emsl16 Protein-protein interactions in cellular signaling
EMSL Project ID
1964
Abstract
The Virtual Biology Center (VBC) is the component of the Environmental Health Initiative (EHI) focused on the development of modeling techniques for biological systems. LDRD-funded research in the VBC is divided into three main catagories (1) whole-organ models, (2) models for cellular signaling pathways, and (3) bioinformatics. In the pathway modeling area, I am working with Tjerk Straastma and Dave Dixon to characterize the protein-protein interactions responsible for signal transduction. To scope the computing resoucres needed in this part of the VBC, we are using NWChem to simulate a complex formed between p21RasGTP and raf-1. An x-ray structure of the complex is available to use as a starting structure for MD simulations. Current, NWchem does not contain module for the guanine triphosphate (GTP) part of the complex. Our first step will be to develop this module, which involves calculation of atomic charges by fiting the electrostatic potential energy from an electronic structure calculation. This is a significant computational effort since GTP contains 44 atoms and the SCF calculation must be carried out with the 6-31g* basis set so that the derived charges are consistent with other components of the force field. After the GTP module has been developed we will perform an MD simulation of the solvated RasGTP:Raf complex. Together with the SFC calcuations, we expect this project to require about 25,000 node hours on the SP.
Project Details
Project type
Capability Research
Start Date
1999-07-20
End Date
2001-10-01
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members