Monte Carlo simulation of denaturation of adsorbed proteins

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 1998-02, Vol.30 (2), p.168-176
• Main Authors: Zhdanov, V.P., Kasemo, B.
• Format: Article
• Language: English
• Subjects: Adsorption; denaturation kinetics; folding temperature; irreversible conformational changes; Kinetics; lattice model; metastable states; Monte Carlo Method; Protein Denaturation; Protein Folding; Proteins - chemistry; Surface Properties
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/(SICI)1097-0134(19980201)30:2<168::AID-PROT6>3.0.CO;2-J

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 > Tc (Tc is the collapse temperature for solution). With decreasing temperature, below Tc but above Tf (Tf is the folding temperature for solution), deviations appear from the first‐order kinetics. For the most interesting temperatures, that is, below Tf, 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 kr. One should rather introduce a distribution of values of this rate constant (different values of kr correspond to the transitions to the altered state via different metastable states). Proteins 30:168–176, 1998. © 1998 Wiley‐Liss, Inc.