Structural significance of hypermodified nucleoside 5-carboxymethylaminomethyluridine (cmnmU) from 'wobble' (34th) position of mitochondrial tRNAs: Molecular modeling and Markov state model studies.

A quantum chemical semi-empirical RM1 approach was used to deduce the structural role of hypermodified nucleoside 5-carboxymethylaminomethyluridine 5'-monophosphate (pcmnmU) from 'wobble' (34th) position of mitochondrial tRNAs. The energetically preferred pcmnmU adopted a 'skew' conformation for C5-substituted side chain (-CH-NH-CH-COO) moiety that orient towards the 5'-ribose-phosphate backbone, which support 'anti' orientation of glycosyl (χ) torsion angle. Preferred conformation of pcmnmU 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.