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Characterization of the conformational space of a triple‐stranded β‐sheet forming peptide with molecular dynamics simulations
Author(s) -
Soto Patricia,
Colombo Giorgio
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20236
Subject(s) - molecular dynamics , folding (dsp implementation) , chemistry , chemical physics , kinetic energy , peptide , polar , crystallography , side chain , protein folding , protein secondary structure , computational chemistry , thermodynamics , physics , classical mechanics , biochemistry , organic chemistry , astronomy , electrical engineering , engineering , polymer
Molecular dynamics (MD) simulations have been performed on a series of mutants of the 20 amino acid peptide Betanova in order to critically assess the ability of MD simulations to reproduce the folding and stability of small β‐sheet–forming peptides on currently accessible timescales. Simulations were performed in both water and in 40% methanol solution, using an explicit solvent model. The simulations suggest that all mutants adopt a wide range of conformations in solution, that the structures are highly flexible, and that stabilization of compact structures is due to a delicate balance of hydrophobic and polar side‐chain interactions. Simulations longer than 100 ns, although not sufficient for a complete thermodynamic and kinetic description of the system, sample an ensemble of compact conformations characterized by the loss of ordered β‐sheet secondary structure. This suggests that no significant free energy barrier separates the different conformations available. Proteins 2004. © 2004 Wiley‐Liss, Inc.