Structure Function Correlation of G-Proteins

University Of Southern California, Los Angeles CA

Investigators

Abstract

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.