Modeling the mechanisms of biological GTP hydrolysis

[Display omitted] •General introduction to GTPases, with a particular emphasis on Ras GTPase and EF-Tu.•Overview of different mechanistic proposals for GTP hydrolysis by Ras and Ras-related enzymes.•Overview of different mechanistic proposals for GTP hydrolysis by EF-Tu.•Discussion of the contribution of computational modeling to understanding the mechanisms of biological GTP hydrolysis.•Future challenges for the field. Enzymes that hydrolyze GTP are currently in the spotlight, due to their molecular switch mechanism that controls many cellular processes. One of the best-known classes of these enzymes are small GTPases such as members of the Ras superfamily, which catalyze the hydrolysis of the γ-phosphate bond in GTP. In addition, the availability of an increasing number of crystal structures of translational GTPases such as EF-Tu and EF-G have made it possible to probe the molecular details of GTP hydrolysis on the ribosome. However, despite a wealth of biochemical, structural and computational data, the way in which GTP hydrolysis is activated and regulated is still a controversial topic and well-designed simulations can play an important role in resolving and rationalizing the experimental data. In this review, we discuss the contributions of computational biology to our understanding of GTP hydrolysis on the ribosome and in small GTPases.