(Q40623105)

English

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme

scientific article published on May 2010

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme (English)

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

0 references

crystal structure

1 reference

based on heuristic

inferred from title

5

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

7

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

3

0 references

author name string

Vojtech Mlýnský

1

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

Pavel Banás

2

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

Kamila Réblová

4

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

Jirí Sponer

6

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

language of work or name

0 references

publication date

1 May 2010

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

114

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

19

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

6642-6652

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

1 reference

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A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm

1 reference

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Classification and energetics of the base-phosphate interactions in RNA

1 reference

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Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.

1 reference

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Comparative enzymology and structural biology of RNA self-cleavage

1 reference

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Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

1 reference

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Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme

1 reference

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Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.

1 reference

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1 reference

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Molecular dynamics study of the ribosomal A-site.

1 reference

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22 September 2017

1 reference

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Catalytic strategies of self-cleaving ribozymes

1 reference

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Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme

1 reference

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22 September 2017

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Recent advances in the study of nucleic acid flexibility by molecular dynamics

1 reference

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Towards a molecular dynamics consensus view of B-DNA flexibility

1 reference

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22 September 2017

Ribozyme catalysis revisited: is water involved?

1 reference

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22 September 2017

Molecular dynamics simulations and their application to four-stranded DNA.

1 reference

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22 September 2017

Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

1 reference

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22 September 2017

Nucleic acid solvation: from outside to insight.

1 reference

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22 September 2017

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

1 reference

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22 September 2017

Molecular dynamics simulations of RNA: an in silico single molecule approach.

1 reference

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22 September 2017

Trapped water molecules are essential to structural dynamics and function of a ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

1 reference

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22 September 2017

Molecular dynamics simulations of sarcin-ricin rRNA motif.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer

1 reference

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22 September 2017

Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Role of an active site adenine in hairpin ribozyme catalysis

1 reference

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Empirical force fields for biological macromolecules: overview and issues.

1 reference

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Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

1 reference

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Simulation and modeling of nucleic acid structure, dynamics and interactions

1 reference

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22 September 2017

Transition state stabilization by a catalytic RNA

1 reference

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Comparative analysis of hairpin ribozyme structures and interference data

1 reference

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22 September 2017

Functional involvement of G8 in the hairpin ribozyme cleavage mechanism

1 reference

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Geometric nomenclature and classification of RNA base pairs

1 reference

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Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

1 reference

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22 September 2017

Structure and function of the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Solution structure of the loop B domain from the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone

1 reference

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22 September 2017

Autolytic processing of a phosphorothioate diester bond

1 reference

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Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA.

1 reference

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22 September 2017

Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

22 September 2017

Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation

1 reference

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Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

1 reference

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Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

1 reference

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Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis

1 reference

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Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite

1 reference

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Role of Solvent Dynamics in Stabilizing the Transition State of RNA Hydrolysis by Hairpin Ribozyme.

1 reference

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20 August 2018

NMR spectroscopic characterization of the adenine-dependent hairpin ribozyme.

1 reference

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Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

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1 reference

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1 reference

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1 reference

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Functional analysis of hairpin ribozyme active site architecture

1 reference

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Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

1 reference

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20 August 2018

Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations

1 reference

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20 August 2018

Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue

1 reference

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20 August 2018

Catalytic roles for proton transfer and protonation in ribozymes

1 reference

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Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function

1 reference

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Dependence of A-RNA simulations on the choice of the force field and salt strength

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872159

2 December 2018

A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/20420375

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The hairpin ribozyme: structure, assembly and catalysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/20420375

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JP1001258

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

22 September 2017

ResearchGate publication ID

0 references

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