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Folding Very Short Peptides Using Molecular Dynamics
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BibTeX
@MISC{Ho_foldingvery,
author = {Bosco K. Ho and Ken A. Dill},
title = {Folding Very Short Peptides Using Molecular Dynamics},
year = {}
}
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Abstract
Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solventaccessible electrostatic approximation to water) implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85 % of the converged cases (41 peptides), the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the b hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.
Keyphrases
short peptide using molecular dynamic native structure preferred structure gb sa different protein present simulation coarse-grained backbone description bioinformatics-based i-sites library pick conformational preference converged case early nucleus native-like structure implicit solvent peptide fragment replica-exchange molecular dynamic protein-structure prediction method physics-based modeling generalized-born solventaccessible electrostatic approximation 8-mer fragment
