A study on the role of Mg²⁺ in a Ras protein by MD simulation

Abstract

Ras protein is a kind of small G protein that functions as a molecular switch or a timer alternating between the inactive GDP-bound and active GTP-bound form. Ras requires Mg²⁺ as a cofactor for its full activity. Recently, in another small G protein family, the release of Mg²⁺ coordinated by GDP was found to play an important role in binding the guanine nucleotide exchanging factor (GEF) that promotes the GDP/GTP exchange reaction. Here we calculated Mg²⁺-bound and Mg²⁺-unbound conformations of the GDP-bound Ras by molecular dynamics (MD) simulation. In the Mg²⁺-unbound conformation, significant conformational changes in the switch 1 region were observed, in which the switch region opened to expose the nucleotide-binding site. The distance between the switch 1 and switch 2 regions increased, resulting in the appearance of a groove. These conformations of the switch regions were very similar to that of Ras bound to its GEF: SOS (Son Of Sevenless). These structural changes were not observed in the Mg²⁺+-bound conformation. These results demonstrate the regulatory role of Mg²⁺ in GEF binding and suggest that the GDP dissociation occurs by a stepwise mechanism; (1) Releasing of Mg²⁺; (2) Conformational changes of the switch regions (semi-open form); (3) GEF binding (complete-open form); and (4) GDP dissociation. We suggest that the concentration of Mg²⁺ ions may regulate the binding between small G-proteins and GEFs.