(Q35083854)

6 August 2017

title

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

1 reference

6 August 2017

Kin-Yiu Wong

1

1 reference

6 August 2017

Jiali Gao

series ordinal

2

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6 August 2017

language of work or name

English

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publication date

14 June 2011

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6 August 2017

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6 August 2017

volume

278

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6 August 2017

issue

14

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6 August 2017

page(s)

2579-2595

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

6 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Understanding the effect of magnesium ion concentration on the catalytic activity of ribonuclease H through computation: does a third metal binding site modulate endonuclease catalysis?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

CHARMM: the biomolecular simulation program

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Biochemistry and physiology of cyclic nucleotide phosphodiesterases: essential components in cyclic nucleotide signaling

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Crystal structures of phosphodiesterases and implications on substrate specificity and inhibitor selectivity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Characterization of a catalytic ligand bridging metal ions in phosphodiesterases 4 and 5 by molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

The catalytic mechanisms of binuclear metallohydrolases.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Mechanisms and free energies of enzymatic reactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Phosphodiesterase-4 as a potential drug target

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Multiple elements jointly determine inhibitor selectivity of cyclic nucleotide phosphodiesterases 4 and 7.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Persistent improvement in synaptic and cognitive functions in an Alzheimer mouse model after rolipram treatment

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

A glutamine switch mechanism for nucleotide selectivity by phosphodiesterases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis,

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Gene Cloning, purification, and characterization of a phosphodiesterase from Delftia acidovorans

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Quantum mechanical methods for enzyme kinetics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Binuclear Metallohydrolases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Identification of overlapping but distinct cAMP and cGMP interaction sites with cyclic nucleotide phosphodiesterase 3A by site-directed mutagenesis and molecular modeling based on crystalline PDE4B

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Atomic structure of PDE4: insights into phosphodiesterase mechanism and specificity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Rolipram, a type IV-specific phosphodiesterase inhibitor, facilitates the establishment of long-lasting long-term potentiation and improves memory

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Sildenafil: an orally active type 5 cyclic GMP-specific phosphodiesterase inhibitor for the treatment of penile erectile dysfunction.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

VMD: visual molecular dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Determination of the structure of the N-terminal splice region of the cyclic AMP-specific phosphodiesterase RD1 (RNPDE4A1) by 1H NMR and identification of the membrane association domain using chimeric constructs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Design, synthesis, and characterization of a potent xylose isomerase inhibitor, D-threonohydroxamic acid, and high-resolution X-ray crystallographic structure of the enzyme-inhibitor complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Effect of selective phosphodiesterase type IV inhibitor, rolipram, on fluid and cellular phases of inflammatory response

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Purification, characterization and analysis of rolipram inhibition of a human type-IVA cyclic AMP-specific phosphodiesterase expressed in yeast

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

MOPAC: a semiempirical molecular orbital program

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Characterization of the zinc binding site of bacterial phosphotriesterase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3128672

Cyclic nucleotide research -- still expanding after half a century

8 July 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Sildenafil (VIAGRATM), a potent and selective inhibitor of type 5 cGMP phosphodiesterase with utility for the treatment of male erectile dysfunction

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Photolabeling of Prostaglandin Endoperoxide H Synthase-1 with 3-Trifluoro-3-(m-Iiodophenyl)diazirine as a Probe of Membrane Association and the Cyclooxygenase Active Site

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Crystal structures of the catalytic domain of phosphodiesterase 4B complexed with AMP, 8-Br-AMP, and rolipram.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Evidence for direct attack by hydroxide in phosphodiester hydrolysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

First computational evidence for a catalytic bridging hydroxide ion in a phosphodiesterase active site.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

A facile and improved synthesis of sildenafil (Viagra) analogs through solid support microwave irradiation possessing tyrosinase inhibitory potential, their conformational analysis and molecular dynamics simulation studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Quantum dynamics of hydride transfer catalyzed by bimetallic electrophilic catalysis: synchronous motion of Mg(2+) and H(-) in xylose isomerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Density-functional thermochemistry. III. The role of exact exchange

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Ground states of molecules. 38. The MNDO method. Approximations and parameters

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Optimization of parameters for semiempirical methods I. Method

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Molecular Electronic-Structure Theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Molecular dynamics simulations at constant pressure and/or temperature

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

A semiempirical model for the two-center repulsion integrals in the NDDO approximation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Extension of the MNDO formalism tod orbitals: Integral approximations and preliminary numerical results

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Extension ofMNDO tod orbitals: Parameters and results for the halogens

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2011.08187.X

On the equilibrium of the adenylate cyclase reaction

21 January 2018

1 reference

12 December 2020

The mechanism of cyclic nucleotide hydrolysis in the phosphodiesterase catalytic site

1 reference

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Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands

1 reference

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The role of cAMP regulation in controlling inflammation

1 reference

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A substrate selectivity and inhibitor design lesson from the PDE10-cAMP crystal structure: a computational study

1 reference

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PM3-compatible zinc parameters optimized for metalloenzyme active sites

1 reference

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AM1/d Parameters for Magnesium in Metalloenzymes

1 reference

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Lennard-Jones triple-point conductivity via weak external fields: Additional calculations

1 reference

12 December 2020

10.1111/J.1742-4658.2011.08187.X

Identifiers

DOI

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6 August 2017

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6 August 2017

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