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Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at “Wobble” 34th Position in the Anticodon Loop of tRNA

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Abstract

Conformational preferences of modified nucleoside, N(4)-acetylcytidine, ac4C have been investigated using quantum chemical semi-empirical RM1 method. Automated geometry optimization using PM3 method along with ab initio methods HF SCF (6-31G**), and density functional theory (DFT; B3LYP/6-31G**) have also been made to compare the salient features. The most stable conformation of N(4)-acetyl group of ac4C prefers “proximal” orientation. This conformation is stabilized by intramolecular hydrogen bonding between O(7)···HC(5), O(2)···HC2′, and O4′···HC(6). The “proximal” conformation of N(4)-acetyl group has also been observed in another conformational study of anticodon loop of E. coli elongator tRNAMet. The solvent accessible surface area (SASA) calculations revealed the role of ac4C in anticodon loop. The explicit molecular dynamics simulation study also shows the “proximal” orientation of N(4)-acetyl group. The predicted “proximal” conformation would allow ac4C to interact with third base of codon AUG/AUA whereas the ‘distal’ orientation of N(4)-acetyl cytidine side-chain prevents such interactions. Single point energy calculation studies of various models of anticodon–codon bases revealed that the models ac4C(34)(Proximal):G3, and ac4C(34)(Proximal):A3 are energetically more stable as compared to models ac4C(34)(Distal):G3, and ac4C(34)(Distal):A3, respectively. MEPs calculations showed the unique potential tunnels between the hydrogen bond donor–acceptor atoms of ac4C(34)(Proximal):G3/A3 base pairs suggesting role of ac4C in recognition of third letter of codons AUG/AUA. The “distal” conformation of ac4C might prevent misreading of AUA codon. Hence, this study could be useful to understand the role of ac4C in the tertiary structure folding of tRNA as well as in the proper recognition of codons during protein biosynthesis process.

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Acknowledgments

This study was supported by the University Grants Commission, New Delhi under the major research project sanctioned to KDS. BVK and ADK are thankful to UGC for providing project fellowship.

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  1. Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416 004, Maharashtra, India

    Bajarang V. Kumbhar, Asmita D. Kamble & Kailas D. Sonawane

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Kumbhar, B.V., Kamble, A.D. & Sonawane, K.D. Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at “Wobble” 34th Position in the Anticodon Loop of tRNA. Cell Biochem Biophys 66, 797–816 (2013). https://doi.org/10.1007/s12013-013-9525-8

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