LONG TIME-SCALE DYNAMICS OF G-PROTEIN COUPLED RECEPTORS IN EXPLICIT LIPID ENVIR

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 G蛋白偶联受体（GPCR）是细胞与外界环境进行通讯的最大的膜蛋白家族。缺乏良好的表达水平和结晶问题阻碍了获得这些蛋白质的实验结构，这些蛋白质占目前药物靶标的约50%。我们的小组已经开发了方法[1]来获得这些GPCR在载脂蛋白和配体结合形式的结构，并成功地将它们应用于许多GPCR [2]。为了获得对这些蛋白质功能的详细分子视角，在不存在和存在配体的情况下，在其天然细胞环境中以激活和失活形式采样和理解其结构是至关重要的。已知与激活相关的构象变化发生在这些受体中的时间尺度为微米至毫秒，并且仍然超出当前全原子分子动力学模拟的范围。开发资助申请将侧重于使用NAMD [3]进行这些模拟，以实验验证这些蛋白质的结构模型所需的时间尺度，并测试载脂蛋白和配体结合蛋白在显式脂质环境中的稳定性。还将使用转向动力学研究这些蛋白质的构象变化，以探索其激活和失活形式之间的相互转化。这是要求延长以前的发展赠款提案，因为我们由于其他紧迫的项目而无法利用这些资源。我们目前有一些GPCR系统已准备好进行动力学研究，因此，这种扩展将是非常有价值的，我们在做初步的动力学研究，并获得必要的信息，一个完整的MRAC/LRAC的建议，专注于一些药物靶GPCR的动力学和功能的理解将提供潜在的候选药物的线索，可以作为选择性和有效的激动剂或拮抗剂。[1]Vaidehi等人，Proc. Natl. Acad.科学，USA 99，12622（2002）。[2]戈达德和Abrol，J Nutr 137，1528 S（2007）. [3]菲利普斯等人，J.Comp.Chem.26，1781（2005）。

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).