(Q34234062)

English

QM/MM analysis suggests that Alkaline Phosphatase (AP) and nucleotide pyrophosphatase/phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP supe

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scholarly article

1 reference

Europe PubMed Central

31 July 2017

QM/MM analysis suggests that Alkaline Phosphatase (AP) and nucleotide pyrophosphatase/phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP supe (English)

1 reference

Europe PubMed Central

31 July 2017

author name string

Guanhua Hou

1

1 reference

Europe PubMed Central

31 July 2017

Qiang Cui

2

1 reference

Europe PubMed Central

31 July 2017

language of work or name

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publication date

8 December 2011

1 reference

Europe PubMed Central

31 July 2017

Journal of the American Chemical Society

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Europe PubMed Central

31 July 2017

134

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Europe PubMed Central

31 July 2017

229-246

1 reference

Europe PubMed Central

31 July 2017

1

1 reference

Europe PubMed Central

31 July 2017

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

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Theoretical Modeling on the Reaction Mechanism of p-Nitrophenylmethylphosphate Alkaline Hydrolysis and its Kinetic Isotope Effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

An implicit solvent model for SCC-DFTB with Charge-Dependent Radii

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Theoretical study of phosphodiester hydrolysis in nucleotide pyrophosphatase/phosphodiesterase. Environmental effects on the reaction mechanism.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Enzyme promiscuity: a mechanistic and evolutionary perspective

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

CHARMM: the biomolecular simulation program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

QM/MM methods for biomolecular systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active-Site Metal Ion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Mechanistic study of protein phosphatase-1 (PP1), a catalytically promiscuous enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

A new member of the alkaline phosphatase superfamily with a formylglycine nucleophile: structural and kinetic characterisation of a phosphonate monoester hydrolase/phosphodiesterase from Rhizobium leguminosarum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Arginine Coordination in Enzymatic Phosphoryl Transfer: Evaluation of the Effect of Arg166 Mutations in Escherichia coli Alkaline Phosphatase † ‡

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

De novo computational design of retro-aldol enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Structure-based activity prediction for an enzyme of unknown function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Minimalist active-site redesign: teaching old enzymes new tricks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Looking at self-consistent-charge density functional tight binding from a semiempirical perspective.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Enzyme promiscuity: evolutionary and mechanistic aspects.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Advances in methods and algorithms in a modern quantum chemistry program package.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

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=3257412

6 July 2018

Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

The 'evolvability' of promiscuous protein functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

The rate of hydrolysis of phosphomonoester dianions and the exceptional catalytic proficiencies of protein and inositol phosphatases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Enzymes with extra talents: moonlighting functions and catalytic promiscuity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Comparison of the binuclear metalloenzymes diphosphoglycerate-independent phosphoglycerate mutase and alkaline phosphatase: their mechanism of catalysis via a phosphoserine intermediate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

A revised mechanism for the alkaline phosphatase reaction involving three metal ions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Two-metal-Ion catalysis in adenylyl cyclase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Catalytic promiscuity and the evolution of new enzymatic activities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

A model of the transition state in the alkaline phosphatase reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Density-functional exchange-energy approximation with correct asymptotic behavior

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

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A general two-metal-ion mechanism for catalytic RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Structure and mechanism of alkaline phosphatase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Enzyme recruitment in evolution of new function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

6 July 2018

Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

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Dinuclear Zn(II) complex catalyzed phosphodiester cleavage proceeds via a concerted mechanism: a density functional theory study.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

The far reaches of enzymology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

Predicting substrates by docking high-energy intermediates to enzyme structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

Optimized atomic radii for protein continuum electrostatics solvation forces.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

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pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

Evidence for direct attack by hydroxide in phosphodiester hydrolysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

Alkaline phosphatase revisited: hydrolysis of alkyl phosphates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

The nature of the transition state for enzyme-catalyzed phosphoryl transfer. Hydrolysis of O-aryl phosphorothioates by alkaline phosphatase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257412

28 October 2018

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

1 reference

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28 October 2018

SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute−Water Clusters

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9 December 2018

A Critical Evaluation of Different QM/MM Frontier Treatments with SCC-DFTB as the QM Method

1 reference

https://pubmed.ncbi.nlm.nih.gov/22097879

12 December 2020

based on heuristic

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1 reference

https://pubmed.ncbi.nlm.nih.gov/22097879

12 December 2020

based on heuristic

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Automatized parametrization of SCC-DFTB repulsive potentials: application to hydrocarbons

1 reference

https://pubmed.ncbi.nlm.nih.gov/22097879

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mutation of Arg-166 of Alkaline Phosphatase Alters the Thio Effect but Not the Transition State for Phosphoryl Transfer. Implications for the Interpretation of Thio Effects in Reactions of Phosphatases†

1 reference

https://pubmed.ncbi.nlm.nih.gov/22097879

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Theoretical modeling of the reaction mechanism of phosphate monoester hydrolysis in alkaline phosphatase

1 reference

https://pubmed.ncbi.nlm.nih.gov/22097879

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules

1 reference

https://pubmed.ncbi.nlm.nih.gov/22097879

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mapping catalytic promiscuity in the alkaline phosphatase superfamily

1 reference

20 August 2023

https://opencitations.net/index/coci/api/v1/citations/10.1351/PAC-CON-08-10-20

Identifiers

10.1021/JA205226D

1 reference

Europe PubMed Central

31 July 2017

1 reference

Europe PubMed Central

31 July 2017

1 reference

Europe PubMed Central

31 July 2017

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