RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
The chemical repertoire of natural ribozymes
Although RNA is generally thought to be a passive genetic blueprint, some RNA molecules,
called ribozymes, have intrinsic enzyme-like activity—they can catalyse chemical reactions …
called ribozymes, have intrinsic enzyme-like activity—they can catalyse chemical reactions …
Correlating structural dynamics and function in single ribozyme molecules
We have studied the correlation between structural dynamics and function of the hairpin
ribozyme. The enzyme-substrate complex exists in either docked (active) or undocked …
ribozyme. The enzyme-substrate complex exists in either docked (active) or undocked …
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
Background: The catalytic activity of RNA enzymes is thought to require divalent metal ions,
which are believed to facilitate RNA folding and to play a direct chemical role in the reaction …
which are believed to facilitate RNA folding and to play a direct chemical role in the reaction …
Ribozyme speed limits
GM Emilsson, S Nakamura, A Roth, RR Breaker - Rna, 2003 - rnajournal.cshlp.org
The speed at which RNA molecules decompose is a critical determinant of many biological
processes, including those directly involved in the storage and expression of genetic …
processes, including those directly involved in the storage and expression of genetic …
Structure and function of the hairpin ribozyme
MJ Fedor - Journal of molecular biology, 2000 - Elsevier
The hairpin ribozyme belongs to the family of small catalytic RNAs that cleave RNA
substrates in a reversible reaction that generates 2′, 3′-cyclic phosphate and 5 …
substrates in a reversible reaction that generates 2′, 3′-cyclic phosphate and 5 …
Aminoglycoside–RNA interactions
The structural and physico-chemical parameters promoting the binding of aminoglycosides
to RNAs are becoming clear. The strength of the interaction is dominated by electrostatics …
to RNAs are becoming clear. The strength of the interaction is dominated by electrostatics …
Single-molecule transition-state analysis of RNA folding
How RNA molecules fold into functional structures is a problem of great significance given
the expanding list of essential cellular RNA enzymes and the increasing number of …
the expanding list of essential cellular RNA enzymes and the increasing number of …
Group II introns: structure and catalytic versatility of large natural ribozymes
K Lehmann, U Schmidt - Critical reviews in biochemistry and …, 2003 - Taylor & Francis
Group II introns are large, natural catalytic RNAs or ribozymes that were discovered in
organelles of certain protists, fungi, algae, and plants and more recently also in prokaryotic …
organelles of certain protists, fungi, algae, and plants and more recently also in prokaryotic …
Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …