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Helical Segments (helical + segment)
Selected AbstractsFlexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation studyBIOPOLYMERS, Issue 1 2009Rakina Yaneva Abstract Major histocompatibility (MHC) Class II cell surface proteins present antigenic peptides to the immune system. Class II structures in complex with peptides but not in the absence of peptide are known. Comparative molecular dynamics (MD) simulations of a Class II protein (HLA-DR3) with and without CLIP (invariant chain-associated protein) peptide were performed starting from the CLIP-bound crystal structure. Depending on the protonation of acidic residues in the P6 peptide-binding pocket the simulations stayed overall close to the start structure. The simulations without CLIP showed larger conformational fluctuations especially of ,-helices flanking the binding cleft. Largest fluctuations without CLIP were observed in a helical segment near the peptide C-terminus binding region matching a segment recognized by antibodies specific for empty Class II proteins. Simulations on a Val86Tyr mutation that fills the peptide N-terminus binding P1 pocket or of a complex with a CLIP fragment (dipeptide) bound to P1 showed an unexpected long range effect. In both simulations the mobility not only of P1 but also of the entire binding cleft was reduced compared to simulations without CLIP. It correlates with the experimental finding that the CLIP fragment binding to P1 is sufficient to prevent antibody recognition specific for the empty form at a site distant from P1. The results suggest a mechanism how a local binding event of small peptides or of an exchange factor near P1 may promote peptide binding and exchange through a long range stabilization of the whole binding cleft in a receptive (near bound) conformation. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 14,27, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Effects of segment substitution on the structure and stability of immunoglobulin G binding domain of streptococcal protein GBIOPOLYMERS, Issue 1 2005Hai-Ning Du Abstract Structural formation of segments plays pivotal roles in protein folding and stability, but how the segment influences the structural ensemble remains elusive. We engineered two hybrid proteins by replacing the central helical segment of immunoglobulin G binding domain of streptococcal protein G with an ,-helix or ,2 -strand element of a structural homologue, the immunoglobulin G binding domain of streptococcal protein L. The results show that substitution by the ,-helical sequence retains a folded structure predominantly with a three-stranded ,-sheet but slightly destabilizes the compact ensemble, while substitution by the ,2 -strand sequence completely destroys the structural formation. The finding implies that the local segment may influence the tertiary structure and overall stability, and the tertiary interactions may modulate structural formation of the segment, which might be considered when studying protein folding, prediction, design, and engineering. © 2005 Wiley Periodicals, Inc. Biopolymers 79: 9,17, 2005 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Influence of a Joining Helix on the BLUF Domain of the YcgF Photoreceptor from Escherichia coliCHEMBIOCHEM, Issue 15 2008Claudia Schroeder Abstract BLUF-domain-comprising photoreceptors sense blue light by utilizing FAD as a chromophore. The ycgF gene product of Escherichia coli is composed of a N-terminal BLUF domain and a C-terminal EAL domain, with the latter postulated to catalyze c-di-GMP hydrolysis. The linkage between these two domains involves a predominantly helical segment. Its role on the function of the YcgF photoreceptor domain was examined by characterizing BLUF domains with and without this segment and reconstituting them with either FAD, FMN or riboflavin. The stability of the light-adapted state of the YcgF BLUF domain depends on the presence of this joining, helical segment and the adenosine diphosphate moiety of FAD. In contrast to other BLUF domains, two-dimensional 1H,15N and one-dimensional 1H NMR spectra of isotope-labeled YcgF-(1,137) revealed large conformational changes during reversion from the light- to the dark-adapted state. Based on these results the function of the joining helix in YcgF during signal transfer and the role of the BLUF domain in regulating c-di-GMP levels is discussed. [source] NMR investigations of subunit c of the ATP synthase from Propionigenium modestum in chloroform/methanol/water (4 : 4 : 1)FEBS JOURNAL, Issue 7 2002Ulrich Matthey The subunit c from the ATP synthase of Propionigenium modestum was studied by NMR in chloroform/methanol/water (4 : 4 : 1). In this solvent, subunit c consists of two helical segments, comprised of residues L5 to I26 and G29 to N82, respectively. On comparing the secondary structure of subunit c from P. modestum in the organic solvent mixture with that in dodecylsulfate micelles several deviations became apparent: in the organic solvent, the interruption of the ,,helical structure within the conserved GXGXGXGX motif was shortened from five to two residues, the prominent interruption of the ,,helical structure in the cystoplasmic loop region was not apparent, and neither was there a break in the ,,helix after the sodium ion-binding Glu65 residue. The folding of subunit c of P. modestum in the organic solvent also deviated from that of Escherichia coli in the same environment, the most important difference being that subunit c of P. modestum did not adopt a stable hairpin structure like subunit c of E. coli. [source] A minor ,-structured conformation is the active state of a fusion peptide of vesicular stomatitis virus glycoprotein,JOURNAL OF PEPTIDE SCIENCE, Issue 4 2008Carolina G. Sarzedas Abstract Entry of enveloped animal viruses into their host cells always depends on a step of membrane fusion triggered by conformational changes in viral envelope glycoproteins. Vesicular stomatitis virus (VSV) infection is mediated by virus spike glycoprotein G, which induces membrane fusion at the acidic environment of the endosomal compartment. In a previous work, we identified a specific sequence in the VSV G protein, comprising the residues 145,164, directly involved in membrane interaction and fusion. In the present work we studied the interaction of pep[145,164] with membranes using NMR to solve the structure of the peptide in two membrane-mimetic systems: SDS micelles and liposomes composed of phosphatidylcholine and phosphatidylserine (PC:PS vesicles). The presence of medium-range NOEs showed that the peptide has a tendency to form N - and C -terminal helical segments in the presence of SDS micelles. Analysis of the chemical shift index indicated helix,coil equilibrium for the C -terminal helix under all conditions studied. At pH 7.0, the N -terminal helix also displayed a helix,coil equilibrium when pep[145-164] was free in solution or in the presence of PC:PS. Remarkably, at the fusogenic pH, the region of the N -terminal helix in the presence of SDS or PC:PS presented a third conformational species that was in equilibrium with the helix and random coil. The N -terminal helix content decreases pH and the minor ,-structured conformation becomes more prevalent at the fusogenic pH. These data point to a ,-conformation as the fusogenic active structure-which is in agreement with the X-ray structure, which shows a ,-hairpin for the region corresponding to pep[145-164]. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between ,-helical and ,-hairpin conformations mediated by collapsed conformational statesJOURNAL OF PEPTIDE SCIENCE, Issue 5 2007Sunita Patel Abstract The peptide TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase adopts a helical conformation in the crystal structure and is a site for two hydrated helical segments, which are thought to be helical folding intermediates. Overlapping sequences of four to five residues from the peptide, sample both helical and strand conformations in known protein structures, which are dissimilar to glyceraldehyde-3-phosphate dehydrogenase suggesting that the peptide may have a structural ambivalence. Molecular dynamics simulations of the peptide sequence performed for a total simulation time of 1.2 µs, starting from the various initial conformations using GROMOS96 force field under NVT conditions, show that the peptide samples a large number of conformational forms with transitions from ,-helix to ,-hairpin and vice versa. The peptide, therefore, displays a structural ambivalence. The mechanism from ,-helix to ,-hairpin transition and vice versa reveals that the compact bends and turns conformational forms mediate such conformational transitions. These compact structures including helices and hairpins have similar hydrophobic radius of gyration (Rgh) values suggesting that similar hydrophobic interactions govern these conformational forms. The distribution of conformational energies is Gaussian with helix sampling lowest energy followed by the hairpins and coil. The lowest potential energy of the full helix may enable the peptide to take up helical conformation in the crystal structure of the glyceraldehyde-3-phosphate dehydrogenase, even though the peptide has a preference for hairpin too. The relevance of folding and unfolding events observed in our simulations to hydrophobic collapse model of protein folding are discussed. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Maximum-likelihood density modification using pattern recognition of structural motifsACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2001Thomas C. Terwilliger The likelihood-based approach to density modification [Terwilliger (2000), Acta Cryst. D56, 965,972] is extended to include the recognition of patterns of electron density. Once a region of electron density in a map is recognized as corresponding to a known structural element, the likelihood of the map is reformulated to include a term that reflects how closely the map agrees with the expected density for that structural element. This likelihood is combined with other aspects of the likelihood of the map, including the presence of a flat solvent region and the electron-density distribution in the protein region. This likelihood-based pattern-recognition approach was tested using the recognition of helical segments in a largely helical protein. The pattern-recognition method yields a substantial phase improvement over both conventional and likelihood-based solvent-flattening and histogram-matching methods. The method can potentially be used to recognize any common structural motif and incorporate prior knowledge about that motif into density modification. [source] The Structural Basis for Docking in Modular Polyketide BiosynthesisCHEMBIOCHEM, Issue 3 2006Kira J. Weissman Dr. Abstract Polyketide natural products such as erythromycin and rapamycin are assembled on polyketide synthases (PKSs), which consist of modular sets of catalytic activities distributed across multiple protein subunits. Correct protein,protein interactions among the PKS subunits which are critical to the fidelity of biosynthesis are mediated in part by "docking domains" at the termini of the proteins. The NMR solution structure of a representative docking domain complex from the erythromycin PKS (DEBS) was recently solved, and on this basis it has been proposed that PKS docking is mediated by the formation of an intermolecular four - ,-helix bundle. Herein, we report the genetic engineering of such a docking domain complex by replacement of specific helical segments and analysis of triketide synthesis by mutant PKSs in vivo. The results of these helix swaps are fully consistent with the model and highlight residues in the docking domains that may be targeted to alter the efficiency or specificity of subunit,subunit docking in hybrid PKSs. [source] | ||||||||||