DMCA
Excluded Volume in Protein Sidechain Packing (2008)
| Citations: | 5 - 0 self |
BibTeX
@MISC{Kussell08excludedvolume,
author = {Edo Kussell and Jun Shimada and Eugene I. Shakhnovich},
title = {Excluded Volume in Protein Sidechain Packing},
year = {2008}
}
Share
 |
 |
 |
 |
||
OpenURL
Abstract
The excluded volume occupied by protein sidechains and the requirement of high packing density in the protein interior should severely limit the number of sidechain conformations compatible with a given native backbone. To examine the relationship between sidechain geometry and sidechain packing, we use an all-atom Monte Carlo simulation to sample the large space of sidechain conformations. We study three models of excluded volume and use umbrella sampling to effectively explore the entire space. We find that while excluded volume constraints reduce the size of conformational space by many orders of magnitude, the number of allowed conformations is still large. An average repacked conformation has 20 % of its χ angles in a non-native state, a marked reduction from the expected 67 % in the absence of excluded volume. Interestingly, well-packed conformations with up to 50 % non-native χ’s exist. The repacked conformations have native packing density as measured by a standard Voronoi procedure. Entropy is distributed non-uniformly over positions, and we partially explain the observed distribution using rotamer probabilities derived from the pdb database. 1 In several cases, native rotamers which occur infrequently in the pdb database are seen with high probability in our simulation, indicating that sequence-specific excluded volume interactions can
Keyphrases
excluded volume protein sidechain packing sidechain conformation pdb database standard voronoi procedure native packing density allowed conformation all-atom monte carlo simulation sidechain geometry high probability observed distribution large space native rotamers sequence-specific excluded volume interaction non-native state well-packed conformation average repacked conformation conformational space marked reduction many order repacked conformation protein sidechains excluded volume constraint sidechain packing native backbone use umbrella protein interior entire space several case
