Computationally Intensive Research Project
Complex Enzymatic Reactions
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Volkhard Helms,1 T. P. Straatsma,2 Thereza A. Soares Da Silva,2 Hartmut Michel,3 Markus Elstner4
1Saarland University, Germany, 2Pacific Northwest National Laboratory, 3Max Planck Institute of Biophysics, Germany, 4Technical University Braunschweig, Germany
FY07 Allocation - 1,200,000
Abstract
This proposal seeks computational resources for the continued development and application of modeling capabilities for the study of complex enzymatic reactions, in particular those that involve proton transfer steps, and novel free energy methodologies for enzymatic design. Understanding of the molecular-level processes, including proton transfer steps in long-time conformational protein dynamical processes as well as the rational design of enzymes with improved specificity requires extending computational tools and techniques beyond what is currently available. The primary approach is that of new developments in the QHOP and DFTB methodologies which will be implemented as new capabilities of NWChem. The second approach deals with a novel application of free-energy perturbation techniques. Both approaches will involve design and implementation of a meta-simulation engine that controls the launch and analysis of individual MD trajectories.
