THEORETICAL STUDIES ON THE DYNAMIC ASPECTS OF MACROMOLECULAR FUNCTION

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A Molecular theory for the rate of nonadiabatic electron transfer was developed and its relation to classical Marcus theory was established. The rate was found to be determined by the probability density of the energy gap, which is defined as the instantaneous change in solvation energy upon moving an electron from the donor to the acceptor. It was shown how this probability density can be obtained from the free energies of transferring varying amounts of charge between the donor and acceptor (as specified by a charging parameter). A simple algorithm was proposed for calculating these free-energy changes (and hence the energy gap probability density) from computer simulations on just three states; the reactant,t he product, and an "anti" product formed by transferring a positive unit charge from the donor to the acceptor. The Marcus relation (i.e., the activation energy as a parabolic function of the free-energy change of reaction) was derived in a way that clearly shows that it is a good approximation in the normal region even when the solvent response is significantly nonlinear. A simple generalization of this relation, in which the activation energy is given by parabolic functions with different curvatures in the normal and inverted regions, was proposed. A novel method has been developed to analyze NMR relaxation experiments on unfolded proteins. It was shown how the spectral density function describing the dynamics of amide bond vectors can be determined at specific frequencies using N15 relaxation parameters alone. Experimental data on the folded and unfolded forms of a small protein was used to establish the validity of this procedure A continuum model of electrostatic interactions in protein has been used to analyze the energetics of a positionally disordered water molecule within an apparently hydrophobic cavity of a protein, as has recently been bound experimentally using NMR.