Nonlinear Vibrations in a 2-Dimensional Protein Cluster Model with Linear Bonds

Abstract

A two-dimensional model for the unchanged part of the substrate inside a pocket of an active site of enzyme as a vibrational system is presented. The parameters of the system are evaluated for ff-chymotrypsin molecule. The case of internal resonant condition is considered. For that resonant case the energy concentrated on a certain degree of freedom is several times larger than in the non-resonant case. Analytical and numerical results are presented also for the case of harmonic excitation. The results can be used for the estimation of probability of the catalytic event for the case of different unchanged parts of substrates bound in a pocket of active sites. I. INTRODUCTION Proteins and, in particular, enzymes and enzyme-substrate complexes are very complicated nonlinear vibrational systems from a physical point of view. In these complex systems we would observe different types of dynamic motion and complicated energy distributions. Usually such macromolecules are investigated using m..