This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. implicit solvent models g-protein coupled receptors microenvironments pH dependent electrostatic effects Abstract: A grant of 186,400 SU is requested for using the Lemieux platform to support the computational needs of the extramurally funded project Functional Properties of Protein Segments in Receptors using a newly developed Implicit Solvent Model for Fast Computer Simulations on Biological Systems. The long term goals of the project are to obtain deeper understanding and insight of the determinants of functional action of protein segments as part of a larger macromolecular system, in particular G-Protein Coupled Receptors (GPCRs). To help achieve these goals an implicit solvent model has been implemented for Monte Carlo and Molecular Dynamics simulations that incorporates the effects of bulk solvent in the potential function defining the system. Such an approach will allow much longer calculations on more realistic systems to be performed. The new simulation methods will be used in this and other projects. The approach has been programmed into the CHARMM suite of programs. However, to utilize the full power of the Lemieux architecture (750 node Compaq Alphaserver with 4 cpu/node) the new method will be incorporated into the NAMD Molecular Simulation program because of its excellent scaling properties. Time is being requested on the Lemieux platform because of its power and outstanding suitability to meet our computational needs. The goals of the grant are to complete the algorithmic developments outlined in the proposal, and to carry out the calculations required to achieve the long term goal of the underlying extramural project: to gain new and deeper insights into the determinants of functional action of protein segments in the context of the complete system and its environment
Showing the most recent 10 out of 292 publications
