(Q47101458)

8 January 2018

title

QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes (English)

1 reference

8 January 2018

author name string

D Roston

series ordinal

1

1 reference

8 January 2018

Q Cui

series ordinal

2

1 reference

8 January 2018

language of work or name

English

0 references

publication date

1 July 2016

1 reference

8 January 2018

published in

Methods in Enzymology

1 reference

8 January 2018

volume

577

1 reference

8 January 2018

page(s)

213-250

1 reference

8 January 2018

QM/MM free energy simulations: recent progress and challenges

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Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

23 May 2018

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Activation pathway of Src kinase reveals intermediate states as targets for drug design

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Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase

23 May 2018

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Precision is essential for efficient catalysis in an evolved Kemp eliminase

23 May 2018

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Ground state destabilization by anionic nucleophiles contributes to the activity of phosphoryl transfer enzymes

23 May 2018

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Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily

23 May 2018

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23 May 2018

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Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints

23 May 2018

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23 May 2018

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23 May 2018

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23 May 2018

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23 May 2018

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Transition states of native and drug-resistant HIV-1 protease are the same

23 May 2018

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23 May 2018

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23 May 2018

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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

23 May 2018

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High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography

23 May 2018

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Isotope-edited FTIR of alkaline phosphatase resolves paradoxical ligand binding properties and suggests a role for ground-state destabilization

23 May 2018

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23 May 2018

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Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks

23 May 2018

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Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

23 May 2018

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23 May 2018

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Atomic-Level Characterization of the Structural Dynamics of Proteins

23 May 2018

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Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

23 May 2018

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Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

23 May 2018

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23 May 2018

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23 May 2018

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23 May 2018

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At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

23 May 2018

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23 May 2018

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23 May 2018

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Enzymatic transition states and dynamic motion in barrier crossing

23 May 2018

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23 May 2018

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23 May 2018

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23 May 2018

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23 May 2018

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Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies

23 May 2018

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Transition-path theory and path-finding algorithms for the study of rare events

23 May 2018

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

23 May 2018

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23 May 2018

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Calculation of protein-ligand binding free energy by using a polarizable potential

23 May 2018

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

23 May 2018

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Kemp elimination catalysts by computational enzyme design

23 May 2018

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A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

23 May 2018

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Color Tuning in Rhodopsins: The Mechanism for the Spectral Shift between Bacteriorhodopsin and Sensory Rhodopsin II

23 May 2018

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Enzymatic mechanisms of phosphate and sulfate transfer.

23 May 2018

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Mechanisms and free energies of enzymatic reactions

23 May 2018

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Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions

23 May 2018

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An NMR perspective on enzyme dynamics

23 May 2018

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

23 May 2018

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

23 May 2018

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

23 May 2018

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Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

23 May 2018

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

23 May 2018

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A perspective on enzyme catalysis.

23 May 2018

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Challenges in enzyme mechanism and energetics

23 May 2018

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Free energy simulations come of age: protein-ligand recognition

23 May 2018

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Principles of docking: An overview of search algorithms and a guide to scoring functions

23 May 2018

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Quantum mechanical methods for enzyme kinetics

23 May 2018

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Transition path sampling: throwing ropes over rough mountain passes, in the dark.

23 May 2018

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

23 May 2018

1 reference

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Trapping the transition state of an ATP-binding cassette transporter: evidence for a concerted mechanism of maltose transport

23 May 2018

1 reference

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

23 May 2018

1 reference

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A model of the transition state in the alkaline phosphatase reaction

23 May 2018

1 reference

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Analysis of zinc binding sites in protein crystal structures

23 May 2018

1 reference

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

23 May 2018

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Crystal structure of bovine low molecular weight phosphotyrosyl phosphatase complexed with the transition state analog vanadate

23 May 2018

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Crystal structures of rat acid phosphatase complexed with the transition-state analogs vanadate and molybdate. Implications for the reaction mechanism

23 May 2018

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

23 May 2018

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Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site

23 May 2018

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Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase

15 August 2018

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Entangled quantum electronic wavefunctions of the Mn₄CaO₅ cluster in photosystem II.

15 August 2018

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A cartography of the van der Waals territories.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Implementation of the solvent macromolecule boundary potential and application to model and realistic enzyme systems.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Ab initio quantum chemistry for protein structures

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Microscopic pKa analysis of Glu286 in cytochrome c oxidase (Rhodobacter sphaeroides): toward a calibrated molecular model

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

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.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

High-accuracy computation of reaction barriers in enzymes.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Calculating absorption shifts for retinal proteins: computational challenges.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Quantum mechanical continuum solvation models.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Binding Energy and Catalysis: The Implications for Transition-State Analogs and Catalytic Antibodies.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Long-Range Electrostatic Effects in QM/MM Studies of Enzymatic Reactions: Application of the Solvated Macromolecule Boundary Potential

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface

1 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Infrared spectral marker bands characterizing a transient water wire inside a hydrophobic membrane protein

1 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

1 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705176

Catalysis of the hydrolysis of phosphorylated pyridines by alkaline phosphatase has little or no dependence on the pKa of the leaving group

1 December 2018

1 reference

12 December 2020

Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations

1 reference

12 December 2020

Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme

1 reference

12 December 2020

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

1 reference

12 December 2020

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

1 reference

12 December 2020

1 reference

12 December 2020

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

1 reference

12 December 2020

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

12 December 2020

10.1016/BS.MIE.2016.05.016

Identifiers

DOI

1 reference

8 January 2018

PMC publication ID

5705176

1 reference

8 January 2018

PubMed publication ID

27498640

1 reference

8 January 2018