We propose to extend a new computational technique, """"""""Dynamic Importance Sampling"""""""" (DIMS) to the study conformational transitions in peptides and proteins. Our long term goals are to study the kinetics and thermodynamics of a type VI turn and, ultimately, of the fatty acid binding protein (FABP). These systems ideal subjects for the DIMS technique because the three-dimensional structures of the different states conformational states in the type VI turn and ligand bound/unbound states in FABP) are known. From such known start and end structures, DIMS is capable of computing (a) reaction rates, (b) transition paths, and equilibrium state populations. The method has proved efficient in small systems because it gathers all necessary information on the very short timescale in which a transition event (i.e., barrier crossing) occurs, rather than on the much longer timescale between transitions - which limits many traditional techniques like molecular dynamics.
Our specific aims are to compute (a) - (c) for the following all-atom systems, modeled by the AMBER potential in the """"""""Molecular Modelling Toolkit"""""""": (I) isomerizations in implicitly-solvated butane alanine dipeptide; (II) isomerizations in butane and alanine dipeptide in explicit water; (III) conformational transitions for a type VI turn; and, (IV) fatty acid entrance and exit in FABP.
| Zuckerman, Daniel M; Woolf, Thomas B (2002) Theory of a systematic computational error in free energy differences. Phys Rev Lett 89:180602 |
