(Q36857675)

English

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

scientific article published on 22 March 2007

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

16 August 2017

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9. (English)

1 reference

Europe PubMed Central

16 August 2017

author name string

Shenglong Wang

1

1 reference

Europe PubMed Central

16 August 2017

Po Hu

2

1 reference

Europe PubMed Central

16 August 2017

Yingkai Zhang

3

1 reference

Europe PubMed Central

16 August 2017

language of work or name

0 references

publication date

22 March 2007

1 reference

Europe PubMed Central

16 August 2017

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

16 August 2017

111

1 reference

Europe PubMed Central

16 August 2017

14

1 reference

Europe PubMed Central

16 August 2017

3758-3764

1 reference

Europe PubMed Central

16 August 2017

QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Electrostatic basis for enzyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Mechanisms and free energies of enzymatic reactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

The diverse functions of histone lysine methylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

The SET-domain protein superfamily: protein lysine methyltransferases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

SET8 recognizes the sequence RHRK20VLRDN within the N terminus of histone H4 and mono-methylates lysine 20.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Specificity and mechanism of the histone methyltransferase Pr-Set7.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Epigenetics--an epicenter of gene regulation: histones and histone-modifying enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Structural and sequence motifs of protein (histone) methylation enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Regulation of p53 activity through lysine methylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Gene-specific modulation of TAF10 function by SET9-mediated methylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

How enzymes work: analysis by modern rate theory and computer simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

SET domains and histone methylation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Histone lysine methylation: a signature for chromatin function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Structural basis for the product specificity of histone lysine methyltransferases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Computer simulations of enzyme catalysis: methods, progress, and insights

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Structure and catalytic mechanism of the human histone methyltransferase SET7/9

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Structure of the SET domain histone lysine methyltransferase Clr4

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Crystal structure and functional analysis of the histone methyltransferase SET7/9

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Structure and catalytic mechanism of a SET domain protein methyltransferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Unsafe SETs: histone lysine methyltransferases and cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

Functional and structural changes due to a serine to alanine mutation in the active-site flap of enolase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

The language of covalent histone modifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

29 September 2017

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

27 June 2018

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Electrostatic interactions dominate the catalytic contribution of arg39 in 4-oxalocrotonate tautomerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

QM/MM determination of kinetic isotope effects for COMT-catalyzed methyl transfer does not support compression hypothesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Theoretical Perspectives on the Reaction Mechanism of Serine Proteases: The Reaction Free Energy Profiles of the Acylation Process

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

S-adenosylmethionine conformations in solution and in protein complexes: conformational influences of the sulfonium group.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 September 2018

Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 December 2018

Structural Insights of the Specificity and Catalysis of a Viral Histone H3 Lysine 27 Methyltransferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2527688

4 December 2018

New Monte Carlo technique for studying phase transitions

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Quantum mechanical free energy barrier for an enzymatic reaction

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si)

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Simulations of Gas-Phase Chemical Reactions: Applications to SN2 Nucleophilic Substitution

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase

1 reference

https://pubmed.ncbi.nlm.nih.gov/17388541

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JP067147I

1 reference

Europe PubMed Central

16 August 2017

1 reference

Europe PubMed Central

16 August 2017

1 reference

Europe PubMed Central

16 August 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q36857675&oldid=2087684768"