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Fine grained sampling of residue characteristics using molecular dynamics simulation

Paper ID Volume ID Publish Year Pages File Format Full-Text
15217 1392 2010 12 PDF Available
Title
Fine grained sampling of residue characteristics using molecular dynamics simulation
Abstract

In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome dataset samples not only the states well represented in the PDB but also the known states that are not well represented in the structural database. In our analysis, we characterized the mutual influence among the backbone ϕ,ψ angles with the first side-chain torsion angles (χ1) and the volumes occupied by the side-chains. The dependencies of these relationships on side-chain environment and amino acids are further explored. We found that residue volumes exhibit dependency on backbone 2° structure conformation: side-chains pack more densely in extended β-sheet than in α-helical structures. As expected, residue volumes on the protein surface were larger than those in the interior. The first side-chain torsion angles are found to be dependent on the backbone conformations in agreement with previous studies, but the dynameome dataset provides higher resolution of rotamer preferences based on the backbone conformation. All three gauche−, gauche+, and trans rotamers show different patterns of ϕ,ψ dependency, and variations in χ1 value are skewed from their canonical values to relieve the steric strains. By demonstrating the utility of dynameomic modeling on the native state ensemble, this study reveals details of the interplay among backbone conformations, residue volumes and side-chain conformations.

Keywords
Molecular dynamics simulation; Residue volume; Side-chain packing; Dynameome; Backbone conformation; Rotamer; Ramachandran plot
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Fine grained sampling of residue characteristics using molecular dynamics simulation
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 34, Issue 3, June 2010, Pages 172–183
Authors
, , , , ,
Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us