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

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 G蛋白偶联受体(GPCRs)是细胞用来与环境沟通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这些蛋白质的实验结构的获得，这些蛋白质约占当前药物靶标的50%。我们的团队已经发展了方法[1]来获得这些以apo和配体结合的形式的GPCRs的结构，并成功地将它们应用于许多GPCRs[2]。为了获得对这些蛋白质功能的详细分子观点，至关重要的是采样和了解它们在天然细胞环境中激活和失活的结构，无论是在没有配体的情况下还是在存在配体的情况下。与激活相关的构象变化已知发生在这些受体的微到毫秒的时间尺度上，仍然超出了当前全原子分子动力学模拟的范围。这项开发拨款的申请将集中于使用NAMD[3]来执行这些模拟，以实验必要和足够的时间尺度来验证这些蛋白质的结构模型，并测试载脂蛋白和配体结合蛋白质在显性脂质环境中的稳定性。这些蛋白质的构象变化也将用导向动力学来研究，以探索它们的激活和非激活形式之间的相互转化。这是要求延长先前的发展赠款提案，因为由于其他紧迫项目，我们无法利用资源。我们目前有一些GPCR系统已经为动力学研究做好了准备，因此这一扩展对于我们进行初步的动力学研究和获得完整的MRAC/LRAC建议集中在几个药物靶标GPCRs上是非常有价值的，对动力学和功能的了解将提供潜在的候选药物线索，可以作为选择性和有效的激动剂或拮抗剂。[1]Vaidehi等人，Proc.娜塔莉。阿卡德。《科学》，美国99,12622(2002年)。[2]Goddard and Abrol，J Nutr 137,1528 S(2007)。[3]Phillips et al.，J.Comp.化学。26,1781(2005)。

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. 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).