QM/MM study on the elongation factor-Tu (EF-Tu)

Abstract

EF-Tu is a member of the GTP binding protein superfamily which consists of proteins carrying information and biological components in cells. When the ternary complex of EF-Tu:GTP:aa tRNA binds to the ribosome, cognate codon anticodon interaction triggers the fast hydrolysis of the EF-Tu bound GTP. The hydrolysis of GTP leads to a remarkable conformation change in EF-Tu as it returns to the GDP (loose) conformation from its GTP (tight) conformation. This conformational change decreases the affinity of EF-Tu to the ribosome and abolishes its affinity towards the aa-tRNA resulting in the release of EF-Tu:GDP complex from aa tRNA and ribosome. As the hydrolysis of GTP to GDP is of central importance in the functioning cycle of G proteins. Considerable amount of computational and experimental studies were directed to elucidate the mechanism of non-enzymatic phosphate hydrolysis in solution. The main mechanistic debate on GTP hydrolysis or phosphate hydrolysis in general is whether it follows an associative or dissociative pathway. The associative pathway can be described by the formation of an intermediate with a penta-coordinated phosphorus atom whereas the dissociative pathway can be described by the formation of a metaphosphate ion as an intermediate. In our study we will mainly emphasize the GTP conformation of the elongation factor Tu (EF-Tu) and investigate the mechanistic pathways in GTP hydrolysis by using Quantum Mechanical/Molecular Mechanical (QM/MM) approach as a hybrid computational method.