THE GTP HYDROLYSIS MECHANISM IN ELONGATION FACTOR –TU (EFTU)

Abstract

Elongation factor Tu (EF-Tu) is a member of G protein family, and as part of a ternary complex with GTP, plays a critical function in translation by delivering aminoacyl-tRNA to the ribosome. Like other G proteins, the function of EF-Tu depends on whether GTP or GDP is bound. When EFTu is complexed with GTP, it can bind the aminoacyl-tRNA. Upon cognate codon-anticodon pairing, GTP is hydrolyzed and EF-Tu is separated from the ribosome leaving the aminoacyl-tRNA at the A-site. Hence, GTP hydrolysis is the critical step for the activity of the protein [1, 2]. To identify the residues involved in GTP hydrolysis mechanism of EF-Tu, we have used QM/MM methods. In particular, we have focused on the roles of Histidine 85 (His85) and Arginine 57 (Arg57) (T. aquaticus numbering). These residues can be situated inside or outside of the active site depending on the conditions. Therefore we have studied three different models: one with His85 in the active, one with Arg57 in the active site and one where both His85 and Arg57 are outside of the active site. Our results indicate that the presence of Arg57 or His85 in the active site decreases the activation energy, indicating that these residues have catalytic roles. Another important issue is to determine whether the hydrolysis reaction proceeds via an associative or dissociative path [3]. To this end, different model structures representing the associative or dissociative path of GTP hydrolysis have been optimised and the energy values have been compared in order to identify the mechanism. All optimised transition structures have associative character. Stationary points involved in a dissociative mechanism could not be located, suggesting that such a mechanism is unlikely, at least for the models studied. We observe that the energy increases at the points where the dissociative path is supposed to occur.