Dynamic Aspects Of Macromolecular Function

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In this reporting period, papers dealing with the following topics appeared in print or have been accepted for publication: (1)Influence of diffusion on the kinetics of excited state association dissociation chemical reactions, (2) Enhancement of association rates by nonspecific binding to DNA and cell membranes (3) Ensemble of transition states for two state protein folding from the eigenvectors of rate matrices and (4) The theory of photon statistics in single molecule Forster resonance energy transfer . The first paper deals with testing the predictions of our general theory or reversible diffusion influenced reactions against the result of many-body computer simulations. In the second paper, we apply this theory to examine the influence of nonspecific binding on the kinetics of binding to receptors on cell membranes and to DNA. In the third paper we propose a new method to analyze kinetic models of protein folding in order to provide insigh into the mechanism. The last and most important paper deals with the theory required to interpret Forster resonance energy transfer experiments on protein folding. In these experiments the number of photons emitted by a donor and an acceptor are monitoried. These contain structural information because the efficiency of energy transfer between tne donor and acceptor depend on the distance between them. Given an arbitrary dynamical scheme we showed how to calculate the probability distribution of the energy transfer obtained for fixed time windows. We have considered the contribution due to shot noise, to conformational dynamics and to translational diffusion in and out of the laser spot. This kind of complete analysis of all contributing factors is essential for the meanigful interpretation of experiments.