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Backbone Dihedral Angles (backbone + dihedral_angle)
Selected AbstractsReconstructing the equilibrium Boltzmann distribution from well-tempered metadynamicsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2009M. Bonomi Abstract Metadynamics is a widely used and successful method for reconstructing the free-energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well-tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solutionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2002Caterina Benzi The conformational behavior of the title compounds has been investigated by Hartree,Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed , turn (,l), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4,0.5 kcal/mol for helical structures and about 2 kcal/mol for ,l structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for ,l structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 341,350, 2002 [source] A statistically derived parameterization for the collagen triple-helixPROTEIN SCIENCE, Issue 11 2002Jan K. Rainey Abstract The triple-helix is a unique secondary structural motif found primarily within the collagens. In collagen, it is a homo- or hetero-tripeptide with a repeating primary sequence of (Gly-X-Y)n, displaying characteristic peptide backbone dihedral angles. Studies of bulk collagen fibrils indicate that the triple-helix must be a highly repetitive secondary structure, with very specific constraints. Primary sequence analysis shows that most collagen molecules are primarily triple-helical; however, no high-resolution structure of any entire protein is yet available. Given the drastic morphological differences in self-assembled collagen structures with subtle changes in assembly conditions, a detailed knowledge of the relative locations of charged and sterically bulky residues in collagen is desirable. Its repetitive primary sequence and highly conserved secondary structure make collagen, and the triple-helix in general, an ideal candidate for a general parameterization for prediction of residue locations and for the use of a helical wheel in the prediction of residue orientation. Herein, a statistical analysis of the currently available high-resolution X-ray crystal structures of model triple-helical peptides is performed to produce an experimentally based parameter set for predicting peptide backbone and C, atom locations for the triple-helix. Unlike existing homology models, this allows easy prediction of an entire triple-helix structure based on all existing high-resolution triple-helix structures, rather than only on a single structure or on idealized parameters. Furthermore, regional differences based on the helical propensity of residues may be readily incorporated. The parameter set is validated in terms of the predicted bond lengths, backbone dihedral angles, and interchain hydrogen bonding. [source] Solution Structure of , -Am2766: A Highly Hydrophobic , -Conotoxin from Conus amadis That Inhibits Inactivation of Neuronal Voltage-Gated Sodium ChannelsCHEMISTRY & BIODIVERSITY, Issue 4 2005Siddhartha The three-dimensional (3D) NMR solution structure (MeOH) of the highly hydrophobic , -conotoxin , -Am2766 from the molluscivorous snail Conus amadis has been determined. Fifteen converged structures were obtained on the basis of 262 distance constraints, 25 torsion-angle constraints, and ten constraints based on disulfide linkages and H-bonds. The root-mean-square deviations (rmsd) about the averaged coordinates of the backbone (N, C,, C) and (all) heavy atoms were 0.62±0.20 and 1.12±0.23,Å, respectively. The structures determined are of good stereochemical quality, as evidenced by the high percentage (100%) of backbone dihedral angles that occupy favorable and additionally allowed regions of the Ramachandran map. The structure of , -Am2766 consists of a triple-stranded antiparallel , -sheet, and of four turns. The three disulfides form the classical ,inhibitory cysteine knot' motif. So far, only one tertiary structure of a , -conotoxin has been reported; thus, the tertiary structure of , -Am2766 is the second such example. Another Conus peptide, Am2735 from C. amadis, has also been purified and sequenced. Am2735 shares 96% sequence identity with , -Am2766. Unlike , -Am2766, Am2735 does not inhibit the fast inactivation of Na+ currents in rat brain Nav1.2 Na+ channels at concentrations up to 200,nM. [source] Characterization of folded conformations in a tetrapeptide containing two tryptophan residues by vibrational circular dichroism,CHIRALITY, Issue 1E 2009Ana G. Petrovic Abstract The intramolecularly hydrogen bonded conformations of the tetrapeptide Boc-Trp-Aib-Gly-Trp-OMe (WUGW) are investigated using experimental and quantum chemical predictions of vibrational circular dichroism (VCD) in the 1800,1550 cm,1 region. The predicted VCD spectrum, for a conformation (conformer A) obtained from optimization of crystal structure, reproduced the dominant negative VCD band observed experimentally in CH3OH and CHCl3 solvents. However, the predicted VCD spectrum of Conformation A also has an extra positive band which is not seen in the experimental spectra. This mismatch appears to be due to the lack of solvent influence in the quantum chemical geometry optimizations. However, Conformations I and II, obtained, respectively, from constrained optimization of crystal and NMR structures, mimic the solvent stabilized structures and are predicted to have dominant negative VCD band as found in the experimental spectra. It is noted that, for the peptide investigated here, unconstrained quantum chemical geometry optimizations in vacuum converged to structures that are not the realistic models of conformations found in solution. It is also noted that undertaking quantum chemical vibrational property calculations directly using geometries obtained from crystal data or NMR data resulted in unrealistic vibrational frequencies and descriptions. However, constraining the backbone dihedral angles to those found in condensed medium, and optimizing the remaining geometrical parameters resulted in a better reproduction of the observed VCD in condensed medium. The vibrational origins of bands in all of the predicted VCD spectra for the WUGW-tetrapeptide have also been presented. Chirality 21:E76,E85, 2009. © 2009 Wiley-Liss, Inc. [source] | ||||||||||