Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations. (Q37265822)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19301836%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

title

Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations (English)

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24 January 2020

1

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24 January 2020

author name string

Hao Hu

series ordinal

2

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24 January 2020

Johannes Rudolph

series ordinal

3

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24 January 2020

Weitao Yang

series ordinal

4

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24 January 2020

language of work or name

English

0 references

publication date

1 April 2009

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Journal of Physical Chemistry B

24 January 2020

published in

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24 January 2020

volume

113

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24 January 2020

issue

15

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24 January 2020

page(s)

5217-5224

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

24 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

CDC25 phosphatases in cancer cells: key players? Good targets?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Cdc25 phosphatases: structure, specificity, and mechanism

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Reaction mechanism of guanidinoacetate methyltransferase, concerted or step-wise

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Free-energy profiles for catalysis by dual-specificity phosphatases.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Dual-specificity phosphatases as targets for antineoplastic agents

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Density functional study of the mechanism of a tyrosine phosphatase: I. Intermediate formation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Molecular reactions of protein phosphatases--insights from structure and chemistry

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Crystal structure of the catalytic subunit of Cdc25B required for G2/M phase transition of the cell cycle

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Roles of active site residues and the NH2-terminal domain in the catalysis and substrate binding of human Cdc25

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

A catalytic mechanism for the dual-specific phosphatases

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Temperature dependence of binding and catalysis for the Cdc25B phosphatase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Mechanistic studies of protein tyrosine phosphatases YopH and Cdc25A with m-nitrobenzyl phosphate.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Nature of the rate-determining steps of the reaction catalyzed by the Yersinia protein-tyrosine phosphatase.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

High-accuracy computation of reaction barriers in enzymes.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Specific parametrisation of a hybrid potential to simulate reactions in phosphatases.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Quadratic string method for determining the minimum-energy path based on multiobjective optimization

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Reactivity of Cdc25 phosphatase at low pH and with thiophosphorylated protein substrate

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

On the role of the conserved aspartate in the hydrolysis of the phosphocysteine intermediate of the low molecular weight tyrosine phosphatase

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Catalytic mechanism of Cdc25.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

The catalytic mechanism of Cdc25A phosphatase

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712249

Dual-specific Cdc25B phosphatase: in search of the catalytic acid

3 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19301836

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19301836

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dual-topology/dual-coordinate free-energy simulation using QM/MM force field

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19301836

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JP805137X

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19301836%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19301836%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

1 reference