Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation

• Published in: Journal of molecular graphics & modelling Vol. 76; pp. 289 - 295
• Main Authors: Rayevsky, A.V., Sharifi, M., Tukalo, M.A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-09-2017
• Subjects: Aminoacyl-tRNA synthetases; Archaea - enzymology; Archaea - genetics; Hydrolysis; Leucine-tRNA Ligase - chemistry; Leucine-tRNA Ligase - metabolism; Leucyl-tRNA synthetase; Molecular Conformation; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Nucleic Acid Conformation; Post-transfer editing; Protein Binding; Pyrococcus horikoshii; RNA Editing; RNA, Transfer - chemistry; RNA, Transfer - genetics; Substrate Specificity; tRNA; Leucyl-tRNA synthetase; tRNA; Molecular dynamics; Pyrococcus horikoshii; Post-transfer editing; Molecular dynamics simulation; Aminoacyl-tRNA synthetases
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2017.06.022

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•Application and combining of in silico methods predicted the pre-intermediate state geometry, preceding the hydrolysis process in CP1 domain.•Based on comparison of structural features in LeuRSs archaeal/eukaryal, distinct modes of water attack and substrate activation were suggested.•Cognate norvaline and non-cognate isoleucine substrates were used to reconstruct steric conditions required to achieve initial state of reaction.•A possible mechanism of the post-transfer editing reaction in archaeal LeuRS system is proposed.
Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNALeu was modeled wherever tRNA’s acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS’s editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNALeu and isoleucyl-tRNALeu. In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS.