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- Title
Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, acC Occur at 'Wobble' 34th Position in the Anticodon Loop of tRNA.
- Authors
Kumbhar, Bajarang; Kamble, Asmita; Sonawane, Kailas
- Abstract
Conformational preferences of modified nucleoside, N(4)-acetylcytidine, acC 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 acC 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 tRNA. The solvent accessible surface area (SASA) calculations revealed the role of acC 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 acC 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 acC(Proximal):G, and acC(Proximal):A are energetically more stable as compared to models acC(Distal):G, and acC(Distal):A, respectively. MEPs calculations showed the unique potential tunnels between the hydrogen bond donor-acceptor atoms of acC(Proximal):G/A base pairs suggesting role of acC in recognition of third letter of codons AUG/AUA. The 'distal' conformation of acC might prevent misreading of AUA codon. Hence, this study could be useful to understand the role of acC in the tertiary structure folding of tRNA as well as in the proper recognition of codons during protein biosynthesis process.
- Subjects
NUCLEOSIDES; MATHEMATICAL optimization; DENSITY functional theory; CONFORMATIONAL analysis; TRANSFER RNA; ACETYL group
- Publication
Cell Biochemistry & Biophysics, 2013, Vol 66, Issue 3, p797
- ISSN
1085-9195
- Publication type
Article
- DOI
10.1007/s12013-013-9525-8