SALT EFFECTS IN SOLUTIONS OF PEPTIDES AND NUCLEIC ACIDS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We will use molecular dynamics simulations and proximal Radial Distribution Functions to study the properties of proteins and nucleic acids in aqueous saline solution. The molecular dynamics simulations will be used to interpret structural and thermodynamic experimental data for the biopolymer projects. Using recent classical force field models these systems will be simulated with molecular dynamics using programs developed in this lab and those available to the community. Additionally, a recent project in development focuses on the calculation of the electrostatic solvation free energy as fast as continuum-based methods and as accurately as explicit simulation by treating the solvent, not as a structure-less dielectric continuum, but as structured. This method uses a special version of the probability distribution function called the proximal Radial Distribution Function (pRDF). The following scientific projects of biochemical/biotechnological significance related to this proposal are described: 1) Salt effect in peptide and protein solutions: non-ideal behavior, 2) DNA/RNA polymorphism and surface-proximity dependence, and 3) Evaluation of and free energies from probability densities. These are an ongoing set of funded projects. Considerable progress has been made with the last allocation. Several manuscripts have been and are being completed; these are listed in a separate section of this document.