(Q43201948)

English

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

scientific article published on 8 August 2008

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility (English)

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

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hepatitis delta virus

object named as

hepatitis delta virus

1 reference

based on heuristic

inferred from title

5

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Europe PubMed Central

PMC publication ID

16 November 2017

7

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

author name string

Pavel Banás

1

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

Lubomír Rulísek

2

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

Veronika Hánosová

3

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

Daniel Svozil

4

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

Jirí Sponer

6

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

language of work or name

0 references

publication date

8 August 2008

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Europe PubMed Central

PMC publication ID

16 November 2017

Journal of Physical Chemistry B

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Europe PubMed Central

PMC publication ID

16 November 2017

112

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

35

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

11177-11187

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2566740

25 May 2018

Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage

1 reference

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25 May 2018

The ribosomal peptidyl transferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2566740

25 May 2018

Structural roles of monovalent cations in the HDV ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2566740

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A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene

1 reference

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25 May 2018

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

1 reference

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25 May 2018

Nucleobase catalysis in ribozyme mechanism

1 reference

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25 May 2018

1 reference

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25 May 2018

Electrostatic basis for enzyme catalysis

1 reference

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25 May 2018

Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme

1 reference

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25 May 2018

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

1 reference

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The catalytic diversity of RNAs

1 reference

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25 May 2018

Ribozyme catalysis: not different, just worse

1 reference

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The contribution of metal ions to the structural stability of the large ribosomal subunit

1 reference

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The role and perspective of ab initio molecular dynamics in the study of biological systems

1 reference

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Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis

1 reference

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Functional involvement of G8 in the hairpin ribozyme cleavage mechanism

1 reference

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Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding

1 reference

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The structural basis of ribosome activity in peptide bond synthesis

1 reference

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25 May 2018

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

1 reference

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Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

1 reference

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Density-functional exchange-energy approximation with correct asymptotic behavior

1 reference

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Crystal structure of a hepatitis delta virus ribozyme

1 reference

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25 May 2018

Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme

1 reference

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A tetrameric DNA structure with protonated cytosine.cytosine base pairs

1 reference

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Crystal structure of intercalated four-stranded d(C3T) at 1.4 A resolution

1 reference

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Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

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Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods.

1 reference

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Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme

1 reference

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Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons

1 reference

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Theoretical examination of two opposite mechanisms proposed for hepatitis delta virus ribozyme

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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Density functional theory investigation on the mechanism of the hepatitis delta virus ribozyme

1 reference

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Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study.

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Two-metal-ion mechanism for hammerhead-ribozyme catalysis

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General acid catalysis by the hepatitis delta virus ribozyme

1 reference

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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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1 reference

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Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme

1 reference

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A conformational switch controls hepatitis delta virus ribozyme catalysis

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Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence

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Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: An ab initio study on the free enzyme

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Identifiers

10.1021/JP802592Z

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

16 November 2017

ResearchGate publication ID

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