Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at 'wobble' position in anticodon loop of tRNALeu: A molecular modeling approach

• Published in: PloS one 2017, Vol.12 (4), p.e0176756-e0176756
• Main Authors: Kamble, Asmita S, Fandilolu, Prayagraj M, Sambhare, Susmit B, Sonawane, Kailas D
• Format: Article
• Language: English
• Subjects: Acidosis; Animals; Anticodon - metabolism; Biochemistry; Bioinformatics; Biology and Life Sciences; Bonding; Codon - metabolism; Codons; Crystal structure; Dynamic structural analysis; Encephalopathy; Humans; Hydrogen; Hydrogen Bonding; Lactic acidosis; MELAS syndrome; Mitochondria; Molecular dynamics; Molecular Dynamics Simulation; Molecular modelling; Myopathy; Nucleosides; Physical Sciences; Protein Biosynthesis; Recognition; Research and Analysis Methods; RNA - metabolism; RNA, Ribosomal - metabolism; RNA, Transfer, Leu - chemistry; RNA, Transfer, Leu - metabolism; rRNA; Simulation; Stroke; Stroke-like episodes; Transfer RNA; Uridine - analogs & derivatives; Uridine - metabolism
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0176756

Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by 'wobble' as well as a novel 'single' hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons.