Structure Function Correlation of G-Proteins

G蛋白几乎完全控制和调节信息的交流，告诉活细胞如何运作，并在许多生命过程的调解中发挥重要作用。因此，获得定量的G-蛋白质的结构功能相关性是一个问题，其解决方案在分子水平上理解生物过程方面具有重大的前景。在这个项目中进行的以前的研究开发和完善的模拟方法的研究GTdR反应在溶液中，在Ras和相关系统。模拟探索了突变导致细胞功能障碍的残基的关键作用，并表明这些残基通过变构机制进行操作，其中远端效应改变了活性位点的作用。试图证实这一发现，并达到更独特的机制的结论，包括系统的高层次的从头算量子力学研究磷酸盐在溶液中的水解，以及初步的从头算QM/MM研究的RasGAP复合物。这些研究再现了关键的实验结果，同时对这些系统的能量景观的性质提供了新的见解。上述进展使该项目处于一个关键点，它准备利用G蛋白和相关系统结构研究的巨大进展。因此，目前的研究正在以下几个方面平行进行：（i）将以前的研究扩展到不使用与Ras相同的关键残基的其他系统;（ii）对不同G蛋白的作用进行比较研究，并确定它们是否具有共同的机制;（iii）通过双突变分析探索RasGAP中以及Ras与其效应子之间的信息传递;（iv）通过对Ras的双突变分析，研究Ras与其效应子之间的信息传递。（iv）了解ATP水解如何激活分子马达;及（v）通过比较不同的从头算QM/MM计算结果，推动生物学和化学中磷酸盐水解性质的共识。上述研究的进展已经通过以下方式整合到教学和培训计划中：（i）开发和教授计算机建模课程;（ii）编写一本广泛使用的关于酶模拟的书;（iii）开发关键的模拟方法（例如，QM/MM和EVB方法）;（iv）生成关于GTdR和ATP酶反应性质的影片（参见http://futura.usc.edu）;（v）在不同的大学开设关于酶催化的专门课程和讲座;（vi）对博士后、博士生和本科生进行现代模拟和复杂生物功能分析方面的培训;（vii）在普通化学讲座中介绍Ras和ATP酶的模拟技术。该项目的未来方向将涉及在四个方面更积极地加强上述努力：（i）编写一本关于磷酸盐作为生物学中心分子的教科书（前三章已经完成），并在这本书中包括关于信号转导，能量转换和复制的章节。这本书将用于化学生物学的高级本科生和研究生课程。(ii)制作电影，说明细胞信号转导的过程及其分子基础。这部电影将与南加州大学电影学院合作制作。这些电影将分发给高中，它们应该提高对该领域迷人问题的兴趣，并鼓励年轻人在这一领域进行研究。它也可以用于向公众展示。(iii)打开一个网站，准备运行MOLARIS的EVB输入文件，用于磷酰基转移反应的所有可能变体以及在生物反应建模中使用这些文件的示例。这将允许学生和科学家以用户友好的方式模拟关键反应，并可用于世界各地的分子建模课程。(iv)该项目将继续为博士后和博士生提供模拟关键生物过程的高级培训。

G-Proteins almost exclusively control and regulate the communication of the messages that tell living cells how to operate and play a major role in the mediation of many life processes. Thus, obtaining quantitative structure function correlations for G-proteins is a problem whose solution holds major promises in terms of the understanding biological processes on a molecular level. Previous studies conducted in this project developed and refined simulation methods for studies of the GTPase reaction in solution, in Ras and in related systems. The simulations explored the key role of residues whose mutations lead to cell malfunction, and indicated that these residues operate by an allosteric mechanism, where a distant effects change the action at the active site. Attempts to confirm this finding and to reach more unique mechanistic conclusions included systematic high level ab initio quantum mechanics studies of phosphate hydrolysis in solution, as well as a preliminary ab initio QM/MM study of the RasGAP complex. These studies reproduced key experimental findings while giving new insights into the nature of the energy landscape of such systems. The above advances have placed the project at a pivotal point, where it is poised to exploit the enormous progress in structural studies of G-proteins and related systems. Thus, the research is now moving in a parallel way on the following fronts: (i) extending previous studies to other systems that do not use the same key residues as Ras; (ii) conducting comparative studies of the action of different G-proteins and determining whether or not they share a common mechanism; (iii) exploring the information transfer in RasGAP and between Ras and its effectors by double mutation analyses; (iv) learning how the hydrolysis of ATP activates molecular motors; and (v) pushing for a consensus on the nature of phosphate hydrolysis in biology and chemistry by comparing the results of different ab initio QM/MM calculations. The advances in the above research have been integrated into teaching and training programs by: (i) developing and teaching a computer modeling course; (ii) writing a widely used book on enzyme simulations; (iii) developing key simulation methods (e.g., the QM/MM and EVB methods); (iv) generating movies on the nature of GTPase and ATPase reactions (see http://futura.usc.edu); (v) giving specialized courses and lectures on enzyme catalysis in different universities; (vi) training postdocs, PhD students and undergraduates in modern simulations and in the analysis of complex biological functions; and (vii) presentation of the simulation techniques of Ras and ATPase, in general chemistry lectures. The future direction of the project will involve more aggressive enhancement of the above effort in four ways: (i) writing a text book on phosphate as the central molecule in biology (the first three chapters have been completed) and including in this book chapters on signal transduction, energy conversion and replication. This book will be used in advanced undergraduate and graduate classes on chemical biology. (ii) Producing movies that illustrate the process of cellular signal transduction and its molecular foundations. The movie will be produced in collaboration with the USC School of Cinema. The movies will be distributed to high schools where they should raise interest in the fascinating issues of the field and encourage young people to pursue research in this field. It can also be used in presentations to the wide public. (iii) Opening a site with ready to run EVB input files for MOLARIS for all the possibly variants of phosphoryl transfer reactions and examples of using these files in modeling biological reactions. This will allow students and scientist to model key reactions in a user friendly way and could be used in molecular modeling classes over the world. (iv) The project will continue to provide advanced training in modeling key biological processes to postdocs and PhD students.