Computer simulations of enzyme catalysis: finding out what has been optimized by evolution. (Q36255425)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9600897 AND SRC:MED&resulttype=core&format=json

11 November 2019

title

Computer simulations of enzyme catalysis: finding out what has been optimized by evolution (English)

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11 November 2019

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2

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11 November 2019

1

A Warshel

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11 November 2019

language of work or name

English

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publication date

1 May 1998

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Proceedings of the National Academy of Sciences of the United States of America

11 November 2019

number of pages

6

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based on heuristic

inferred from page(s)

published in

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11 November 2019

volume

95

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11 November 2019

issue

11

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11 November 2019

page(s)

5950-5955

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On the concept of orbital steering in catalytic reactions

11 November 2019

cites work

1 reference

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A source for the special catalytic power of enzymes: orbital steering

30 September 2017

1 reference

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Active Site of alpha-Chymotrypsin Activation by Association-Desolvation

30 September 2017

1 reference

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Non-enzymatic and enzymatic hydrolysis of alkyl halides: a haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction

30 September 2017

1 reference

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Nonenzymatic and enzymatic hydrolysis of alkyl halides: a theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides.

30 September 2017

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A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase

30 September 2017

1 reference

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Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Computer simulation of the triosephosphate isomerase catalyzed reaction

30 September 2017

1 reference

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Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Computer modelling of enzyme catalysed reaction mechanisms.

30 September 2017

1 reference

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Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Low-barrier hydrogen bonds and enzymic catalysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

30 September 2017

1 reference

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A low-barrier hydrogen bond in the catalytic triad of serine proteases

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Calculations of electrostatic interactions in biological systems and in solutions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

The Three-Dimensional Structure of an Enzyme Molecule

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Physical Organic Models for the Mechanism of Lysozyme Action

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Transition-state stabilization in the mechanism of tyrosyl-tRNA synthetase revealed by protein engineering

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Alternative view of enzyme reactions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Enzymes work by solvation substitution rather than by desolvation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Functional interaction among catalytic residues in subtilisin BPN'.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Electrostatic interactions in macromolecules: theory and applications

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Enzyme Dynamics: The Statistical Physics Approach

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Energetics of enzyme catalysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Binding Energy, Specificity, and Enzymic Catalysis: The Circe Effect

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Evaluation of catalytic free energies in genetically modified proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=34499

Hydrogen tunneling in enzyme reactions

29 June 2018

1 reference

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Viscosity-dependent structural fluctuations in enzyme catalysis

29 June 2018

1 reference

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Picosecond dynamics of tyrosine side chains in proteins

29 June 2018

1 reference

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Molecular Architecture and Biological Reactions

29 June 2018

1 reference

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Rates of Uncatalyzed Peptide Bond Hydrolysis in Neutral Solution and the Transition State Affinities of Proteases

21 January 2018

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Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

21 January 2018

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Entropy, Binding Energy, and Enzymic Catalysis

21 January 2018

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Mechanisms of thiamine-catalyzed reactions. Decarboxylation of 2-(1-carboxy-l-hydroxyethyl)-3,4-dimethylthiazolium chloride

21 January 2018

1 reference

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Mechanism of the chain extension step in the biosynthesis of fatty acids

21 January 2018

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A specific, highly active malate dehydrogenase by redesign of a lactate dehydrogenase framework

21 January 2018

1 reference

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Computer simulation and analysis of the reaction pathway of triosephosphate isomerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.95.11.5950

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.95.11.5950

21 January 2018

Identifiers

DOI

10.1073/PNAS.95.11.5950

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9600897 AND SRC:MED&resulttype=core&format=json

11 November 2019

0 references

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11 November 2019

PubMed publication ID

9600897

1 reference