Monte Carlo simulation of denaturation of adsorbed proteins

✍ Scribed by V.P. Zhdanov; B. Kasemo

• Publisher: John Wiley and Sons
• Year: 1998
• Tongue: English
• Weight: 210 KB
• Volume: 30
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/(sici)1097-0134(19980201)30:2<168::aid-prot6>3.0.co;2-j

✦ Synopsis

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 G 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).