Abstract:
:Protein flexibility and conformational diversity is well known to be a key characteristic of the function of many proteins. Human blood coagulation proteins have multiple substrates, and various protein-protein interactions are required for the smooth functioning of the coagulation cascade to maintain blood hemostasis. To address how a protein may cope with multiple interactions with its structurally diverse substrates and the accompanied structural changes that may drive these changes, we studied human Factor X. We employed 20 ns of molecular dynamics (MD) and steered molecular dynamics (SMD) simulations on two different conformational forms of Factor X, open and closed, and observed an interchangeable conformational transition from one to another. This work also demonstrates the roles of various aromatic residues involved in aromatic-aromatic interactions, which make this dynamic transition possible.
journal_name
Biopolymersjournal_title
Biopolymersauthors
Singh N,Briggs JMdoi
10.1002/bip.21062subject
Has Abstractpub_date
2008-12-01 00:00:00pages
1104-13issue
12eissn
0006-3525issn
1097-0282journal_volume
89pub_type
杂志文章相关文献
BIOPOLYMERS文献大全abstract::The hinge region links the antigen binding Fab part to the constant Fc domain in immunoglobulins. For the hinge peptide derivative [AcThr(OtBu)-Cys-Pro-Pro-Cys-Pro-Ala-ProNH2]2 the assignment of the 1H and 13C resonances was achieved by two-dimensional nmr techniques: total correlation spectroscopy (TOCSY), nuclear Ov...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360311007
更新日期:1991-09-01 00:00:00
abstract::The comprehensive understanding of disassembly mechanism of amyloid fibrils requires nano-scale characterization of the mechanical properties of amyloid fibrils during the disassembly process. In this work, gemini surfactant C12 C6 C12 Br2 micelles were used as a probe to disassemble Aβ(1-40) fibrils. The microstructu...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22992
更新日期:2017-02-01 00:00:00
abstract::Fourier transform IR (FTIR) spectroscopy has been successfully applied in recent years to examine the functional and structural properties of the membrane protein rhodopsin, a prototype G protein coupled receptor. Unlike UV-visible spectroscopy, FTIR spectroscopy is structurally sensitive. It may give us both global i...
journal_title:Biopolymers
pub_type: 杂志文章,评审
doi:10.1002/bip.10407
更新日期:2003-01-01 00:00:00
abstract::Aromatic stacking and hydrogen bonding between nucleobases are two of the key interactions responsible for stabilization of DNA double-helical structures. The present work aims at defining the specific contributions of these interactions to the stability of individual base pairs in DNA. The two DNA double helices inve...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20811
更新日期:2007-10-05 00:00:00
abstract::Reactive oxygen species (ROS) have generated a great deal of interest in the clinical field since experimental studies showed the involvement of these species in carcinogenesis. This paper reports the detection of ROS during the decomposition of H2O2 in the presence of samples obtained from tissues of 16 patients with...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20068
更新日期:2004-08-05 00:00:00
abstract::Additive physical properties of DNA double strand polymers have been expanded in terms of 8 irreducible parameters. This provided consistency relations among the corresponding 10 duplex dimer contributions. To allow for oligomer analysis, end parameters were often added, and this would add extra degrees of freedom to ...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22214
更新日期:2013-08-01 00:00:00
abstract::An improved model for calculating the CD of polypeptides has been developed. Excited state wavefunctions were derived from CNDO/S (complete neglect of differential overlap, spectroscopic) calculations on N-methylacetamide. Four discrete peptide-localized transitions were employed: pi 0 pi* (NV1), pi* + pi* (NV2), n pi...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360310511
更新日期:1991-04-01 00:00:00
abstract::Near uv CD spectra of Trp residues in proteins frequently show a complex line shape deriving from the overlap of 1La and 1Lb electronic transitions. This study presents an original empirical method of resolving these components, based on the near uv CD spectra of well-defined complexes of calmodulin domains with targe...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/(SICI)1097-0282(199806)45:7<493::AID-BIP3>
更新日期:1998-06-01 00:00:00
abstract::Vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide-27 (PACAP27) are members of the secretin-glucagon family containing 28 and 27 residues, respectively. NMR spectroscopy studies suggest that the N-terminus exhibit consecutive beta-turns whereas the central and C-terminal parts o...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.21147
更新日期:2009-05-01 00:00:00
abstract::A detailed description of the two observed solution conformations of the pentapeptide lactone fragment of actinomycin D is presented using the distance constraints obtained from two-dimensional nuclear Overhauser enhancement spectra in combination with minimum energy calculations. Low energy conformational states that...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360281010
更新日期:1989-10-01 00:00:00
abstract::A short peptide-based molecule has been found to form a strong hydrogel at phosphate buffer solution of pH 7.46. The hydrogel has been characterized thoroughly using various techniques including field emission scanning electron microscopy (FE-SEM), wide angle powder X-ray diffraction (PXRD), and rheological analysis. ...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22915
更新日期:2017-01-01 00:00:00
abstract::Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as d...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.23014
更新日期:2017-07-01 00:00:00
abstract::Nanoparticle based delivery systems can offer opportunities for targeting, controlled release, and enhanced stability of their drug, protein, or gene therapy payload. This study investigated the use of chitosan in combination with the ionic additives sulfobutyl-ether-7-beta-cyclodextrin (SB-CD) or SB-CD/dextran sulfat...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.21055
更新日期:2008-01-01 00:00:00
abstract::To optimize antigen-antibody reactions, we have synthesized chemically well-defined hydrophilic microspheres. Proteins or haptens were covalently linked to these carriers. When the microsphere conjugates were agglutinated by the corresponding antiserum, the size of the complex artificially increased during the immunol...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360320808
更新日期:1992-08-01 00:00:00
abstract::Depsipeptide analogues of peptide sequences can help in elucidating the role of specific hydrogen bonds in determining the conformation in peptides. The repeating pentapeptide and hexapeptide sequences of elastin have been suggested to contain a type II beta-turn with a 4----1 hydrogen bond. Depsipeptide analogues of ...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360291212
更新日期:1990-10-01 00:00:00
abstract::In order to check our current knowledge on the principles involved in beta-hairpin formation, we have modified the sequence of a 3:5 beta-hairpin forming peptide with two different purposes, first to increase the stability of the formed 3:5 beta-hairpin, and second to convert the 3:5 beta-hairpin into a 2:2 beta-hairp...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20345
更新日期:2005-10-15 00:00:00
abstract::A de novo polypeptide GH(6)[(GA)(3)GY(GA)(3)GE](8)GAH(6) (YE8) was designed and genetically engineered to form antiparallel beta-strands of GAGAGA repeats. Modulation of pH enables control of solubility, folding, and aggregation of YE8 by control of the overall polypeptide charge, a consequence of the protonation or d...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20730
更新日期:2007-07-01 00:00:00
abstract::In this article, the pulsed double electron-electron resonance in electron spin-echo (PELDOR) technique is applied to study the self-aggregation of spin-labeled zervamicin IIA, a hexadecapeptide antibiotic of fungal origin, which is known to form ion channels in a phospholipid double layer. Measurements of the ion cha...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.10208
更新日期:2002-09-01 00:00:00
abstract::Several new biocompatible and degradable materials were prepared by chemical modification of sodium hyaluronate. The method of activation of hyaluronate by cyanogen bromide was used and subsequent reaction with nucleophile led to the formation of carbamate. This modification of hydroxyl groups of glycosaminoglycans pr...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20461
更新日期:2006-05-01 00:00:00
abstract::Computer simulations can provide in principle quantitative correlation between the structures of DNA polymerases and the replication fidelity. This paper describes our progress in this direction. Using several theoretical approaches, including the free energy perturbation (FEP), linear response approximation (LRA), an...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.10244
更新日期:2003-03-01 00:00:00
abstract::We suggest, using dynamical simulations of a simple heteropolymer modelling the alpha-carbon sequence in a protein, that generically the folded states of globular proteins correspond to statistically well-defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several fre...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360320610
更新日期:1992-06-01 00:00:00
abstract::Human saliva contains hundreds of small proline-rich peptides originated by the proteolytic cleavage of the salivary basic Proline-Rich Proteins. Nevertheless only for few of them a specific biological activity has been assigned to date. Among them, the 1932 Da peptide (p1932) has been patented as an anti-HIV agent. I...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22889
更新日期:2016-09-01 00:00:00
abstract::The formation mechanism of an alanine-based peptide has been studied by all-atom molecular dynamics simulations with a recently developed all-atom point-charge force field and the Generalize Born continuum solvent model at an effective salt concentration of 0.2M. Thirty-two simulations were conducted. Each simulation ...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.10216
更新日期:2003-01-01 00:00:00
abstract::We have previously described [K. M. Sullivan and D. M. J. Lilley (1986) Cell 47, 817-827] a set of sequences, called C-type inducing sequences, which cause cruciform extrusion by adjacent inverted repeats to occur by an abnormal kinetic pathway involving a large denatured region of DNA. In this paper we apply statisti...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360280810
更新日期:1989-08-01 00:00:00
abstract::Chiral interaction of helical peptide with chiral molecule, and concomitant induction in its helix sense have been demonstrated in optically inactive nonapeptide (1) possessing Gly at its N-terminus: H-Gly-(Delta(Z)Phe-Aib)(4)-OCH(3) (1: Delta(Z)Phe = Z-dehydrophenylalanine; Aib = alpha-aminoisobutyric acid). Spectros...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20557
更新日期:2006-11-01 00:00:00
abstract::Ribonuclease A is the archetype of a functionally diverse superfamily of vertebrate-specific ribonucleases. Inhibitors of its action have potential use in the elucidation of the in vivo roles of these enzymes and in the treatment of pathologies associated therewith. Derivatives of adenosine 5'-pyrophosphate are the mo...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.21158
更新日期:2009-12-01 00:00:00
abstract::Molecular dynamics simulation, with backbone constraints for 20 ps of equilibration and simulation, of a repeating polypeptide segment, Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-Met-(Gln-Pro-Leu )4, constituting residues 112-138 of bovine amelolgenin, a 19.35 kD hydrophobic protein, are discussed. It is ...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360280130
更新日期:1989-01-01 00:00:00
abstract::RADA-16-I is a self-assembling peptide which forms biocompatible fibrils and hydrogels. We used molecular dynamics simulations, atomic-force microscopy, NMR spectroscopy, and thioflavin T binding assay to examine size, structure, and morphology of RADA-16-I aggregates. We used the native form of RADA-16-I (H-(ArgAlaAs...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22755
更新日期:2016-01-01 00:00:00
abstract::The conformational behavior of the synthetic peptide, Boc-Gly-Val-Gly-Gly-Leu-OMe, containing the X-Gly-Gly and Gly-Gly-X (X = Val or Leu) repeating sequences and constituting a fragment of elastin was investigated by molecular mechanics and molecular dynamics (MD) simulation. The results suggest that, irrespective of...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360320206
更新日期:1992-02-01 00:00:00
abstract::The pulsed-field gel electrophoresis (PFG) is a newly developing technique used in the fractionation of large DNA fragments. Advances in PFG demand a better understanding in the corresponding mechanisms of DNA dynamics in the gel network. Detailed experiments are needed to verify and to extend existing theoretical pre...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360290408
更新日期:1990-03-01 00:00:00