocalized with SNARE-associated protein snapin, a protein involved in synaptic vesicle docking and fusion, and PAP-deficient mice display altered subcellular distribution of snapin. We have previously shown TMPAP to reside in prostatic exosomes and we propose that TMPAP is involved in the control of GABAergic tone in the brain also through exocytosis, and that PAP deficiency produces a distinct neurological phenotype.

  12. The generic geometry of helices and their close-packed structures

    DEFF Research Database (Denmark)

    Olsen, Kasper; Bohr, Jakob

    2010-01-01

    with values from the literature for helical polypeptide backbone structures, the alpha-, pi-. 3-10-, and gamma-helices. The alpha-helices are close to being optimally packed in the sense of efficient use of space, i.e. close-packed. They are more densely packed than the other three types of helices...

  13. What Helicity Can Tell Us about Solar Magnetic Fields Alexei A ...

    Indian Academy of Sciences (India)

    Figure 1. Knot (a) and figure-8, (b) as two examples of topological objects, which can be transformed to a simple O-ring. Right panel shows helicity meter that can be used to determine helicity of two objects shown to the left. Numbers next to helicity meter show corresponding helicity. Figure 2. A ribbon (a) demonstration of ...

  14. Particle orbit analysis for LHD helical axis configurations

    International Nuclear Information System (INIS)

    Guasp, J.; Yamazaki, K.; Motojima, O.

    1993-04-01

    Fast ion orbits for helical magnetic axis configurations in LHD (Large Helical Device) are analyzed and compared with the standard circular axis case. Boundaries between passing and helically trapped particle regions show clear differences: in the non-planar axis case the helically trapped region spreads, near the magnetic axis, over a much wider band across the 90deg pitch angle value and shows a very marked asymmetry. The locally trapped particle region is also wider than in the standard case. The differences in the loss cone boundaries of the two cases are rather small, however, the effects of re-entering criteria are very important in both cases. On the contrary, effects of finite coil size are not significant. (author)

  15. Energy and helicity of magnetic torus knots and braids

    Science.gov (United States)

    Oberti, Chiara; Ricca, Renzo L.

    2018-02-01

    By considering steady magnetic fields in the shape of torus knots and unknots in ideal magnetohydrodynamics, we compute some fundamental geometric and physical properties to provide estimates for magnetic energy and helicity. By making use of an appropriate parametrization, we show that knots with dominant toroidal coils that are a good model for solar coronal loops have negligible total torsion contribution to magnetic helicity while writhing number provides a good proxy. Hence, by the algebraic definition of writhe based on crossing numbers, we show that the estimated values of writhe based on image analysis provide reliable information for the exact values of helicity. We also show that magnetic energy is linearly related to helicity, and the effect of the confinement of magnetic field can be expressed in terms of geometric information. These results can find useful application in solar and plasma physics, where braided structures are often present.

  16. Investigation into the heat transfer performance of helically ribbed surfaces

    International Nuclear Information System (INIS)

    Firth, R.J.

    1981-12-01

    The first part of an investigation into flow and heat transfer in annular channels and seven pin clusters is described. One of the main aims of the project is to improve cluster heat transfer prediction codes for helically ribbed surfaces. A study is made of the heat transfer and flow characteristics of a helically ribbed pin in an annular channel. It is shown that the swirling flow, which is induced by the helical ribs, gives rise to substantially enhanced diffusivity levels. This phenomenon had not been taken into account by previous analysis techniques. The methods for analysing heat transfer and pressure drop data from annular channels which were originally developed for non-swirling flow are generalised to accommodate swirling flow. The new methods are shown to be consistent with empirical data. Roughness parameter data is presented for helically ribbed surfaces with an axial rib pitch into height ratio of about 7. (author)

  17. Microfabricated, 94 GHz, 25 W, Helical Traveling Wave Tube Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Teraphysics Corporation completed the Phase I objectives for the electrical design of a 94 GHz, 26 W TWT with 53% overall efficiency, including the helical circuit...

  18. Macroscopic ordering of helical pores for arraying guest molecules noncentrosymmetrically

    Science.gov (United States)

    Li, Chunji; Cho, Joonil; Yamada, Kuniyo; Hashizume, Daisuke; Araoka, Fumito; Takezoe, Hideo; Aida, Takuzo; Ishida, Yasuhiro

    2015-09-01

    Helical nanostructures have attracted continuous attention, not only as media for chiral recognition and synthesis, but also as motifs for studying intriguing physical phenomena that never occur in centrosymmetric systems. To improve the quality of signals from these phenomena, which is a key issue for their further exploration, the most straightforward is the macroscopic orientation of helices. Here as a versatile scaffold to rationally construct this hardly accessible structure, we report a polymer framework with helical pores that unidirectionally orient over a large area (~10 cm2). The framework, prepared by crosslinking a supramolecular liquid crystal preorganized in a magnetic field, is chemically robust, functionalized with carboxyl groups and capable of incorporating various basic or cationic guest molecules. When a nonlinear optical chromophore is incorporated in the framework, the resultant complex displays a markedly efficient nonlinear optical output, owing to the coherence of signals ensured by the macroscopically oriented helical structure.

  19. Studies of Helicity Injection in a Spheromak Formed by a Large Area Planar Coaxial Gun

    Science.gov (United States)

    Hsu, Scott; Bellan, Paul; Pracko, Steven

    2000-10-01

    A new planar coaxial gun has been constructed in order to study the process of helicity injection during spheromak formation. Improvements in helicity injection, a key method for poloidal field sustainment in spheromaks, would increase the attractiveness of the spheromak configuration as a fusion energy scheme. The goal of this research is to create simple, well-defined experiments allowing the details of helicity injection to be resolved and better understood. The design of the new gun, which was motivated by insights gained from ongoing solar prominence experiments [Bellan and Hansen, Phys. Plasmas 5, 1991 (1998)], involves large planar electrodes with a low field solenoid, in contrast to smaller cylindrical guns with high field solenoids commonly in existence. More efficient spheromak formation and better ``λ-matching'' should be possible in the new setup. The formation and dynamical evolution of twisted flux tubes will be studied using a variety of optical and probe diagnostics, including (1) visible light photography using a pair of fast, gated intensified CCD cameras, (2) local magnetic field measurements using an array of small pickup coils, (3) density and electron temperature measurements using a triple Langmuir probe, and (4) measurements of local ion distribution functions using laser-induced fluorescence. Details of the new gun design and initial experimental results will be presented.

  20. Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides.

    Science.gov (United States)

    Oparin, Peter B; Mineev, Konstantin S; Dunaevsky, Yakov E; Arseniev, Alexander S; Belozersky, Mikhail A; Grishin, Eugene V; Egorov, Tsezi A; Vassilevski, Alexander A

    2012-08-15

    A new peptide trypsin inhibitor named BWI-2c was obtained from buckwheat (Fagopyrum esculentum) seeds by sequential affinity, ion exchange and reversed-phase chromatography. The peptide was sequenced and found to contain 41 amino acid residues, with four cysteine residues involved in two intramolecular disulfide bonds. Recombinant BWI-2c identical to the natural peptide was produced in Escherichia coli in a form of a cleavable fusion with thioredoxin. The 3D (three-dimensional) structure of the peptide in solution was determined by NMR spectroscopy, revealing two antiparallel α-helices stapled by disulfide bonds. Together with VhTI, a trypsin inhibitor from veronica (Veronica hederifolia), BWI-2c represents a new family of protease inhibitors with an unusual α-helical hairpin fold. The linker sequence between the helices represents the so-called trypsin inhibitory loop responsible for direct binding to the active site of the enzyme that cleaves BWI-2c at the functionally important residue Arg(19). The inhibition constant was determined for BWI-2c against trypsin (1.7×10(-1)0 M), and the peptide was tested on other enzymes, including those from various insect digestive systems, revealing high selectivity to trypsin-like proteases. Structural similarity shared by BWI-2c, VhTI and several other plant defence peptides leads to the acknowledgement of a new widespread family of plant peptides termed α-hairpinins.

  1. Towards online patient imaging during helical radiotherapy

    International Nuclear Information System (INIS)

    Yu, L.; Lancaster, C.M.; Sylvander, S.R.; Poole, C.M.

    2015-01-01

    Exit-detector data from helical radiation therapy have been studied extensively for delivery verification and dose reconstruction. Since the same radiation source is used for both imaging and treatment, this work investigates the possibility of utilising exit-detector raw data for imaging purposes. This gives rise to potential clinical applications such as retrospective daily setup verification and inter-fractional setup error detection. The exit-detector raw data were acquired and independently analysed using Python programming language. The raw data were extracted from the treatment machine’s onboard computer, and converted into 2D array files. The contours of objects (phantom or patient) were acquired by applying a logarithmic function to the ratio of two sinograms, one with the object in the beam and one without. The setup variation between any two treatment deliveries can be detected by applying the same function to their corresponding exit-detector sinograms. The contour of the object was well defined by the secondary radiation from the treatment beam and validated with the imaging beam, although no internal structures were discernible due to the interference from the primary radiation. The sensitivity of the setup variation detection was down to 2 mm, which was mainly limited by the resolution of the exit-detector itself. The exit-detector data from treatment procedures contain valuable photon exit fluence maps which can be utilised for contour definition and verification of patient alignment without reconstruction.

  2. Helical Screw Expander Evaluation Project. Final report

    Energy Technology Data Exchange (ETDEWEB)

    McKay, R.

    1982-03-01

    A functional 1-MW geothermal electric power plant that featured a helical screw expander was produced and then tested in Utah in 1978 to 1979 with a demonstrated average performance of approximately 45% machine efficiency over a wide range of test conditions in noncondensing operation on two-phase geothermal fluids. The Project also produced a computer-equipped data system, an instrumentation and control van, and a 1000-kW variable load bank, all integrated into a test array designed for operation at a variety of remote test sites. Additional testing was performed in Mexico in 1980 under a cooperative test program using the same test array, and machine efficiency was measured at 62% maximum with the rotors partially coated with scale, compared with approximately 54% maximum in Utah with uncoated rotors, confirming the importance of scale deposits within the machine on performance. Data are presented for the Utah testing and for the noncondensing phases of the testing in Mexico. Test time logged was 437 hours during the Utah tests and 1101 hours during the Mexico tests.

  3. Tokamak startup using point-source dc helicity injection.

    Science.gov (United States)

    Battaglia, D J; Bongard, M W; Fonck, R J; Redd, A J; Sontag, A C

    2009-06-05

    Startup of a 0.1 MA tokamak plasma is demonstrated on the ultralow aspect ratio Pegasus Toroidal Experiment using three localized, high-current density sources mounted near the outboard midplane. The injected open field current relaxes via helicity-conserving magnetic turbulence into a tokamaklike magnetic topology where the maximum sustained plasma current is determined by helicity balance and the requirements for magnetic relaxation.

  4. Pulmonary artery aneurysm in Bechcet's disease: helical computed tomography study

    International Nuclear Information System (INIS)

    Munoz, J.; Caballero, P.; Olivera, M. J.; Cajal, M. L.; Caniego, J. L.

    2000-01-01

    Behcet's disease is a vasculitis of unknown etiology that affects arteries and veins of different sizes and can be associated with pulmonary artery aneurysms. We report the case of a patient with Behcet's disease and a pulmonary artery aneurysm who was studied by means of plain chest X ray, helical computed tomography and pulmonary arteriography. Helical computed tomography is a reliable technique for the diagnosis and follow-up of these patients. (Author) 9 refs

  5. Comparison between helical computed tomography angiography and intraoperative findings

    Directory of Open Access Journals (Sweden)

    Abijit Shetty

    2014-01-01

    Conclusions: Helical CT is important in delineating the arterial, venous, and ureteral anatomy and can show the important incidental findings. Left renal donors and males have more variations in their renal anatomy. Technically challenging laparoscopic nephrectomy on the multiple-vessel-side donor is possible with the aid of helical CT. The importance of the CT in evaluating donor renal anatomy for a technically challenging laparoscopic donor nephrectomy is commendable.

  6. Progressive and resonant wave helices application to electron paramagnetic resonance

    International Nuclear Information System (INIS)

    Volino, F.

    1969-01-01

    We show that helices can be used as resonant systems. Their properties are theoretically and experimentally studied. We describe resonant helices for electron paramagnetic resonance in X-band and develop a comparison between their sensitivity and the sensitivity of a normal resonant cavity. For cylindrical samples less than 3 mm diameter, the helix is more sensitive and can produce more intense microwave magnetic fields. (author) [fr

  7. Transmembrane topology of the acetylcholine receptor examined in reconstituted vesicles

    International Nuclear Information System (INIS)

    McCrea, P.D.

    1987-01-01

    Each of the five acetylcholine receptor (AChR) subunits, α 2 β-γδ, is believed to have the same number of transmembrane crossing and to share the same general folding pattern. AChR isolated from the electric organ of electric fish is predominantly dimeric. We have used this bridge as a marker for the C-terminus of the δ subunit, and presumably that of the other subunits in addition. The disulfide's accessibility to hydrophilic reductants, principally glutathione (GSH), was tested in a reconstituted vesicle system. The reduction of the δ-δ desulfide, as evidenced by the transition of AChrR dimers to monomers, was quantitatively monitored on velocity sedimentation sucrose gradients. Alternatively, the reduction of δ 2 to δ was followed by employing non-reducing SDS-PAGE. Reductants such as GSH were able to access the bridge in intact right-side-out vesicles. No acceleration of this process was evident when the vesicles were disrupted by freeze-thaw or by detergents. Control experiments which determined the rate of reduction of entrapped diphtheria toxin, or that of 3 H-GSH efflux, demonstrated that intact reconstituted vesicles provide an adequate permeability barrier to GSH access of their intravesicular space

  8. Transmembrane channel-like (tmc) gene regulates Drosophila larval locomotion.

    Science.gov (United States)

    Guo, Yanmeng; Wang, Yuping; Zhang, Wei; Meltzer, Shan; Zanini, Damiano; Yu, Yue; Li, Jiefu; Cheng, Tong; Guo, Zhenhao; Wang, Qingxiu; Jacobs, Julie S; Sharma, Yashoda; Eberl, Daniel F; Göpfert, Martin C; Jan, Lily Yeh; Jan, Yuh Nung; Wang, Zuoren

    2016-06-28

    Drosophila larval locomotion, which entails rhythmic body contractions, is controlled by sensory feedback from proprioceptors. The molecular mechanisms mediating this feedback are little understood. By using genetic knock-in and immunostaining, we found that the Drosophila melanogaster transmembrane channel-like (tmc) gene is expressed in the larval class I and class II dendritic arborization (da) neurons and bipolar dendrite (bd) neurons, both of which are known to provide sensory feedback for larval locomotion. Larvae with knockdown or loss of tmc function displayed reduced crawling speeds, increased head cast frequencies, and enhanced backward locomotion. Expressing Drosophila TMC or mammalian TMC1 and/or TMC2 in the tmc-positive neurons rescued these mutant phenotypes. Bending of the larval body activated the tmc-positive neurons, and in tmc mutants this bending response was impaired. This implicates TMC's roles in Drosophila proprioception and the sensory control of larval locomotion. It also provides evidence for a functional conservation between Drosophila and mammalian TMCs.

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

    DEFF Research Database (Denmark)

    Högel, Philipp; Götz, Alexander; Kuhne, Felix

    2018-01-01

    the measured exchange kinetics and reveal, at atomic resolution, a severe packing defect at glycine that enhances local hydration. Furthermore, glycine alters H-bond occupancies and triggers a redistribution of α-helical and 310-helical H-bonds. These effects facilitate local helix bending at the glycine site...

  10. Helical Birods: An Elastic Model of Helically Wound Double-Stranded Rods

    KAUST Repository

    Prior, Christopher

    2014-03-11

    © 2014, Springer Science+Business Media Dordrecht. We consider a geometrically accurate model for a helically wound rope constructed from two intertwined elastic rods. The line of contact has an arbitrary smooth shape which is obtained under the action of an arbitrary set of applied forces and moments. We discuss the general form the theory should take along with an insight into the necessary geometric or constitutive laws which must be detailed in order for the system to be complete. This includes a number of contact laws for the interaction of the two rods, in order to fit various relevant physical scenarios. This discussion also extends to the boundary and how this composite system can be acted upon by a single moment and force pair. A second strand of inquiry concerns the linear response of an initially helical rope to an arbitrary set of forces and moments. In particular we show that if the rope has the dimensions assumed of a rod in the Kirchhoff rod theory then it can be accurately treated as an isotropic inextensible elastic rod. An important consideration in this demonstration is the possible effect of varying the geometric boundary constraints; it is shown the effect of this choice becomes negligible in this limit in which the rope has dimensions similar to those of a Kirchhoff rod. Finally we derive the bending and twisting coefficients of this effective rod.

  11. Folding and insertion thermodynamics of the transmembrane WALP peptide.

    Science.gov (United States)

    Bereau, Tristan; Bennett, W F Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

    2015-12-28

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum-in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

  12. Electrohydrodynamic (EHD) vortices in helical turbulence

    International Nuclear Information System (INIS)

    Kikuchi, H.

    1996-01-01

    The study of large-scale coherent hydrodynamic (HD) vortex generation has been extended to electrified charged dusty vortices to be termed as electrohydrodynamic (EHD) vortices, incorporating helical turbulence in electric and magnetic fields into that in fluid velocity, which are all created by an external DC electric field on the background. A new equation of EHD vortices is introduced on the basis of a set of EHD or electromagnetohydrodynamic (EMHD) equations, including equations of state and a full set of Maxwell's equations by using functional techniques for estimating equations for an ensemble average, turbulent background, and additional random field. In fact, EHD vortices for a charged dusty fluid can be more explosive with larger instabilities than HD vortices. In addition, it is inferred that an external DC electric field could provide the origin of additional self-organization to a coalescence of fluid vortex and electric field lines as a manifestation of a new frozen-in field concept for electric fields when the electric Reynolds number is sufficiently high. This is discussed on the basis of a set of general transport equations for fluid vorticity, magnetic and electric fields that are rederived concisely. In particular, a novel concept of electric field line merging-reconnection is developed in close relation to fluid vortex line merging, indicating a coalescence of fluid vortex breakdown or merging point and electric field line reconnection point, X-type or O-type with possible application to tornadic thunderstorms. In fact, a thundercloud charge distribution so as to provide a coalescence of fluid vortex and electric field lines is quite possible without theoretical inconsistency, and is thought most likely to occur from observations available so far. (orig.)

  13. Visualizing water molecules in transmembrane proteins using radiolytic labeling methods.

    Science.gov (United States)

    Orban, Tivadar; Gupta, Sayan; Palczewski, Krzysztof; Chance, Mark R

    2010-02-09

    Essential to cells and their organelles, water is both shuttled to where it is needed and trapped within cellular compartments and structures. Moreover, ordered waters within protein structures often colocalize with strategically placed polar or charged groups critical for protein function, yet it is unclear if these ordered water molecules provide structural stabilization, mediate conformational changes in signaling, neutralize charged residues, or carry out a combination of all these functions. Structures of many integral membrane proteins, including G protein-coupled receptors (GPCRs), reveal the presence of ordered water molecules that may act like prosthetic groups in a manner quite unlike bulk water. Identification of "ordered" waters within a crystalline protein structure requires sufficient occupancy of water to enable its detection in the protein's X-ray diffraction pattern, and thus, the observed waters likely represent a subset of tightly bound functional waters. In this review, we highlight recent studies that suggest the structures of ordered waters within GPCRs are as conserved (and thus as important) as conserved side chains. In addition, methods of radiolysis, coupled to structural mass spectrometry (protein footprinting), reveal dynamic changes in water structure that mediate transmembrane signaling. The idea of water as a prosthetic group mediating chemical reaction dynamics is not new in fields such as catalysis. However, the concept of water as a mediator of conformational dynamics in signaling is just emerging, because of advances in both crystallographic structure determination and new methods of protein footprinting. Although oil and water do not mix, understanding the roles of water is essential to understanding the function of membrane proteins.

  14. Modeling the Structure of SARS 3a Transmembrane Protein Using a ...

    Indian Academy of Sciences (India)

    Modeling the structure of SARS 3a Transmembrane protein using a minimum unfavorable contact approach. S RAMAKRISHNA, SILADITYA PADHI and U DEVA PRIYAKUMAR*. Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India.

  15. Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors

    Directory of Open Access Journals (Sweden)

    Zied Gaieb

    2017-01-01

    Full Text Available Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7 bound to its ligand CCL21.

  16. Magnetic Helicity and Large Scale Magnetic Fields: A Primer

    Science.gov (United States)

    Blackman, Eric G.

    2015-05-01

    Magnetic fields of laboratory, planetary, stellar, and galactic plasmas commonly exhibit significant order on large temporal or spatial scales compared to the otherwise random motions within the hosting system. Such ordered fields can be measured in the case of planets, stars, and galaxies, or inferred indirectly by the action of their dynamical influence, such as jets. Whether large scale fields are amplified in situ or a remnant from previous stages of an object's history is often debated for objects without a definitive magnetic activity cycle. Magnetic helicity, a measure of twist and linkage of magnetic field lines, is a unifying tool for understanding large scale field evolution for both mechanisms of origin. Its importance stems from its two basic properties: (1) magnetic helicity is typically better conserved than magnetic energy; and (2) the magnetic energy associated with a fixed amount of magnetic helicity is minimized when the system relaxes this helical structure to the largest scale available. Here I discuss how magnetic helicity has come to help us understand the saturation of and sustenance of large scale dynamos, the need for either local or global helicity fluxes to avoid dynamo quenching, and the associated observational consequences. I also discuss how magnetic helicity acts as a hindrance to turbulent diffusion of large scale fields, and thus a helper for fossil remnant large scale field origin models in some contexts. I briefly discuss the connection between large scale fields and accretion disk theory as well. The goal here is to provide a conceptual primer to help the reader efficiently penetrate the literature.

  17. A new look at time dependent transport of magnetic helicity

    International Nuclear Information System (INIS)

    Moses, R.W.

    1991-01-01

    This paper has two purposes. First, a new definition of magnetic helicity is presented to give a sharper distinction between inductive and parallel-electrostatic magnetic helicity transport. Second, a theorem is described which states that only parallel-electrostatic transport can indefinitely sustain magnetic helicity dissipation in a torus, where the boundary moves to maintain a constant volume averaged toroidal flux. The concept of magnetic helicity lends considerable simplification to the descriptions of plasma relaxation, current drive, or Ohmic dissipation. The definition of magnetic helicity, K ≡ ∫A·BdV, used in 2 cited references is only applicable to closed volumes where no magnetic field penetrates the surface. In a torus, gauge invariance is maintained by subtracting, from A, the contribution due to transformer flux through the core of the torus. When magnetic field penetrates the surface under consideration, K can be made gauge invariant by subtracting a vacuum field term, A p ·P. The electric field E =-∇φ-∂A/∂t is now divided into explicitly electrostatic, φ, and inductive, A, components. If the macroscopic nature of B and the linked transformer flux do not change over a long period of time, then ∫E·BdV = ∫ηJ·BdV = - ∫φB·ds when averaged over time. This result is well known for time independent fields, and now it clearly extends to time varying fields that undergo no macroscopic change over an extended period. If magnetic helicity dissipation is an essential part of plasma sustainment, there is no inductive mechanism that can transport magnetic helicity into a volume without connecting field lines across the surface of that volume. 5 refs

  18. THE ROLE OF MAGNETIC HELICITY IN STRUCTURING THE SOLAR CORONA

    Energy Technology Data Exchange (ETDEWEB)

    Knizhnik, K. J. [Department of Physics and Astronomy, The Johns Hopkins University, Baltimore, MD 21287 (United States); Antiochos, S. K.; DeVore, C. R. [Heliophysics Science Division, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States)

    2017-01-20

    Two of the most widely observed and striking features of the Sun's magnetic field are coronal loops, which are smooth and laminar, and prominences or filaments, which are strongly sheared. Loops are puzzling because they show little evidence of tangling or braiding, at least on the quiet Sun, despite the chaotic nature of the solar surface convection. Prominences are mysterious because the origin of their underlying magnetic structure—filament channels—is poorly understood at best. These two types of features would seem to be quite unrelated and wholly distinct. We argue that, on the contrary, they are inextricably linked and result from a single process: the injection of magnetic helicity into the corona by photospheric motions and the subsequent evolution of this helicity by coronal reconnection. In this paper, we present numerical simulations of the response of a Parker (1972) corona to photospheric driving motions that have varying degrees of helicity preference. We obtain four main conclusions: (1) in agreement with the helicity condensation model of Antiochos (2013), the inverse cascade of helicity by magnetic reconnection in the corona results in the formation of filament channels localized about polarity inversion lines; (2) this same process removes most complex fine structure from the rest of the corona, resulting in smooth and laminar coronal loops; (3) the amount of remnant tangling in coronal loops is inversely dependent on the net helicity injected by the driving motions; and (4) the structure of the solar corona depends only on the helicity preference of the driving motions and not on their detailed time dependence. We discuss the implications of our results for high-resolution observations of the corona.

  19. Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogaster embryogenesis

    Directory of Open Access Journals (Sweden)

    González Mauricio

    2009-09-01

    Full Text Available Abstract Background Morphogenetic events that shape the Drosophila melanogaster embryo are tightly controlled by a genetic program in which specific sets of genes are up-regulated. We used a suppressive subtractive hybridization procedure to identify a group of developmentally regulated genes during early stages of D. melanogaster embryogenesis. We studied the spatiotemporal activity of these genes in five different intervals covering 12 stages of embryogenesis. Results Microarrays were constructed to confirm induction of expression and to determine the temporal profile of isolated subtracted cDNAs during embryo development. We identified a set of 118 genes whose expression levels increased significantly in at least one developmental interval compared with a reference interval. Of these genes, 53% had a phenotype and/or molecular function reported in the literature, whereas 47% were essentially uncharacterized. Clustering analysis revealed demarcated transcript groups with maximum gene activity at distinct developmental intervals. In situ hybridization assays were carried out on 23 uncharacterized genes, 15 of which proved to have spatiotemporally restricted expression patterns. Among these 15 uncharacterized genes, 13 were found to encode putative secreted and transmembrane proteins. For three of them we validated our protein sequence predictions by expressing their cDNAs in Drosophila S2R+ cells and analyzed the subcellular distribution of recombinant proteins. We then focused on the functional characterization of the gene CG6234. Inhibition of CG6234 by RNA interference resulted in morphological defects in embryos, suggesting the involvement of this gene in germ band retraction. Conclusion Our data have yielded a list of developmentally regulated D. melanogaster genes and their expression profiles during embryogenesis and provide new information on the spatiotemporal expression patterns of several uncharacterized genes. In particular, we

  20. Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogaster embryogenesis.

    Science.gov (United States)

    Zúñiga, Alejandro; Hödar, Christian; Hanna, Patricia; Ibáñez, Freddy; Moreno, Pablo; Pulgar, Rodrigo; Pastenes, Luis; González, Mauricio; Cambiazo, Verónica

    2009-09-22

    Morphogenetic events that shape the Drosophila melanogaster embryo are tightly controlled by a genetic program in which specific sets of genes are up-regulated. We used a suppressive subtractive hybridization procedure to identify a group of developmentally regulated genes during early stages of D. melanogaster embryogenesis. We studied the spatiotemporal activity of these genes in five different intervals covering 12 stages of embryogenesis. Microarrays were constructed to confirm induction of expression and to determine the temporal profile of isolated subtracted cDNAs during embryo development. We identified a set of 118 genes whose expression levels increased significantly in at least one developmental interval compared with a reference interval. Of these genes, 53% had a phenotype and/or molecular function reported in the literature, whereas 47% were essentially uncharacterized. Clustering analysis revealed demarcated transcript groups with maximum gene activity at distinct developmental intervals. In situ hybridization assays were carried out on 23 uncharacterized genes, 15 of which proved to have spatiotemporally restricted expression patterns. Among these 15 uncharacterized genes, 13 were found to encode putative secreted and transmembrane proteins. For three of them we validated our protein sequence predictions by expressing their cDNAs in Drosophila S2R+ cells and analyzed the subcellular distribution of recombinant proteins. We then focused on the functional characterization of the gene CG6234. Inhibition of CG6234 by RNA interference resulted in morphological defects in embryos, suggesting the involvement of this gene in germ band retraction. Our data have yielded a list of developmentally regulated D. melanogaster genes and their expression profiles during embryogenesis and provide new information on the spatiotemporal expression patterns of several uncharacterized genes. In particular, we recovered a substantial number of unknown genes encoding

  1. Deletion of the transmembrane transporter ABCG1 results in progressive pulmonary lipidosis.

    Science.gov (United States)

    Baldán, Angel; Tarr, Paul; Vales, Charisse S; Frank, Joy; Shimotake, Thomas K; Hawgood, Sam; Edwards, Peter A

    2006-09-29

    We show that mice lacking the ATP-binding cassette transmembrane transporter ABCG1 show progressive and age-dependent severe pulmonary lipidosis that recapitulates the phenotypes of different respiratory syndromes in both humans and mice. The lungs of chow-fed Abcg1(-/-) mice, >6-months old, exhibit extensive subpleural cellular accumulation, macrophage, and pneumocyte type 2 hypertrophy, massive lipid deposition in both macrophages and pneumocytes and increased levels of surfactant. No such abnormalities are observed at 3 months of age. However, gene expression profiling reveals significant changes in the levels of mRNAs encoding key genes involved in lipid metabolism in both 3- and 8-month-old Abcg1(-/-) mice. These data suggest that the lungs of young Abcg1(-/-) mice maintain normal lipid levels by repressing lipid biosynthetic pathways and that such compensation is inadequate as the mice mature. Studies with A-549 cells, a model for pneumocytes type 2, demonstrate that overexpression of ABCG1 specifically stimulates the efflux of cellular cholesterol by a process that is dependent upon phospholipid secretion. In addition, we demonstrate that Abcg1(-/-), but not wild-type macrophages, accumulate cholesterol ester droplets when incubated with surfactant. Together, these data provide a mechanism to explain the lipid accumulation in the lungs of Abcg1(-/-)mice. In summary, our results demonstrate that ABCG1 plays essential roles in pulmonary lipid homeostasis.

  2. Transmembrane collagen XVII modulates integrin dependent keratinocyte migration via PI3K/Rac1 signaling.

    Directory of Open Access Journals (Sweden)

    Stefanie Löffek

    Full Text Available The hemidesmosomal transmembrane component collagen XVII (ColXVII plays an important role in the anchorage of the epidermis to the underlying basement membrane. However, this adhesion protein seems to be also involved in the regulation of keratinocyte migration, since its expression in these cells is strongly elevated during reepithelialization of acute wounds and in the invasive front of squamous cell carcinoma, while its absence in ColXVII-deficient keratinocytes leads to altered cell motility. Using a genetic model of murine Col17a1⁻/⁻ keratinocytes we elucidated ColXVII mediated signaling pathways in cell adhesion and migration. Col17a1⁻/⁻ keratinocytes exhibited increased spreading on laminin 332 and accelerated, but less directed cell motility. These effects were accompanied by increased expression of the integrin subunits β4 and β1. The migratory phenotype, as evidenced by formation of multiple unstable lamellipodia, was associated with enhanced phosphoinositide 3-kinase (PI3K activity. Dissection of the signaling pathway uncovered enhanced phosphorylation of the β4 integrin subunit and the focal adhesion kinase (FAK as activators of PI3K. This resulted in elevated Rac1 activity as a downstream consequence. These results provide mechanistic evidence that ColXVII coordinates keratinocyte adhesion and directed motility by interfering integrin dependent PI3K activation and by stabilizing lamellipodia at the leading edge of reepithelializing wounds and in invasive squamous cell carcinoma.

  3. Residues in the hendra virus fusion protein transmembrane domain are critical for endocytic recycling.

    Science.gov (United States)

    Popa, Andreea; Carter, James R; Smith, Stacy E; Hellman, Lance; Fried, Michael G; Dutch, Rebecca Ellis

    2012-03-01

    Hendra virus is a highly pathogenic paramyxovirus classified as a biosafety level four agent. The fusion (F) protein of Hendra virus is critical for promoting viral entry and cell-to-cell fusion. To be fusogenically active, Hendra virus F must undergo endocytic recycling and cleavage by the endosomal/lysosomal protease cathepsin L, but the route of Hendra virus F following internalization and the recycling signals involved are poorly understood. We examined the intracellular distribution of Hendra virus F following endocytosis and showed that it is primarily present in Rab5- and Rab4-positive endosomal compartments, suggesting that cathepsin L cleavage occurs in early endosomes. Hendra virus F transmembrane domain (TMD) residues S490 and Y498 were found to be important for correct Hendra virus F recycling, with the hydroxyl group of S490 and the aromatic ring of Y498 important for this process. In addition, changes in association of isolated Hendra virus F TMDs correlated with alterations to Hendra virus F recycling, suggesting that appropriate TMD interactions play an important role in endocytic trafficking.

  4. Brucella Intracellular Life Relies on the Transmembrane Protein CD98 Heavy Chain.

    Science.gov (United States)

    Keriel, Anne; Botella, Eric; Estrach, Soline; Bragagnolo, Gabriel; Vergunst, Annette C; Feral, Chloe C; O'Callaghan, David

    2015-06-01

    Brucella are intracellular bacterial pathogens that use a type IV secretion system (T4SS) to escape host defenses and create a niche in which they can multiply. Although the importance of Brucella T4SS is clear, little is known about its interactions with host cell structures. In this study, we identified the eukaryotic protein CD98hc as a partner for Brucella T4SS subunit VirB2. This transmembrane glycoprotein is involved in amino acid transport, modulation of integrin signaling, and cell-to-cell fusion. Knockdown of CD98hc expression in HeLa cells demonstrated that it is essential for Brucella infection. Using knockout dermal fibroblasts, we confirmed its role for Brucella but found that it is not required for Salmonella infection. CD98hc transiently accumulates around the bacteria during the early phases of infection and is required for both optimal bacterial uptake and intracellular multiplication of Brucella. These results provide new insights into the complex interplay between Brucella and its host. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Transmembrane prostatic acid phosphatase (TMPAP interacts with snapin and deficient mice develop prostate adenocarcinoma.

    Directory of Open Access Journals (Sweden)

    Ileana B Quintero

    Full Text Available The molecular mechanisms underlying prostate carcinogenesis are poorly understood. Prostatic acid phosphatase (PAP, a prostatic epithelial secretion marker, has been linked to prostate cancer since the 1930's. However, the contribution of PAP to the disease remains controversial. We have previously cloned and described two isoforms of this protein, a secretory (sPAP and a transmembrane type-I (TMPAP. The goal in this work was to understand the physiological function of TMPAP in the prostate. We conducted histological, ultra-structural and genome-wide analyses of the prostate of our PAP-deficient mouse model (PAP(-/- with C57BL/6J background. The PAP(-/- mouse prostate showed the development of slow-growing non-metastatic prostate adenocarcinoma. In order to find out the mechanism behind, we identified PAP-interacting proteins byyeast two-hybrid assays and a clear result was obtained for the interaction of PAP with snapin, a SNARE-associated protein which binds Snap25 facilitating the vesicular membrane fusion process. We confirmed this interaction by co-localization studies in TMPAP-transfected LNCaP cells (TMPAP/LNCaP cells and in vivo FRET analyses in transient transfected LNCaP cells. The differential gene expression analyses revealed the dysregulation of the same genes known to be related to synaptic vesicular traffic. Both TMPAP and snapin were detected in isolated exosomes. Our results suggest that TMPAP is involved in endo-/exocytosis and disturbed vesicular traffic is a hallmark of prostate adenocarcinoma.

  6. Cdon and Boc: Two transmembrane proteins implicated in cell-cell communication.

    Science.gov (United States)

    Sanchez-Arrones, Luisa; Cardozo, Marcos; Nieto-Lopez, Francisco; Bovolenta, Paola

    2012-05-01

    Cdon and Boc, and their Drosophila homologues Ihog and Boi, are evolutionary conserved transmembrane glycoproteins belonging to a subgroup of the Immunoglobulin superfamily of cell adhesion molecules (CAMs). Initially isolated in vertebrates as CAMs that link cadherin function with MAPK signaling in myoblast differentiation, they have thereafter been shown to act as essential receptors for the Hedgehog (Hh) family of secreted proteins. They associate with both ligand and other Hh receptor components, including Ptch and Gas1, thus forming homo- and heteromeric complexes. In Drosophila, they are also involved in ligand processing and release from Hh producing cells. Cdon/Boc and Ihog/Boi can substitute one another and play redundant functions is some contexts. In addition, Boc, but not Cdon, mediates axon guidance information provided by Hh in specific neuronal populations, whereas mutations in the CDON cause holoprosencephaly, a human congenital anomaly defined by forebrain midline defects prominently associated with diminished Hh pathway activity. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Tryptophan Substitutions at Lipid-exposed Positions of the Gamma M3 Transmembrane Domain Increase the Macroscopic Ionic Current Response of the Torpedo californica Nicotinic Acetylcholine Receptor

    Science.gov (United States)

    Cruz-Martín, A.; Mercado, J.L.; Rojas, L.V.; McNamee, M.G.; Lasalde-Dominicci, J.A.

    2015-01-01

    Our previous amino-acid substitutions at the postulated lipid-exposed transmembrane segment M4 of the Torpedo californica acetylcholine receptor (AChR) focused on the alpha subunit. In this study we have extended the mutagenesis analysis using single tryptophan replacements in seven positions (I288, M291, F292, S294, L296, M299 and N300) near the center of the third transmembrane domain of the gamma subunit (γM3). All the tryptophan substitution mutants were expressed in Xenopus laevis oocytes following mRNA injections at levels close to wild type. The functional response of these mutants was evaluated using macroscopic current analysis in voltage-clamped oocytes. For all the substitutions the concentration for half-maximal activation, EC50, is similar to wild type using acetylcholine. For F292W, L296W and M299W the normalized macroscopic responses are 2- to 3-fold higher than for wild type. Previous photolabeling studies demonstrated that these three positions were in contact with membrane lipids. Each of these M3 mutations was co-injected with the previously characterized αC418W mutant to examine possible synergistic effects of single lipid-exposed mutations on two different subunits. For the γM3/αM4 double mutants, the EC50s were similar to those measured for the αC418W mutant alone. Tryptophan substitutions at positions that presumably face the interior of the protein (S294 and M291) or neighboring helices (I288) did not cause significant inhibition of channel function or surface expression of AChRs. PMID:11547353

  8. Stable double helical iodine chains inside single-walled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Zhen [College of Science, Liaoning University of Technology, Jinzhou, Liaoning, 121001 (China); Liu, Chun-Jian [College of Mathematics and Physics, Bohai University, Jinzhou, Liaoning, 121000 (China); Lv, Hang [Institute of New Energy, Bohai University, Jinzhou, Liaoning, 121000 (China); Liu, Bing-Bing, E-mail: liubb@jlu.edu.cn [State Key Laboratory of Superhard Materials, Jilin University, Changchun, 130012 (China)

    2016-08-12

    The helicity of stable double helical iodine chains inside single-walled carbon nanotubes (SWCNTs) is studied by calculating the systematic interaction energy. Our results present clear images of stable double helical structures inside SWCNTs. The optimum helical radius and helical angle increase and decrease with increasing diameter, respectively. The tube's diameter plays a leading role in the helicity of encapsulated structures, while the tube's chirality may induce different metastable structures. This study indicates that the observed double helical iodine chains in experiments are not necessarily the optimum structures, but may also be metastable structures. - Highlights: • The stable double helical iodine chain inside single-walled carbon nanotubes is proposed. • The influence of tube's diameter and chirality on the stability of encapsulated iodine chains is studied. • The metastable double helical structures may be co-existence with the stable structure but not in the same tubes.

  9. l=1 helical axis heliotron device in Kyoto university

    International Nuclear Information System (INIS)

    Nagasaki, K.; Sano, F.; Mizuuchi, T.; Hanatani, K.; Okada, H.; Obiki, T.

    1999-01-01

    Helical systems are an attractive candidate for magnetic fusion reactor. Recently, there has been great progress in theoretical research of three dimensional magnetic field structures, resulting in several kinds of confinement optimization being proposed for toroidal magnetic confinement system. For example, some sophisticated ideas have appeared on stage such as quasi-helical symmetry and quasi-isodynamic system. To find experimentally which way is the best Optimisation, a new helical axis heliotron device, so called 'Heliotron J', is under construction in the Institute of Advanced Energy, Kyoto University, Japan. In this conference, the basic concept and the present status will be presented. In the conventional plane axis helical system, it was difficult to have both good particle confinement and good MHD stability simultaneously. The goal of Heliotron J project is to clarify their compatibility in the spatial axis toroidal device. The best way for Optimising the helical magnetic field configuration will be explored by investigating the plasma response to the change in the field components. The main subjects for plasma experiment are: demonstration of the existence of good magnetic flux surfaces, reduction of neoclassical transport in collisionless regime, MHD Stabilisation in high β plasma, controllability of bootstrap current, good confinement of high energy particles

  10. Chirality of Intermediate Filaments and Magnetic Helicity of Active Regions

    Science.gov (United States)

    Lim, Eun-Kyung; Chae, J.

    2009-05-01

    Filaments that form either between or around active regions (ARs) are called intermediate filaments. Even though there have been many theoretical studies, the origin of the chirality of filaments is still unknown. We investigated how intermediate filaments are related to their associated ARs, especially from the point of view of magnetic helicity and the orientation of polarity inversion lines (PILs). The chirality of filaments has been determined based on the orientations of barbs observed in the full-disk Hα images taken at Big Bear Solar Observatory during the rising phase of solar cycle 23. The sign of magnetic helicity of ARs has been determined using S/inverse-S shaped sigmoids from Yohkoh SXT images. As a result, we have found a good correlation between the chirality of filaments and the magnetic helicity sign of ARs. Among 45 filaments, 42 filaments have shown the same sign as helicity sign of nearby ARs. It has been also confirmed that the role of both the orientation and the relative direction of PILs to ARs in determining the chirality of filaments is not significant, against a theoretical prediction. These results suggest that the chirality of intermediate filaments may originate from magnetic helicity of their associated ARs.

  11. Gynecological applications of helical CT using SmartPrep

    Energy Technology Data Exchange (ETDEWEB)

    Sakurada, Akira; Kakizaki, Dai; Abe, Kimihiko [Tokyo Medical Coll. (Japan)

    1999-11-01

    SmartPrep is software program for scanning a given region of interest (ROI) at optimal contrast density. An operator can arbitrarily define ROI and preset the CT value at which scanning should be started. After the injection of a contrast medium, system conducts continuous monitoring of the ROI and the operator starts helical scanning of the planned region when the present CT value has been reached. In comparison with conventional helical CT that requires a period of time from the beginning of contrast medium injection to the beginning of scanning, SmartPrep minimizes personal error and better depicts the artery-predominant phase under optimal conditions. In this study we examine the usefulness of contrast-enhanced helical CT using SmartPrep in the evaluation of gynecological disease. When the contrast medium was injected into the dorsal vein of the hand at a rate of 3 ml/sec, strong staining of pelvic arteries was observed in the CT images started at 17 to 23 sec after injection. The early-phase helical CT obtained under these conditions provided good depiction of lesions in cases of placenta accreta and invasive mole, as well as clear demonstration of tumor angiogenesis and evaluation of laterality in cases of cervical cancer. Comparison of the early and delayed phase also facilitated easier evaluation of lymph nodes than conventional comparison of simple and contrast-enhanced CT. The results thus suggest the usefulness of contrast-enhanced helical CT using SmartPrep in gynecology. (author)

  12. Reduced bispectrum seeded by helical primordial magnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Hortúa, Héctor Javier [Universidad Nacional de Colombia-Bogotá, Facultad de Ciencias, Departamento de Física, Carrera 30 Calle 45-03, C.P. 111321 Bogotá (Colombia); Castañeda, Leonardo, E-mail: hjhortuao@unal.edu.co, E-mail: lcastanedac@unal.edu.co [Grupo de Gravitación y Cosmología, Observatorio Astronómico Nacional, Universidad Nacional de Colombia, cra 45 No 26-85, Edificio Uriel Gutierréz, Bogotá, D.C. (Colombia)

    2017-06-01

    In this paper, we investigate the effects of helical primordial magnetic fields (PMFs) on the cosmic microwave background (CMB) reduced bispectrum. We derive the full three-point statistics of helical magnetic fields and numerically calculate the even contribution in the collinear configuration. We then numerically compute the CMB reduced bispectrum induced by passive and compensated PMF modes on large angular scales. There is a negative signal on the bispectrum due to the helical terms of the fields and we also observe that the biggest contribution to the bispectrum comes from the non-zero IR cut-off for causal fields, unlike the two-point correlation case. For negative spectral indices, the reduced bispectrum is enhanced by the passive modes. This gives a lower value of the upper limit for the mean amplitude of the magnetic field on a given characteristic scale. However, high values of IR cut-off in the bispectrum, and the helical terms of the magnetic field relaxes this bound. This demonstrates the importance of the IR cut-off and helicity in the study of the nature of PMFs from CMB observations.

  13. Microscopic Processes in Global Relativistic Jets Containing Helical Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Ken-Ichi Nishikawa

    2016-09-01

    Full Text Available In the study of relativistic jets one of the key open questions is their interaction with the environment on the microscopic level. Here, we study the initial evolution of both electron–proton ( e − – p + and electron–positron ( e ± relativistic jets containing helical magnetic fields, focusing on their interaction with an ambient plasma. We have performed simulations of “global” jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability (kKHI and the Mushroom instability (MI. In our initial simulation study these kinetic instabilities are suppressed and new types of instabilities can grow. In the e − – p + jet simulation a recollimation-like instability occurs and jet electrons are strongly perturbed. In the e ± jet simulation a recollimation-like instability occurs at early times followed by a kinetic instability and the general structure is similar to a simulation without helical magnetic field. Simulations using much larger systems are required in order to thoroughly follow the evolution of global jets containing helical magnetic fields.

  14. Progesterone modulation of transmembrane helix-helix interactions between the α-subunit of Na/K-ATPase and phospholipid N-methyltransferase in the oocyte plasma membrane

    Directory of Open Access Journals (Sweden)

    Askari Amir

    2010-05-01

    Full Text Available Abstract Background Progesterone binding to the surface of the amphibian oocyte initiates the meiotic divisions. Our previous studies with Rana pipiens oocytes indicate that progesterone binds to a plasma membrane site within the external loop between the M1 and M2 helices of the α-subunit of Na/K-ATPase, triggering a cascade of lipid second messengers and the release of the block at meiotic prophase. We have characterized this site, using a low affinity ouabain binding isoform of the α1-subunit. Results Preparations of isolated plasma membranes from Rana oocytes demonstrate that physiological levels of progesterone (or the non-metabolizable progestin R5020 successively activate phosphatidylethanolamine-N-methyltransferase (PE-NMT and sphingomyelin synthase within seconds. Inhibition of PE-NMT blocks the progesterone induction of meiosis in intact oocytes, whereas its initial product, phosphatidylmonomethylethanolamine (PME, can itself initiate meiosis in the presence of the inhibitor. Published X-ray crystallographic data on Na/K-ATPase, computer-generated 3D projections, heptad repeat analysis and hydrophobic cluster analysis of the transmembrane helices predict that hydrophobic residues L, V, V, I, F and Y of helix M2 of the α1-subunit interact with F, L, G, L, L and F, respectively, of helix M3 of PE-NMT. Conclusion We propose that progesterone binding to the first external loop of the α1-subunit facilitates specific helix-helix interactions between integral membrane proteins to up-regulate PE-NMT, and, that successive interactions between two or more integral plasma membrane proteins induce the signaling cascades which result in completion of the meiotic divisions.

  15. Transmembrane TNF-dependent uptake of anti-TNF antibodies.

    Science.gov (United States)

    Deora, Arun; Hegde, Subramanya; Lee, Jacqueline; Choi, Chee-Ho; Chang, Qing; Lee, Cheryl; Eaton, Lucia; Tang, Hua; Wang, Dongdong; Lee, David; Michalak, Mark; Tomlinson, Medha; Tao, Qingfeng; Gaur, Nidhi; Harvey, Bohdan; McLoughlin, Shaun; Labkovsky, Boris; Ghayur, Tariq

    TNF-α (TNF), a pro-inflammatory cytokine is synthesized as a 26 kDa protein, anchors in the plasma membrane as transmembrane TNF (TmTNF), and is subjected to proteolysis by the TNF-α converting enzyme (TACE) to release the 15 kDa form of soluble TNF (sTNF). TmTNF and sTNF interact with 2 distinct receptors, TNF-R1 (p55) and TNF-R2 (p75), to mediate the multiple biologic effects of TNF described to date. Several anti-TNF biologics that bind to both forms of TNF and block their interactions with the TNF receptors are now approved for the treatment of a variety of immune-mediated diseases. Several reports suggest that binding of anti-TNFs to TmTNF delivers an outside-to-inside 'reverse' signal that may also contribute to the efficacy of anti-TNFs. Some patients, however, develop anti-TNF drug antibody responses (ADA or immunogenicity). Here, we demonstrate biochemically that TmTNF is transiently expressed on the surface of lipopolysaccharide-stimulated primary human monocytes, macrophages, and monocyte-derived dendritic cells (DCs) and expression of TmTNF on the cell surface is enhanced following treatment of cells with TAPI-2, a TACE inhibitor. Importantly, binding of anti-TNFs to TmTNF on DCs results in rapid internalization of the anti-TNF/TmTNF complex first into early endosomes and then lysosomes. The internalized anti-TNF is processed and anti-TNF peptides can be eluted from the surface of DCs. Finally, tetanus toxin peptides fused to anti-TNFs are presented by DCs to initiate T cell recall proliferation response. Collectively, these observations may provide new insights into understanding the biology of TmTNF, mode of action of anti-TNFs, biology of ADA response to anti-TNFs, and may help with the design of the next generation of anti-TNFs.

  16. Effects of multiple-helicity fields on ion temperature gradient modes

    Energy Technology Data Exchange (ETDEWEB)

    Kuroda, T. [National Inst. for Fusion Science, Toki, Gifu (Japan); Sugama, H. [Graduate Univ. for Advanced Studies, Toki, Gigu (Japan)

    2001-04-01

    Effects of multiple-helicity magnetic fields on ion temperature gradient (ITG) modes in toroidal helical systems like the Large Helical Device (LHD) are studied by means of the linear gyrokinetic theory. Especially, dependence of the real frequency, growth rate, and the eigenfunction of the ITG mode on sideband-helicity fields added to the main helical component is investigated. Comparison between multiple-helicity effects on the ITG mode with those on the neoclassical ripple transport is presented, and optimization of the magnetic configuration for better plasma confinement is discussed. (author)

  17. Stable single helical C- and I-chains inside single-walled carbon nanotubes

    International Nuclear Information System (INIS)

    Yao Z; Li Y; Jing X D; Meng F S; Zhao X; Li J H; Qiu Z Y; Yuan Q; Wang W X; Bi L; Liu H; Zhang Y P; Liu C J; Zheng S P; Liu B B

    2016-01-01

    The helicity of stable single helical carbon chains and iodine chains inside single-walled carbon nanotubes (SWCNTs) is studied by calculating the systematic van der Waals interaction energy. The results show that the optimal helical radius increases linearly with increasing tube radius, which produces a constant separation between the chain structure and the tube wall. The helical angle exhibits a ladder-like decrease with increasing tube radius, indicating that a large tube can produce a small helicity in the helical structures. (paper)

  18. Fabrication of a magnetic helical mesostructured silica rod

    Science.gov (United States)

    Zhang, Lei; Zhang Qiao, Shi; Cheng, Lina; Yan, Zifeng; Qing Lu, Gao Max

    2008-10-01

    We report a one-step synthesis of magnetic helical mesostructured silica (MHMS) by self-assembly of an achiral surfactant, magnetic nanocrystals with stearic acid ligands and silicate. This core-shell structured material consists of an Fe3O4 superparamagnetic nanocrystal core and a highly ordered periodic helical mesoporous silica shell. We propose that the formation of the helical structure is induced by the interaction between the surfactant and dissociated stearic acid ligands. The MHMS obtained possesses superparamagnetism, uniform mesostructure, narrow pore size distribution, high surface area, and large pore volume. Furthermore, the drug release process is demonstrated using aspirin as a drug model and MHMS as a drug carrier in a sodium phosphate buffer solution.

  19. New reconstruction algorithm in helical-volume CT

    International Nuclear Information System (INIS)

    Toki, Y.; Rifu, T.; Aradate, H.; Hirao, Y.; Ohyama, N.

    1990-01-01

    This paper reports on helical scanning that is an application of continuous scanning CT to acquire volume data in a short time for three-dimensional study. In a helical scan, the patient couch sustains movement during continuous-rotation scanning and then the acquired data is processed to synthesize a projection data set of vertical section by interpolation. But the synthesized section is not thin enough; also, the image may have artifacts caused by couch movement. A new reconstruction algorithm that helps resolve such problems has been developed and compared with the ordinary algorithm. The authors constructed a helical scan system based on TCT-900S, which can perform 1-second rotation continuously for 30 seconds. The authors measured section thickness using both algorithms on an AAPM phantom, and we also compared degree of artifacts on clinical data

  20. Giant hepatic cavernous hemangioma. Findings on computed helical tomography

    International Nuclear Information System (INIS)

    Castrillon, German A; Montoya, Maria del Pilar; Soto, Jorge A

    2010-01-01

    Objective: To describe computed helical tomography characteristics of the giant hepatic cavernous hemangioma. Method: During five years, we evaluated 21 patients with 21 giant hepatic cavernous hemangiomas with computed helical and multislice tomography. We included 18 women (86%) and 3 men (14%) with a mean age of 45 years. Results: The mean size of hemangiomas was 10.4 cm. Non enhanced computed tomography Showed 21 hemangiomas with lower density than adjacent hepatic parenchyma , all hemangiomas showed a central cleft area with low density. None hemangioma showed calcifications neither internal septa. In enhanced helical tomography all lesions demonstrated a globular, peripheral enhancing pattern with centripetal filling that begin in the arterial phase and continued in portal and delayed phases. None of the lesions showed complete filling. Conclusion: giant hepatic cavernous hemangiomas showed low attenuation in non enhanced computed tomography. central cleft area was very frequently seen. The enhancement pattern is characteristic, starting at the periphery with centripetal filling but it was never complete.

  1. Stability of helical tip vortices in a rotor far wake

    DEFF Research Database (Denmark)

    Okulov, Valery; Sørensen, Jens Nørkær

    2007-01-01

    , corresponding to Rankine, Gaussian and Scully vortices, at radial extents ranging from the core radius of a tip vortex to several rotor radii. The analysis shows that the stability of tip vortices largely depends on the radial extent of the hub vorticity as well as on the type of vorticity distribution. As part......As a means of analysing the stability of the wake behind a multi-bladed rotor the stability of a multiplicity of helical vortices embedded in an assigned flow field is addressed. In the model the tip vortices in the far wake are approximated by infinitely long helical vortices with constant pitch...... and radius. The work is a further development of a model developed in Okulov (J. Fluid Mech., vol. 521, p. 319) in which the linear stability of N equally azimuthally spaced helical vortices was considered. In the present work the analysis is extended to include an assigned vorticity field due to root...

  2. Imploding to equilibrium of helically symmetric theta pinches

    Energy Technology Data Exchange (ETDEWEB)

    Sharky, N.N.

    1978-01-01

    The time-dependent, single-fluid, dissipative magnetohydrodynamic equations are solved in helical coordinates (r,phi), where phi = THETA-kz, k = 2..pi../L and L is the periodicity length in the z-direction. The two-dimensional numerical calculations simulate theta pinches which have an l = 1 helical field added to them. Given the applied magnetic fields and the initial state of the plasma, we study the time evolution of the system. The plasma is found to experience two kinds of oscillations, occurring on different time scales. These are the radial compression oscillations, and the slower helical oscillations of the plasma column. The plasma motion is followed until these oscillations disappear and an equilibrium is nearly reached. Hence given the amplitude and the rise time of the applied magnetic fields, the calculations allow one to relate the initial state of a cold, homogeneous plasma to its final equilibrium state where it is heated and compressed.

  3. Effect of loss cone on confinement in toroidal helical device

    International Nuclear Information System (INIS)

    Itoh, K.; Itoh, S.-I.; Fukuyama, A.; Hanatani, K.

    1988-12-01

    Analytical estimation is given on the loss cone in the toroidal helical devices in the presence of the radial electric field and the modulation of the helical ripple. The minimum energy of particles entering the loss cone is calculated. The modulation is not always effective in reducing the loss in the presence of the radial electric field. The plasma loss due to the loss cone is estimated in the collisionless limit. The radial electric field is estimated in the presence of the loss cone. It is found that the transition to the solution with positive radial electric field, which is necessary to achieve the high-ion-temperature mode, becomes difficult. This difficulty is large for the systems with the small helical ripple. (author)

  4. Cooperative polymerization of α-helices induced by macromolecular architecture

    Science.gov (United States)

    Baumgartner, Ryan; Fu, Hailin; Song, Ziyuan; Lin, Yao; Cheng, Jianjun

    2017-07-01

    Catalysis observed in enzymatic processes and protein polymerizations often relies on the use of supramolecular interactions and the organization of functional elements in order to gain control over the spatial and temporal elements of fundamental cellular processes. Harnessing these cooperative interactions to catalyse reactions in synthetic systems, however, remains challenging due to the difficulty in creating structurally controlled macromolecules. Here, we report a polypeptide-based macromolecule with spatially organized α-helices that can catalyse its own formation. The system consists of a linear polymeric scaffold containing a high density of initiating groups from which polypeptides are grown, forming a brush polymer. The folding of polypeptide side chains into α-helices dramatically enhances the polymerization rate due to cooperative interactions of macrodipoles between neighbouring α-helices. The parameters that affect the rate are elucidated by a two-stage kinetic model using principles from nucleation-controlled protein polymerizations; the key difference being the irreversible nature of this polymerization.

  5. Divertors for Helical Devices: Concepts, Plans, Results, and Problems

    International Nuclear Information System (INIS)

    Koenig, R.; Grigull, P.; McCormick, K.

    2004-01-01

    With Large Helical Device (LHD) and Wendelstein 7-X (W7-X), the development of helical devices is now taking a large step forward on the path to a steady-state fusion reactor. Important issues that need to be settled in these machines are particle flux and heat control and the impact of divertors on plasma performance in future continuously burning fusion plasmas. The divertor concepts that will initially be explored in these large machines were prepared in smaller-scale devices like Heliotron E, Compact Helical System (CHS), and Wendelstein 7-AS (W7-AS). While advanced divertor scenarios relevant for W7-X were already studied in W7-AS, other smaller-scale experiments like Heliotron-J, CHS, and National Compact Stellarator Experiment will be used for the further development of divertor concepts. The two divertor configurations that are being investigated are the helical and the island divertor, as well as the local island divertor, which was successfully demonstrated on CHS and just went into operation on LHD. At present, on its route to a fully closed helical divertor, LHD operates in an open helical divertor configuration. W7-X will be equipped right from the start with an actively cooled discrete island divertor that will allow quasi-continuous operation. The divertor design is very similar to the one explored on W7-AS. For sufficiently large island sizes and not too long field line connection lengths, this divertor gives access to a partially detached quasi-steady-state operating scenario in a newly found high-density H-mode operating regime, which benefits from high energy and low impurity confinement times, with edge radiation levels of up to 90% and sufficient neutral compression in the subdivertor region (>10) for active pumping. The basic physics of the different divertor concepts and associated implementation problems, like asymmetries due to drifts, accessibility of essential operating scenarios, toroidal asymmetries due to symmetry breaking error fields

  6. Variation in the helical structure of native collagen.

    Directory of Open Access Journals (Sweden)

    Joseph P R O Orgel

    Full Text Available The structure of collagen has been a matter of curiosity, investigation, and debate for the better part of a century. There has been a particularly productive period recently, during which much progress has been made in better describing all aspects of collagen structure. However, there remain some questions regarding its helical symmetry and its persistence within the triple-helix. Previous considerations of this symmetry have sometimes confused the picture by not fully recognizing that collagen structure is a highly complex and large hierarchical entity, and this affects and is effected by the super-coiled molecules that make it. Nevertheless, the symmetry question is not trite, but of some significance as it relates to extracellular matrix organization and cellular integration. The correlation between helical structure in the context of the molecular packing arrangement determines which parts of the amino acid sequence of the collagen fibril are buried or accessible to the extracellular matrix or the cell. In this study, we concentrate primarily on the triple-helical structure of fibrillar collagens I and II, the two most predominant types. By comparing X-ray diffraction data collected from type I and type II containing tissues, we point to evidence for a range of triple-helical symmetries being extant in the molecules native environment. The possible significance of helical instability, local helix dissociation and molecular packing of the triple-helices is discussed in the context of collagen's supramolecular organization, all of which must affect the symmetry of the collagen triple-helix.

  7. Conformal avoidance helical tomotherapy for dogs with nasopharyngeal tumors

    International Nuclear Information System (INIS)

    Welsh, J.S.; Turek, M.; Mackie, T.R.; Miller, P.; Mehta, M.P.; Forrest, L.J.

    2003-01-01

    Helical tomotherapy provides a unique means of delivering intensity-modulated radiation therapy (IMRT) using a novel treatment unit, which merges features of a linear accelerator with a helical CT scanner. Thanks to the CT imaging capacity, targeted regions can be visualized prior to, during, or immediately after each treatment. Such image-guidance through megavoltage CT will allow the realization and refinement of the concept of adaptive radiotherapy - the reconstruction of the actually delivered daily dose (as opposed to planned dose) accompanied by prescription adjustments when appropriate. In addition to this unique feature, helical tomotherapy promises further improvements in the specific avoidance of critical normal structures, i.e. conformal avoidance, the counterpart of conformal therapy. The first definitive treatment protocol using helical tomotherapy is presently underway for dogs with nasopharyngeal tumors. In general, such tumors can be treated with conventional external beam radiation therapy but at the cost of severe ocular toxicity due to the anatomy of the canine head. These are readily measurable toxicities and are almost universal in incidence; therefore, the canine nasopharyngeal tumor presents an ideal model to assess the ability to conformally avoid critical structures. It is hoped that conformal avoidance helical tomotherapy will improve tumor control via dose-escalation while reducing ocular toxicity in these veterinary patients. A total of 10 fractions are scheduled for these patients; the first 3 dogs have all received at least 7 fractions delivered via helical tomotherapy. Although preliminary, the first 3 dogs treated have not shown any evidence of ocular toxicity in this ongoing study

  8. Transmembrane-sequence-dependent overexpression and secretion of glycoproteins in Saccharomyces cerevisiae.

    Science.gov (United States)

    Schuster, M; Wasserbauer, E; Aversa, G; Jungbauer, A

    2001-02-01

    Protein expression using the secretory pathway in Saccharomyces cerevisiae can lead to high amounts of overexpressed and secreted proteins in culture supernatants in a short period of time. These post-translational modified expression products can be purified up to >90% in a single step. The overexpression and secretion of the transmembrane glycoprotein signaling lymphocytic activation molecule (SLAM) was studied. SLAM belongs to the immunoglobulin superfamily and its engagement results in T-cell expansion and INF-gamma production. The molecule is composed of an extracellular, a single-span transmembrane and a cytoplasmatic domain. The extracellular part may be relevant for stimulation studies in vitro since SLAM is a high-affinity self-ligand. Therefore several fragments of this region have been expressed as Flag-fusions in S. cerevisiae: a full-length fragment containing the transmembrane region and the autologous signal sequence, another without the transmembrane region, and two fragments without the autologous signal sequence with and without the transmembrane region. By molecular cloning, the different deletion mutants of the cDNA encoding the full-length construct have been inserted in a yeast episomal plasmid. Upstream of the cDNA, the alpha-leader sequence of a yeast mating pheromone has been cloned to direct the fusion proteins into the secretory protein maturation pathway. All four fragments were expressed but yield, location, and maturation were highly influenced by the transmembrane domain and the autologous signal sequence. Only the fragment without autologous signal sequence and transmembrane domain could be efficiently secreted. High-mannose glycosylation was analyzed by lectin mapping and digestion with specific glycosidases. After enzyme treatment, a single band product with the theoretical size could be detected and identified as SLAM by a specific monoclonal antibody. The fusion protein concentration in the supernatant was 30 microg/ml. The

  9. Demonstration of a helical armature for a superconducting generator

    International Nuclear Information System (INIS)

    Conley, P.L.; Kirtley, J.L. Jr.; Hagman, W.H.; Ula, A.H.M.S.

    1979-01-01

    This is a report on the design, construction and testing of an experimental helical armature for a superconducting geneator. Rated at 60 kVA, this armature was built to be operated in conjunction with the rotor of the first experimental superconducting machine built at MIT. It incorporates, in addition to the helical winding form, a high density edge-brazed end turn geometry, molded bar groups, and silicone fluid coolant and insulation impregnant. Tests showed that the thermal performance of the armature was within reasonable limits, magnetic analyses leading to the computation of reactance and voltage geneation were approximately correct. No abnormal cheating was observed. 9 refs

  10. Helicity Selection Rules and Non-Interference for BSM Amplitudes

    CERN Document Server

    Azatov, Aleksandr; Machado, Camila S.; Riva, Francesco

    2017-01-01

    Precision studies of scattering processes at colliders provide powerful indirect constraints on new physics. We study the helicity structure of scattering amplitudes in the SM and in the context of an effective Lagrangian description of BSM dynamics. Our analysis reveals a novel set of helicity selection rules according to which, in the majority of 2 to 2 scattering processes at high energy, the SM and the leading BSM effects do not interfere. In such situations, the naive expectation that dimension-6 operators represent the leading BSM contribution is compromised, as corrections from dimension-8 operators can become equally (if not more) important well within the validity of the effective field theory approach.

  11. Spin Hall insulators beyond the helical Luttinger model

    Science.gov (United States)

    Mastropietro, Vieri; Porta, Marcello

    2017-12-01

    We consider the interacting, spin-conserving, extended Kane-Mele-Hubbard model, and we rigorously establish the exact quantization of the edge spin conductance and the validity of the helical Luttinger liquid relations for Drude weights and susceptibilities. Our analysis takes fully into account lattice effects, typically neglected in the helical Luttinger model approximation, which play an essential role for universality. The analysis is based on exact renormalization-group methods and on a combination of lattice and emergent Ward identities, which enable the emergent chiral anomaly to be related with the finite renormalizations due to lattice corrections.

  12. Point contacts and localization in generic helical liquids

    Science.gov (United States)

    Orth, Christoph P.; Strübi, Grégory; Schmidt, Thomas L.

    2013-10-01

    We consider two helical liquids on opposite edges of a two-dimensional topological insulator, which are connected by one or several local tunnel junctions. In the presence of spatially inhomogeneous Rashba spin-orbit coupling, the spin of the helical edge states is momentum dependent, and this spin texture can be different on opposite edges. We demonstrate that this has a strong impact on the electron transport between the edges. In particular, in the case of many random tunnel contacts, the localization length depends strongly on the spin textures of the edge states.

  13. Epicyclic Helical Channels for Parametric Resonance Ionization Cooling

    Energy Technology Data Exchange (ETDEWEB)

    Andrei Afanaciev, Alex Bogacz, Yaroslav Derbenev, Kevin Beard, Valentin Ivanov, Rolland Johnson, Guimei Wang, Katsuya Yonehara

    2009-05-01

    In order to achieve cooling of muons in addition to 6D helical cooling channel (HCC) [1], we develop a technique based on a parametric resonance. The use of parametric resonances requires alternating dispersion, minimized at locations of thin absorbers, but maximized in between in order to compensate for chromatic aberrations [2]. These solutions can be combined in an Epicyclic Helical Cooling Channel (EHCC) that meets requirements of alternating dispersion of beam periodic orbit with best conditions for maintenance of stable beam transport in a continuous solenoid-type field [3]. We discuss here basic features and new simulation results for EHCC.

  14. Synthesis, model and stability of helically coiled carbon nanotubes

    DEFF Research Database (Denmark)

    Fejes, Dora; Raffai, Manuella; Hernadi, Klara

    2013-01-01

    Structural model of helically coiled carbon nanotubes is proposed. It is constructed by means of topological coordinate method. Relaxation and cohesive energy calculation are performed by molecular mechanics, using second-generation bond order potential for hydrocarbons introduced by D. W. Brenner....... Our experiments focused on the production and development of catalysts for the synthesis of helically coiled CNTs (carbon nanotubes). The catalysts were tested in the decomposition of acetylene by CCVD (Catalytic Chemical Vapor Deposition) method. The carbon deposit was imaged by TEM (Transmission...

  15. Helical CT of traumatic injuries of the thoracic aorta

    International Nuclear Information System (INIS)

    Mengozzi, E.; Burzi, M.; Miceli, M.; Lipparini, M.; Sartoni Galloni, S.

    2000-01-01

    Acute thoracic aortic injuries account for up to 10-20% of fatalities in high-speed deceleration road accidents and have an estimated immediate fatality rate of 80-90%. Untreated survivors to acute trauma (10-20%) have a dismal prognosis: 30% of them die within 6 hours, 40-50% die within 24 hours, and 90% within 4 months. It was investigated the diagnostic accuracy of Helical Computed Tomography (Helical CT) in acute traumatic injuries of the thoracic aorta, and the role of this technique in the diagnostic management of trauma patients with a strong suspicion of aortic rupture. It was compared retrospectively the chest Helical CT findings of 256 trauma patients examined June 1995 through August 1999. Chest Helical CT examinations were performed according to trauma score, to associated traumatic lesions and to plain chest radiographic findings. All the examinations were performed with no intravenous contrast agent administration and the pitch 2 technique. After a previous baseline study, contrast-enhanced scans were acquired with pitch 1 in 87 patients. Helical CT showed aortic lesions in 9 of 256 patients examined. In all the 9 cases it was found a mediastinal hematoma and all of them had positive plain chest radiographic findings of mediastinal enlargement. Moreover, in 6 cases aortic knob blurring was also evident on plain chest film and in 5 cases depressed left mainstem bronchus and trachea deviation rightwards were observed. All aortic lesions were identified on axial scans and located at the isthmus of level. Aortic rupture was always depicted as pseudo diverticulum of the proximal descending tract and intimal flap. It was also found that periaortic hematoma in 6 cases and intramural hematoma in 1 case. There were non false positive results in the series: 7 patients with Helical CT diagnosis of aortic rupture were submitted to conventional aortography that confirmed both type and extension of the lesions as detected by Helical CT, and all findings were

  16. Free energy determinants of secondary structure formation: I. alpha-Helices.

    Science.gov (United States)

    Yang, A S; Honig, B

    1995-09-22

    The Zimm-Bragg parameters s and sigma are calculated for the helix-coil transition of poly-L-alanine. The theoretical approach involves evaluating gas phase conformational energies for both coil and helical states using the CHARMM potential function and accounting for solvation effects with various continuum solvation models. Conformational free energies are then incorporated into a formalism developed by Go et al. for the calculation of s and sigma. Calculated values for both s and sigma as well as the enthalpy change associated with helix formation are in good agreement with experimental data when the Finite Difference Poisson-Boltzmann (FDPB) method is used to treat solvent effects. The driving force for the helix-coil transition is analyzed in terms of individual free energy components. Hydrogen bond formation is found to contribute little to helix stability because the internal hydrogen bonding energy is largely canceled by the large free energy cost associated with removing polar groups from water. The entropic cost associated with fixing backbone dihedral angles in the helical conformation is found to be approximately 7 e.u./residue (about 2 kcal/mol at room temperature). The major driving force favoring helix formation can be associated with interactions including enhanced van der Waals interactions in the close-packed helix conformation and the hydrophobic effect. These contribute about 2 kcal/mol favoring the helical state. The differences in helical propensities between alanine and glycine are attributed primarily to hydrophobic and packing interactions involving the C beta with a smaller contribution arising from increased conformational freedom for glycine in the coil state. The description of helix formation presented here is consistent with previous conclusions regarding tertiary structure formation which suggest that hydrophobic and close-packed interactions provide stability while hydrogen bond formation constitutes a structural constraint imposed

  17. Self-Assembling Organic Nanopores as Synthetic Transmembrane Channels with Tunable Functions

    Science.gov (United States)

    Wei, Xiaoxi

    A long-standing goal in the area of supramolecular self-assembly involves the development of synthetic ion/water channels capable of mimicking the mass-transport characteristics of biological channels and pores. Few examples of artificial transmembrane channels with large lumen, high conductivity and selectivity are known. A review of pronounced biological transmembrane protein channels and some representative synthetic models have been provided in Chapter 1, followed by our discovery and initial investigation of shape-persistent oligoamide and phenylene ethynylene macrocycles as synthetic ion/water channels. In Chapter 2, the systematic structural modification of oligoamide macrocycles 1, the so-called first-generation of these shape-persistent macrocycles, has led to third-generation macrocycles 3. The third generation was found to exhibit unprecedented, strong intermolecular association in both the solid state and solution via multiple techniques including X-ray diffraction (XRD), SEM, and 1H NMR. Fluorescence spectroscopy paired with dynamic light scattering (DLS) revealed that macrocycles 3 can assemble into a singly dispersed nanotubular structure in solution. The resultant self-assembling pores consisting of 3 were examined by HPTS-LUVs assays and BLM studies (Chapter 3) and found to form cation-selective (PK+/PCl- = 69:1) transmembrane ion channels with large conductance (200 ˜ 2000 pS for alkali cations) and high stability with open times reaching to 103 seconds. Tuning the aggregation state of macrocycles by choosing an appropriate polar solvent mixture (i.e., 3:1, THF:DMF, v/v) and concentration led to the formation of ion channels with well-defined square top behavior. A parallel study using DLS to examine the size of aggregates was used in conjunction with channel activity assays (LUVs/BLM) to reveal the effects of the aggregation state on channel activity. Empirical evidence now clearly indicates that a preassembled state, perhaps that of a

  18. Helicity injection with moving vacuum--plasma boundary with arbitrary flux surfaces

    International Nuclear Information System (INIS)

    Bellan, P.M.

    1988-01-01

    If a toroidal plasma has arbitrary nested magnetic flux surfaces and a moving plasma--vacuum interface, then any helicity injected by modulating the magnetic fields is simply consumed by an increase in helicity dissipation due to the modulated fields

  19. HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.

    Science.gov (United States)

    Tsaousis, Georgios N; Bagos, Pantelis G; Hamodrakas, Stavros J

    2014-02-01

    During the last two decades a large number of computational methods have been developed for predicting transmembrane protein topology. Current predictors rely on topogenic signals in the protein sequence, such as the distribution of positively charged residues in extra-membrane loops and the existence of N-terminal signals. However, phosphorylation and glycosylation are post-translational modifications (PTMs) that occur in a compartment-specific manner and therefore the presence of a phosphorylation or glycosylation site in a transmembrane protein provides topological information. We examine the combination of phosphorylation and glycosylation site prediction with transmembrane protein topology prediction. We report the development of a Hidden Markov Model based method, capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites along the protein sequence. Our method integrates a novel feature in transmembrane protein topology prediction, which results in improved performance for topology prediction and reliable prediction of phosphorylation and glycosylation sites. The method is freely available at http://bioinformatics.biol.uoa.gr/HMMpTM. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Expression of Trans-Membrane Proteins in vitro Using a Cell Free System

    Science.gov (United States)

    Weisse, Natalie; Noireaux, Vincent; Chalmeau, Jerome

    2010-10-01

    Trans-membrane proteins represent a significant portion of the proteins expressed by cells. The expression of proteins in vitro, however, remains a challenge. Numerous expression approaches have been developed with cell free expression (CFE) being one of the most promising. CFE is based on a transcription-translation system that has been extracted from E. coli bacteria. Adding the desired DNA allows expression of a selected protein, and in the presence of phospholipids the expression of trans-membrane proteins becomes possible. In order to express trans-membrane proteins in a closed native environment, the cell free system (CFS) is encapsulated with a phospholipid bilayer, creating an artificial cell. To verify protein expression, AquaporinZ (AqpZ), a well-known trans-membrane protein tagged with a green fluorescent protein (eGFP), was used so the expressed proteins could be seen under a fluorescent microscope. These artificial cells will serve as an experimental platform for testing the viability of the expressed trans-membrane proteins. Results from the manipulation of these artificial cells by attaching them to the slide surface through streptavidin-biotin bonding will be presented.

  1. Transmembrane domain quality control systems operate at the endoplasmic reticulum and Golgi apparatus.

    Science.gov (United States)

    Briant, Kit; Johnson, Nicholas; Swanton, Eileithyia

    2017-01-01

    Multiple protein quality control systems operate to ensure that misfolded proteins are efficiently cleared from the cell. While quality control systems that assess the folding status of soluble domains have been extensively studied, transmembrane domain (TMD) quality control mechanisms are poorly understood. Here, we have used chimeras based on the type I plasma membrane protein CD8 in which the endogenous TMD was substituted with transmembrane sequences derived from different polytopic membrane proteins as a mode to investigate the quality control of unassembled TMDs along the secretory pathway. We find that the three TMDs examined prevent trafficking of CD8 to the cell surface via potentially distinct mechanisms. CD8 containing two distinct non-native transmembrane sequences escape the ER and are subsequently retrieved from the Golgi, possibly via Rer1, leading to ER localisation at steady state. A third chimera, containing an altered transmembrane domain, was predominantly localised to the Golgi at steady state, indicating the existence of an additional quality control checkpoint that identifies non-native transmembrane domains that have escaped ER retention and retrieval. Preliminary experiments indicate that protein retained by quality control mechanisms at the Golgi are targeted to lysosomes for degradation.

  2. Rationally designed transmembrane peptide mimics of the multidrug transporter protein Cdr1 act as antagonists to selectively block drug efflux and chemosensitize azole-resistant clinical isolates of Candida albicans.

    Science.gov (United States)

    Maurya, Indresh Kumar; Thota, Chaitanya Kumar; Verma, Sachin Dev; Sharma, Jyotsna; Rawal, Manpreet Kaur; Ravikumar, Balaguru; Sen, Sobhan; Chauhan, Neeraj; Lynn, Andrew M; Chauhan, Virander Singh; Prasad, Rajendra

    2013-06-07

    Drug-resistant pathogenic fungi use several families of membrane-embedded transporters to efflux antifungal drugs from the cells. The efflux pump Cdr1 (Candida drug resistance 1) belongs to the ATP-binding cassette (ABC) superfamily of transporters. Cdr1 is one of the most predominant mechanisms of multidrug resistance in azole-resistant (AR) clinical isolates of Candida albicans. Blocking drug efflux represents an attractive approach to combat the multidrug resistance of this opportunistic human pathogen. In this study, we rationally designed and synthesized transmembrane peptide mimics (TMPMs) of Cdr1 protein (Cdr1p) that correspond to each of the 12 transmembrane helices (TMHs) of the two transmembrane domains of the protein to target the primary structure of the Cdr1p. Several FITC-tagged TMPMs specifically bound to Cdr1p and blocked the efflux of entrapped fluorescent dyes from the AR (Gu5) isolate. These TMPMs did not affect the efflux of entrapped fluorescent dye from cells expressing the Cdr1p homologue Cdr2p or from cells expressing a non-ABC transporter Mdr1p. Notably, the time correlation of single photon counting fluorescence measurements confirmed the specific interaction of FITC-tagged TMPMs with their respective TMH. By using mutant variants of Cdr1p, we show that these TMPM antagonists contain the structural information necessary to target their respective TMHs of Cdr1p and specific binding sites that mediate the interactions between the mimics and its respective helix. Additionally, TMPMs that were devoid of any demonstrable hemolytic, cytotoxic, and antifungal activities chemosensitize AR clinical isolates and demonstrate synergy with drugs that further improved the therapeutic potential of fluconazole in vivo.

  3. Alpha-Effect, Current and Kinetic Helicities for Magnetically Driven ...

    Indian Academy of Sciences (India)

    tribpo

    driven by a (given) Lorentz force in a non stratified but rotating convection zone. The main result confirms the numerical findings of Brandenburg & Schmitt that in the northern hemisphere the α effect and the kinetic helicity are positive (and negative in the northern hemisphere), this being just opposite to what occurs for the ...

  4. Study of a Large Helical Eruptive Prominence Associated with ...

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... Here we present a preliminary analysis of a helical eruptive prominence at the east limb of the Sun on 21 April 2001. Unusually this eruption is associated with a double CME. We have tried to study the morphology of the event, energy budget of the prominence and associated CMEs. Our analysis shows ...

  5. Helicity and other conservation laws in perfect fluid motion

    Science.gov (United States)

    Serre, Denis

    2018-03-01

    In this review paper, we discuss helicity from a geometrical point of view and see how it applies to the motion of a perfect fluid. We discuss its relation with the Hamiltonian structure, and then its extension to arbitrary space dimensions. We also comment about the existence of additional conservation laws for the Euler equation, and its unlikely integrability in Liouville's sense.

  6. Is gadolinium a helical antiferromagnet or a collinear ferromagnet?

    Indian Academy of Sciences (India)

    they rule out the possibility of a helical spin structure in Gd and clearly bring out the role of long- range dipolar interactions in stabilising collinear ferromagnetic ... Symposium on Advances in Superconductivity and Mag- netism: Materials, Mechanisms and Devices, ASMM2D-2001, 25–28 September 2001, Mangalore,. India ...

  7. Helquats: A facile, modular, scalable route to novel helical dications

    Czech Academy of Sciences Publication Activity Database

    Adriaenssens, Louis; Severa, Lukáš; Šálová, Tereza; Císařová, I.; Pohl, Radek; Šaman, David; Rocha, S. V.; Finney, N. S.; Pospíšil, Lubomír; Slavíček, P.; Teplý, Filip

    2009-01-01

    Roč. 15, č. 5 (2009), s. 1072-1076 ISSN 0947-6539 Grant - others:GA MŠk(CZ) OC 140 Program:OC Institutional research plan: CEZ:AV0Z40550506 Keywords : air-tolerant cycloisomerization * diquat * elektrochemistry * helical structures Subject RIV: CC - Organic Chemistry Impact factor: 5.382, year: 2009

  8. Pair production of helicity-flipped neutrinos in supernovae

    Science.gov (United States)

    Perez, Armando; Gandhi, Raj

    1989-01-01

    The emissivity was calculated for the pair production of helicity-flipped neutrinos, in a way that can be used in supernova calculations. Also presented are simple estimates which show that such process can act as an efficient energy-loss mechanism in the shocked supernova core, and this fact is used to extract neutrino mass limits from SN 1987A neutrino observations.

  9. Is gadolinium a helical antiferromagnet or a collinear ferromagnet?

    Indian Academy of Sciences (India)

    as low as 15 Oe suffice to transform the helical antiferromagnetism into collinear ferro- magnetism. This picture of the spin structure in Gd had to be discarded after subsequent. £Article presented at the International Symposium on Advances in Superconductivity and Mag- netism: Materials, Mechanisms and Devices, ...

  10. Standard and Nonstandard Craniospinal Radiotherapy Using Helical TomoTherapy

    International Nuclear Information System (INIS)

    Parker, William; Brodeur, Marylene; Roberge, David; Freeman, Carolyn

    2010-01-01

    Purpose: To show the advantages of planning and delivering craniospinal radiotherapy with helical TomoTherapy (TomoTherapy Inc., Madison, WI) by presenting 4 cases treated at our institution. Methods and Materials: We first present a standard case of craniospinal irradiation in a patient with recurrent myxopapillary ependymoma (MPE) and follow this with 2 cases requiring differential dosing to multiple target volumes. One of these, a patient with recurrent medulloblastoma, required a lower dose to be delivered to the posterior fossa because the patient had been previously irradiated to the full dose, and the other required concurrent boosts to leptomeningeal metastases as part of his treatment for newly diagnosed MPE. The final case presented is a patient with pronounced scoliosis who required spinal irradiation for recurrent MPE. Results: The four cases presented were planned and treated successfully with Helical Tomotherapy. Conclusions: Helical TomoTherapy delivers continuous arc-based intensity-modulated radiotherapy that gives high conformality and excellent dose homogeneity for the target volumes. Increased healthy tissue sparing is achieved at higher doses albeit at the expense of larger volumes of tissue receiving lower doses. Helical TomoTherapy allows for differential dosing of multiple targets, resulting in very elegant dose distributions. Daily megavoltage computed tomography imaging allows for precision of patient positioning, permitting a reduction in planning margins and increased healthy tissue sparing in comparison with standard techniques.

  11. Signs of helicity in solar prominences and related features

    Science.gov (United States)

    Martin, S.

    This review illustrates several ways to identify the chirality (handedness) of solar prominences (filaments) from their structure and the structure of their surrounding magnetic fields in the chromosphere and corona. For prominences, these structural elements include the axial magnetic field direction, orientation of barbs, and direction of the prominence fine structure. The surrounding structures include the pattern of fibrils beneath the prominences and the pattern of coronal loops above the prominences. These ways of identifying chirality are then interpreted in terms of the formal definitions of helicity to yield a consistent set of one-to-one helicity relationships for all features. The helicity of some prominences can also be independently determined during their eruption by their fine structure, apparent crossings in the line-of-sight of different parts of the same prominence, and by large- scale twist of the prominence structure. Unlike observations of prominences (filaments) observed prior to eruption, in some cases evidence of both signs of helicity are found within the same erupting prominence. This indicates the continued application of forces on the prominences during the eruption process or the possible introduction of force(s) not present during earlier stages of their evolution.

  12. Helical undulator based on partial redistribution of uniform magnetic field

    Directory of Open Access Journals (Sweden)

    N. Balal

    2017-12-01

    Full Text Available A new type of helical undulator based on redistribution of magnetic field of a solenoid by ferromagnetic helix has been proposed and studied both in theory and experiment. Such undulators are very simple and efficient for promising sources of coherent spontaneous THz undulator radiation from dense electron bunches formed in laser-driven photo-injectors.

  13. Helical undulator based on partial redistribution of uniform magnetic field

    Science.gov (United States)

    Balal, N.; Bandurkin, I. V.; Bratman, V. L.; Fedotov, A. E.

    2017-12-01

    A new type of helical undulator based on redistribution of magnetic field of a solenoid by ferromagnetic helix has been proposed and studied both in theory and experiment. Such undulators are very simple and efficient for promising sources of coherent spontaneous THz undulator radiation from dense electron bunches formed in laser-driven photo-injectors.

  14. Study of a Large Helical Eruptive Prominence Associated with ...

    Indian Academy of Sciences (India)

    2001-04-21

    Apr 21, 2001 ... Abstract. Here we present a preliminary analysis of a helical eruptive prominence at the east limb of the Sun on 21 April 2001. Unusually this eruption is associated with a double CME. We have tried to study the morphology of the event, energy budget of the prominence and associated. CMEs. Our analysis ...

  15. Chiral and achiral helical coordination polymers of zinc and ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 5. Chiral and achiral helical ... Ganapathi Anantharaman. Special issue on Chemical Crystallography Volume 126 Issue 5 September 2014 pp 1423-1431 ... Anantharaman1. Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India ...

  16. The Hemispheric Sign Rule of Current Helicity during the Rising ...

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... We compute the signs of two different current helicity parameters (i.e., best and ) for 87 active regions during the rise of cycle 23. The results indicate that 59% of the active regions in the northern hemisphere have negative best and 65% in the southern hemisphere have positive. This is consistent ...

  17. Helical instability of charged vortices in layered superconductors

    OpenAIRE

    Gurevich, A.

    2010-01-01

    It is shown that the electric charge of vortices can result in a helical instability of straight vortex lines in layered superconductors, particularly Bi-based cuprates or organic superconductors. This instability may result in a phase transition to a uniformly twisted vortex state, which could be detected by torque magnetometry, neutron diffraction, electromagnetic or calorimetric measurements.

  18. HELAS: HELicity Amplitude Subroutines for Feynman diagram evaluations

    International Nuclear Information System (INIS)

    Murayama, H.; Watanabe, I.; Hagiwara, K.

    1992-01-01

    HELAS is a set of the FORTRAN 77 subroutines which enable to compute the helicity amplitude of an arbitrary tree level Feynman diagram with a simple sequence of CALL SUBROUTINE statements. It is easy to write down a FORTRAN program to calculate the helicity amplitude of a given process by calling the HELAS subroutines. The example of evaluating the helicity amplitude of the process W + W - →t anti-t is shown. The compactness of the helicity amplitude programs is the main advantage of using the HELAS. Another advantage is that it is very easy to allow external heavy particles to decay into light quarks and leptons without losing the spin correlation. The procedure of calculating the cross section of an arbitrary process with the help of the HELAS and noteworthy characteristics of the HELAS system are shown. How to use the HELAS package is explained about the above example. The HELAS subroutines are grouped in wave functions, nine vertices and tools and standard model coupling constants. HELAS CHECK messages makes the job to find mistake easy. (K.I.)

  19. Wave packet dynamics in a helical optical waveguide

    International Nuclear Information System (INIS)

    Longhi, Stefano

    2005-01-01

    Beam propagation in a helically twisted optical waveguide is theoretically studied and shown to provide an optical analog to the electron wave packet dynamics of a two-dimensional atom subject to a high-frequency and high-intensity circularly polarized laser field

  20. Study of electric field pulsation in helical plasmas

    International Nuclear Information System (INIS)

    Toda, S; Itoh, K

    2011-01-01

    A model for the experimental results of the periodic oscillation of the electric field, so-called the electric field pulsation, observed in the Compact Helical Device (Fujisawa et al 1998 Phys. Rev. Lett. 81 2256) and the Large Helical Device (Shimizu et al 2010 Plasma Fusion Res. 5 S1015) is presented. A self-generated oscillation of the radial electric field is shown as the simulation result in helical plasmas. The reduction of the anomalous transport diffusivity in the core region is observed due to the strong shear of the radial electric field when the positive electric field is shown in the core region in the periodic oscillation of E r . Two different time scales are found in the self-generated oscillation, which are the transport time scale and the fast time scale at the transition of the radial electric field. This oscillation because of the hysteresis characteristic is attributed to the electric field pulsation observed in helical plasmas. The parameter region of the condition for the self-generated oscillation is derived. It is shown that the multiple solutions of the radial electric field for the ambipolar condition are necessary but not sufficient for obtaining the self-generated oscillation.

  1. Helicity of Solar Active Regions from a Dynamo Model Piyali ...

    Indian Academy of Sciences (India)

    Key words. MHD—Sun: activity—Sun: magnetic fields—sunspots. 1. Introduction. Typically, solar active regions are known to have helicity associated with them and the ... hemisphere and positive in the southern hemisphere), in spite of a very large statistical ... When a new toroidal flux tube with positive Bφ moves upwards.

  2. Helical Phase Inflation and Monodromy in Supergravity Theory

    Directory of Open Access Journals (Sweden)

    Tianjun Li

    2015-01-01

    Full Text Available We study helical phase inflation which realizes “monodromy inflation” in supergravity theory. In the model, inflation is driven by the phase component of a complex field whose potential possesses helicoid structure. We construct phase monodromy based on explicitly breaking global U(1 symmetry in the superpotential. By integrating out heavy fields, the phase monodromy from single complex scalar field is realized and the model fulfills natural inflation. The phase-axion alignment is achieved from explicitly symmetry breaking and gives super-Planckian phase decay constant. The F-term scalar potential provides strong field stabilization for all the scalars except inflaton, which is protected by the approximate global U(1 symmetry. Besides, we show that helical phase inflation can be naturally realized in no-scale supergravity with SU(2,1/SU(2×U(1 symmetry since the supergravity setup needed for phase monodromy is automatically provided in the no-scale Kähler potential. We also demonstrate that helical phase inflation can be reduced to another well-known supergravity inflation model with shift symmetry. Helical phase inflation is free from the UV-sensitivity problem although there is super-Planckian field excursion, and it suggests that inflation can be effectively studied based on supersymmetric field theory while a UV-completed framework is not prerequisite.

  3. Nucleonic helicity distributions revisited with an emphasis on their ...

    Indian Academy of Sciences (India)

    dimensions and our results are in conformity with the work presented in ref. [10]. This work, in association with our previous work in ref. [6], gives a satisfactory description of various parts of helicity distributions and their evolutions in the gauge-fixed light-front. Hamiltonian formulation. Including the work presented in refs [8,9] ...

  4. Variation in the Helical Structure of Native Collagen

    Science.gov (United States)

    2014-02-24

    2211 collagen, molecular structure, variability, xray diffraction REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR...indicates the triple-helix begins to associate at the (GPO)5 region as suggested previously [29,30], but must transition from the non-helical

  5. Interaction of 18-residue peptides derived from amphipathic helical ...

    Indian Academy of Sciences (India)

    Madhsudhan

    amphipathic peptides having potent antimicrobial activities;. Biochemistry 31 12688–12694. Cornell R B and Taneva S G 2006 Amphipathic helices as mediators of the membrane interaction of amphitropic proteins, and as modulators of bilayer physical properties; Curr. Protein. Pept. Sci. 6 539–552. Dathe M, Schumann M, ...

  6. Experimental evaluation of helically coiled tube flocculators for ...

    African Journals Online (AJOL)

    The constant need to improve water treatment techniques allows for the emergence of new technologies for obtaining adequate water, both in terms of quality and quantity. In order to obtain an efficient, rapid and low-cost clarification system, this study proposes the use of helically coiled tubes (HCTs) as a ...

  7. Helical Feed Milling with MQL for Boring of Aluminum Alloy

    Science.gov (United States)

    Sasahara, Hiroyuki; Kawasaki, Makoto; Tsutsumi, Masaomi

    MQL is applied to the helical feed milling hole-making process of aluminum alloy. It is difficult to drill on aluminum alloy without cutting fluid because the adhesion to the tool leads to a chip jam, the tool breakage or low accuracy. By employing the helical feed milling, cutting temperature will decrease, each chip length will become short and a chip jam in a hole will be avoided, because the intermittent cutting is realized. As a result of employing the helical feed milling with MQL, it was shown that the shape error is decreased, a burr formation is decreased, machining temperature becomes low and the cutting force becomes small comparing with drilling process. Shape error by helical feed milling with MQL is comparable with that with flood coolant. In this case, small mist particle counts under 5μm, which affects working environment, are almost constant if the spindle speed varies. Scattered mist particle counts are less when MQL is employed over 20000 min-1 spindle speed comparing with the flood coolant.

  8. The Hemispheric Sign Rule of Current Helicity during the Rising ...

    Indian Academy of Sciences (India)

    tribpo

    netic chirality (handedness) exists throughout the solar atmosphere, such as sunspot whirls (Richardson 1941), signs of current helicity in active regions (see Table 1), quiescent filaments (Martin et al. 1994), sigmoid coronal loops (Rust & Kumar 1996) and interplanetary magnetic clouds (Rust 1994). Table 1 shows that the ...

  9. Experimental and theoretical studies on a novel helical architecture ...

    Indian Academy of Sciences (India)

    A novel two-dimensional (2D), layered, helical supramolecular architecture constructed via cooperative hydrogen bond and halogen bonds was synthesized and characterized: [(BMBA)₂(TPB)]n (1) [BMBA= 3-bromo-2-methylbenzoic acid, TPB = 1,2,3,4-tetra-(4-pyridyl)-butane]. Density functional theory (DFT) calculations ...

  10. Experimental and theoretical studies on a novel helical architecture ...

    Indian Academy of Sciences (India)

    Sci. Vol. 128, No. 12, December 2016, pp. 1895–1904. c Indian Academy of Sciences. DOI 10.1007/s12039-016-1195-9. Experimental and theoretical studies on a novel helical architecture driven by hydrogen and halogen bonding interactions. QING ZHU LIUa, SHAN SHAN WANGa, TENG FEI WANGa, JIAN GUO LINa,∗.

  11. The role of dual-phase helical CT in assessing resectability of carcinoma of the gallbladder

    Energy Technology Data Exchange (ETDEWEB)

    Kumaran, Vinay; Pande, Girish Kumar; Sahni, Peush; Chattopadhyay, Tushar Kanti [Department of Gastrointestinal Surgery, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029 (India); Gulati, Manpreet Singh; Paul, Shashi Bala [Department of Radiodiagnosis, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029 (India)

    2002-08-01

    Our objective was to assess the ability of dual-phase helical CT (DHCT) to predict resectability of carcinoma of gallbladder (CaGB). Thirty-two consecutive patients suspected of having CaGB on clinical examination and sonography presented to our centre over 10-month period. All these 32 patients underwent DHCT. Fifteen patients were considered inoperable and 2 had xanthogranulomatous cholecystitis. The remaining 15 patients (10 women, 5 men; age range 33-72 years) underwent surgery and had histopathological confirmation of CaGB and were included in the study based on the following criteria: presence of mass in gallbladder fossa on sonography and DHCT, and confirmation at surgery and histopathological examination. Axial reconstructions of 2 mm were obtained (collimation 3 mm, table speed 4.5 mm/s) for arterial (scan delay 20 s) and venous (scan delay 60 s) phases on a helical scanner. The criteria used for unresectability were: distant metastasis (liver, peritoneum, lymph nodes), extensive local contiguous organ spread, involvement of secondary biliary confluence of both lobes of liver, tumoral invasion of main portal vein, or proper hepatic artery or simultaneous invasion of one side hepatic artery and the other side portal vein. The CT findings related to unresectability were correlated with surgical findings. On the basis of CT findings, 10 patients were unresectable and 5 were resectable. Of the 10 patients considered unresectable, 9 had tumours that were unresectable at surgery (sensitivity 100%, positive predictive value 90%). Five patients had more than one reason and 4 had one reason alone for being unresectable (lymph nodes, n=2; hepatic metastasis, n=1; and vascular invasion, n=1). All 5 patients considered resectable based on CT findings had resectable tumours at surgery (negative predictive value 100%). The overall accuracy of CT was 93.3%. Dual-phase helical CT comprehensively evaluates CaGB and may be a useful tool in preoperative staging of this

  12. 76 FR 72722 - Helical Spring Lock Washers From China and Taiwan

    Science.gov (United States)

    2011-11-25

    ... COMMISSION Helical Spring Lock Washers From China and Taiwan Determination On the basis of the record \\1... antidumping duty orders on helical spring lock washers from China and Taiwan would be likely to lead to... with respect to helical spring lock washers from Taiwan. Background The Commission instituted these...

  13. Numerical analysis of fluid flow and heat transfer in a helical ...

    African Journals Online (AJOL)

    Helical channels are widely applied in different application areas. In a converging diverging nozzle, helical channels are mainly used for cooling of its wall. The characteristics of fluid flow and heat transfer inside helical duct for a converging diverging nozzle is not commonly dealt in present literatures. In this paper CFD ...

  14. Expression of transmembrane protein 26 (TMEM26) in breast cancer and its association with drug response

    Science.gov (United States)

    Nass, Norbert; Dittmer, Angela; Hellwig, Vicky; Lange, Theresia; Beyer, Johanna Mirjam; Leyh, Benjamin; Ignatov, Atanas; Weiβenborn, Christine; Kirkegaard, Tove; Lykkesfeldt, Anne E.; Kalinski, Thomas; Dittmer, Jürgen

    2016-01-01

    We have previously shown that stromal cells desensitize breast cancer cells to the anti-estrogen fulvestrant and, along with it, downregulate the expression of TMEM26 (transmembrane protein 26). In an effort to study the function and regulation of TMEM26 in breast cancer cells, we found that breast cancer cells express non-glycosylated and N-glycosylated isoforms of the TMEM26 protein and demonstrate that N-glycosylation is important for its retention at the plasma membrane. Fulvestrant induced significant changes in expression and in the N-glycosylation status of TMEM26. In primary breast cancer, TMEM26 protein expression was higher in ERα (estrogen receptor α)/PR (progesterone receptor)-positive cancers. These data suggest that ERα is a major regulator of TMEM26. Significant changes in TMEM26 expression and N-glycosylation were also found, when MCF-7 and T47D cells acquired fulvestrant resistance. Furthermore, patients who received aromatase inhibitor treatment tend to have a higher risk of recurrence when tumoral TMEM26 protein expression is low. In addition, TMEM26 negatively regulates the expression of integrin β1, an important factor involved in endocrine resistance. Data obtained by spheroid formation assays confirmed that TMEM26 and integrin β1 can have opposite effects in breast cancer cells. These data are consistent with the hypothesis that, in ERα-positive breast cancer, TMEM26 may function as a tumor suppressor by impeding the acquisition of endocrine resistance. In contrast, in ERα-negative breast cancer, particularly triple-negative cancer, high TMEM26 expression was found to be associated with a higher risk of recurrence. This implies that TMEM26 has different functions in ERα-positive and -negative breast cancer. PMID:27224909

  15. Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1.

    Directory of Open Access Journals (Sweden)

    Michael Mühle

    Full Text Available The transmembrane envelope (TM protein gp41 of the human immunodeficiency virus-1 (HIV-1 plays an important role during virus infection inducing the fusion of the viral and cellular membranes. In addition, there are indications that the TM protein plays a role in the immunopathogenesis leading to the acquired immunodeficiency syndrome (AIDS. Inactivated virus particles and recombinant gp41 have been reported to inhibit lymphocyte proliferation, as well as to alter cytokine release and gene expression. The same was shown for a peptide corresponding to a highly conserved domain of all retroviral TM proteins, the immunosuppressive domain. Due to its propensity to aggregate and to be expressed at low levels, studies comprising authentic gp41 produced in eukaryotic cells are extremely rare. Here we describe the production of a secreted, soluble recombinant gp41 in 293 cells. The antigen was purified to homogeneity and characterised thoroughly by various biochemical and immunological methods. It was shown that the protein was glycosylated and assembled into trimers. Binding studies by ELISA and surface plasmon resonance using conformation-specific monoclonal antibodies implied a six-helix bundle conformation. The low binding of broadly neutralising antibodies (bnAb directed against the membrane proximal external region (MPER suggested that this gp41 is probably not suited as vaccine to induce such bnAb. Purified gp41 bound to monocytes and to a lesser extent to lymphocytes and triggered the production of specific cytokines when added to normal peripheral blood mononuclear cells. In addition, gp41 expressed on target cells inhibited the antigen-specific response of murine CD8+ T cells by drastically impairing their IFNγ production. To our knowledge, this is the first comprehensive analysis of a gp41 produced in eukaryotic cells including its immunosuppressive properties. Our data provide another line of evidence that gp41 might be directly involved in

  16. 3D Architecture of the Trypanosoma brucei Flagella Connector, a Mobile Transmembrane Junction

    Science.gov (United States)

    Höög, Johanna L.; Lacomble, Sylvain; Bouchet-Marquis, Cedric; Briggs, Laura; Park, Kristin; Hoenger, Andreas; Gull, Keith

    2016-01-01

    Background Cellular junctions are crucial for the formation of multicellular organisms, where they anchor cells to each other and/or supportive tissue and enable cell-to-cell communication. Some unicellular organisms, such as the parasitic protist Trypanosoma brucei, also have complex cellular junctions. The flagella connector (FC) is a three-layered transmembrane junction that moves with the growing tip of a new flagellum and attaches it to the side of the old flagellum. The FC moves via an unknown molecular mechanism, independent of new flagellum growth. Here we describe the detailed 3D architecture of the FC suggesting explanations for how it functions and its mechanism of motility. Methodology/Principal Findings We have used a combination of electron tomography and cryo-electron tomography to reveal the 3D architecture of the FC. Cryo-electron tomography revealed layers of repetitive filamentous electron densities between the two flagella in the interstitial zone. Though the FC does not change in length and width during the growth of the new flagellum, the interstitial zone thickness decreases as the FC matures. This investigation also shows interactions between the FC layers and the axonemes of the new and old flagellum, sufficiently strong to displace the axoneme in the old flagellum. We describe a novel filament, the flagella connector fibre, found between the FC and the axoneme in the old flagellum. Conclusions/Significance The FC is similar to other cellular junctions in that filamentous proteins bridge the extracellular space and are anchored to underlying cytoskeletal structures; however, it is built between different portions of the same cell and is unique because of its intrinsic motility. The detailed description of its structure will be an important tool to use in attributing structure / function relationships as its molecular components are discovered in the future. The FC is involved in the inheritance of cell shape, which is important for the life

  17. Transmembrane Prostatic Acid Phosphatase (TMPAP) Interacts with Snapin and Deficient Mice Develop Prostate Adenocarcinoma

    Science.gov (United States)

    Quintero, Ileana B.; Herrala, Annakaisa M.; Araujo, César L.; Pulkka, Anitta E.; Hautaniemi, Sampsa; Ovaska, Kristian; Pryazhnikov, Evgeny; Kulesskiy, Evgeny; Ruuth, Maija K.; Soini, Ylermi; Sormunen, Raija T.; Khirug, Leonard; Vihko, Pirkko T.

    2013-01-01

    The molecular mechanisms underlying prostate carcinogenesis are poorly understood. Prostatic acid phosphatase (PAP), a prostatic epithelial secretion marker, has been linked to prostate cancer since the 1930's. However, the contribution of PAP to the disease remains controversial. We have previously cloned and described two isoforms of this protein, a secretory (sPAP) and a transmembrane type-I (TMPAP). The goal in this work was to understand the physiological function of TMPAP in the prostate. We conducted histological, ultra-structural and genome-wide analyses of the prostate of our PAP-deficient mouse model (PAP−/−) with C57BL/6J background. The PAP−/− mouse prostate showed the development of slow-growing non-metastatic prostate adenocarcinoma. In order to find out the mechanism behind, we identified PAP-interacting proteins byyeast two-hybrid assays and a clear result was obtained for the interaction of PAP with snapin, a SNARE-associated protein which binds Snap25 facilitating the vesicular membrane fusion process. We confirmed this interaction by co-localization studies in TMPAP-transfected LNCaP cells (TMPAP/LNCaP cells) and in vivo FRET analyses in transient transfected LNCaP cells. The differential gene expression analyses revealed the dysregulation of the same genes known to be related to synaptic vesicular traffic. Both TMPAP and snapin were detected in isolated exosomes. Our results suggest that TMPAP is involved in endo-/exocytosis and disturbed vesicular traffic is a hallmark of prostate adenocarcinoma. PMID:24039861

  18. SAXS analysis of a soluble cytosolic NgBR construct including extracellular and transmembrane domains.

    Directory of Open Access Journals (Sweden)

    Joshua Holcomb

    Full Text Available The Nogo-B receptor (NgBR is involved in oncogenic Ras signaling through directly binding to farnesylated Ras. It recruits farnesylated Ras to the non-lipid-raft membrane for interaction with downstream effectors. However, the cytosolic domain of NgBR itself is only partially folded. The lack of several conserved secondary structural elements makes this domain unlikely to form a complete farnesyl binding pocket. We find that inclusion of the extracellular and transmembrane domains that contain additional conserved residues to the cytosolic region results in a well folded protein with a similar size and shape to the E.coli cis-isoprenyl transferase (UPPs. Small Angle X-ray Scattering (SAXS analysis reveals the radius of gyration (Rg of our NgBR construct to be 18.2 Å with a maximum particle dimension (Dmax of 61.0 Å. Ab initio shape modeling returns a globular molecular envelope with an estimated molecular weight of 23.0 kD closely correlated with the calculated molecular weight. Both Kratky plot and pair distribution function of NgBR scattering reveal a bell shaped peak which is characteristic of a single globularly folded protein. In addition, circular dichroism (CD analysis reveals that our construct has the secondary structure contents similar to the UPPs. However, this result does not agree with the currently accepted topological orientation of NgBR which might partition this construct into three separate domains. This discrepancy suggests another possible NgBR topology and lends insight into a potential molecular basis of how NgBR facilitates farnesylated Ras recruitment.

  19. 3D Architecture of the Trypanosoma brucei Flagella Connector, a Mobile Transmembrane Junction.

    Directory of Open Access Journals (Sweden)

    Johanna L Höög

    2016-01-01

    Full Text Available Cellular junctions are crucial for the formation of multicellular organisms, where they anchor cells to each other and/or supportive tissue and enable cell-to-cell communication. Some unicellular organisms, such as the parasitic protist Trypanosoma brucei, also have complex cellular junctions. The flagella connector (FC is a three-layered transmembrane junction that moves with the growing tip of a new flagellum and attaches it to the side of the old flagellum. The FC moves via an unknown molecular mechanism, independent of new flagellum growth. Here we describe the detailed 3D architecture of the FC suggesting explanations for how it functions and its mechanism of motility.We have used a combination of electron tomography and cryo-electron tomography to reveal the 3D architecture of the FC. Cryo-electron tomography revealed layers of repetitive filamentous electron densities between the two flagella in the interstitial zone. Though the FC does not change in length and width during the growth of the new flagellum, the interstitial zone thickness decreases as the FC matures. This investigation also shows interactions between the FC layers and the axonemes of the new and old flagellum, sufficiently strong to displace the axoneme in the old flagellum. We describe a novel filament, the flagella connector fibre, found between the FC and the axoneme in the old flagellum.The FC is similar to other cellular junctions in that filamentous proteins bridge the extracellular space and are anchored to underlying cytoskeletal structures; however, it is built between different portions of the same cell and is unique because of its intrinsic motility. The detailed description of its structure will be an important tool to use in attributing structure / function relationships as its molecular components are discovered in the future. The FC is involved in the inheritance of cell shape, which is important for the life cycle of this human parasite.

  20. Photosensitized electron transport across lipid vesicle walls: Enhancement of quantum yield by ionophores and transmembrane potentials

    Science.gov (United States)

    Laane, Colja; Ford, William E.; Otvos, John W.; Calvin, Melvin

    1981-01-01

    The photosensitized reduction of heptylviologen in the bulk aqueous phase of phosphatidylcholine vesicles containing EDTA inside and a membrane-bound tris(2,2′-bipyridine)ruthenium(2+) derivative is enhanced by a factor of 6.5 by the addition of valinomycin in the presence of K+. A 3-fold stimulation by gramicidin and carbonyl cyanide m-chlorophenylhydrazone is observed. The results suggest that, under these conditions, the rate of photoinduced electron transfer across vesicle walls in the absence of ion carriers is limited by cotransport of cations. The rate of electron transfer across vesicle walls could be influenced further by generating transmembrane potentials with K+ gradients in the presence of valinomycin. When vesicles are made with transmembrane potentials, interior more negative, the quantum yield of heptylviologen reduction is doubled, and, conversely, when vesicles are made with transmembrane potentials, interior more positive, the quantum yield is decreased and approaches the value found in the absence of valinomycin. PMID:16593002

  1. High temperature helical tubular receiver for concentrating solar power system

    Science.gov (United States)

    Hossain, Nazmul

    In the field of conventional cleaner power generation technology, concentrating solar power systems have introduced remarkable opportunity. In a solar power tower, solar energy concentrated by the heliostats at a single point produces very high temperature. Falling solid particles or heat transfer fluid passing through that high temperature region absorbs heat to generate electricity. Increasing the residence time will result in more heat gain and increase efficiency. A novel design of solar receiver for both fluid and solid particle is approached in this paper which can increase residence time resulting in higher temperature gain in one cycle compared to conventional receivers. The helical tubular solar receiver placed at the focused sunlight region meets the higher outlet temperature and efficiency. A vertical tubular receiver is modeled and analyzed for single phase flow with molten salt as heat transfer fluid and alloy625 as heat transfer material. The result is compared to a journal paper of similar numerical and experimental setup for validating our modeling. New types of helical tubular solar receivers are modeled and analyzed with heat transfer fluid turbulent flow in single phase, and granular particle and air plug flow in multiphase to observe the temperature rise in one cyclic operation. The Discrete Ordinate radiation model is used for numerical analysis with simulation software Ansys Fluent 15.0. The Eulerian granular multiphase model is used for multiphase flow. Applying the same modeling parameters and boundary conditions, the results of vertical and helical receivers are compared. With a helical receiver, higher temperature gain of heat transfer fluid is achieved in one cycle for both single phase and multiphase flow compared to the vertical receiver. Performance is also observed by varying dimension of helical receiver.

  2. Control of transmembrane protein diffusion within the postsynaptic density assessed by simultaneous single-molecule tracking and localization microscopy

    Directory of Open Access Journals (Sweden)

    Thomas A Blanpied

    2016-07-01

    Full Text Available Postsynaptic transmembrane proteins are critical elements of synapses, mediating trans-cellular contact, sensitivity to neurotransmitters and other signaling molecules, and flux of Ca and other ions. Positioning and mobility of each member of this large class of proteins is critical to their individual function at the synapse. One critical example is that the position of glutamate receptors within the postsynaptic density (PSD strongly modulates their function by aligning or misaligning them with sites of presynaptic vesicle fusion. In addition, the regulated ability of receptors to move in or out of the synapse is critical for activity-dependent plasticity. However, factors that control receptor mobility within the boundaries of the synapse are not well understood. Notably, PSD scaffold molecules accumulate in domains much smaller than the synapse. Within these nanodomains, the density of proteins is considerably higher than that of the synapse as a whole, so high that steric hindrance is expected to reduce receptor mobility substantially. However, while numerical modeling has demonstrated several features of how the varying protein density across the face of a single PSD may modulate receptor motion, there is little experimental information about the extent of this influence. To address this critical aspect of synaptic organizational dynamics, we performed single-molecule tracking of transmembrane proteins using uPAINT over PSDs whose internal structure was simultaneously resolved using PALM. The results provide important experimental confirmation that PSD scaffold density protein strongly influences the mobility of transmembrane proteins. Tracking a protein with a cytosolic domain that does not bind PSD-95 still was slowed in regions of high PSD-95 density, suggesting that crowding by scaffold molecules and perhaps other proteins is sufficient to stabilize receptors even in the absence of binding. Because numerous proteins thought to be

  3. Formation and sustainment of a very low aspect ratio tokamak using coaxial helicity injection (the Helicity Injected Torus [HIT] experiment)

    International Nuclear Information System (INIS)

    Jarboe, T.R.; Nelson, B.A.

    1992-01-01

    In the paper we will detail the progress of the HIT experiment construction, including the following components: preliminary data and interpretation; diagnostic systems; vacuum vessel and pumping system; helicity source and power supplies; toroidal field coil and power supply; data acquisition system; collaboration with general atomics, with a brief summary given on each

  4. Expression of transmembrane carbonic anhydrases, CAIX and CAXII, in human development

    Directory of Open Access Journals (Sweden)

    Lerman Michael I

    2009-03-01

    Full Text Available Abstract Background Transmembrane CAIX and CAXII are members of the alpha carbonic anhydrase (CA family. They play a crucial role in differentiation, proliferation, and pH regulation. Expression of CAIX and CAXII proteins in tumor tissues is primarily induced by hypoxia and this is particularly true for CAIX, which is regulated by the transcription factor, hypoxia inducible factor-1 (HIF-1. Their distributions in normal adult human tissues are restricted to highly specialized cells that are not always hypoxic. The human fetus exists in a relatively hypoxic environment. We examined expression of CAIX, CAXII and HIF-1α in the developing human fetus and postnatal tissues to determine whether expression of CAIX and CAXII is exclusively regulated by HIF-1. Results The co-localization of CAIX and HIF-1α was limited to certain cell types in embryonic and early fetal tissues. Those cells comprised the primitive mesenchyma or involved chondrogenesis and skin development. Transient CAIX expression was limited to immature tissues of mesodermal origin and the skin and ependymal cells. The only tissues that persistently expressed CAIX protein were coelomic epithelium (mesothelium and its remnants, the epithelium of the stomach and biliary tree, glands and crypt cells of duodenum and small intestine, and the cells located at those sites previously identified as harboring adult stem cells in, for example, the skin and large intestine. In many instances co-localization of CAIX and HIF-1α was not evident. CAXII expression is restricted to cells involved in secretion and water absorption such as parietal cells of the stomach, acinar cells of the salivary glands and pancreas, epithelium of the large intestine, and renal tubules. Co-localization of CAXII with CAIX or HIF-1α was not observed. Conclusion The study has showed that: 1 HIF-1α and CAIX expression co- localized in many, but not all, of the embryonic and early fetal tissues; 2 There is no evidence of

  5. Human Cytomegalovirus Exploits Interferon-Induced Transmembrane Proteins To Facilitate Morphogenesis of the Virion Assembly Compartment

    Science.gov (United States)

    Xie, Maorong; Xuan, Baoqin; Shan, Jiaoyu; Pan, Deng; Sun, Yamei; Shan, Zhao; Zhang, Jinping; Yu, Dong

    2014-01-01

    ABSTRACT Recently, interferon-induced transmembrane proteins (IFITMs) have been identified to be key effector molecules in the host type I interferon defense system. The invasion of host cells by a large range of RNA viruses is inhibited by IFITMs during the entry step. However, the roles of IFITMs in DNA virus infections have not been studied in detail. In this study, we report that human cytomegalovirus (HCMV), a large human DNA virus, exploits IFITMs to facilitate the formation of the virion assembly compartment (vAC) during infection of human fibroblasts. We found that IFITMs were expressed constitutively in human embryonic lung fibroblasts (MRC5 cells). HCMV infection inhibited IFITM protein accumulation in the later stages of infection. Overexpression of an IFITM protein in MRC5 cells slightly enhanced HCMV production and knockdown of IFITMs by RNA interference reduced the virus titer by about 100-fold on day 8 postinfection, according to the findings of a virus yield assay at a low multiplicity of infection. Virus gene expression and DNA synthesis were not affected, but the typical round structure of the vAC was not formed after the suppression of IFITMs, thereby resulting in defective virion assembly and the production of less infectious virion particles. Interestingly, the replication of herpes simplex virus, a human herpesvirus that is closely related to HCMV, was not affected by the suppression of IFITMs in MRC5 cells. These results indicate that IFITMs are involved in a specific pathway required for HCMV replication. IMPORTANCE HCMV is known to repurpose the interferon-stimulated genes (ISGs) viperin and tetherin to facilitate its replication. Our results expand the range of ISGs that can be exploited by HCMV for its replication. This is also the first report of a proviral function of IFITMs in DNA virus replication. In addition, whereas previous studies showed that IFITMs modulate virus entry, which is a very early stage in the virus life cycle, we

  6. Use of Membrane Potential to Achieve Transmembrane Modification with an Artificial Receptor.

    Science.gov (United States)

    Hatanaka, Wataru; Kawaguchi, Miki; Sun, Xizheng; Nagao, Yusuke; Ohshima, Hiroyuki; Hashida, Mitsuru; Higuchi, Yuriko; Kishimura, Akihiro; Katayama, Yoshiki; Mori, Takeshi

    2017-02-15

    We developed a strategy to modify cell membranes with an artificial transmembrane receptor. Coulomb force on the receptor, caused by the membrane potential, was used to achieve membrane penetration. A hydrophobically modified cationic peptide was used as a membrane potential sensitive region that was connected to biotin through a transmembrane oligoethylene glycol (OEG) chain. This artificial receptor gradually disappeared from the cell membrane via penetration despite the presence of a hydrophilic OEG chain. However, when the receptor was bound to streptavidin (SA), it remained on the cell membrane because of the large and hydrophilic nature of SA.

  7. Novel mutations in the transmembrane natriuretic peptide receptor ...

    Indian Academy of Sciences (India)

    skeletal growth is slow (Bartels et al. 2004). Radiographic findings include abnormal growth plates and short bones in the limbs detectable by two years of age. Involvement of the axial skeleton differentiates it from acromesomelic dys- plasia of Hunter–Thompson type which is caused by muta- tions in GDF5 gene. Recently ...

  8. Alignment of helical membrane protein sequences using AlignMe.

    Directory of Open Access Journals (Sweden)

    Marcus Stamm

    Full Text Available Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S matching was combined with evolutionary information (using a position-specific substitution matrix (P, in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T, in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set.

  9. Exosome-related multi-pass transmembrane protein TSAP6 is a target of rhomboid protease RHBDD1-induced proteolysis.

    Directory of Open Access Journals (Sweden)

    Chunhua Wan

    Full Text Available We have previously reported that rhomboid domain containing 1 (RHBDD1, a mammalian rhomboid protease highly expressed in the testis, can cleave the Bcl-2 protein Bik. In this study, we identified a multi-pass transmembrane protein, tumor suppressor activated pathway-6 (TSAP6 as a potential substrate of RHBDD1. RHBDD1 was found to induce the proteolysis of TSAP6 in a dose- and activity-dependent manner. The cleavage of TSAP6 was not restricted to its glycosylated form and occurred in three different regions. In addition, mass spectrometry and mutagenesis analyses both indicated that the major cleavage site laid in the C-terminal of the third transmembrane domain of TSAP6. A somatic cell knock-in approach was used to genetically inactivate the endogenous RHBDD1 in HCT116 and RKO colon cancer cells. Exosome secretion was significantly elevated when RHBDD1 was inactivated in the two cells lines. The increased exosome secretion was verfied through the detection of certain exosomal components, including Tsg101, Tf-R, FasL and Trail. In addition, the elevation of exosome secretion by RHBDD1 inactivation was reduced when TSAP6 was knocked down, indicating that the role of RHBDD1 in regulating exosomal trafficking is very likely to be TSAP6-dependent. We found that the increase in FasL and Trail increased exosome-induced apoptosis in Jurkat cells. Taken together, our findings suggest that RHBDD1 is involved in the regulation of a nonclassical exosomal secretion pathway through the restriction of TSAP6.

  10. SDN-1/Syndecan Acts in Parallel to the Transmembrane Molecule MIG-13 to Promote Anterior Neuroblast Migration.

    Science.gov (United States)

    Sundararajan, Lakshmi; Norris, Megan L; Lundquist, Erik A

    2015-05-28

    The Q neuroblasts in Caenorhabditis elegans display left-right asymmetry in their migration, with QR and descendants on the right migrating anteriorly, and QL and descendants on the left migrating posteriorly. Initial QR and QL migration is controlled by the transmembrane receptors UNC-40/DCC, PTP-3/LAR, and the Fat-like cadherin CDH-4. After initial migration, QL responds to an EGL-20/Wnt signal that drives continued posterior migration by activating MAB-5/Hox activity in QL but not QR. QR expresses the transmembrane protein MIG-13, which is repressed by MAB-5 in QL and which drives anterior migration of QR descendants. A screen for new Q descendant AQR and PQR migration mutations identified mig-13 as well as hse-5, the gene encoding the glucuronyl C5-epimerase enzyme, which catalyzes epimerization of glucuronic acid to iduronic acid in the heparan sulfate side chains of heparan sulfate proteoglycans (HSPGs). Of five C. elegans HSPGs, we found that only SDN-1/Syndecan affected Q migrations. sdn-1 mutants showed QR descendant AQR anterior migration defects, and weaker QL descendant PQR migration defects. hse-5 affected initial Q migration, whereas sdn-1 did not. sdn-1 and hse-5 acted redundantly in AQR and PQR migration, but not initial Q migration, suggesting the involvement of other HSPGs in Q migration. Cell-specific expression studies indicated that SDN-1 can act in QR to promote anterior migration. Genetic interactions between sdn-1, mig-13, and mab-5 suggest that MIG-13 and SDN-1 act in parallel to promote anterior AQR migration and that SDN-1 also controls posterior migration. Together, our results indicate previously unappreciated complexity in the role of multiple signaling pathways and inherent left-right asymmetry in the control of Q neuroblast descendant migration. Copyright © 2015 Sundararajan et al.

  11. More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology.

    Directory of Open Access Journals (Sweden)

    Wing-Cheong Wong

    Full Text Available Large-scale genome sequencing gained general importance for life science because functional annotation of otherwise experimentally uncharacterized sequences is made possible by the theory of biomolecular sequence homology. Historically, the paradigm of similarity of protein sequences implying common structure, function and ancestry was generalized based on studies of globular domains. Having the same fold imposes strict conditions over the packing in the hydrophobic core requiring similarity of hydrophobic patterns. The implications of sequence similarity among non-globular protein segments have not been studied to the same extent; nevertheless, homology considerations are silently extended for them. This appears especially detrimental in the case of transmembrane helices (TMs and signal peptides (SPs where sequence similarity is necessarily a consequence of physical requirements rather than common ancestry. Thus, matching of SPs/TMs creates the illusion of matching hydrophobic cores. Therefore, inclusion of SPs/TMs into domain models can give rise to wrong annotations. More than 1001 domains among the 10,340 models of Pfam release 23 and 18 domains of SMART version 6 (out of 809 contain SP/TM regions. As expected, fragment-mode HMM searches generate promiscuous hits limited to solely the SP/TM part among clearly unrelated proteins. More worryingly, we show explicit examples that the scores of clearly false-positive hits, even in global-mode searches, can be elevated into the significance range just by matching the hydrophobic runs. In the PIR iProClass database v3.74 using conservative criteria, we find that at least between 2.1% and 13.6% of its annotated Pfam hits appear unjustified for a set of validated domain models. Thus, false-positive domain hits enforced by SP/TM regions can lead to dramatic annotation errors where the hit has nothing in common with the problematic domain model except the SP/TM region itself. We suggest a workflow of

  12. High temperature technological heat exchangers and steam generators with helical coil assembly tube bundle

    International Nuclear Information System (INIS)

    Korotaev, O.J.; Mizonov, N.V.; Nikolaevsky, V.B.; Nazarov, E.K.

    1990-01-01

    Analysis of thermal hydraulics characteristics of nuclear steam generators with different tube bundle arrangements and waste heat boilers for ammonia production units was performed on the basis of operating experience results and research and development data. The present report involves the obtained information. The estimations of steam generator performances and repair-ability are given. The significant temperature profile of the primary and secondary coolant flows are attributed to all steam generator designs. The intermediate mixing is found to be an effective means of temperature profile overcoming. At present the only means to provide an effective mixing in heat exchangers of the following types: straight tubes, field tubes, platen tubes and multibank helical coil tubes (with complicated bend distribution along their length) are section arrangements in series in conjunction with forced and natural mixing in connecting lines. Development of the unificated system from mini helical coil assemblies allows to design and manufacture heat exchangers and steam generators within the wide range of operating conditions without additional expenses on the research and development work

  13. Probing conserved helical modules of portal complexes by mass spectrometry-based hydrogen/deuterium exchange.

    Science.gov (United States)

    Kang, Sebyung; Poliakov, Anton; Sexton, Jennifer; Renfrow, Matthew B; Prevelige, Peter E

    2008-09-05

    The Double-stranded DNA bacteriophage P22 has a ring-shaped dodecameric complex composed of the 84 kDa portal protein subunit that forms the central channel of the phage DNA packaging motor. The overall morphology of the P22 portal complex is similar to that of the portal complexes of Phi29, SPP1, T3, T7 phages and herpes simplex virus. Secondary structure prediction of P22 portal protein and its threading onto the crystal structure of the Phi29 portal complexes suggested that the P22 portal protein complex shares conserved helical modules that were found in the dodecameric interfaces of the Phi29 portal complex. To identify the amino acids involved in intersubunit contacts in the P22 portal ring complexes and validate the threading model, we performed comparative hydrogen/deuterium exchange analysis of monomeric and in vitro assembled portal proteins of P22 and the dodecameric Phi29 portal. Hydrogen/deuterium exchange experiments provided evidence of intersubunit interactions in the P22 portal complex similar to those in the Phi29 portal that map to the regions predicted to be conserved helical modules.

  14. Probing Conserved Helical Modules of Portal Complexes by Mass Spectrometry based Hydrogen/deuterium Exchange

    Science.gov (United States)

    Kang, Sebyung; Poliakov, Anton; Sexton, Jennifer; Renfrow, Matthew B.; Prevelige, Peter E.

    2008-01-01

    The dsDNA bacteriophage P22 has a ring shaped dodecameric complex composed of the 84 kDa portal protein subunit which forms the central channel of the phage’s DNA packaging motor. The overall morphology of the P22 portal complex is similar to that of the portal complexes of Phi29, SPP1, T3, T7 phages and herpes simplex virus. Secondary structure prediction of P22 portal protein and its threading onto the crystal structure of the Phi29 portal complexes suggested that P22 portal protein complex shares conserved helical modules which were found in the dodecameric interfaces of the Phi29 portal complex. To identify the amino acids involved in inter-subunit contacts in the P22 portal ring complexes and validate the threading model, we performed comparative hydrogen/deuterium exchange analysis of monomeric and in vitro assembled portal proteins of P22 and the dodecameric Phi29 portal. Hydrogen/deuterium exchange experiments provided evidence of inter-subunit interactions in the P22 portal complex similar to those in the Phi29 portal which map to the regions predicted to be conserved helical modules. PMID:18621389

  15. Contractile and chiral activities codetermine the helicity of swimming droplet trajectories

    Science.gov (United States)

    Tjhung, Elsen; Cates, Michael E.; Marenduzzo, Davide

    2017-05-01

    Active fluids are a class of nonequilibrium systems where energy is injected into the system continuously by the constituent particles themselves. Many examples, such as bacterial suspensions and actomyosin networks, are intrinsically chiral at a local scale, so that their activity involves torque dipoles alongside the force dipoles usually considered. Although many aspects of active fluids have been studied, the effects of chirality on them are much less known. Here, we study by computer simulation the dynamics of an unstructured droplet of chiral active fluid in three dimensions. Our model considers only the simplest possible combination of chiral and achiral active stresses, yet this leads to an unprecedented range of complex motilities, including oscillatory swimming, helical swimming, and run-and-tumble motion. Strikingly, whereas the chirality of helical swimming is the same as the microscopic chirality of torque dipoles in one regime, the two are opposite in another. Some of the features of these motility modes resemble those of some single-celled protozoa, suggesting that underlying mechanisms may be shared by some biological systems and synthetic active droplets.

  16. Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Granzin, Joachim [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany); Huang, Ying; Topbas, Celalettin [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Huang, Wenying [Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Wu, Zhiping [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Misra, Saurav [Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Hazen, Stanley L. [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Blanton, Ronald E. [Department of Infectious Diseases, Case Western Reserve University, Cleveland, OH 44190 (United States); Lee, Xavier [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany)

    2012-06-01

    The crystal structure of ShSPI, a serpin from the blood fluke S. haematobium, reveals some peculiar features of the helical subdomain which have not been observed previously in the serpin superfamily. Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite–host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.

  17. Cryogenic system for the Large Helical Device. The helium refrigerator/liquefier for Large Helical Device

    International Nuclear Information System (INIS)

    Maekawa, Ryuji; Mito, Toshiyuki; Satoh, Sadao

    1997-01-01

    A large-scale helium refrigerator/liquefier has been developed to provide reliable and safe operation for the Large Helical Device (LHD). The refrigerator is required to satisfy four different types of cooling methods: forced-flow supercritical helium, a pool boiling method, two-phase helium flow and forced-flow low-temperature (40-80 K) helium gas. The forced-flow supercritical helium is widely used in modern large-scale superconducting magnets. This method requires a much more complex refrigeration system than does pool boiling because of the circulation of low-temperature helium within a very long cooling path. The overall refrigeration system is fairly complicated because of these multi-refrigeration requirements. As a matter of fact, it is not likely to find this type of refrigeration plant in the world. The helium refrigerator has a total refrigeration capacity of 5.65 kW at 4.4 K and 20.6 kW at 80 K and 650 l/h liquefaction. The refrigerator was designed to have high processing efficiency since the construction expense is much less than the operating cost. In order to achieve this, the refrigerator has two precooling cycles (300 to 80 K and 80 to 20 K) and has two turboexpanders running in parallel with different temperature levels at the cold end. To achieve a high mass flow rate in a low-temperature regime, eight screw-type compressors are operated at room temperature. There are two compressor groups, group A and group B, to reduce the overall work load. Each group consists of 1st and 2nd stage compression processes. The total mass flow rate becomes 960 g/s at 1.864 MPa. This article reviews the basic characteristics of a 10 kW class helium refrigerator/liquefier and a simple refrigeration cycle. (author)

  18. The conservation of helicity in hurricane Andrew (1992) and the formation of the spiral rainband

    Science.gov (United States)

    Xu, Yamei; Wu, Rongsheng

    2003-11-01

    The characteristics of helicity in a hurricane are presented by calculating the MM5 model output in addition to theoretical analysis. It is found that helicity in a hurricane mainly depends on its horizontal component, whose magnitude is about 100 to 1000 times larger than its vertical component. It is also found that helicity is approximately conserved in the hurricane. Since the fluid has the intention to adjust the wind shear to satisfy the conservation of helicity, the horizontal vorticity is even larger than the vertical vorticity, and the three-dimensional vortices slant to the horizontal plane except in the inner eye. There are significant horizontal vortices and inhomogeneous helical flows in the hurricane. The formation of the spiral rainband is discussed by using the law of horizontal helical flows. It is closely related to the horizontal strong vortices and inhomogeneous helical flows.

  19. The role of transmembrane segment II in 7TM receptor activation

    DEFF Research Database (Denmark)

    Benned-Jensen, Tau; Rosenkilde, M M

    2009-01-01

    During the two past decades tremendous effort has been put into uncovering the activation mechanism of 7TM receptors. The majority of such studies have focused on the major binding pocket, comprised of transmembrane segments (TM) -III through -VII, as most non-peptide and peptide ligands, in addi...

  20. Self-assembly of small-molecule fumaramides allows transmembrane chloride channel formation.

    Science.gov (United States)

    Roy, Arundhati; Gautam, Amitosh; Malla, Javid Ahmad; Sarkar, Sohini; Mukherjee, Arnab; Talukdar, Pinaki

    2018-02-20

    This study reports the formation of self-assembled transmembrane anion channels by small-molecule fumaramides. Such artificial ion channel formation was confirmed by ion transport across liposomes and by planar bilayer conductance measurements. The geometry-optimized model of the channel and Cl - ion selectivity within the channel lumen was also illustrated.

  1. Intact transmembrane isoforms of the neural cell adhesion molecule are released from the plasma membrane

    DEFF Research Database (Denmark)

    Olsen, M; Krog, L; Edvardsen, K

    1993-01-01

    . By density-gradient centrifugation it was shown that shed transmembrane NCAM-B was present in fractions of high, as well as low, density, indicating that a fraction of the shed NCAM is associated with minor plasma membrane fragments. Finally, it was shown that isolated soluble NCAM inhibited cell binding......-s1 and NCAM-s2 and the function of soluble NCAM forms were investigated. It was shown that all three soluble forms could be released from brain membranes with M(r) values identical to the three major membrane-associated forms: the large transmembrane 190,000-M(r) form (NCAM-A), the smaller...... intact soluble form from membranes of cells transfected with this isoform. Thus, NCAM-s1 and NCAM-s2 probably represent intact released transmembrane NCAM-A and NCAM-B. The soluble transmembrane forms are likely to exist in vivo, as NCAM-s1 and NCAM-s2 were readily demonstrated in cerebrospinal fluid...

  2. CoPreTHi: a Web tool which combines transmembrane protein segment prediction methods

    OpenAIRE

    Promponas, Vasilis; Palaios, Giorgos; Pasquier, Claude; Hamodrakas, Ioannis; Hamodrakas, Stavros

    2009-01-01

    International audience; CoPreTHi is a Java based web application, which combines the results of methods that predict the location of transmembrane segments in protein sequences into a joint prediction histogram. Clearly, the joint prediction algorithm, produces superior quality results than individual prediction schemes. The program is available at http://o2.db.uoa.gr/CoPreTHi.

  3. Transmembrane Domain Single-Nucleotide Polymorphisms Impair Expression and Transport Activity of ABC Transporter ABCG2

    NARCIS (Netherlands)

    Sjostedt, N.; Heuvel, J.J.M.W. van den; Koenderink, J.B.; Kidron, H.

    2017-01-01

    PURPOSE: To study the function and expression of nine naturally occurring single-nucleotide polymorphisms (G406R, F431L, S441N, P480L, F489L, M515R, L525R, A528T and T542A) that are predicted to reside in the transmembrane regions of the ABC transporter ABCG2. METHODS: The transport activity of the

  4. Detergent properties influence the stability of the glycophorin A transmembrane helix dimer in lysophosphatidylcholine micelles.

    Science.gov (United States)

    Stangl, Michael; Veerappan, Anbazhagan; Kroeger, Anja; Vogel, Peter; Schneider, Dirk

    2012-12-19

    Detergents might affect membrane protein structures by promoting intramolecular interactions that are different from those found in native membrane bilayers, and fine-tuning detergent properties can be crucial for obtaining structural information of intact and functional transmembrane proteins. To systematically investigate the influence of the detergent concentration and acyl-chain length on the stability of a transmembrane protein structure, the stability of the human glycophorin A transmembrane helix dimer has been analyzed in lyso-phosphatidylcholine micelles of different acyl-chain length. While our results indicate that the transmembrane protein is destabilized in detergents with increasing chain-length, the diameter of the hydrophobic micelle core was found to be less crucial. Thus, hydrophobic mismatch appears to be less important in detergent micelles than in lipid bilayers and individual detergent molecules appear to be able to stretch within a micelle to match the hydrophobic thickness of the peptide. However, the stability of the GpA TM helix dimer linearly depends on the aggregation number of the lyso-PC detergents, indicating that not only is the chemistry of the detergent headgroup and acyl-chain region central for classifying a detergent as harsh or mild, but the detergent aggregation number might also be important. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  5. The trans-membrane potential of biological membranes in computer simulation

    Czech Academy of Sciences Publication Activity Database

    Melcr, Josef; Timr, Štěpán; Jungwirth, Pavel

    2015-01-01

    Roč. 44, Suppl 1 (2015), S170 ISSN 0175-7571. [EBSA European Biophysics Congress /10./. 18.07.2015-22.07.2015, Dresden] Institutional support: RVO:61388963 Keywords : molecular dynamics * trans-membrane potential Subject RIV: CF - Physical ; Theoretical Chemistry

  6. Simulations of Skin Barrier Function: Free Energies of Hydrophobic and Hydrophilic Transmembrane Pores in Ceramide Bilayers

    NARCIS (Netherlands)

    Notman, Rebecca; Anwar, Jamshed; Briels, Willem J.; Noro, Massimo G.; den Otter, Wouter K.

    2008-01-01

    Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO)

  7. Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments

    Czech Academy of Sciences Publication Activity Database

    Vít, O.; Man, Petr; Kádek, Alan; Hausner, Jiří; Sklenář, A.; Harant, K.; Novák, Petr; Scigelová, M.; Wofferndin, G.; Petrák, J.

    2016-01-01

    Roč. 146, SI (2016), s. 15-22 ISSN 1874-3919 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : Integral membrane proteins * CNBr * Transmembrane Subject RIV: CE - Biochemistry Impact factor: 3.914, year: 2016

  8. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server

    DEFF Research Database (Denmark)

    Käll, Lukas; Krogh, Anders; Sonnhammer, Erik L L

    2007-01-01

    When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30-65% of all predicted signal peptides and 25-35% of al...

  9. Intrinsic potential of cell membranes: opposite effects of lipid transmembrane asymmetry and asymmetric salt ion distribution

    DEFF Research Database (Denmark)

    Gurtovenko, Andrey A; Vattulainen, Ilpo

    2009-01-01

    Using atomic-scale molecular dynamics simulations, we consider the intrinsic cell membrane potential that is found to originate from a subtle interplay between lipid transmembrane asymmetry and the asymmetric distribution of monovalent salt ions on the two sides of the cell membrane. It turns out...

  10. The transmembrane region is responsible for targeting of adaptor protein LAX into "heavy rafts''

    Czech Academy of Sciences Publication Activity Database

    Hrdinka, Matouš; Otáhal, Pavel; Hořejší, Václav

    2012-01-01

    Roč. 7, č. 5 (2012), e36330 E-ISSN 1932-6203 R&D Projects: GA ČR GEMEM/09/E011; GA MŠk 1M0506 Institutional research plan: CEZ:AV0Z50520514 Keywords : LAX * transmembrane domain * DRM Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.730, year: 2012

  11. Modeling the structure of SARS 3a transmembrane protein using a ...

    Indian Academy of Sciences (India)

    Abstract. 3a is an accessory protein from SARS coronavirus that is known to play a significant role in the proliferation of the virus by forming tetrameric ion channels. Although the monomeric units are known to consist of three transmembrane (TM) domains, there are no solved structures available for the complete monomer.

  12. Structure, function and physiological consequences of virally encoded chemokine seven transmembrane receptors

    NARCIS (Netherlands)

    Rosenkilde, M.M.; Smit, M.J.; Waldhoer, M.

    2008-01-01

    A number of human and animal herpes viruses encode G-protein coupled receptors with seven transmembrane (7TM) segments - most of which are clearly related to human chemokine receptors. It appears, that these receptors are used by the virus for immune evasion, cellular transformation, tissue

  13. Effects of Magnetic and Kinetic Helicities on the Growth of Magnetic Fields in Laminar and Turbulent Flows by Helical Fourier Decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Linkmann, Moritz; Sahoo, Ganapati; Biferale, Luca [Department of Physics and INFN, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, I-00133 Rome (Italy); McKay, Mairi; Berera, Arjun [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, EH9 3FD, Edinburgh (United Kingdom)

    2017-02-10

    We present a numerical and analytical study of incompressible homogeneous conducting fluids using a helical Fourier representation. We analytically study both small- and large-scale dynamo properties, as well as the inverse cascade of magnetic helicity, in the most general minimal subset of interacting velocity and magnetic fields on a closed Fourier triad. We mainly focus on the dependency of magnetic field growth as a function of the distribution of kinetic and magnetic helicities among the three interacting wavenumbers. By combining direct numerical simulations of the full magnetohydrodynamics equations with the helical Fourier decomposition, we numerically confirm that in the kinematic dynamo regime the system develops a large-scale magnetic helicity with opposite sign compared to the small-scale kinetic helicity, a sort of triad-by-triad α -effect in Fourier space. Concerning the small-scale perturbations, we predict theoretically and confirm numerically that the largest instability is achived for the magnetic component with the same helicity of the flow, in agreement with the Stretch–Twist–Fold mechanism. Vice versa, in the presence of Lorentz feedback on the velocity, we find that the inverse cascade of magnetic helicity is mostly local if magnetic and kinetic helicities have opposite signs, while it is more nonlocal and more intense if they have the same sign, as predicted by the analytical approach. Our analytical and numerical results further demonstrate the potential of the helical Fourier decomposition to elucidate the entangled dynamics of magnetic and kinetic helicities both in fully developed turbulence and in laminar flows.

  14. A rotating helical sealing joint capable of partially melting

    International Nuclear Information System (INIS)

    Martin, Jean; Ollier, J.-L.; Petit, Paul.

    1973-01-01

    A coagulated rotating helical joint providing gas and liquid tightness along a rotating shaft, comprising: a metal sleeve connected to the wall through which passes the rotating sleeve, an intermediate sleeve made of a fusible material, inert with respect to the fluid to be sealingly retained, and finally the rotating shaft provided with an engraved helical thread in register with the intermediate sleeve. Means are provided for regulating the intermediate sleeve temperature so that a thin melted film is formed on said intermediate sleeve when in contact with the rotating threaded shaft. This can be applied in the nuclear industry, including cases when the intermediate sleeve is constituted by the fluid itself, then in the solid state [fr

  15. Compensating Faraday Depolarization by Magnetic Helicity in the Solar Corona

    Energy Technology Data Exchange (ETDEWEB)

    Brandenburg, Axel; Ashurova, Mohira B. [Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, CO 80303 (United States); Jabbari, Sarah, E-mail: brandenb@nordita.org [School of Mathematical Sciences and Monash Centre for Astrophysics, Monash University, Clayton, VIC 3800 (Australia)

    2017-08-20

    A turbulent dynamo in spherical geometry with an outer corona is simulated to study the sign of magnetic helicity in the outer parts. In agreement with earlier studies, the sign in the outer corona is found to be opposite to that inside the dynamo. Line-of-sight observations of polarized emission are synthesized to explore the feasibility of using the local reduction of Faraday depolarization to infer the sign of helicity of magnetic fields in the solar corona. This approach was previously identified as an observational diagnostic in the context of galactic magnetic fields. Based on our simulations, we show that this method can be successful in the solar context if sufficient statistics are gathered by using averages over ring segments in the corona separately for the regions north and south of the solar equator.

  16. Fluid motion and mixing in helical static mixers

    Science.gov (United States)

    Jones, S. Casey; Sotiropoulos, Fotis

    2001-11-01

    Helical static mixers are used for mixing in a variety of industrial settings under a wide range of flow conditions. To obtain a more fundamental understanding of how these mixers operate, a detailed computational fluid dynamics model study of the helical static mixer was performed using a second-order accurate method for solving the incompressible Navier-Stokes equations on fine computational grids. We investigate the fluid structure in the mixers as a function the Reynolds number and the number of mixer elements. The Reynolds number was varied from 100 to 500, and the number of elements was varied from two to six. Mixing was investigated by applying dynamical systems techniques to the trajectories of a large number of particles released from the inlet of the mixer. We also consider closely two numerical issues: the length of the inlet and outlet sections attached to the mixer and the periodicity of the flow field within the mixer sections.

  17. Creating Helical Tool Paths for Single Point Incremental Forming

    DEFF Research Database (Denmark)

    Skjødt, Martin; Hancock, Michael H.; Bay, Niels

    2007-01-01

    Single point incremental forming (SPIF) is a relatively new sheet forming process. A sheet is clamped in a rig and formed incrementally using a rotating single point tool in the form of a rod with a spherical end. The process is often performed on a CNC milling machine and the tool movement...... is programed using CAM software intended for surface milling. Often the function called profile milling or contour milling is applied. Using this milling function the tool only has a continuous feed rate in two directions X and Y, which is the plane of the undeformed sheet. The feed in the vertical Z direction...... from the profile milling code and converts them into a helical tool path with continuous feed in all three directions. Using the helical tool path the scarring is removed, the part is otherwise unchanged and a major disadvantage of using milling software for SPIF is removed. The solution...

  18. Organocatalyzed Asymmetric Synthesis of Axially, Planar, and Helical Chiral Compounds.

    Science.gov (United States)

    Shirakawa, Seiji; Liu, Shiyao; Kaneko, Shiho

    2016-02-04

    Axially, planar, and helical chiral compounds are indispensable building blocks in modern organic synthesis. A wide variety of chiral ligands and catalysts were designed based on these chiral scaffolds, and these chiral ligands and catalysts were used for various catalytic asymmetric transformations to produce important chiral compounds in an optically enriched form. Furthermore, these chiral skeletons are found in the structure of biologically active natural products. Thus, the development of efficient enantioselective methods for the synthesis of these chiral compounds is an important task in the field of organic chemistry. In the last few years, organocatalyzed approaches, which are one of the most reliable catalytic asymmetric methods, became a hot topic. This Focus Review summarizes asymmetric organocatalytic methods for the synthesis of axially, planar, and helical chiral compounds as useful chiral building blocks. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Small-x Asymptotics of the Quark Helicity Distribution.

    Science.gov (United States)

    Kovchegov, Yuri V; Pitonyak, Daniel; Sievert, Matthew D

    2017-02-03

    We construct a numerical solution of the small-x evolution equations derived in our recent work [J. High Energy Phys. 01 (2016) 072.JHEPFG1029-847910.1007/JHEP01(2016)072] for the (anti)quark transverse momentum dependent helicity TMDs and parton distribution functions (PDFs) as well as the g_{1} structure function. We focus on the case of large N_{c}, where one finds a closed set of equations. Employing the extracted intercept, we are able to predict directly from theory the behavior of the quark helicity PDFs at small x, which should have important phenomenological consequences. We also give an estimate of how much of the proton's spin carried by the quarks may be at small x and what impact this has on the spin puzzle.

  20. Study on reinforced concrete beams with helical transverse reinforcement

    Science.gov (United States)

    Kaarthik Krishna, N.; Sandeep, S.; Mini, K. M.

    2018-02-01

    In a Reinforced Concrete (R.C) structure, major reinforcement is used for taking up tensile stresses acting on the structure due to applied loading. The present paper reports the behavior of reinforced concrete beams with helical reinforcement (transverse reinforcement) subjected to monotonous loading by 3-point flexure test. The results were compared with identically similar reinforced concrete beams with rectangular stirrups. During the test crack evolution, load carrying capacity and deflection of the beams were monitored, analyzed and compared. Test results indicate that the use of helical reinforcement provides enhanced load carrying capacity and a lower deflection proving to be more ductile, clearly indicating the advantage in carrying horizontal loads. An analysis was also carried out using ANSYS software in order to compare the test results of both the beams.

  1. Magnetic field due to helical currents on a torus

    International Nuclear Information System (INIS)

    Sy, W.N.C.

    1981-01-01

    By means of coordinate transformations on different forms of the Biot-Savart law, general expressions are derived for both the magnetic vector potential and the magnetic field in two systems of toroidal coordinates. For the cases of interest, it is shown that the integrations can be performed exactly in proper toroidal coordinates, whereas approximations are necessary in quasi-toroidal coordinates. Different forms of helical windings are discussed. The results are applied to the calculation of a stellarator magnetic field of arbitrary polarity l, produced by a distribution of helical current filaments on a torus. The components of the magnetic field are given in terms of infinite series. In the intermediate region, away from the external separatrices and the central region, simple analytic expressions for the magnetic surfaces are obtained. (author)

  2. A 3D printed helical antenna with integrated lens

    KAUST Repository

    Farooqui, Muhammad Fahad

    2015-10-26

    A novel antenna configuration comprising a helical antenna with an integrated lens is demonstrated in this work. The antenna is manufactured by a unique combination of 3D printing of plastic material (ABS) and inkjet printing of silver nano-particle based metallic ink. The integration of lens enhances the gain by around 7 dB giving a peak gain of about 16.4 dBi at 9.4 GHz. The helical antenna operates in the end-fire mode and radiates a left-hand circularly polarized (LHCP) pattern. The 3-dB axial ratio (AR) bandwidth of the antenna with lens is 3.2 %. Due to integration of lens and fully printed processing, this antenna configuration offers high gain performance and requires low cost for manufacturing.

  3. Helicity dependence of the γ {sup 3}He → πX reactions in the Δ(1232) resonance region

    Energy Technology Data Exchange (ETDEWEB)

    Costanza, S.; Rigamonti, F. [INFN, Sezione di Pavia, Pavia (Italy); Universita di Pavia, Dipartimento di Fisica, Pavia (Italy); Mushkarenkov, A.; Braghieri, A.; Pedroni, P. [INFN, Sezione di Pavia, Pavia (Italy); Romaniuk, M.; Mandaglio, G. [INFN, Sezione di Catania, Catania (Italy); Universita di Messina, Dipartimento di Fisica e Scienze della Terra, Messina (Italy); Aguar Bartolome, P.; Ahrens, J.; Arends, H.J.; Heid, E.; Jahn, O.; Kashevarov, V.L.; Ostrick, M.; Ortega, H.; Otte, P.B.; Oussena, B.; Schumann, S.; Thomas, A.; Unverzagt, M. [Universitaet Mainz, Institut fuer Kernphysik, Mainz (Germany); Annand, J.R.M.; Hamilton, D.; Howdle, D.; Livingston, K.; MacGregor, I.J.D.; Mancell, J.; McGeorge, J.C.; Rosner, G. [University of Glasgow, SUPA School of Physics and Astronomy, Glasgow (United Kingdom); Beck, R. [University of Bonn, Helmholtz-Institut fuer Strahlen und Kernphysik, Bonn (Germany); Bekrenev, V.; Kruglov, S.; Kulbardis, A. [Petersburg Nuclear Physics Institute, Gatchina (Russian Federation); Berghaeuser, H.; Drexler, P.; Metag, V.; Thiel, M. [University of Giessen, II Physikalisches Institut, Giessen (Germany); Briscoe, W.J.; Downie, E.J. [The George Washington University, Washington, DC (United States); Cherepnya, S.N.; Fil' kov, L.V.; Lisin, V.; Polonski, A. [Institute for Nuclear Research, Moscow (Russian Federation); Collicott, C. [Dalhousie University, Halifax, NS (Canada); Saint Mary' s University, Halifax, NS (Canada); Fix, A. [Tomsk Polytechnic University, Tomsk (Russian Federation); Glazier, D.I. [University of Glasgow, SUPA School of Physics and Astronomy, Glasgow (United Kingdom); University of Edinburgh, SUPA School of Physics and Astronomy, Edinburgh (United Kingdom); Heil, W.; Krimmer, J. [Universitaet Mainz, Institut fuer Physik, Mainz (Germany); Hornidge, D.; Middleton, D.G. [Mount Allison University, Sackville, NB (Canada); Jaegle, I.; Keshelashvili, I.; Krusche, B.; Oberle, M.; Pheron, F.; Rostomyan, T.; Werthmueller, D. [University of Basel, Institut fuer Physik, Basel (Switzerland); Huber, G.M. [University of Regina, Regina, SK (Canada); Jude, T.; Watts, D.P. [University of Edinburgh, SUPA School of Physics and Astronomy, Edinburgh (United Kingdom); Kondratiev, R. [Lebedev Physical Institute, Moscow (Russian Federation); Korolija, M.; Supek, I. [Rudjer Boskovic Institute, Zagreb (Croatia); Manley, D.M. [Kent State University, Kent, Ohio (United States); Nefkens, B.M.K.; Starostin, A. [University of California, Los Angeles, California (United States); Nikolaev, A. [Universita di Pavia, Dipartimento di Fisica, Pavia (Italy); Prakhov, S. [Universitaet Mainz, Institut fuer Kernphysik, Mainz (Germany); The George Washington University, Washington, DC (United States); University of California, Los Angeles, California (United States); Sarty, A.J. [Saint Mary' s University, Halifax, NS (Canada); Collaboration: A2 Collaboration

    2014-11-15

    The helicity dependences of the differential cross sections for the semi-inclusive γ {sup 3}He → π{sup 0} X and γ {sup 3}He → π{sup ±} X reactions have been measured for the first time in the energy region 200 < E{sub γ} 450 MeV. The experiment was performed at the tagged photon beam facility of the MAMI accelerator in Mainz using a longitudinally polarised high-pressure {sup 3}He gas target. Hadronic products were measured with the large-acceptance Crystal Ball detector complemented with additional devices for charged-particle tracking and identification. Unpolarised differential cross sections and their helicity dependence are compared with theoretical calculations using the Fix-Arenhoevel model. The effect of the intermediate excitation of the Δ(1232) resonance can be clearly seen from this comparison, especially for the polarised case, where nuclear effects are relatively small. The model provides a better theoretical description of the unpolarised charged pion photoproduction data than the neutral pion channel. It does significantly better in describing the helicity-dependent data in both channels. These comparisons provide new information on the mechanisms involved in pion photoproduction on {sup 3}He and suggest that a polarised {sup 3}He target can provide valuable information on the corresponding polarised quasi-free neutron reactions. (orig.)

  4. Vibration of helical springs in cross water flow

    International Nuclear Information System (INIS)

    Axisa, F.; Brunet, G.

    1987-05-01

    The purpose of this paper is to present new experimental data on vortex-shedding induced vibration on helical springs subjected to cross-flows. Intense locked-in vibration were observed on the natural modes of axial displacement. A simplified model is tentatively proposed to interpret the experimental data which is based on an analogy with vortex-shedding as observed on straight tube rows

  5. Formation of helical electron beams by electrostatic pumping

    International Nuclear Information System (INIS)

    Barroso, J.J.; Spassovsky, L.P.; Stellati, C.

    1993-01-01

    A non-adiabatic gun for a 35 GHz, 100 kw gyrotron is presented. A 50 kV, 10 A laminar helical electron beam has been achieved with a perpendicular to parallel velocity ratio of 1.9. A non-adiabatic change of the pumping electric field is used to impart rotational velocity to the beam particles which are extracted at the cathode surface in a direction parallel to the guiding magnetic field. (author)

  6. Light scattering measurements supporting helical structures for chromatin in solution.

    Science.gov (United States)

    Campbell, A M; Cotter, R I; Pardon, J F

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model.

  7. Domain Walls in Helical Magnets: Elasticity and Pinning

    OpenAIRE

    Nattermann, Thomas

    2012-01-01

    Recently completely new types of domain walls (DWs) have been discovered in helical magnets, consisting generically of a regular array of {\\it pairs} of magnetic vortex lines \\cite{Li+12}. Only for special orientations DWs are free of vortices. In this article we calculate their elastic and pinning properties, using the pitch angle $\\theta$ as a small parameter. In particular we show that vortex free DWs exhibit long range elasticity which makes them very stiff and suppresses their pinning by...

  8. New Classes of Quasi-helically Symmetric Stellarators

    International Nuclear Information System (INIS)

    Ku, L.P.; Boozer, A.H.

    2010-01-01

    New classes of quasi-helically symmetric stellarators with aspect ratios (le) 10 have been found which are stable to the perturbation of magnetohydrodynamic modes at plasma pressures of practical interest. These configurations have large rotational transform and good quality of flux surfaces. Characteristics of some selected examples are discussed in detail. The feasibility of using modular coils for these stellarators has been investigated. It is shown that practical designs for modular coils can be achieved.

  9. Colonic metastasis from renal cell carcinoma: helical-CT demonstration

    International Nuclear Information System (INIS)

    Diaz-Candamio, M.J.; Pombo, S.; Pombo, F.

    2000-01-01

    Clinically evident colonic metastasis from renal cell carcinoma (RCC) is rare. In the present study a hypervascular sigmoid mass was demonstrated on arterial-phase helical CT using a water enema in a patient who had suffered left nephrectomy 8 years previously for RCC. The intense and early enhancement of the lesion suggested the possibility of a solitary colonic metastasis from RCC, a diagnosis which was pathologically confirmed. (orig.)

  10. Hepatic abscess : three-phase helical CT appearance

    International Nuclear Information System (INIS)

    Chung, Il Gyu; Lee, Won Jae; Lim, Hyo Keun; Lee, Soon Jin; Kim, Seung Hoon; Choi, Sang Hee; Lim, Jae Hoon

    1999-01-01

    The purpose of this study was to evaluate the enhancement patterns and morphologic features of hepatic abscesses, as seen on three-phase helical CT images. Three-phase helical CT images of 22 clinically and pathologically proven hepatic abscesses more than 3 cm in diameter in 21 patients were retrospectively reviewed. Three-phase helical CT scans were obtained at 30 sec(hepatic arterial phase, AP), 70 sec(portal venous phase, PP) and 3 min(equilibrium phase, EP) after the start of intravenous infusion of contrast material. We analyzed the number of abscess layers and their enhancement patterns during each phase, and evaluated the size and shape of abscess, the CT attenuation and presence of septae in the abscess cavity, and the thickness and maturation of the granulation layer and collagenous wall. AP images showed that 13 abscesses(59%) had four layers; on PP images, half the abscesses were seen to have three layers, while EP images showed that two-thirds had two layers. Among the 13 abscesses with four layers seen on AP images, all abscess cavities and granulation layers were hypo- and hyperattenuating, respectively, during all three phases. Most hypoattenuating collagenous walls seen on AP images became iso- or hyperattenuating on EP images, while hyperattenuating hyperperfusion zones seen on AP images became isoattenuating during later phases. The degree of maturation of the collagenous wall correlated with the number of abscess layers. As seen on AP, PP and EP three-phase helical CT images, hepatic abscess frequently had four, three, or two layers respectively. More mature collagenous walls tended to have more abscess layers

  11. FITTING HELICAL SNAKE AND ROTATOR FIELD STRENGTH MEASUREMENTS IN RHIC

    International Nuclear Information System (INIS)

    RANJBAR, V.; LUCCIO, A.U.; MACKAY, W.W.; TSOUPAS, N.

    2001-01-01

    We examined recent multi-pole measurements for the helical snakes and rotators in RHIC to generate a full field map. Since multi-pole measurements yield real field values for B, field components we developed a unique technique to evaluate the full fields using a traditional finite element analysis software [1]. From these measurements we employed SNIG [2] to generate orbit and Spin plots. From orbit values we generated a transfer matrix for the first snake

  12. Revisiting the Helical Cooperativity of Synthetic Polypeptides in Solution.

    Science.gov (United States)

    Ren, Yuan; Baumgartner, Ryan; Fu, Hailin; van der Schoot, Paul; Cheng, Jianjun; Lin, Yao

    2017-08-14

    Using synthetic polypeptides as a model system, the theories of helix-coil transition were developed into one of the most beautiful and fruitful subjects in macromolecular science. The classic models proposed by Schellman and Zimm-Bragg more than 50 years ago, differ in the assumption on whether the configuration of multiple helical sequences separated by random coil sections is allowed in a longer polypeptide chain. Zimm also calculated the critical chain lengths that facilitate such interrupted helices in different solvent conditions. The experimental validation of Zimm's prediction, however, was not carefully examined at that time. Herein, we synthesize a series of homopolypeptide samples with different lengths, to systematically examine their helix-coil transition and folding cooperativity in solution. We find that for longer chains, polypeptides do exist as interrupted helices with scattered coil sections even in helicogenic solvent conditions, as predicted in the Zimm-Bragg model. The critical chain lengths that facilitate such interrupted helices, however, are substantially smaller than Zimm's original estimation. The inaccuracy is in part due to an approximation that Zimm made in simplifying the calculation. But more importantly, we find there exist intramolecular interactions between different structural segments in the longer polypeptides, which are not considered in the classic helix-coil theories. As such, even the Zimm-Bragg model in its exact form cannot fully describe the transition behavior and folding cooperativity of longer polypeptides. The results suggest that long "all-helix" chains may be much less prevalent in solution than previously imagined, and a revised theory is required to accurately account for the helix-coil transition of the longer chains with potential "non-local" intramolecular interactions.

  13. Cylindrical Taylor states conserving total absolute magnetic helicity

    Science.gov (United States)

    Low, B. C.; Fang, F.

    2014-09-01

    The Taylor state of a three-dimensional (3D) magnetic field in an upright cylindrical domain V is derived from first principles as an extremum of the total magnetic energy subject to a conserved, total absolute helicity Habs. This new helicity [Low, Phys. Plasmas 18, 052901 (2011)] is distinct from the well known classical total helicity and relative total helicity in common use to describe wholly-contained and anchored fields, respectively. A given field B, tangential along the cylindrical side of V, may be represented as a unique linear superposition of two flux systems, an axially extended system along V and a strictly transverse system carrying information on field-circulation. This specialized Chandrasekhar-Kendall representation defines Habs and permits a neat formulation of the boundary-value problem (BVP) for the Taylor state as a constant-α force-free field, treating 3D wholly-contained and anchored fields on the same conceptual basis. In this formulation, the governing equation is a scalar integro-partial differential equation (PDE). A family of series solutions for an anchored field is presented as an illustration of this class of BVPs. Past treatments of the constant-α field in 3D cylindrical geometry are based on a scalar Helmholtz PDE as the governing equation, with issues of inconsistency in the published field solutions discussed over time in the journal literature. The constant-α force-free equation reduces to a scalar Helmholtz PDE only as special cases of the 3D integro-PDE derived here. In contrast, the constant-α force-free equation and the scalar Helmholtz PDE are absolutely equivalent in the spherical domain as discussed in Appendix. This theoretical study is motivated by the investigation of the Sun's corona but the results are also relevant to laboratory plasmas.

  14. Electric Control of Spin Helicity in a Magnetic Ferroelectric

    International Nuclear Information System (INIS)

    Yamasaki, Y.; Goto, T.; Sagayama, H.; Matsuura, M.; Hirota, K.; Arima, T.; Tokura, Y.

    2007-01-01

    Magnetic ferroelectrics or multiferroics, which are currently extensively explored, may provide a good arena to realize a novel magnetoelectric function. Here we demonstrate the genuine electric control of the spiral magnetic structure in one such magnetic ferroelectric, TbMnO 3 . A spin-polarized neutron scattering experiment clearly shows that the spin helicity, clockwise or counterclockwise, is controlled by the direction of spontaneous polarization and hence by the polarity of the small electric field applied on cooling

  15. Determining the helicity structure of third generation resonances

    International Nuclear Information System (INIS)

    Papaefstathiou, Andreas

    2011-11-01

    We examine methods that have been proposed for determining the helicity structure of decays of new resonances to third generation quarks and/or leptons. We present analytical and semi-analytical predictions and assess the applicability of the relevant variables in realistic reconstruction scenarios using Monte Carlo-generated events, including the effects of QCD radiation and multiple parton interactions, combinatoric ambiguities and fast detector simulation. (orig.)

  16. Electrochemical Platform for the Detection of Transmembrane Proteins Reconstituted into Liposomes.

    Science.gov (United States)

    Vacek, Jan; Zatloukalova, Martina; Geleticova, Jaroslava; Kubala, Martin; Modriansky, Martin; Fekete, Ladislav; Masek, Josef; Hubatka, Frantisek; Turanek, Jaroslav

    2016-04-19

    The development of new methods and strategies for the investigation of membrane proteins is limited by poor solubility of these proteins in an aqueous environment and hindered by a number of other problems linked to the instability of the proteins outside lipid bilayers. Therefore, current research focuses on an analysis of membrane proteins incorporated into model lipid membrane, most frequently liposomes. In this work, we introduce a new electrochemical methodology for the analysis of transmembrane proteins reconstituted into a liposomal system. The proposed analytical approach is based on proteoliposomal sample adsorption on the surface of working electrodes followed by analysis of the anodic and cathodic signals of the reconstituted proteins. It works based on the fact that proteins are electroactive species, in contrast to the lipid components of the membranes under the given experimental conditions. Electroanalytical experiments were performed with two transmembrane proteins; the Na(+)/K(+)ATPase that contains transmembrane as well as large extramembraneous segments and the mitochondrial uncoupling protein 1, which is a transmembrane protein essentially lacking extramembraneous segments. Electrochemical analyses of proteoliposomes were compared with analyses of both proteins solubilized with detergents (C12E8 and octyl-PoE) and supported by the following complementary methods: microscopy techniques, protein activity testing, molecular model visualizations, and immunochemical identification of both proteins. The label-free electrochemical platform presented here enables studies of reconstituted transmembrane proteins at the nanomolar level. Our results may contribute to the development of new electrochemical sensors and microarray systems applicable within the field of poorly water-soluble proteins.

  17. Effect of flow rate and temperature on transmembrane blood pressure drop in an extracorporeal artificial lung.

    Science.gov (United States)

    Park, M; Costa, E L V; Maciel, A T; Barbosa, E V S; Hirota, A S; Schettino, G de P; Azevedo, L C P

    2014-11-01

    Transmembrane pressure drop reflects the resistance of an artificial lung system to blood transit. Decreased resistance (low transmembrane pressure drop) enhances blood flow through the oxygenator, thereby, enhancing gas exchange efficiency. This study is part of a previous one where we observed the behaviour and the modulation of blood pressure drop during the passage of blood through artificial lung membranes. Before and after the induction of multi-organ dysfunction, the animals were instrumented and analysed for venous-venous extracorporeal membrane oxygenation, using a pre-defined sequence of blood flows. Blood flow and revolutions per minute (RPM) of the centrifugal pump varied in a linear fashion. At a blood flow of 5.5 L/min, pre- and post-pump blood pressures reached -120 and 450 mmHg, respectively. Transmembrane pressures showed a significant spread, particularly at blood flows above 2 L/min; over the entire range of blood flow rates, there was a positive association of pressure drop with blood flow (0.005 mmHg/mL/minute of blood flow) and a negative association of pressure drop with temperature (-4.828 mmHg/(°Celsius). These associations were similar when blood flows of below and above 2000 mL/minute were examined. During its passage through the extracorporeal system, blood is exposed to pressure variations from -120 to 450 mmHg. At high blood flows (above 2 L/min), the drop in transmembrane pressure becomes unpredictable and highly variable. Over the entire range of blood flows investigated (0-5500 mL/min), the drop in transmembrane pressure was positively associated with blood flow and negatively associated with body temperature. © The Author(s) 2014.

  18. Scattering bottleneck for spin dynamics in metallic helical antiferromagnetic dysprosium

    Science.gov (United States)

    Langner, M. C.; Roy, S.; Kemper, A. F.; Chuang, Y.-D.; Mishra, S. K.; Versteeg, R. B.; Zhu, Y.; Hertlein, M. P.; Glover, T. E.; Dumesnil, K.; Schoenlein, R. W.

    2015-11-01

    Ultrafast studies of magnetization dynamics have revealed fundamental processes that govern spin dynamics, and the emergence of time-resolved x-ray techniques has extended these studies to long-range spin structures that result from interactions with competing symmetries. By combining time-resolved resonant x-ray scattering and ultrafast magneto-optical Kerr studies, we show that the dynamics of the core spins in the helical magnetic structure occur on much longer time scales than the excitation of conduction electrons in the lanthanide metal Dy. The observed spin behavior differs markedly from that observed in the ferromagnetic phase of other lanthanide metals or transition metals and is strongly dependent on temperature and excitation fluence. This unique behavior results from coupling of the real-space helical spin structure to the shape of the conduction electron Fermi surface in momentum space, which creates a bottleneck in spin scattering events that transfer the valence excitation to the core spins. The dependence of the dynamics on the intersite interactions renders the helical ordering much more robust to perturbations than simple ferromagnetic or antiferromagnetic ordering, where dynamics are driven primarily by on-site interactions.

  19. Passive base isolation with superelastic nitinol SMA helical springs

    International Nuclear Information System (INIS)

    Huang, Bin; Zhang, Haiyang; Wang, Han; Song, Gangbing

    2014-01-01

    Seismic isolation of structures such as multi-story buildings, nuclear reactors, bridges, and liquid storage tanks should be designed to preserve structural integrity. By implementing seismic isolation technology, the deformation of superstructures can be dramatically reduced, consequently helping to protect their safety as well. In this paper, an innovative type of passive base isolation system, which is mainly composed of superelastic nitinol SMA helical springs, is developed. In order to verify the effectiveness of the proposed system, a two-story experimental steel frame model is constructed, and two superelastic SMA helical springs are thermo-mechanically built in the laboratory. To describe the nonlinear mechanical properties of the superelastic SMA helical springs under reciprocating load, a phenomenological model is presented in terms of a series of tensile tests. Afterwards, a numerical model of the two-story frame with the suggested isolation system is set up to simulate the response of the isolated frame subjected to an earthquake. Both the experimental and the numerical simulation results indicate that the proposed base isolation system can remarkably suppress structural vibrations and has improved isolation effects when compared with a steel spring isolation system. Due to the capabilities of energy dissipation as well as fully re-centering, it is very applicable to utilize the suggested isolation system in base isolated structures to resist earthquakes. (paper)

  20. Flexibility of LHD configuration with multi-layer helical coils

    Energy Technology Data Exchange (ETDEWEB)

    Ichiguchi, Katsuji; Motojima, Osamu; Yamazaki, Kozo; Nakajima, Noriyoshi; Okamoto, Masao

    1995-11-01

    The Large Helical Device (LHD) is a heliotron device with two helical coils, each of which has a structure of three current layers. It is designed so that the current in each layer should be controlled independently. By changing the combination of the coil current in the layers, it is possible to vary the effective minor radius of the helical coils, which enlarges the flexibility of the configuration. The properties of the plasmas for several combinations of the layers are investigated numerically. In the vacuum configuration, it is obtained that the combination of the layers corresponding to a large effective coil radius has a large outermost surface. In this case, the rotational transform decreases and the magnetic hill is reduced compared with the configuration with all three layers. The large Shafranov shift which is due to the small rotational transform enhances the magnetic well and the magnetic shear to stabilize the Mercier mode, however, it degrades the equilibrium beta limit. In the case of the combination for a small effective coil radius, the Mercier mode is destabilized, because the magnetic hill is enhanced. The effect on the bootstrap current is also studied. (author).

  1. Helical instability in film blowing process: Analogy to buckling instability

    Science.gov (United States)

    Lee, Joo Sung; Kwon, Ilyoung; Jung, Hyun Wook; Hyun, Jae Chun

    2017-12-01

    The film blowing process is one of the most important polymer processing operations, widely used for producing bi-axially oriented film products in a single-step process. Among the instabilities observed in this film blowing process, i.e., draw resonance and helical motion occurring on the inflated film bubble, the helical instability is a unique phenomenon portraying the snake-like undulation motion of the bubble, having the period on the order of few seconds. This helical instability in the film blowing process is commonly found at the process conditions of a high blow-up ratio with too low a freezeline position and/or too high extrusion temperature. In this study, employing an analogy to the buckling instability for falling viscous threads, the compressive force caused by the pressure difference between inside and outside of the film bubble is introduced into the simulation model along with the scaling law derived from the force balance between viscous force and centripetal force of the film bubble. The simulation using this model reveals a close agreement with the experimental results of the film blowing process of polyethylene polymers such as low density polyethylene and linear low density polyethylene.

  2. Helical cone beam CT with an asymmetrical detector

    International Nuclear Information System (INIS)

    Zamyatin, Alexander A.; Taguchi, Katsuyuki; Silver, Michael D.

    2005-01-01

    If a multislice or other area detector is shifted to one side to cover a larger field of view, then the data are truncated on one side. We propose a method to restore the missing data in helical cone-beam acquisitions that uses measured data on the longer side of the asymmetric detector array. The method is based on the idea of complementary rays, which is well known in fan beam geometry; in this paper we extend this concept to the cone-beam case. Different cases of complementary data coverage and dependence on the helical pitch are considered. The proposed method is used in our prototype 16-row CT scanner with an asymmetric detector and a 700 mm field of view. For evaluation we used scanned body phantom data and computer-simulated data. To simulate asymmetric truncation, the full, symmetric datasets were truncated by dropping either 22.5% or 45% from one side of the detector. Reconstructed images from the prototype scanner with the asymmetrical detector show excellent image quality in the extended field of view. The proposed method allows flexible helical pitch selection and can be used with overscan, short-scan, and super-short-scan reconstructions

  3. Dual electromagnetism: helicity, spin, momentum and angular momentum

    International Nuclear Information System (INIS)

    Bliokh, Konstantin Y; Nori, Franco; Bekshaev, Aleksandr Y

    2013-01-01

    The dual symmetry between electric and magnetic fields is an important intrinsic property of Maxwell equations in free space. This symmetry underlies the conservation of optical helicity and, as we show here, is closely related to the separation of spin and orbital degrees of freedom of light (the helicity flux coincides with the spin angular momentum). However, in the standard field-theory formulation of electromagnetism, the field Lagrangian is not dual symmetric. This leads to problematic dual-asymmetric forms of the canonical energy–momentum, spin and orbital angular-momentum tensors. Moreover, we show that the components of these tensors conflict with the helicity and energy conservation laws. To resolve this discrepancy between the symmetries of the Lagrangian and Maxwell equations, we put forward a dual-symmetric Lagrangian formulation of classical electromagnetism. This dual electromagnetism preserves the form of Maxwell equations, yields meaningful canonical energy–momentum and angular-momentum tensors, and ensures a self-consistent separation of the spin and orbital degrees of freedom. This provides a rigorous derivation of the results suggested in other recent approaches. We make the Noether analysis of the dual symmetry and all the Poincaré symmetries, examine both local and integral conserved quantities and show that only the dual electromagnetism naturally produces a complete self-consistent set of conservation laws. We also discuss the observability of physical quantities distinguishing the standard and dual theories, as well as relations to quantum weak measurements and various optical experiments. (paper)

  4. Seismic analysis of a helical coil type heat exchanger

    International Nuclear Information System (INIS)

    Nishiguchi, I.; Baba, O.; Yatabe, H.

    1984-01-01

    The intermediate heat exchanger (IHX) which forms the reactor coolant pressure boundary is one of the most important components of the Multi-purpose Experimental Very High Temperature Gas-cooled Reactor (ex. VHTR) under development at Japan Atomic Energy Research Institute. This paper presents the results of the finite element modeling, eigenvalue analysis and dynamic response analysis of the IHX. For the modeling, the structure of the IHX was separated into a helical tube bundle, inner and outer vessels, and a center pipe. The eigenvalue analysis was made for each structure with a detailed three-dimensional finite element model. Then the simplified model of the whole structure of the IHX was constructed using the result of the eigenvalue analysis. A dynamic response analysis was made for the simplified model with and without stoppers of the helical tube bundle supports and the center pipe. The effect of stoppers on the behavior of the center pipe, the helical tube, and the connecting tube is discussed. (author)

  5. Enhanced Control for Local Helicity Injection on the Pegasus ST

    Science.gov (United States)

    Pierren, C.; Bongard, M. W.; Fonck, R. J.; Lewicki, B. T.; Perry, J. M.

    2017-10-01

    Local helicity injection (LHI) experiments on Pegasus rely upon programmable control of a 250 MVA modular power supply system that drives the electromagnets and helicity injection systems. Precise control of the central solenoid is critical to experimental campaigns that test the LHI Taylor relaxation limit and the coupling efficiency of LHI-produced plasmas to Ohmic current drive. Enhancement and expansion of the present control system is underway using field programmable gate array (FPGA) technology for digital logic and control, coupled to new 10 MHz optical-to-digital transceivers for semiconductor level device communication. The system accepts optical command signals from existing analog feedback controllers, transmits them to multiple devices in parallel H-bridges, and aggregates their status signals for fault detection. Present device-level multiplexing/de-multiplexing and protection logic is extended to include bridge-level protections with the FPGA. An input command filter protects against erroneous and/or spurious noise generated commands that could otherwise cause device failures. Fault registration and response times with the FPGA system are 25 ns. Initial system testing indicates an increased immunity to power supply induced noise, enabling plasma operations at higher working capacitor bank voltage. This can increase the applied helicity injection drive voltage, enable longer pulse lengths and improve Ohmic loop voltage control. Work supported by US DOE Grant DE-FG02-96ER54375.

  6. Properties of the electrostatically driven helical plasma state

    Science.gov (United States)

    Akçay, Cihan; Finn, John M.; Nebel, Richard A.; Barnes, Daniel C.; Martin, Neal

    2018-02-01

    A novel plasma state has been found [Akçay et al., Phys. Plasmas 24, 052503 (2017)] in the presence of a uniform applied axial magnetic field in periodic cylindrical geometry. This state is driven by external electrostatic fields provided by helical electrodes with a (m =1 ,n =1 ) (helical) symmetry where m and n represent the poloidal and axial harmonics. The resulting plasma is a function of the cylinder radius r mean current density, with a mean-field line safety factor q0(r ) just above the pitch of the electrodes m /n =1 in the interior, where the plasma is nearly force-free. However, at the edge the current density has a component perpendicular to the magnetic field B. This perpendicular current density drives nearly Alfvénic helical plasma flows, a notable feature of these states. This state is being studied for its possible application in DC electrical transformers. We present results on several issues of importance for these applications: the transient leading to the steady state; the twist and writhe of the field lines and their relation with the current density; the properties of the current density streamlines and length of the current density lines connected to the electrodes; the sensitivity to changes in the velocity boundary conditions; the effect of varying the radial resistivity profile; and the effects of a concentrated electrode potential.

  7. Influence of Helical Cell Shape on Motility of Helicobacter Pylori

    Science.gov (United States)

    Hardcastle, Joseph; Martinez, Laura; Salama, Nina; Bansil, Rama; Boston University Collaboration; University of Washington Collaboration

    2014-03-01

    Bacteria's body shape plays an important role in motility by effecting chemotaxis, swimming mechanisms, and swimming speed. A prime example of this is the bacteria Helicobacter Pylori;whose helical shape has long been believed to provide an advantage in penetrating the viscous mucus layer protecting the stomach lining, its niche environment. To explore this we have performed bacteria tracking experiments of both wild-type bacteria along with mutants, which have a straight rod shape. A wide distribution of speeds was found. This distribution reflects both a result of temporal variation in speed and different shape morphologies in the bacterial population. Our results show that body shape plays less role in a simple fluid. However, in a more viscous solution the helical shape results in increased swimming speeds. In addition, we use experimentally obtained cell shape measurements to model the hydrodynamic influence of cell shape on swimming speed using resistive force theory. The results agree with the experiment, especially when we fold in the temporal distribution. Interestingly, our results suggest distinct wild-type subpopulations with varying number of half helices can lead to different swimming speeds. NSF PHY

  8. Crystal Engineering of Hand-Twisted Helical Crystals.

    Science.gov (United States)

    Saha, Subhankar; Desiraju, Gautam R

    2017-02-08

    A strategy is outlined for the design of hand-twisted helical crystals. The starting point in the exercise is the one-dimensional (1D) plastic crystal, 1,4-dibromobenzene, which is then changed to a 1D elastic crystal, exemplified by 4-bromophenyl 4'-chlorobenzoate, by introduction of a molecular synthon -O-CO- in lieu of the supramolecular synthon Br···Br in the precursor. The 1D elastic crystals are next modified to two-dimensional (2D) elastic crystals, of the type 4-bromophenyl 4'-nitrobenzoate where the halogen bonding and C-H···O hydrogen bonding are well-matched. Finally, varying the interaction strengths in these 2D elastic crystals gives plastic crystals with two pairs of bendable faces but without slip planes. Typical examples are 4-chlorophenyl and 4-bromophenyl 4'-nitrobenzoate. This type of 2D plasticity represents a new type of bendable crystals in which plastic behavior is seen with a fair degree of isotropic character in the crystal packing. The presence of two sets of bendable faces, generally orthogonal to each other, allows for the possibility of hand-twisting of the crystals to give grossly helical morphologies. Accordingly, we propose the name hand-twisted helical crystals for these substances.

  9. Experiments on helical modes in magnetized thin foil-plasmas

    Science.gov (United States)

    Yager-Elorriaga, David

    2017-10-01

    This paper gives an in-depth experimental study of helical features on magnetized, ultrathin foil-plasmas driven by the 1-MA linear transformer driver at University of Michigan. Three types of cylindrical liner loads were designed to produce: (a) pure magneto-hydrodynamic (MHD) modes (defined as being void of the acceleration-driven magneto-Rayleigh-Taylor instability, MRT) using a non-imploding geometry, (b) pure kink modes using a non-imploding, kink-seeded geometry, and (c) MRT-MHD coupled modes in an unseeded, imploding geometry. For each configuration, we applied relatively small axial magnetic fields of Bz = 0.2-2.0 T (compared to peak azimuthal fields of 30-40 T). The resulting liner-plasmas and instabilities were imaged using 12-frame laser shadowgraphy and visible self-emission on a fast framing camera. The azimuthal mode number was carefully identified with a tracking algorithm of self-emission minima. Our experiments show that the helical structures are a manifestation of discrete eigenmodes. The pitch angle of the helix is simply m / kR , from implosion to explosion, where m, k, and R are the azimuthal mode number, axial wavenumber, and radius of the helical instability. Thus, the pitch angle increases (decreases) during implosion (explosion) as R becomes smaller (larger). We found that there are one, or at most two, discrete helical modes that arise for magnetized liners, with no apparent threshold on the applied Bz for the appearance of helical modes; increasing the axial magnetic field from zero to 0.5 T changes the relative weight between the m = 0 and m = 1 modes. Further increasing the applied axial magnetic fields yield higher m modes. Finally, the seeded kink instability overwhelms the intrinsic instability modes of the plasma. These results are corroborated with our analytic theory on the effects of radial acceleration on the classical sausage, kink, and higher m modes. Work supported by US DOE award DE-SC0012328, Sandia National Laboratories

  10. What makes single-helical metamaterials generate "pure" circularly polarized light?

    Science.gov (United States)

    Wu, Lin; Yang, ZhenYu; Zhao, Ming; Zhang, Peng; Lu, ZeQing; Yu, Yang; Li, ShengXi; Yuan, XiuHua

    2012-01-16

    Circular polarizers with left-handed helical metamaterials can transmit right-handed circularly polarized (RCP) light with few losses. But a certain amount of left-handed circularly polarized (LCP) light will occur in the transmitted light, which is the noise of the circular polarizer. Therefore, we defined the ratio of the RCP light intensity to the LCP light intensity as the signal-to-noise (S/N) ratio. In our previous work, it's found that circular polarizers with multi-helical metamaterials have two orders higher S/N ratios than that of single-helical metamaterials. However, it has been a great challenge to fabricate such multi-helical structures with micron or sub-micron feature sizes. Is it possible for the single-helical metamaterials to obtain equally high S/N ratios as the multi-helical ones? To answer this question, we systematically investigated the influences of structure parameters of single-helical metamaterials on the S/N ratios using the finite-different time-domain (FDTD) method. It was found that the single-helical metamaterials can also reach about 30dB S/N ratios, which are equal to the multi-helical ones. Furthermore, we explained the phenomenon by the antenna theory and optimized the performances of the single-helical circular polarizers.

  11. Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes

    Directory of Open Access Journals (Sweden)

    Reiner Ribarics

    2015-01-01

    Full Text Available MHC α-helices form the antigen-binding cleft and are of particular interest for immunological reactions. To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices. Each resulting axis was fitted by polynomials in a least-squares sense and the curvature integral was computed. To find the appropriate polynomial degree, the method was tested on two artificially modelled helices, one performing a bending movement and another a hinge movement. We found that second-order polynomials retrieve predefined parameters of helical motion with minimal relative error. From MD simulations we selected those parts of α-helices that were stable and also close to the TCR/MHC interface. We monitored the curvature integral, generated a ruled surface between the two MHC α-helices, and computed interhelical area and surface torsion, as they changed over time. We found that MHC α-helices undergo rapid but small changes in conformation. The curvature integral of helices proved to be a sensitive measure, which was closely related to changes in shape over time as confirmed by RMSD analysis. We speculate that small changes in the conformation of individual MHC α-helices are part of the intrinsic dynamics induced by engagement with the TCR.

  12. Local and nonlocal advected invariants and helicities in magnetohydrodynamics and gas dynamics I: Lie dragging approach

    International Nuclear Information System (INIS)

    Webb, G M; Dasgupta, B; McKenzie, J F; Hu, Q; Zank, G P

    2014-01-01

    In this paper advected invariants and conservation laws in ideal magnetohydrodynamics (MHD) and gas dynamics are obtained using Lie dragging techniques. There are different classes of invariants that are advected or Lie dragged with the flow. Simple examples are the advection of the entropy S (a 0-form), and the conservation of magnetic flux (an invariant 2-form advected with the flow). The magnetic flux conservation law is equivalent to Faraday's equation. The gauge condition for the magnetic helicity to be advected with the flow is determined. Different variants of the helicity in ideal fluid dynamics and MHD including: fluid helicity, cross helicity and magnetic helicity are investigated. The fluid helicity conservation law and the cross-helicity conservation law in MHD are derived for the case of a barotropic gas. If the magnetic field lies in the constant entropy surface, then the gas pressure can depend on both the entropy and the density. In these cases the conservation laws are local conservation laws. For non-barotropic gases, we obtain nonlocal conservation laws for fluid helicity and cross helicity by using Clebsch variables. These nonlocal conservation laws are the main new results of the paper. Ertel's theorem and potential vorticity, the Hollman invariant, and the Godbillon–Vey invariant for special flows for which the magnetic helicity is zero are also discussed. (paper)

  13. The Selective Autophagy Receptor p62 Forms a Flexible Filamentous Helical Scaffold

    Directory of Open Access Journals (Sweden)

    Rodolfo Ciuffa

    2015-05-01

    Full Text Available The scaffold protein p62/SQSTM1 is involved in protein turnover and signaling and is commonly found in dense protein bodies in eukaryotic cells. In autophagy, p62 acts as a selective autophagy receptor that recognizes and shuttles ubiquitinated proteins to the autophagosome for degradation. The structural organization of p62 in cellular bodies and the interplay of these assemblies with ubiquitin and the autophagic marker LC3 remain to be elucidated. Here, we present a cryo-EM structural analysis of p62. Together with structures of assemblies from the PB1 domain, we show that p62 is organized in flexible polymers with the PB1 domain constituting a helical scaffold. Filamentous p62 is capable of binding LC3 and addition of long ubiquitin chains induces disassembly and shortening of filaments. These studies explain how p62 assemblies provide a large molecular scaffold for the nascent autophagosome and reveal how they can bind ubiquitinated cargo.

  14. Identification of amino acids essential for estrone-3-sulfate transport within transmembrane domain 2 of organic anion transporting polypeptide 1B1.

    Directory of Open Access Journals (Sweden)

    Nan Li

    Full Text Available As an important structure in membrane proteins, transmembrane domains have been found to be crucial for properly targeting the protein to cell membrane as well as carrying out transport functions in transporters. Computer analysis of OATP sequences revealed transmembrane domain 2 (TM2 is among those transmembrane domains that have high amino acid identities within different family members. In the present study, we identify four amino acids (Asp70, Phe73, Glu74, and Gly76 that are essential for the transport function of OATP1B1, an OATP member that is specifically expressed in the human liver. A substitution of these four amino acids with alanine resulted in significantly reduced transport activity. Further mutagenesis showed the charged property of Asp70 and Glu74 is critical for proper function of the transporter protein. Comparison of the kinetic parameters indicated that Asp70 is likely to interact with the substrate while Glu74 may be involved in stabilizing the binding site through formation of a salt-bridge. The aromatic ring structure of Phe73 seems to play an important role because substitution of Phe73 with tyrosine, another amino acid with a similar structure, led to partially restored transport function. On the other hand, replacement of Gly76 with either alanine or valine could not recover the function of the transporter. Considering the nature of a transmembrane helix, we proposed that Gly76 may be important for maintaining the proper structure of the protein. Interestingly, when subjected to transport function analysis of higher concentration of esteone-3-sulfate (50 µM that corresponds to the low affinity binding site of OATP1B1, mutants of Phe73, Glu74, and Gly76 all showed a transport function that is comparable to that of the wild-type, suggesting these amino acids may have less impact on the low affinity component of esteone-3-sulfate within OATP1B1, while Asp 70 seems to be involved in the interaction of both sites.

  15. Hydrogen recycling and transport in the helical divertor of TEXTOR

    Energy Technology Data Exchange (ETDEWEB)

    Clever, Meike

    2010-07-01

    The aim of this thesis was to investigate the hydrogen recycling at the target plates of the helical divertor in TEXTOR and by this the capability of this divertor configuration to access such favourable operational regimes. In order to study the different divertor density regimes in TEXTOR, discharges were performed in which the total plasma density was increased continuously up to the density limit. The recycling was investigated in a fixed helical divertor structure where four helical strike points with a poloidal width of about 8-10 cm are created at the divertor target plates. The experimental investigation of the hydrogen recycling was carried out using mainly spectroscopic methods supplemented by Langmuir probe, interferometric and atomic beam measurements. In the framework of this thesis a spectroscopic multi camera system has been built that facilitates the simultaneous observation of four different spectral lines, recording images of the divertor target plates and the plasma volume close to the target. The system facilitates the simultaneous measurement of the poloidal and toroidal pattern of the recycling flux at the divertor target without the need for sweeping the plasma structure. The simultaneous observation of different spectral lines reduces the uncertainty in the analysis based on several lines, as the contribution from uncertainties in the reproducibility of plasma parameters in different discharges are eliminated and only the uncertainty of the measurement method limits the accuracy. The spatial resolution of the system in poloidal and toroidal direction (0.8 mm{+-}0.01 mm) is small compared to the separation of the helical strike points, the capability of the measurement method to resolve these structures is therefore limited by the line-of-sight integration and the penetration depth of the light emitting species. The measurements showed that the recycling flux increases linearly with increasing plasma density, a high recycling regime is not

  16. Hydrogen recycling and transport in the helical divertor of TEXTOR

    International Nuclear Information System (INIS)

    Clever, Meike

    2010-01-01

    The aim of this thesis was to investigate the hydrogen recycling at the target plates of the helical divertor in TEXTOR and by this the capability of this divertor configuration to access such favourable operational regimes. In order to study the different divertor density regimes in TEXTOR, discharges were performed in which the total plasma density was increased continuously up to the density limit. The recycling was investigated in a fixed helical divertor structure where four helical strike points with a poloidal width of about 8-10 cm are created at the divertor target plates. The experimental investigation of the hydrogen recycling was carried out using mainly spectroscopic methods supplemented by Langmuir probe, interferometric and atomic beam measurements. In the framework of this thesis a spectroscopic multi camera system has been built that facilitates the simultaneous observation of four different spectral lines, recording images of the divertor target plates and the plasma volume close to the target. The system facilitates the simultaneous measurement of the poloidal and toroidal pattern of the recycling flux at the divertor target without the need for sweeping the plasma structure. The simultaneous observation of different spectral lines reduces the uncertainty in the analysis based on several lines, as the contribution from uncertainties in the reproducibility of plasma parameters in different discharges are eliminated and only the uncertainty of the measurement method limits the accuracy. The spatial resolution of the system in poloidal and toroidal direction (0.8 mm±0.01 mm) is small compared to the separation of the helical strike points, the capability of the measurement method to resolve these structures is therefore limited by the line-of-sight integration and the penetration depth of the light emitting species. The measurements showed that the recycling flux increases linearly with increasing plasma density, a high recycling regime is not

  17. Transmembrane signaling through major histocompatibility complex (MHC) encoded molecules

    International Nuclear Information System (INIS)

    Newell, M.K.

    1987-01-01

    The importance of the major histocompatibility complex (MHC) encoded molecules has traditionally been ascribed to the role these molecules play as restriction elements for T lymphocytes. This is, in order for T cell activation to occur the T cell must recognize antigen in association with MHC molecules. More controversial, however, is the potential role MHC molecules play as signal transducing receptors/acceptors to the B lymphocyte. In other words, do class II MHC molecules (Ia antigens) actively transduce a signal to the B cell which drives its differentiation into an antibody secreting cell? Two approaches to this question are described. The first involves biochemical characterization of those molecules which consistently copurify with I-A/sup k/ by two dimensional gel electrophoresis. The second approach utilizes two types of analyses: first, an examination of the biochemical changes which occur in the cell as a result of Ia ligation; and second, analysis of changes in the B cell's physiological response as a result of Ia perturbation. Molecules were examined which may couple the antigen binding event in the B lymphocyte to the antigen driven signal transduction cascade which ultimately leads to immunoglobulin secretion. In these experiments, cells were labelled with [ 32 P] and stimulated cells with phorbol myristate acetate. The membrane form of immunoglobulin was then isolated from detergent lysates of whole cells and passed over an anti-k affinity column. The eluates were analyzed by SDS-PAGE

  18. Right- and Left-Handed Helices, What is in between? Interconversion of Helical Structures of Alternating Pyridinedicarboxamide/m-(phenylazo)azobenzene Oligomers.

    Science.gov (United States)

    Tao, Peng; Parquette, Jon R; Hadad, Christopher M

    2012-12-11

    Some unnatural polymers/oligomers have been designed to adopt a well-defined, compact, three-dimensional folding capability. Azobenzene units are common linkages in these oligomer designs. Two alternating pyridinedicarboxamide/m-(phenylazo)azobenzene oligomers that can fold into both right- and left-handed helices were studied computationally in order to understand their dynamical properties. Helical structures were shown to be the global minima among the many different conformations generated from the Monte Carlo simulations, and extended conformations have higher potential energies than compact ones. To understand the interconversion process between right- and left-handed helices, replica-exchange molecular dynamic (REMD) simulations were performed on both oligomers, and with this method, both right- and left-handed helices were successfully sampled during the simulations. REMD trajectories revealed twisted conformations as intermediate structures in the interconversion pathway between the two helical forms of these azobenzene oligomers. This mechanism was observed in both oligomers in current study and occurred locally in the larger oligomer. This discovery indicates that the interconversion between helical structures with different handedness goes through a compact and partially folded structure instead of globally unfold and extended structure. This is also verified by the nudged elastic band (NEB) calculations. The temperature weighted histogram analysis method (T-WHAM) was applied on the REMD results to generate contour maps of the potential of mean force (PMF). Analysis showed that right- and left-handed helices are equally sampled in these REMD simulations. In large oligomers, both right- and left-handed helices can be adopted by different parts of the molecule simultaneously. The interconversion between two helical forms can occur in the middle of the helical structure and not necessarily at the termini of the oligomer.

  19. Evolutionary dynamics of the interferon-induced transmembrane gene family in vertebrates.

    Directory of Open Access Journals (Sweden)

    Zhao Zhang

    Full Text Available Vertebrate interferon-induced transmembrane (IFITM genes have been demonstrated to have extensive and diverse functions, playing important roles in the evolution of vertebrates. Despite observance of their functionality, the evolutionary dynamics of this gene family are complex and currently unknown. Here, we performed detailed evolutionary analyses to unravel the evolutionary history of the vertebrate IFITM family. A total of 174 IFITM orthologous genes and 112 pseudogenes were identified from 27 vertebrate genome sequences. The vertebrate IFITM family can be divided into immunity-related IFITM (IR-IFITM, IFITM5 and IFITM10 sub-families in phylogeny, implying origins from three different progenitors. In general, vertebrate IFITM genes are located in two loci, one containing the IFITM10 gene, and the other locus containing IFITM5 and various numbers of IR-IFITM genes. Conservation of evolutionary synteny was observed in these IFITM genes. Significant functional divergence was detected among the three IFITM sub-families. No gene duplication or positive selection was found in IFITM5 sub-family, implying the functional conservation of IFITM5 in vertebrate evolution, which is involved in bone formation. No IFITM5 locus was identified in the marmoset genome, suggesting a potential association with the tiny size of this monkey. The IFITM10 sub-family was divided into two groups: aquatic and terrestrial types. Functional divergence was detected between the two groups, and five IFITM10-like genes from frog were dispersed into the two groups. Both gene duplication and positive selection were observed in aquatic vertebrate IFITM10-like genes, indicating that IFITM10 might be associated with the adaptation to aquatic environments. A large number of lineage- and species-specific gene duplications were observed in IR-IFITM sub-family and positive selection was detected in IR-IFITM of primates and rodents. Because primates have experienced a long history of

  20. Transmembrane Adaptor Protein PAG/CBP Is Involved in both Positive and Negative Regulation of Mast Cell Signaling

    Czech Academy of Sciences Publication Activity Database

    Dráberová, Lubica; Bugajev, Viktor; Potůčková, Lucie; Hálová, Ivana; Bambousková, Monika; Polakovičová, Iva; Xavier, R.J.; Seed, B.; Dráber, Petr

    2014-01-01

    Roč. 34, č. 23 (2014), s. 4285-4300 ISSN 0270-7306 R&D Projects: GA ČR GA301/09/1826; GA ČR GAP302/10/1759; GA ČR(CZ) GBP302/12/G101; GA ČR(CZ) GD204/09/H084; GA MŠk LD12073; GA ČR(CZ) GA14-00703S; GA ČR(CZ) GA14-09807S Institutional support: RVO:68378050 Keywords : plasma membrane * cel signaling * IgE receptor Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.777, year: 2014