THEORETICAL STUDIES ON THE DYNAMIC ASPECTS OF MACROMOLECULAR FUNCTION

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In this reporting period, papers dealing with the following projects appeared in print: (1) Reaction dynamics on a thermally fluctuating potential; (2) Theory of the fluorescence of singlymolecules undergoing multistate conformational dynamics; (3) Asimple model for protein folding that illustrates a large numberof concepts needed to understand this process, including entropic barriers, transition states, funnels and the origin of single exponential folding kinetics. The first paper deals with the important problem of how fluctuations in the environment, such as those that occur in the active site of an enzyme, influence the rate of a chemical reaction. The second paper addresses the problem of how one should interpret recent and novel fluorescence experiments not on bulk samples but on individual molecules. The third paper introduces the simplest model that captures themost fundamental aspect of protein folding, namely that both the entropy (that is the number of configurations) and the energy decrease as folding occurs. This is in contrast to most chemical reactions where bonds are first broken, leading to an increase in energy. The interesting finding is that this "bare bones"model is able to account for a surprising number of experimental trends, showing how such results follow from the simplest physical assumptions.