Computer simulation of the decay of nonlinear subglobular oscillations in aqueous solutions of protein molecules

摘要

The efficiency of the molecular machines can be determined by the Q-factor of oscillations in the selected degrees of freedom. In particular, the quasi-harmonic oscillations of chymotrypsin decrease the threshold for the diffusion limitation of its functioning as molecular scissors. It was demonstrated by the methods of molecular dynamics that the Q-factor of the subglobular oscillations of proteins in water at the frequencies ω about 10~(12) Hz can reach 10, although the Raman bands in the corresponding spectral range were found only in crystal samples. Q quadratically increases with ω. The earlier hypothesis regarding the catalytic importance of the Fermi resonance for the oscillations of ligands and atomic groups in the enzyme-substrate complexes was not proved in experiments with simple models. The Fermi resonance can be observed if the Q-factor of the selected degree of freedom exceeds 100.