THEORETICAL STUDIES ON THE DYNAMIC ASPECTS OF MACROMOLECULAR FUNCTION

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The theory of absorbance measurements on a system (e.g. a chromophore in a protein) that undergoes a sequence of reactions initiated by a linearly polarized laser pulse of arbitrary intensity is developed. In order to provide a complete framework that could be used to analyze experiments, a wide variety of complications (e.g. reorientational motion on the same time scale as the intense excitation pulse,the influence of internal motions and chemical kinetics) were explicitly treated. In order to describe the dynamics of macromolecules on time scales where comformational transitions (barrier crossings) occur, we showed that memory function corrections must be added to the optimized Rouse-Zimm theory and developed a new, computationally efficient way of doing so. A simple analytic theory required to analyze fluorescence studies of cell-cell fusion has been developed. This theory is based on the realization that the diffusive transfer of probes between two cell surfaces connected by a small pore can be accurately described by two state chemical kinetics. The rate constants were expressed in terms of microscopic parameters by exploiting a rigorous mapping of the cell problem onto one involving diffusion on a one dimensional bistable potential with an entropic barrier. An analytic theory for the response of a dipolar lattice to a newly created change has been formulated based on a dynamic mean spherical approximation. The predictions of this theory for solvation dynamics has been tested against computer simulations. The influence of electrostatic interactions and diffusion on the rate of protein-protein association kinetics have been examined. A new method (boundary elements) for calculating the electrostastic interaction energy between two macromolecules has been developed. This procedure can handle the irregular shape of the molecular surfaces, the small dielectric constant in the interior and the presence of salt ions in solution.