Keep on moving: discovering and perturbing the conformational dynamics of enzymes (Q28080602)

main subject

physiological phenomenon

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20 August 2019

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28 September 2019

1

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James S Fraser

series ordinal

3

object named as

James S. Fraser

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Justin T. Biel

2

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Accounts of Chemical Research

Crossref

language of work or name

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17 February 2015

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20 August 2019

28 September 2019

3 references

20 August 2019

28 September 2019

48

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issue

2

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page(s)

423-30

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Catalytic efficiency of designed catalytic proteins

cites work

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Precision is essential for efficient catalysis in an evolved Kemp eliminase

20 March 2017

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Divergent evolution of protein conformational dynamics in dihydrofolate reductase

20 March 2017

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20 March 2017

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Evolution of a designed retro-aldolase leads to complete active site remodeling

20 March 2017

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Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans

20 March 2017

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20 March 2017

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Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes

20 March 2017

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Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

20 March 2017

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Functional modulation of a protein folding landscape via side-chain distortion

20 March 2017

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Iterative approach to computational enzyme design

20 March 2017

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A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis

20 March 2017

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Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

20 March 2017

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Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series

20 March 2017

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Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

20 March 2017

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Kemp elimination catalysts by computational enzyme design

20 March 2017

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De novo computational design of retro-aldol enzymes

20 March 2017

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Network of coupled promoting motions in enzyme catalysis

20 March 2017

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Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence

20 March 2017

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Isomorphous crystal structures of Escherichia coli dihydrofolate reductase complexed with folate, 5-deazafolate, and 5,10-dideazatetrahydrofolate: mechanistic implications

20 March 2017

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Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state

20 March 2017

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Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding

20 March 2017

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

20 March 2017

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Prolyl cis-trans isomerization as a molecular timer

20 March 2017

1 reference

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Cyclophilin, TRIM5, and innate immunity to HIV-1

20 March 2017

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Structure, dynamics, and catalytic function of dihydrofolate reductase

20 March 2017

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20 March 2017

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Structure and dynamics of the G121V dihydrofolate reductase mutant: lessons from a transition-state inhibitor complex

6 April 2017

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Preservation of protein dynamics in dihydrofolate reductase evolution

20 March 2017

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Dynamic personalities of proteins

20 March 2017

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The dynamic energy landscape of dihydrofolate reductase catalysis

7 April 2017

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Intrinsic dynamics of an enzyme underlies catalysis

7 April 2017

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Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics

7 April 2017

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Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism

29 September 2017

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Understanding the mechanism of proteasome 20S core particle gating

29 September 2017

1 reference

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Protein-guided RNA dynamics during early ribosome assembly.

29 September 2017

1 reference

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The effect of the hydrophobic environment on the retro-aldol reaction: comparison to a computationally-designed enzyme

29 September 2017

1 reference

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Protein conformational populations and functionally relevant substates.

29 September 2017

1 reference

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Side-chain conformational heterogeneity of intermediates in the Escherichia coli dihydrofolate reductase catalytic cycle

29 September 2017

1 reference

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Computational enzyme design

29 September 2017

1 reference

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Biochemistry. Integrative structural biology

29 September 2017

1 reference

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Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Barrier Crossing in Dihydrofolate Reductasedoes not involve a rate-promoting vibration

29 September 2017

1 reference

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Conformational selection or induced fit? A critical appraisal of the kinetic mechanism

29 September 2017

1 reference

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Biomolecular simulation: a computational microscope for molecular biology

29 September 2017

1 reference

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A Bayesian view on cryo-EM structure determination.

29 September 2017

1 reference

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Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

29 September 2017

1 reference

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Automated electron-density sampling reveals widespread conformational polymorphism in proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

The role of conformational entropy in molecular recognition by calmodulin

29 September 2017

1 reference

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Origins of catalysis by computationally designed retroaldolase enzymes

29 September 2017

1 reference

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The influence of protein dynamics on the success of computational enzyme design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Conformational selection or induced fit: a flux description of reaction mechanism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

A 21st century revisionist's view at a turning point in enzymology

29 September 2017

1 reference

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Protein dynamism and evolvability.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Single-molecule approach to molecular biology in living bacterial cells

29 September 2017

1 reference

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Conformational entropy in molecular recognition by proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

New tools provide new insights in NMR studies of protein dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Enzyme dynamics during catalysis

29 September 2017

1 reference

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Enzyme-like proteins by computational design

29 September 2017

1 reference

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Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Insights into enzyme function from studies on mutants of dihydrofolate reductase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Conformational motions regulate phosphoryl transfer in related protein tyrosine phosphatases.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Evaluation and ranking of enzyme designs

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Diagnostic chemical shift markers for loop conformation and substrate and cofactor binding in dihydrofolate reductase complexes

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Probing the functional role of threonine-113 of Escherichia coli dihydrofolate reductase for its effect on turnover efficiency, catalysis, and binding.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334266

Effects of point mutation in a flexible loop on the stability and enzymatic function of Escherichia coli dihydrofolate reductase.

27 November 2018

1 reference

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The role of mobility in the substrate binding and catalytic machinery of enzymes.

27 November 2018

1 reference

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27 November 2018

Identifiers

DOI

10.1021/AR5003158

1 reference

release_3crsuthbvzggbbqwimhr7rpzzu

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/3crsuthbvzggbbqwimhr7rpzzu

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

1 reference

PubMed publication ID

25539415

1 reference