Molecular dynamics simulations of the Rap1A reveal unique features in the active site

Abstract

GTPases are hydrolytic proteins that convert GTP into GDP and serve as bivalent switches, where the GTP-bound state is active and the GDP-bound state is inactive. Rap1A is a GTPase with 50% sequence homology and similar tertiary structure to the archetypal GTPase Ras, with a key difference occurring at position 61. In Ras Q61 participates in the hydrolysis mechanism and mutation leads to oncogenesis, while the role of T61 in Rap1A is not clear. The goal of this project is to explore the Rap1A active site and its mechanism of intrinsic hydrolysis. Two crystal structures were obtained with differing conformations of T61 in the Rap1A active site. Accelerated molecular dynamic simulations were run for 200 ns, starting with each of the structures, to sample the variety of motion present in Rap1A. Results indicate coordinated movements between the switch I, switch II, and helix 3 regions. Further, switch II appears less mobile than in simulations with Ras isoforms. Although Ras and Rap proteins are highly similar in structure, their dynamics are clearly different and this may have consequences for catalysis and allosteric modulation associated with function.