Effect of solvent on the structure of a protein (H3.1) with a coarse-grained model with knowledge-based interactions

Quality of solvent plays a critical role in modulating the structure of a protein along with the temperature. Using a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ[1], BT[2], BFKV[3]) we examine the structure and dynamics of a histone (H3.1). The empty lattice sites constitute the effective solvent medium in which the protein is embedded. Residue-solvent characteristic interaction is based on the hydropathy index while the residue-residue interaction is used from the knowledge-based contact matrices derived from ensembles of protein structures in the protein data bank. Large scale simulations are performed to analyze the structure of protein for a range of residue-solvent interaction strength, a measure of the solvent quality with each potential. Unlike the monotonic thermal response, the radius of gyration of the protein exhibits non-monotonic dependence of the solvent strength. Quantitative comparison of the structure and dynamics emerging from three knowledge-based potentials will be presented in this talk. \\[4pt] [1] S. Miyazawa and R.L. Jernigan, Macromolecules 18, 534 (1985).\\[0pt] [2] M.R. Betancourt and D. Thirumalai, Protein Sci. 2, 361 (1999).\\[0pt] [3] U. Bastolla et al. Proteins 44, 79 (2001).