Investigation of translation initiation factor through protein–protein interactions and molecular dynamics approaches

Abstract

ABSTRACT A crucial biological process that involves both transcription and translation is protein synthesis. While, the translation mechanism endures protein synthesis with the help of messenger RNA, translation initiation factors, initiator tRNA and ribosomal small subunit, which efficiently recruit mRNA and start protein synthesis. This study focuses on the archaea, which is an attractive target of its evolutionary aspects. aIF2 plays a key regulatory roles in the archaea. This work mainly focuses on the initiation mechanism of Pyrococcus horikoshii OT3 and analyzes the structural interaction pattern between proteins. Here, the crystal structure of PH0702 was retrieved from the Protein Data Bank (PDB id: 6A34). Further, a molecular docking was carried out with the PH0702 protein, GTP and tRNA using the Glide module of Schrödinger and PATCHDOCK online server. Result shows the residues (Arg57, Gln206 and Lys258) interact with the oxygen group of 1st, 2nd and 3rd phosphoric acid. The three hydrogen bonds were formed between the Guanine (560) and Ser (300). Similarly, Modeling of 30S ribosomal subunit and mRNA of P. horikoshii OT3 were carried and their stability was analyzed using the molecular dynamics approach. Hence, this study paved a good platform for elucidating the overall mechanism of the protein initiation process.