Simbios Talk by Yun-Dong Wu, Department of Chemistry, The Hong Kong University of Science & Technology, March 30, 2009

Title: A United-Atom Protein Force Field in Coarse-Grained Solvent

Abstract: Despite improvement of computer power and conformational sampling technique, all-atom molecular dynamics simulations of proteins remain formidable. We set out to develop a protein model that can achieve atomistic details but fast enough for the simulation of real proteins, so that it can become a general tool for the simulation of protein folding and protein/protein interaction. We adopt a united-atom model for the protein coupled with coarse-grained water (four water molelcules as a particle). In this lecture I will present our strategies for the development of the protein model and successful applications of the model that has been achieved so far, including (1) coil-to-helix transition free energies of Ac-(Ala)6-X-(Ala)7-NHMe, X = Gly, Ala, Leu; (2) the transfer free energies of 19 amino acid side-chain analogous (excluding glycine) from cyclohexane; (3) the folding of a 73-residue protein model into 4-helix bundles; and (4) the folding of Trp-cage mini protein.