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Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A. Three‐dimensional lattice model of lysozyme
Author(s) -
Ueda Yuzo,
Taketomi Hiroshi,
Gō Nobuhiro
Publication year - 1978
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.1978.360170612
Subject(s) - lysozyme , chemistry , lattice (music) , native state , protein folding , monte carlo method , chemical physics , crystallography , limiting , folding (dsp implementation) , statistical physics , thermodynamics , lattice protein , physics , biochemistry , mechanical engineering , statistics , mathematics , electrical engineering , acoustics , engineering
A three‐dimensional lattice model of protein designed to assimilate lysozyme is introduced. An attractive interaction is assumed to work between preassigned specific pairs of units, when they occupy the nearest‐nighbor lattice points. The behavior of this lattice lysozyme is studied by a Monte Carlo simulation method. Because of the specific interunit interactions,“native state” of the lattice lysozyme is stable at low temperatures. Conformational fluctuations in the native state are observed to occur at both termini and loop regions of the main chain existing on the surface. The process of unfolding and denatured states of this model are discussed. Complete refolding from a denatured state was not observed. However, by starting from partially folded structures, the native conformation could be attained. From these observation it is concluded that, in the process of folding of proteins as simplified in a lattice model, nulceation is a rate‐limiting factor. The artificial character of this model and possible improvement are discussed.