title: Comparative Structural Dynamics of tRNA(Phe) with Respect to Hinge Region Methylated Guanosine: A Computational Approach.
abstract: Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for maintaining the structural stability of tRNAs. However, their significance for upholding the tRNA structure has not been investigated in detail at the atomic level. In this study, molecular dynamic simulations have been performed to assess the effects of methylated nucleic acid bases, N (2)-methylguanosine (m(2)G) and N (2)-N (2)-dimethylguanosine (m 2 (2) G) at position 26, i.e., the hinge region of E. coli tRNA(Phe) on its structure and dynamics. The results revealed that tRNA(Phe) having unmodified guanosine in the hinge region (G26) shows structural rearrangement in the core of the molecule, resulting in lack of base stacking interactions, U-turn feature of the anticodon loop, and TΨC loop. We show that in the presence of the unmodified guanosine, the overall fold of tRNA(Phe) is essentially not the same as that of m(2)G26 and m 2 (2) G26 containing tRNA(Phe). This structural rearrangement arises due to intrinsic factors associated with the weak hydrogen-bonding patterns observed in the base triples of the tRNA(Phe) molecule. The m(2)G26 and m 2 (2) G26 containing tRNA(Phe) retain proper three-dimensional fold through tertiary interactions. Single-point energy and molecular electrostatics potential calculation studies confirmed the structural significance of tRNAs containing m(2)G26 and m 2 (2) G26 compared to tRNA with normal G26, showing that the mono-methylated (m(2)G26) and dimethylated (m 2 (2) G26) modifications are required to provide structural stability not only in the hinge region but also in the other parts of tRNA(Phe). Thus, the present study allows us to better understand the effects of modified nucleosides and ionic environment on tRNA folding.
authors.affiliation: Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra (M.S.), 416 004, India. kds_biochem@unishivaji.ac.in.|Department of Microbiology, Shivaji University, Kolhapur, Maharashtra (M.S.), 416 004, India. kds_biochem@unishivaji.ac.in.
authors.forename: Kailas D
authors.initials: KD
authors.lastname: Sonawane
authors.affiliation: Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra (M.S.), 416 004, India.|Computational Biology and Bioinformatics Lab (CBBL), Department of Biochemistry, Gyeongsang National University, jinju, South Korea.
authors.forename: Rohit S
authors.initials: RS
authors.lastname: Bavi
authors.affiliation: Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra (M.S.), 416 004, India.
authors.forename: Susmit B
authors.initials: SB
authors.lastname: Sambhare
authors.affiliation: Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra (M.S.), 416 004, India.
authors.forename: Prayagraj M
authors.initials: PM
authors.lastname: Fandilolu
mesh_terms: D020029:Base Pairing; D006151:Guanosine / Q000378:metabolism*; D006860:Hydrogen Bonding; D008274:Magnesium / Q000378:metabolism; D008745:Methylation; D008958:Models, Molecular; D012331:RNA, Fungal / Q000737:chemistry / Q000378:metabolism; D012360:RNA, Transfer, Phe / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D012331:RNA, Fungal; D012360:RNA, Transfer, Phe; D006151:Guanosine; D008274:Magnesium
keywords: Modified nucleosides; Molecular dynamic simulations; N 2,N 2-dimethylguanosine (m 2 2 G); N 2-methylguanosine (m2G); tRNA