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Helix‐coil and beta sheet‐coil transitions in a simplified, yet realistic protein model
Author(s) -
Ilkowski Bartosz,
Skolnick Jeffrey,
Kolinski Andrzej
Publication year - 2000
Publication title -
macromolecular theory and simulations
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.37
H-Index - 56
eISSN - 1521-3919
pISSN - 1022-1344
DOI - 10.1002/1521-3919(20001101)9:8<523::aid-mats523>3.0.co;2-i
Subject(s) - cooperativity , globular protein , chemistry , hydrogen bond , crystallography , lattice protein , monte carlo method , beta sheet , helix (gastropod) , protein structure , chemical physics , protein folding , molecule , ecology , biochemistry , statistics , mathematics , organic chemistry , snail , biology
A reduced model of polypeptide chains and protein stochastic dynamics is employed in Monte Carlo studies of the coil‐globule transition. The model assumes a high‐resolution lattice representation of protein conformational space. The interaction scheme is derived from a statistical analysis of structural regularities seen in known three‐dimensional protein structures. It is shown that model polypeptides containing residues that have strong propensities towards locally expanded conformations collapse to β‐like globular conformations, while polypeptides containing residues with helical propensities form globules of closely packed helices. A more cooperative transition is observed for β‐type systems. It is also demonstrated that hydrogen bonding is an important factor for protein cooperativity, although, for systems with suppressed hydrogen bond interactions, a higher cooperativity of β‐type proteins is also observed.