Kumbhar NM, Gopal JS. Structural significance of hypermodified nucleoside 5-carboxymethylaminomethyluridine (cmnm
5U) from 'wobble' (34th) position of mitochondrial tRNAs: Molecular modeling and Markov state model studies.
J Mol Graph Model 2018;
86:66-83. [PMID:
30336453 DOI:
10.1016/j.jmgm.2018.10.004]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/28/2022]
Abstract
A quantum chemical semi-empirical RM1 approach was used to deduce the structural role of hypermodified nucleoside 5-carboxymethylaminomethyluridine 5'-monophosphate (pcmnm5U) from 'wobble' (34th) position of mitochondrial tRNAs. The energetically preferred pcmnm5U(34) adopted a 'skew' conformation for C5-substituted side chain (-CH2-NH2+-CH2-COO-) moiety that orient towards the 5'-ribose-phosphate backbone, which support 'anti' orientation of glycosyl (χ34) torsion angle. Preferred conformation of pcmnm5U(34) was stabilized by O(4) … HC(10), O1P⋯HN(11), O(15) … HN(11), O(15) … HC(10), O4' … HC(6) and O(2) … HC2' hydrogen bonding interactions. The high flexibility of side chain moiety displayed different structural properties for pcmnm5U(34). Three different conformations of pcmnm5U(34) were observed in molecular dynamics simulations and Markov state model studies. The unmodified uracil revealed 'syn' and 'anti' orientations for glycosyl (χ34) torsion angle that substantiate the role of "-CH2-NH2+-CH2-COO-" moiety in maintaining the 'anti' orientation of pcmnm5U(34). The preferred conformation of pcmnm5U(34) helps to recognize Guanosine more proficiently than Adenosine from the third position of codons. The role of pcmnm5U(34) in tRNA biogenesis paves the way to understand its structural significance in usual mitochondrial metabolism and respiration.
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