This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. G-protein coupled receptors (GPCRs) constitute the largest family of membrane proteins used by cells to communicate with their environment. Lack of good expression levels and crystallization issues have obstructed obtaining experimental structures for these proteins, that constitute about 50% of the current pharmaceutical targets. Our group has developed methods [1] to obtain structures of these GPCRs in apo and ligand-bound forms and successfully applied them to many GPCRs [2]. To gain a detailed molecular perspective on the function of these proteins, it is critical to sample and understand their structures in activated and deactivated forms in their native cell environment, both in the absence and presence of ligands. Conformational changes, which are associated with activation, are known to occur in these receptors on micro to millisecond time scales and are still beyond the reach of current all-atom molecular dynamics simulations. This application for a development grant will focus on performing these simulations using NAMD [3] to experiment with the time scales necessary and sufficient to validate structural models of these proteins and to test the stability of apo and ligand-bound proteins in explicit lipid environment. The conformational changes in these proteins will also be studied using steered dynamics to explore interconversions between their activated and inactivated forms. This is a request for an extension of the previous development grant proposal, as we were unable to utilize the resources due to other pressing projects. We current have a number of GPCR systems which are ready for dynamics studies, hence this extension will be extremely valuable for us in doing preliminary dynamical studies and obtaining information necessary for a full MRAC/LRAC proposal to focus on a few pharmaceutical target GPCRs for which an understanding of dynamics and function will provide potential drug candidate leads that can act as selective and effective agonists or antagonists. [1] Vaidehi et al., Proc. Natl. Acad. Sci., USA 99, 12622 (2002). [2] Goddard and Abrol, J Nutr 137, 1528S (2007). [3] Phillips et al., J. Comp. Chem. 26, 1781 (2005).
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