Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras.
Over the last 40 years, we have learnt a great deal about the Ras onco-proteins. These intracellular molecular switches are essential for the function of a variety of physiological processes, including signal transduction cascades responsible for cell growth and proliferation. Molecular simulations and free energy calculations have played an essential role in elucidating the conformational dynamics and energetics underlying the GTP hydrolysis reaction catalysed by Ras. Here we present an overview of the main lessons from molecular simulations on the GTPase reaction and conformational dynamics of this important anti-cancer drug target. In the first part, we summarise insights from quantum mechanical and combined quantum mechanical/molecular mechanical simulations as well as other free energy methods and highlight consensus viewpoints as well as remaining controversies. The second part provides a very brief overview of new insights emerging from large-scale molecular dynamics simulations. We conclude with a perspective regarding future studies of Ras where computational approaches will likely play an active role.
Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, 6431 Fannin St, Houston, TX 77030, USA.
Priyanka
P
Prakash
Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, 6431 Fannin St, Houston, TX 77030, USA.
Alemayehu A
AA
Gorfe
GTP hydrolysis; conformational dynamics; molecular dynamics; molecular mechanics; quantum mechanics