Tuesday, May 20, 2008
Student Union Building, Upper (Queensborough Community College)
507

Coarse-Grain Molecular Dynamics of Tetrapeptides

Kenny Nguyen1, Russell DeVane2, Zhiwei Liu1, and Preston B. Moore1. (1) University of the Sciences in Philadelphia, Philadelphia, PA, (2) University of Pennsylvania, Philadelphia, PA

Coarse-grain molecular dynamics (CGMD) is a reduced model approach that expands existing all-atom (AA) MD techniques. Temporal and spatial scales can be extended by a factor of 1000 at the expense of atomistic details. CGMD simulations have been extensively used on lipid bilayers and have been extended to complex protein systems. A new CG model is presented, which has been parameterized from AAMD simulations of tetrapeptides GXYG in which G represents glycine and XY represents any two amino acid residues (400 combinations). Physicochemical information from AAMD simulations, such as bond lengths, bond angles, and torsions, is used to derive CG parameters. CGMD simulations of tetrapeptides using the derived parameters, as well as parameters derived from PDB structures of proteins are carried out where comparisons are made.