Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis
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Identification of an Imino Group Indispensable for Cleavage by a Small RibozymeA dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations.Molecular modeling of nucleic acid structure: energy and samplingExploring ribozyme conformational changes with X-ray crystallography.Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path.Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations.Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.Multiscale methods for computational RNA enzymology.Molecular simulations of RNA 2'-O-transesterification reaction models in solution.A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.pH-dependent dynamics of complex RNA macromoleculesTowards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobasesIntermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysisMolecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization.Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol.Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.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.Computational approaches to predicting the impact of novel bases on RNA structure and stability.Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods.The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.Molecular modeling of nucleic acid structure: energy and sampling.Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.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.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 inRelative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.Pressure modulates the self-cleavage step of the hairpin ribozyme.Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.Multiple proton relay routes in the reaction mechanism of RNAP II: assessing the effect of structural model.
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Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis
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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 18 March 2008
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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
Quantum mechanical/molecular m ...... of hairpin ribozyme catalysis
@en
Quantum mechanical/molecular m ...... of hairpin ribozyme catalysis.
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type
label
Quantum mechanical/molecular m ...... of hairpin ribozyme catalysis
@en
Quantum mechanical/molecular m ...... of hairpin ribozyme catalysis.
@nl
prefLabel
Quantum mechanical/molecular m ...... of hairpin ribozyme catalysis
@en
Quantum mechanical/molecular m ...... of hairpin ribozyme catalysis.
@nl
P2860
P356
P1476
Quantum mechanical/molecular m ...... of hairpin ribozyme catalysis
@en
P2093
Kwangho Nam
P2860
P304
P356
10.1021/JA0759141
P407
P577
2008-03-18T00:00:00Z