(Q41832665)

12 October 2017

Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding (English)

1 reference

12 October 2017

1 reference

Sharon Hammes-Schiffer

series ordinal

2

object named as

Sharon Hammes-Schiffer

1 reference

12 October 2017

Joshua P Layfield

1

1 reference

PMC publication ID

3547160

12 October 2017

language of work or name

English

0 references

publication date

31 December 2012

1 reference

Journal of the American Chemical Society

12 October 2017

1 reference

12 October 2017

135

1 reference

12 October 2017

2

1 reference

12 October 2017

717-725

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

12 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Evaluation of the energetics of the concerted acid-base mechanism in enzymatic catalysis: the case of ketosteroid isomerase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Phosphate vibrations probe local electric fields and hydration in biomolecules

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Water in the active site of ketosteroid isomerase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Solvation response along the reaction coordinate in the active site of ketosteroid isomerase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Proton affinity of the oxyanion hole in the active site of ketosteroid isomerase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Hydrogen Bond Coupling in the Ketosteroid Isomerase Active Site

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Optimized quantum mechanics/molecular mechanics strategies for nitrile vibrational probes: acetonitrile and para-tolunitrile in water and tetrahydrofuran.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Nitrile groups as vibrational probes: calculations of the CN infrared absorption line shape of acetonitrile in water and tetrahydrofuran.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site?

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Site-specific conversion of cysteine thiols into thiocyanate creates an IR probe for electric fields in proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Comparison of multiple Amber force fields and development of improved protein backbone parameters

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Enzymatic mechanisms for catalysis of enolization: ketosteroid isomerase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

A perspective on enzyme catalysis.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Pseudoreversion of the catalytic activity of Y14F by the additional substitution(s) of tyrosine with phenylalanine in the hydrogen bond network of delta 5-3-ketosteroid isomerase from Pseudomonas putida biotype B

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from Pseudomonas putida biotype B

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Canonical dynamics: Equilibrium phase-space distributions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Solution structure of Delta 5-3-ketosteroid isomerase complexed with the steroid 19-nortestosterone hemisuccinate

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Hydrogen bonding at the active site of delta 5-3-ketosteroid isomerase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Energetics of 3-oxo-delta 5-steroid isomerase: source of the catalytic power of the enzyme

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Carbon-deuterium vibrational probes of amino acid protonation state.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Nitrile and thiocyanate IR probes: molecular dynamics simulation studies.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Nitrile and thiocyanate IR probes: quantum chemistry calculation studies and multivariate least-square fitting analysis.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Computational study of ketosteroid isomerase: insights from molecular dynamics simulation of enzyme bound substrate and intermediate.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Molecular dynamics and quantum chemical studies on the catalytic mechanism of Delta5-3-ketosteroid isomerase: the catalytic diad versus the cooperative hydrogen bond mechanism.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

The CN Stretching Band of Aliphatic Thiocyanate is Sensitive to Solvent Dynamics and Specific Solvation

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547160

Approaches for the calculation of vibrational frequencies in liquids: comparison to benchmarks for azide/water clusters

2 December 2018

1 reference

12 December 2020

Vibrational Spectral Diffusion of Azide in Water†

1 reference

12 December 2020

Vibrational energy relaxation of azide in water

1 reference

12 December 2020

Infrared absorption line shapes in the classical limit: a comparison of the classical dipole and fluctuating frequency approximations

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA3084384

1 reference

12 October 2017

1 reference

PMC publication ID

3547160

12 October 2017

PubMed publication ID

23210919

1 reference

PMC publication ID

3547160