(Q35185648)

English

QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5'-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis

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scholarly article

1 reference

Europe PubMed Central

7 August 2017

QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5'-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis (English)

1 reference

Europe PubMed Central

7 August 2017

5

object named as

K N Houk

1 reference

Europe PubMed Central

7 August 2017

Christopher J. Mundy

object named as

Christopher J Mundy

3

0 references

author name string

Courtney L Stanton

1

1 reference

Europe PubMed Central

7 August 2017

I-Feng W Kuo

2

1 reference

Europe PubMed Central

7 August 2017

Teodoro Laino

4

1 reference

Europe PubMed Central

7 August 2017

language of work or name

0 references

publication date

10 October 2007

1 reference

Europe PubMed Central

7 August 2017

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

7 August 2017

111

1 reference

Europe PubMed Central

7 August 2017

12573-12581

1 reference

Europe PubMed Central

7 August 2017

43

1 reference

Europe PubMed Central

7 August 2017

Metadynamics as a tool for exploring free energy landscapes of chemical reactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Scalable molecular dynamics with NAMD

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Flexible docking in solution using metadynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Escaping free-energy minima

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Catalytic proficiency: the unusual case of OMP decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Electrostatic stress in catalysis: Structure and mechanism of the enzyme orotidine monophosphate decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Anatomy of a proficient enzyme: The structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Density-functional exchange-energy approximation with correct asymptotic behavior

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Intrinsic activity and stability of bifunctional human UMP synthase and its two separate catalytic domains, orotate phosphoribosyltransferase and orotidine-5'-phosphate decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

A proficient enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Investigation of the enzymatic mechanism of yeast orotidine-5'-monophosphate decarboxylase using 13C kinetic isotope effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

A unique catalytic and inhibitor-binding role for Lys93 of yeast orotidylate decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Orotidylate decarboxylase: insights into the catalytic mechanism from substrate specificity studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

Mechanism of decarboxylation of 1,3-dimethylorotic acid. A model for orotidine 5'-phosphate decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

28 July 2018

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Exploring the gating mechanism in the ClC chloride channel via metadynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Why enzymes are proficient catalysts: beyond the Pauling paradigm

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Reconstructing the density of states by history-dependent metadynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Crystal structures of orotidine monophosphate decarboxylase: does the structure reveal the mechanism of nature's most proficient enzyme?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Circe effect versus enzyme preorganization: what can be learned from the structure of the most proficient enzyme?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Yeast orotidine-5'-phosphate decarboxylase: steady-state and pre-steady-state analysis of the kinetic mechanism of substrate decarboxylation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163499

27 September 2018

Assessing the Accuracy of Metadynamics†

1 reference

https://pubmed.ncbi.nlm.nih.gov/17927240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Acetoacetate Decarboxylase. Identification of Lysine at the Active Site*

1 reference

https://pubmed.ncbi.nlm.nih.gov/17927240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Separable dual-space Gaussian pseudopotentials

1 reference

https://pubmed.ncbi.nlm.nih.gov/17927240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The planar conformation of a strained proline ring: a QM/MM study

1 reference

https://pubmed.ncbi.nlm.nih.gov/17927240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Inhibition of orotidine-5'-phosphate decarboxylase by 1-(5'-phospho-beta-d-ribofuranosyl)barbituric acid, 6-azauridine 5'-phosphate, and uridine 5'-phosphate

1 reference

https://pubmed.ncbi.nlm.nih.gov/17927240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Electronic Structure of Compound I in Human Isoforms of Cytochrome P450 from QM/MM Modeling

1 reference

https://pubmed.ncbi.nlm.nih.gov/17927240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JP074858N

1 reference

Europe PubMed Central

7 August 2017

1 reference

Europe PubMed Central

7 August 2017

1 reference

Europe PubMed Central

7 August 2017

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