title: Molecular dynamics simulation study of valyl-tRNA synthetase with its pre- and post-transfer editing substrates.
abstract: The main role of aminoacyl-tRNA synthetases (aaRSs) is to transfer the cognate amino acids to the 3'-end of their tRNA by strictly discriminating from non-cognate amino acids. Some aaRSs accomplish this via proofreading and editing mechanisms, among which valyl-tRNA synthetase (ValRS) hydrolyses the non-cognate amino acid, threonine. In ValRS, existence of pre-transfer editing process is still unclear, although crystal structure of editing site with pre-transfer substrate analog (Thr-AMS) was released. In the case of isoleucyl-tRNA synthetase (IleRS), editing mechanism is well studied and mutational analyses revealed the existence of post- and pre-transfer editing mechanisms. Our aim is to investigate the possibility of pre-transfer editing process by performing molecular dynamics (MD) simulation studies. Simulations were carried out for ValRS with pre-transfer substrates (Thr-AMP/Val-AMP) and post-transfer substrates (Thr-A76/Val-A76) to understand their binding pattern. Two important point mutation studies were performed to observe their effect on editing process. This study also intends to compare and contrast the pre-transfer editing with post-transfer editing of ValRS. Interestingly, the MD simulation results revealed that non-cognate substrates (Thr-AMP/Thr-A76) bind more strongly than the cognate substrates (Val-AMP/Val-A76) in both pre- and post-transfer editing respectively. The editing site mutations (Lys270Ala and Asp279Ala) severely affected the binding ability of pre-transfer substrate (Thr-AMP) by different ways. Even though pre- and post-transfer substrates bind to the same site, specific differences were observed which has led us to believe the existence of the pre-transfer editing process in ValRS.
authors.affiliation: Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea.
authors.forename: Nagakumar
authors.initials: N
authors.lastname: Bharatham
authors.forename: Kavitha
authors.initials: K
authors.lastname: Bharatham
authors.forename: Yuno
authors.initials: Y
authors.lastname: Lee
authors.forename: Keun
authors.initials: K
authors.lastname: Woo Lee
mesh_terms: D000249:Adenosine Monophosphate / Q000737:chemistry / Q000378:metabolism*; D001224:Aspartic Acid / Q000235:genetics; D003198:Computer Simulation; D008239:Lysine / Q000235:genetics; D008958:Models, Molecular; D017354:Point Mutation; D011485:Protein Binding; D011487:Protein Conformation; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity; D016963:Thermus thermophilus / Q000201:enzymology*; D013912:Threonine / Q000737:chemistry / Q000378:metabolism*; D014633:Valine / Q000737:chemistry / Q000378:metabolism*; D014637:Valine-tRNA Ligase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D013912:Threonine; D001224:Aspartic Acid; D000249:Adenosine Monophosphate; D012343:RNA, Transfer; D014637:Valine-tRNA Ligase; D014633:Valine; D008239:Lysine