Conformational Preferences of Modified Nucleoside 5-Taurinomethyluridine, τm(5)U Occur at 'wobble' 34th Position in the Anticodon Loop of tRNA

• Published in: Cell biochemistry and biophysics Vol. 71; no. 3; pp. 1589 - 1603
• Main Authors: Kamble, Asmita S, Kumbhar, Bajarang V, Sambhare, Susmit B, Bavi, Rohit S, Sonawane, Kailas D
• Format: Journal Article
• Language: English
• Published: United States 01-04-2015
• Subjects: Anticodon - metabolism; Escherichia coli - genetics; Hydrogen Bonding; Molecular Conformation; Molecular Dynamics Simulation; Static Electricity; Uridine - analogs & derivatives; Uridine - chemistry; Uridine - metabolism; Molecular electrostatics potential (MEPs); DFT; tRNA; HF; τm5U; RM1
• ISSN: 1559-0283
• DOI: 10.1007/s12013-014-0382-x

Conformational preferences of hypermodified nucleoside 5-taurinomethyluridine 5'-monophoshate 'p-τm(5)U' (-CH2-NH2(+)-CH2-CH2-SO3(-)) have been investigated using semi-empirical RM1 method. Automated geometry optimization using ab initio molecular orbital HF-SCF (6-31G**) and DFT (B3LYP/6-31G**) calculations have also been made to compare the salient features. The RM1 preferred most stable conformation of 'p-τm(5)U' has been stabilized by hydrogen bonding interactions between O(11a)…HN(8), O1P(34)…HN(8), and O1P(34)…HC(10). Another conformational study of 5-taurinomethyluridine side chain has also been performed in context of anticodon loop bases of E. coli tRNA(Leu). The atom O(11a) of τm(5)U(34) side chain interacts with adenosine (A35) as well as ribose-phosphate backbone which might provide structural stability to the anticodon loop. The glycosyl torsion angle of τm(5)U retains 'anti'-conformation. The solvent accessible surface area calculations revealed the role of τm(5)U in tRNA(Leu) anticodon loop. MD simulation results are found in agreement with RM1 preferred stable structure. The MEPs calculations of τm(5)U(34):G3 model show unique potential tunnels between the hydrogen bond donor and acceptor atoms as compared to τm(5)U(34):A3 model. Thus, these results could pave the way to understand the role of τm(5)U(34) to recognize UUG/UUA codons at atomic level in the mitochondrial disease, MELAS.