Influence of intramolecular dynamic structure on the process of energy transfer from the place of original localization to the active site and processes in the active site of enzyme is under consideration. The possibility of realization of "marked"degrees of freedom when the system motion occures in narrow area of phase space was considered within the framework of a simplest cluster model of an enzyme molecule. Under certain conditions the motion of the system becomes complex and perhaps stochastic and the spectrum of oscillations becomes more rich. The role of the interaction potential curve shapes of the system is discussed. Problems of spectral transformation and complexization and characteristic times determination are important for interpretation of the data obtained by the methods of laser spectroscopy and CARS, in particular [1].We discuss the problem of the overcoming of potential energy barrier inside the active site in terms of the location and energy of definite part of substrate within the framework of a two-dimensional model. The special role of fluctuations of atom groups and the substrate influence on the process are taken into account.
We consider here the effect of Fermi resonance on the rate of stochastic transitions over potential barriers. As a typical phenomenon for Fermi resonance we investigate the fading of the energy between the oscillations in different degrees of freedom. Due to this fading phenomenon we see from time to time rather large amplitudes of oscillations along the reaction path which may support transitions over reaction barriers in the underdamped regime. As as an application we study the influence of Fermi resonance on enzyme reactions. In particular we investigate the possible effect of Fermi resonance on the breaking of peptide bonds.
In this work, we continue our research of the problem concerning the proteins' functioning efficiency. The system under study, a three-dimensional harmonic oscillator, placed in a water "drop" which consists of 264 molecules, simulates the fluctuations of atomic groups in a non-stationary charge pattern field of an active center. The latter results in a break of chemical bonds. Damping time and Q-factor calculations of atomic fluctuations at various frequencies, intensities of interaction with the water environment, and also at various atomic weights are carried out. By means of the argon-like model of water molecules the Q-factor of atomic fluctuations is also estimated. The results obtained are compared with those calculated with the SP3-model.
The effect of anomalously enhanced quality factor (small damping decrement) is demonstrated and explained by phase dependence of interaction with particles of medium. The dependence of quality factor on the temperature of the medium is described. The most suitable noise intensity is determined. Molecular dynamics simulations qualitatively confirm the results. The size and mass of real bio-molecules, the frequency, amplitude of their oscillations and the temperature of living body are suitable conditions for this effect.
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