Structural analysis of Small Ras-like GTPases

Abstract

Small Ras-like GTPases are molecular switches that regulate diverse cellular processes including signal transduction, cytoskeletal dynamics, and membrane trafficking. They are majorly divided into five families: Ras, Rho, Rab, Arf, and Ran. Their activity is tightly controlled by four classes of interacting partners: GAPs, GEFs, GDIs, and effectors. The GTPases are inefficient switches without their interacting partners. There are family-specific interacting partners with certain domains found in a particular family only. Understanding this specificity of regulators to a particular family and finding characteristic structural patterns was one of the key objectives of this study. We represented Small Ras-like GTPases as a pyramid with four faces and a base. This pyramidal reference frame helped to systematically visualize and analyze the interaction surfaces of Small Ras-like GTPases. We constructed a dataset of 1,408 Small Ras- like GTPase structures retrieved from the PDB and analyzed them using PDBePISA. A classification methodology for interacting partners of Small Ras-like GTPase was devised in this work. Using this, GAPs were classified into five classes, GEFs into seven and GDIs into four. The face engagement patterns for all the classes clearly showed that face 2 was the most engaged face for the regulators GAPs, GEFs and GDIs. This is because face 2 contains the catalytically important residues and the switch I and switch II which undergo major conformational changes upon GTP hydrolysis. Apart from face 2 there is occurrence of other faces as well in different classes of regulators which suggest different mode by which these regulators act on the GTPases. For all the classes of the regulators we observed family specificity, this points out the families of GTPases have a preferred mechanisms of GAP, GEF and GDIs activity. For example Rab was present in three classes of GAPs whereas Rho was present in only one GAP class. In GEF Rho was found in 6 classes whereas Ras in 2 classes only.