Multiscale simulation methods for protein dynamics and synergistic regulation of enzyme complexes

COMP 187

Chia-en A. Chang,, M. Qaiser Fatmi,, and Rizi Ai. Department of Chemistry, University of California at Riverside, Chemical Sciences Building, Riverside, CA 92507
It has long been of interest to know which mechanisms and rules that proteins utilize for allosteric and synergetic regulations. We develop and apply computational tools to elucidate the role of conformation, dynamics and allosteric regulation in the enzymatic function of multi-enzyme complexes. This study uses the tryptophan synthase complex as a model system, which has been studied as a model for allosteric regulation and substrate channeling within protein complexes for decades. The enzyme is a bienzyme nanomachine. Its catalytic activity is intimately related to allosteric signaling and metabolite transfer between its alpha- and beta-subunits that are connected by a 25 -long channel. Molecular dynamics simulations are carried out to study the allosteric regulation. Moreover, the Brownian dynamics algorithm, together with a coarse-grained model are used to study the travel of the substrate (channeling) within the protein. A new program for analysis of simulations based on Bond-Angle-Torsion coordinates will also be introduced.

Hewlett-Packard Scholar Awards
6:00 PM-8:00 PM, Tuesday, August 18, 2009 Walter E. Washington Convention Center -- Ballroom A, Poster

Division of Computers in Chemistry

The 238th ACS National Meeting, Washington, DC, August 16-20, 2009