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. More specifically, our new Brownian dynamics simulation package Browndye will be enhanced to include many novel theoretical methods, to increase the accuracy and scales of diffusional simulations. A novel approach to the treatment of hydrodynamic interactions will be developed to better describe the significant effects of these interactions in biomolecular associations. A unique, unified polar-apolar implicit solvation theory invented in the current grant (the Variational Implicit Solvent Method) will be extended in a number of important directions to provide unprecedented accuracy in future Brownian dynamics simulations. A unique approach will be developed to couple Brownian dynamics simulations for a proper stochastic treatment in critical domains with efficient continuum treatments elsewhere. Applications will be made to study signal transduction phenomena and channeling of intermediates in enzyme assemblages in engineered and natural settings. 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.
Diffusional interactions among small molecules and macromolecules such as proteins occur continuously in healthy cells, and are disrupted in various ways in diseased cells. In this work, computer simulation methods are being used to create a virtual microscope to observe these diffusional processes, and how they may be altered by external interventions such as the introduction of therapeutic agents. 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.
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