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• W1992015440 endingPage "11082" @default.
• W1992015440 startingPage "11077" @default.
• W1992015440 abstract "We have performed molecular dynamics (MD) calculations by using one of the recently solved crystal structures of a hammerhead ribozyme. By rotating the α, β, γ, δ, ɛ, and ζ torsion angles of the phosphate linkage of residue 17, the nucleobase at the cleavage site was slightly rotated out of the active site toward the solution. Unconstrained MD simulations exceeding 1 ns were performed on this starting structure solvated in water with explicit counter ions and two Mg 2+ ions at the active site. Our results reveal that near attack conformations consistently were formed in the simulation. These near attack conformations are characterized by assumption of the 2′-hydroxyl to a near in-line position for attack on the -O-(PO 2 − )-O- phosphorous. Also during the time course of the MD study, one Mg 2+ moved immediately to associate with a pro -R phosphate oxygen in the conserved core region, and the second Mg 2+ remained associated with the pro -R oxygen on the phosphate linkage undergoing hydrolysis. These results are in accord with a one-metal ion mechanism of catalysis and give insight into the possible roles of many of the conserved residues in the ribozyme." @default.
• W1992015440 created "2016-06-24" @default.
• W1992015440 creator A5040471810 @default.
• W1992015440 creator A5067857067 @default.
• W1992015440 date "1998-09-15" @default.
• W1992015440 modified "2023-09-27" @default.
• W1992015440 title "Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction" @default.
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• W1992015440 doi "https://doi.org/10.1073/pnas.95.19.11077" @default.
• W1992015440 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/21598" @default.
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