Modeling the mechanisms of biological GTP hydrolysis

Abstract

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.

19F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA‐Catalyzed GTP Hydrolysis

“…The rate acceleration provided by GAPs has been broadly attributed to the insertion of an arginine finger into the active site,17 where it provides electrostatic catalysis,7c, 8f makes the β‐phosphate a better leaving group by hydrogen bonding to the β,γ‐bridging oxygen (O3β), and excludes solvent 17, 18. Our results identify two additional roles for Arg85′.…”

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, 19F NMR, and DFT Approaches

“…These studies show that the sidechain of a highly conserved arginine (Arg85′ in RhoGAP), termed the “arginine finger”, is inserted into the active site of RhoA in the RhoA/RhoGAP/GTP complex. Four functions have been proposed for the arginine finger in catalysis 5. First, its sidechain excludes several water molecules from the active site 6.…”

“…Second, the arginine finger stabilizes an eclipsed orientation of the α‐ and β‐phosphoryl oxygen atoms, adding to the existing strained eclipsing of the β‐ and γ‐phosphoryl oxygens 7. Third, the guanidinium moiety facilitates hydrolysis by donating two hydrogen bonds (H‐bonds) to GTP (α‐ and γ‐phosphoryl oxygens) 5. Fourth, its backbone carbonyl group accepts an H‐bond from the sidechain of a conserved glutamine (Gln63 in RhoA), thereby orientating that carboxamide moiety for catalytic function 8.…”

Special issue in computational modeling on biological systems

“…In the first one, Alexandra Carvalho, Klaudia Szeler, Konstantinos Vavitsas, Johan Åqvist and Shina Kamerlin review the contributions of computational biology to the understanding of GTP hydrolysis on the ribosome, and in small GTPases. [8] It is stressed how, 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 computational study on another problem with medical applications; the mechanisms of hydrolysis of two antibiotics in the active site of a mono-nuclear β-lactamase. [12] The study, based on molecular dynamics simulations with multiscale methods, explores the reaction paths and highlights the dramatic conformational changes that can take place in the cavity of the enzyme to accommodate different substrates, which would be the origin of its substrate promiscuity.…”