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Complex regimes in simple methods of molecular dynamics of enzymes

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 occurs in a 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. We discuss the problem of overcoming the potential energy barrier inside the active site in terms of the location and energy of definite parts of the substrate within the framework of a 2D model. The special role of fluctuations of atom groups and the substrate influence on the process are taken into account.