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Monte Carlo simulation of protein folding in the presence of residue‐specific binding sites
Author(s) -
Rossinsky E.,
Srebnik S.
Publication year - 2005
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20365
Subject(s) - monte carlo method , preprint , chemistry , folding (dsp implementation) , protein folding , statistical physics , polar , chain (unit) , chemical physics , crystallography , computational chemistry , thermodynamics , physics , biochemistry , statistics , mathematics , quantum mechanics , astronomy , electrical engineering , engineering
Ensemble growth Monte Carlo (EGMC) and dynamic Monte Carlo (DMC) simulations are used to study sequential folding and thermodynamic stability of hydrophobic–polar (HP) chains that fold to a compact structure. Molecularly imprinted cavities are modeled as hard walls having sites that are attractive to specific polar residues on the chain. Using EGMC simulation, we find that the folded conformation can be stabilized using a small number of carefully selected residue‐specific sites while a random selection of surface‐bound residues may only slightly contribute toward stabilizing the folded conformation, and in some cases may hinder the folding of the chain. DMC simulations of the surface‐bound chain confirm increased stability of the folded conformation over a free chain. However, a different trend of the equilibrium population of folded chains as a function of residue‐external site interactions is predicted with the two simulation methods. © 2005 Wiley Periodicals, Inc. Biopolymers 79: 259–268, 2005 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com