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Monte Carlo simulation of protein folding with orientation‐dependent monomer–monomer interactions
Author(s) -
Zhdanov V.P.,
Kasemo B.
Publication year - 1997
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/(sici)1097-0134(199712)29:4<508::aid-prot10>3.0.co;2-q
Subject(s) - antiparallel (mathematics) , metastability , monte carlo method , crystallography , protein folding , monomer , chemical physics , lattice protein , folding (dsp implementation) , folding funnel , native state , statistical physics , chemistry , energy landscape , physics , downhill folding , thermodynamics , phi value analysis , polymer , mathematics , biochemistry , statistics , organic chemistry , quantum mechanics , magnetic field , electrical engineering , engineering
We present the results of lattice Monte Carlo simulations of protein folding in the framework of a model taking into account (i) the dependence of the energy of interaction of amino‐acid residues on their orientation and (ii) the rigidity of the polypeptide chain with respect to the formation of kinks. If the chain is flexible, the final protein structures are predicted to be compact. Increasing the energy cost of creation of kinks is found to favor the formation of flat structures mimicking an ideal antiparallel β sheet. For compact structures, the kinetics of folding exhibit the standard two‐phase regime (a rapid collapse to one of the metastable state, followed by slow reconfiguration of the chain to the native structure). For flat structures, the transition to the native state is often gradual. Proteins 29:508–516, 1997. © 1997 Wiley‐Liss, Inc.