Kurnikova, M. G. | bioRxiv Science

bioRxiv2025

Time-Resolved Crystallography Reveals the Mechanisms of GTP hydrolysis for N-RAS and the Oncogenic Mutants G12C, G12V and Q61L

The RAS family of small GTPases are molecular switches that convey downstream signals regulating cell proliferation, differentiation, and apoptosis. The signaling competent GTP-bound RAS transitions to its inactive GDP-bound form through {gamma}-phosphate hydrolysis. Oncogenic RAS mutations hamper GTP hydrolysis and are present in up to 30% of all human cancers. Structural studies of RAS proteins bound to non-hydrolysable GTP analogs have revealed snapshots of the enzyme in its possibly active form. Yet, the mechanism of GTP hydrolysis has not been structurally resolved. To visualize this reaction in real time, we performed time-resolved crystallographic experiments employing a photolabile caged-GTP substrate. Fifty-seven distinctive reaction intermediates were captured during hydrolysis of a live GTP for N-RAS, the oncogenic mutants G12C, G12V and Q61L; and Y32R, a fast hydrolytic mutant. The reaction mechanisms and rates for the native and each of the mutants differed significantly; however, they shared common elements: an initially catalytically-defective open state, which transitions into the closed Michaelis complex state with solvent-assisted O3B-P{gamma} bond lengthening and breaking, followed by the release of the Mg2+ stabilized PO3-/PO4-3 species and unfolding of the switch loops. Given the conserved nature of GTP- and ATP-ases active sites, this structural work lays the basis to understand the universal mechanism of {gamma}-phosphate hydrolysis. Furthermore, search for cryptic binding sites during GTP hydrolysis in G12C, G12V, and Q61L mutants reveals the presence of distinctive state-dependent binding pockets that could be targets for structure-based drug discovery of experimentally resolved intermediates states.

cancer biology↗

bioRxiv2019

Microsecond Molecular Dynamics Simulations of Diphtheria Toxin Translocation T-Domain pH-Dependent Unfolding in Solution

Diphtheria toxin is a multi-domain protein that invades cells by using their own endocytosis mechanism. In endocytosis, an endosome, a lipid bilayer vesicle, is formed to encapsulate an extracellular molecule. Subsequent acidification of endosome internal solution induces conformational rearrangements and membrane insertion of such encapsulated diphtheria toxin translocation domain (T-domain). In solution at neutral pH, a stand-alone T-domain adopts an all alpha-helical globular structure; however, atomistic details of the pH-dependent conformational changes of the protein are not completely understood. We model structural rearrangements in T-domain in 18 {micro}s long molecular dynamics (MD) simulations of neutral and low pH T-domain models in explicit solvent. At low pH, six histidine residues of the protein were protonated. Two independent MD trajectories resulted in partial protein unfolding at low pH, in which similar regions of the protein conformational subspace were explored. Notably, a pH induced unfolding transition was initiated by partial unfolding of helix TH4 followed by unfolding of helix TH1. Helix TH2 repeatedly unfolds in the low pH T-domain model, which is consequently predicted to be disordered by a consensus of disorder prediction algorithms. Protonation of histidines disrupted a hydrophobic core containing a putative transmembrane helix TH8, which is encircled by hydrophobic surfaces of helices TH3, TH5 and TH9. Afterwards, the low pH T-domain model was reorganized into an ensemble of partially unfolded structures with increased solvent exposure of hydrophobic and charged sites. Thus, MD simulations suggest the destabilizing role of protonation of histidines, in the neutral pH conformation in solution, which may facilitate the initial stages of T-domain membrane binding. The simulation at neutral pH samples conformations in the vicinity of the native structure of the protein. However, significant fluctuations of the protein, including unfolding and refolding of -helices were observed at these simulation time-scales.

biophysics↗