Structure Function Correlation of G-Proteins

G蛋白几乎完全控制和调节信息的交流，这些信息告诉活细胞如何运作，并在许多生命过程的中介中发挥重要作用。因此，获得G蛋白的定量结构功能相关性是一个问题，它的解决方案在分子水平上理解生物过程方面有着重大的希望。该项目以前进行的研究为研究溶液、RAS和相关体系中的GTPase反应开发和改进了模拟方法。模拟探索了其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工作，其中远处的影响改变了活性部位的作用。为了证实这一发现并得出更独特的机理结论，试图包括系统地对溶液中磷酸水解的高水平从头算量子力学研究，以及对RasGAP络合物的初步从头算QM/MM研究。这些研究复制了关键的实验结果，同时对此类系统的能源格局的性质提供了新的见解。上述进展使该项目处于一个关键时刻，它准备利用G蛋白及其相关系统的结构研究的巨大进展。因此，这项研究目前正在以下方面平行进行：(I)将先前的研究扩展到其他不使用与RAS相同关键残基的系统；(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与其效应器之间的信息传递；(Iv)了解ATP的水解如何激活分子马达；以及(V)通过比较不同从头计算QM/MM的结果，推动就生物和化学中磷酸水解的性质达成共识。上述研究的进展已纳入教学和培训方案：(1)开发和教授计算机建模课程；(2)编写一本关于酶模拟的广泛使用的书；(3)开发关键的模拟方法(例如，QM/MM和EVB方法)；(4)制作关于GTP酶和ATPase反应性质的电影(见http://futura.usc.edu)；(V)在不同大学提供关于酶催化的专门课程和讲座；(6)培训博士后、博士生和本科生现代模拟和复杂生物功能的分析；以及(Vii)在普通化学课程中介绍RAS和ATPase的模拟技术。该项目未来的方向将包括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的中心分子的教科书(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。本书将用于化学生物学的高级本科生和研究生课程。(Ii)制作说明细胞信号转导过程及其分子基础的电影。这部电影将与南加州大学电影学院合作制作。这些电影将被分发给高中，在那里它们应该引起人们对该领域迷人问题的兴趣，并鼓励年轻人在该领域从事研究。它还可以用于向广大公众进行演示。(3)为MOLARIS打开一个网站，提供所有可能的磷酰转移反应变种的可运行EVB输入文件，以及在模拟生物反应中使用这些文件的例子。这将允许学生和科学家以用户友好的方式对关键反应进行建模，并可用于世界各地的分子建模课程。(4)该项目将继续向博士后和博士后提供关键生物过程建模方面的高级培训。

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.