Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.
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Identification of an Imino Group Indispensable for Cleavage by a Small RibozymeExploring ribozyme conformational changes with X-ray crystallography.Metal ions: supporting actors in the playbook of small ribozymes.Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozymeThe pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenineClassification and energetics of the base-phosphate interactions in RNAConstant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme.pH-dependent dynamics of complex RNA macromoleculesTowards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity.Scope and mechanism of interstrand cross-link formation by the C4'-oxidized abasic site.Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Principles of ion recognition in RNA: insights from the group II intron structures.The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe inDirect Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
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P2860
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.
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article científic
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article scientifique
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articolo scientifico
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artigo científico
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bilimsel makale
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scientific article published on 17 February 2009
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vedecký článok
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vetenskaplig artikel
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videnskabelig artikel
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vědecký článek
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name
Molecular dynamics suggest mul ...... lysis of the hairpin ribozyme.
@en
Molecular dynamics suggest mul ...... lysis of the hairpin ribozyme.
@nl
type
label
Molecular dynamics suggest mul ...... lysis of the hairpin ribozyme.
@en
Molecular dynamics suggest mul ...... lysis of the hairpin ribozyme.
@nl
prefLabel
Molecular dynamics suggest mul ...... lysis of the hairpin ribozyme.
@en
Molecular dynamics suggest mul ...... lysis of the hairpin ribozyme.
@nl
P2093
P2860
P50
P356
P1433
P1476
Molecular dynamics suggest mul ...... alysis of the hairpin ribozyme
@en
P2093
Jirí Sponer
Mark A Ditzler
Nils G Walter
P2860
P304
P356
10.1261/RNA.1416709
P407
P577
2009-02-17T00:00:00Z