Continuation support for theoretical studies on aqueous solvation problems relevant to biomolecular structure and process is requested. The research methodology to be used is liquid state statistical thermodynamic Monte Carlo computer simulation based mainly on intermolecular potential functions determined from quantum mechanical or empirical intermolecular interaction energies. Our intended studies range from the solvation of the simplest organizational units of dissolved molecules atoms and functional groups - to studies of the solvation of biological molecules, biomacromolecular fragments, and solvent effects on biomolecular association and conformational stability. We place special emphasis on extracting a useful descriptive physicochemical picture of solvation from the detailed numerical results using quasicomponent molecular distribution functions and the newly developed concepts of statistical state solvation sites and solvent mean positions. We plan to systematically interpret the results on more complex systems in terms of the collected results obtained for simpler constituent systems, and to determine the extent to which the solvation of a complex biomolecular or macro molecular systems can be predicted from a knowledge of the solvation of independent components. Specific problems to be investigated include the aqueous hydration of simple amines, amino acid residues and nucleic acid constituents, the organization of water in biomolecular crystal hydrates and the characteristics of biopolymer hydration including counterion considerations.
| Singhal, Poonam; Jayaram, B; Dixit, Surjit B et al. (2008) Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 94:4173-83 |
