Theory of Biomolecular Diffusion

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PROJECT SUMMARY Molecular diffusion, often steered and accelerated by solute interactions, critically influences the outcomes of many biological processes. Diffusion is known to influence or control the kinetics of many enzymes, and the rates of action of such enzymes may be increased by several orders of magnitude by electrostatic attraction of charged substrates toward the enzyme active sites. Likewise, electrostatically steered diffusion greatly speeds the interaction of proteins with other proteins, with nucleic acids, and with macromolecular assemblages on membranes in a variety of processes essential for cytoskeletal remodeling, cargo transport, gene expression, and signal transduction. The broad objectives of the proposed work are to provide new computer simulation tools that will enable the detailed analysis of the role of molecular diffusion in biological processes at the subcellular and cellular levels, and the application of these tools to selected problems where close contact with experimental work is possible. Development will continue on a novel approach to the treatment of hydrodynamic interactions in order to better describe the significant effects of these interactions in biomolecular associations. A unique, unified polar-apolar implicit solvation theory invented and developed in past and current grant cycles (the Variational Implicit Solvent Method) will be extended in a number of important directions to provide unprecedented accuracy and speed in future Brownian dynamics simulations. Development will continue on a unique approach for coupling Brownian dynamics simulations for a proper stochastic treatment in critical domains with efficient continuum treatments elsewhere. We will develop a method of adding flexible motion to large molecules in Brownian dynamics by making use of well-developed Markov State models of biomolecular conformational changes. These innovations will be implemented in our Brownian dynamics simulation package “Browndye”, and will be used to study a variety of biological systems. The health relatedness of this work lies in the potential of diffusional simulations to reveal the detailed dynamics of molecular interactions within healthy cells and how these dynamics may be altered in pathological situations. This will provide a basis for future work in structure-based drug discovery, in which small molecules are used to modulate the dynamic processes within the cell.