THEORETICAL STUDIES ON THE DYNAMIC ASPECTS OF MACROMOLECULAR FUNCTION

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Several theories for the kinetics of reversible diffusion influenced bimolecular reactions, developed in this laboratory, have been evaluated by comparison with exact results obtained via computer simulations of simple model reactions. No adjustable parameters were used and the good agreement between theory and simulations was found. In particular, the prediction that at long times concentrations relax to equilibrium not exponentially, as expected from simple chemical kinetics, but rather as a power law, has been verified. An analysis of a simple model of protein folding showed that Levinthal's astronomical folding time (10(to the power of 30)years) is reduced to a biologically relevant size (seconds) if correct local conformations are assumed to be more stable than incorrect ones by as little as 1kcal/mol. Computer simulations of u152 amino acid protein in water suggested a molecular picture of the slow (400ps-1ns) motions of N-H bonds that has been inferred from NMR relaxation experiments: the N-H groups of residues in loop regions of the protein undergo large amplitude jumps between conformations stabilized by hydrogen bonds due to infrequent dihedral transitions. The langevin dynamics of a linear molecular in a liquid crystal was simulated in order to test an analytical expression for the flipping rate. The nature of dielectric and orientational relaxation in a brownian dipolar lattice was analyzed using computer simulations and it was found that these relaxations become significantly nonexponential with increasing polarity.