Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.
Cleveland, United States. In Biochim Biophys Acta, Nov 2015
The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state.
[Ribonucleases as antiviral agents].
In Mol Biol (mosk), 2014
The review observes the most known RNases which possess established antiviral effects, actually intracellular RNases (RNase L, MCPIPI protein, eosinophylic RNases) as well as exogenously applied ones (RNase A, BS-RNase, onconase, binase, synthetic RNases).
fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems.
Madrid, Spain. In J Chem Theory Comput, 2014
We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.
It takes two to flirt with a dimeric RNase.
Napoli, Italy. In Biopolymers, 2009
Studies illustrate of the making dimeric pancreatic RNase through removal by directed mutagenesis of most of the N-terminal alpha-helix to the remainder of the protein.
Catalytic strategies of self-cleaving ribozymes.
New Haven, United States. In Acc Chem Res, 2008
All of these RNA enzymes catalyze self-scission of the RNA backbone using a chemical mechanism equivalent to that of RNase A. RNase A uses four basic strategies to promote this reaction: geometric constraints, activation of the nucleophile, transition-state stabilization, and leaving group protonation.
Oxidative folding of proteins.
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Ithaca, United States. In Acc Chem Res, 2000
The oxidative folding of proteins is reviewed and illustrated with bovine pancreatic ribonuclease A (RNase A).