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Monte Carlo simulation of denaturation of adsorbed proteins
Author(s) -
Zhdanov V.P.,
Kasemo B.
Publication year - 1998
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(19980201)30:2<168::aid-prot6>3.0.co;2-j
Subject(s) - metastability , denaturation (fissile materials) , kinetics , chemistry , monte carlo method , thermodynamics , molecule , reaction rate constant , crystallography , chemical physics , physics , organic chemistry , statistics , mathematics , quantum mechanics , nuclear chemistry
Denaturation of model proteinlike molecules at the liquid–solid interface is simulated over a wide temperature range by employing the lattice Monte Carlo technique. Initially, the molecule containing 27 monomers of two types ( A and B ) is assumed to be adsorbed in the native folded state (a 3 × 3 × 3 cube) so that one of its sides is in contact with the surface. The details of the denaturation kinetics are found to be slightly dependent on the choice of the side, but the main qualitative conclusions hold for all the sides. In particular, the kinetics obey approximately the conventional first‐order law at T > T c ( T c is the collapse temperature for solution). With decreasing temperature, below T c but above T f ( T f is the folding temperature for solution), deviations appear from the first‐order kinetics. For the most interesting temperatures, that is, below T f , the denaturation kinetics are shown to be qualitatively different from the conventional ones. In particular, the denaturation process occurs via several intermediate steps due to trapping in metastable states. Mathematically, this means that (i) the transition to the denatured state of a given molecule is nonexponential, and (ii) the denaturation process cannot be described by a single rate constant k r . One should rather introduce a distribution of values of this rate constant (different values of k r correspond to the transitions to the altered state via different metastable states). Proteins 30:168–176, 1998. © 1998 Wiley‐Liss, Inc.