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Dynamic properties of protein‐like heteropolymers: a computer simulation study
Author(s) -
Romiszowski Piotr,
Sikorski Andrzej
Publication year - 2003
Publication title -
macromolecular symposia
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.257
H-Index - 76
eISSN - 1521-3900
pISSN - 1022-1360
DOI - 10.1002/masy.200351333
Subject(s) - polymer , monte carlo method , autocorrelation , chain (unit) , solvent , single chain , materials science , force field (fiction) , protein secondary structure , lattice protein , molecular dynamics , chemical physics , lattice model (finance) , biological system , statistical physics , chemistry , computer science , protein structure , computational chemistry , physics , mathematics , composite material , organic chemistry , biochemistry , statistics , astronomy , artificial intelligence , antibody , immunology , biology
A simple model of a single polypeptide chain was used in the computer simulation. The units in a model polypeptide were located at α‐carbons and embedded in a very flexible [310] lattice. The force field that mimics polymer‐polymer and polymer‐solvent interactions contained a long‐range contact potential between the residues as well as local preferences in forming helical structures. The chain consisted of two types of residues: hydrophilic and hydrophobic. The classic Metropolis simulation algorithm was used. Monte Carlo simulations were carried out for helical sequences of residues and for various temperature conditions. It was shown that the formation of secondary structures in the chain under consideration had an influence on local short‐time dynamic properties. The analysis of the autocorrelation functions enables one to identify the presence of secondary structures. The analysis of the formation of polymer‐polymer and polymer‐solvent contacts in ordered structures was also made.