Cyclic oxyphosphoranes as model intermediates during splicing and cleavage or RNA:Ab initiomolecular orbital calculations on the conformational analysis
- 25 May 1989
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 17 (10), 3699-3708
- https://doi.org/10.1093/nar/17.10.3699
Abstract
Ab initio molecular orbital calculations have been carried out on hydrated adducts of methyl ethylene phosphate as a model intermediate during cleavage of RNA. Upon rotating the apical methoxyl group two kinds of stable conformers and two kinds of rotational transition states are located, the most stable conformation being gs -G where the dihedral angle between the apical methyl group and the basal ring oxygen is calculated to be 76°. In this gs -G conformation one of the lone pairs on the apical oxygen is oriented antiperiplanar to the basal ring ester bond. The torsional energy required to rotate the methyl group about the phosphorus-apical oxygen bond leading to ts -C conformation, where the methyl group is eclipsed with the ring oxygen, is calculated to be 5.2 kcal/mol. Judging from the published substrate's coordinates in the RNase environment, the expected pentacoordinate-intermediate/transition state during the cleavage of RNA appears to be, in fact, the most stable gs -G conformation.Keywords
This publication has 12 references indexed in Scilit:
- Simple RNA enzymes with new and highly specific endoribonuclease activitiesNature, 1988
- Construction of a series of several self‐cleaving RNA duplexes using synthetic 21‐mersFEBS Letters, 1988
- Two histidine residues are essential for ribonuclease T1 activity as is the case for ribonuclease ABiochemistry, 1987
- A small catalytic oligoribonucleotideNature, 1987
- BIOLOGICAL CATALYSIS BY RNAAnnual Review of Biochemistry, 1986
- Ribonuclease P Catalysis Differs from Ribosomal RNA Self-SplicingScience, 1985
- A Catalytic RNA and Its Gene from Salmonella typhimuriumScience, 1985
- In vitro splicing of the ribosomal RNA precursor of tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequenceCell, 1981
- Pentacoordinated molecules. 28. Computer simulation of ribonuclease action on uridylyl-(3'-5')-adenosineJournal of the American Chemical Society, 1978
- Geometry of the First Step in the Action of Ribonuclease-AProceedings of the National Academy of Sciences, 1972