(Q36393515)

English

How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design

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scholarly article

1 reference

Europe PubMed Central

13 August 2017

How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design (English)

1 reference

Europe PubMed Central

13 August 2017

crystal structure

1 reference

based on heuristic

inferred from title

7

object named as

K N Houk

1 reference

Europe PubMed Central

13 August 2017

author name string

Jason Dechancie

1

1 reference

Europe PubMed Central

13 August 2017

Fernando R Clemente

2

1 reference

Europe PubMed Central

13 August 2017

Adam J T Smith

3

1 reference

Europe PubMed Central

13 August 2017

Hakan Gunaydin

4

1 reference

Europe PubMed Central

13 August 2017

Yi-Lei Zhao

5

1 reference

Europe PubMed Central

13 August 2017

Xiyun Zhang

6

1 reference

Europe PubMed Central

13 August 2017

publication date

1 September 2007

1 reference

Europe PubMed Central

13 August 2017

Protein Science

1 reference

Europe PubMed Central

13 August 2017

16

1 reference

Europe PubMed Central

13 August 2017

1851-1866

1 reference

Europe PubMed Central

13 August 2017

9

1 reference

Europe PubMed Central

13 August 2017

Combinatorial methods for small-molecule placement in computational enzyme design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Tyrosyl-DNA phosphodiesterase (Tdp1) participates in the repair of Top2-mediated DNA damage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Understanding nature's catalytic toolkit

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Role of water in aging of human butyrylcholinesterase inhibited by echothiophate: the crystal structure suggests two alternative mechanisms of aging

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Energetics for displacing a single chain from the surface of microcrystalline cellulose into the active site of Acidothermus cellulolyticus Cel5A.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Binding Affinities of Host–Guest, Protein–Ligand, and Protein–Transition‐State Complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

The near attack conformation approach to the study of the chorismate to prephenate reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

HIV-1 protease: mechanism and drug discovery

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Direct experimental observation of the hydrogen-bonding network of a glycosidase along its reaction coordinate revealed by atomic resolution analyses of endoglucanase Cel5A

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Insights into substrate binding and catalytic mechanism of human tyrosyl-DNA phosphodiesterase (Tdp1) from vanadate and tungstate-inhibited structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Observation of covalent intermediates in an enzyme mechanism at atomic resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Modeling the active sites in metalloenzymes. 3. Density functional calculations on models for [Fe]-hydrogenase: structures and vibrational frequencies of the observed redox forms and the reaction mechanism at the Diiron Active Center

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Rapid screening of the aglycone specificity of glycosidases: applications to enzymatic synthesis of oligosaccharides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

The mechanism of the Ni-Fe hydrogenases: a quantum chemical perspective

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Probing the role of the C-terminus of Bacillus subtilis chorismate mutase by a novel random protein-termination strategy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp-containing aspartic proteinase from the flowers of Cynara cardunculus L

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Insights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

A eukaryotic enzyme that can disjoin dead-end covalent complexes between DNA and type I topoisomerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Evidence for the general base mechanism in carboxypeptidase A-catalyzed reactions: partitioning studies on nucleophiles and H2(18)O kinetic isotope effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Molecular structure of an aspartic proteinase zymogen, porcine pepsinogen, at 1.8 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Evolution in the structure and function of aspartic proteases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Mechanism of carboxypeptidase A: hydration of a ketonic substrate analogue

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

30 September 2017

New algorithms and an in silico benchmark for computational enzyme design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

28 June 2018

Fundamental reaction mechanism for cocaine hydrolysis in human butyrylcholinesterase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

28 June 2018

Theozymes and compuzymes: theoretical models for biological catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

28 June 2018

Effect of pH on the activities of penicillopepsin and Rhizopus pepsin and a proposal for the productive substrate binding mode in penicillopepsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

28 June 2018

Human immunodeficiency virus-1 protease. 1. Initial velocity studies and kinetic characterization of reaction intermediates by 18O isotope exchange

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

28 June 2018

Molecular Architecture and Biological Reactions

1 reference

https://api.crossref.org/works/10.1110%2FPS.072963707

21 January 2018

Elucidation of the mechanism of selenoprotein glutathione peroxidase (GPx)-catalyzed hydrogen peroxide reduction by two glutathione molecules: a density functional study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 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=2206971

21 September 2018

Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Computational design of a biologically active enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Theoretical investigation of the origins of catalysis of a retro-Diels-Alder reaction by antibody 10F11.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

A comparative study of claisen and cope rearrangements catalyzed by chorismate mutase. An insight into enzymatic efficiency: transition state stabilization or substrate preorganization?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Just a near attack conformer for catalysis (chorismate to prephenate rearrangements in water, antibody, enzymes, and their mutants).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Theozyme for antibody aldolases. Characterization of the transition-state analogue

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

A comparison of the mechanism for the reductive half-reaction between pea seedling and other copper amine oxidases (CAOs).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Metal-bridging mechanism for O-O bond cleavage in cytochrome C oxidase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Comparison of Formation of Reactive Conformers (NACs) for the Claisen Rearrangement of Chorismate to Prephenate in Water and in the E. coli Mutase: The Efficiency of the Enzyme Catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Experimental determination of the absolute enantioselectivity of an antibody-catalyzed Diels-Alder reaction and theoretical explorations of the origins of stereoselectivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Catalysis on the coastline: theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Origins and predictions of stereoselective antibody catalysis: theoretical analysis of Diels-Alder catalysis by 39A11 and its germ-line antibody

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Analysis of catalytic residues in enzyme active sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Is the bis-mu-oxo Cu2(III,III) state an intermediate in tyrosinase?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2206971

21 September 2018

Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase

1 reference

https://api.crossref.org/works/10.1110%2FPS.072963707

21 January 2018

Calculation of the electronic structure and spectra of model cytochrome P450 compound I

1 reference

https://pubmed.ncbi.nlm.nih.gov/17766382

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nonparallelism between reaction rate and dienophile-catalyst affinity in catalytic enantioselective Diels-Alder reactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/17766382

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case

1 reference

https://pubmed.ncbi.nlm.nih.gov/17766382

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modeling enzymatic reactions involving transition metals

1 reference

https://pubmed.ncbi.nlm.nih.gov/17766382

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nature of Forces between Large Molecules of Biological Interest*

1 reference

https://pubmed.ncbi.nlm.nih.gov/17766382

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate

1 reference

https://pubmed.ncbi.nlm.nih.gov/17766382

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1110/PS.072963707

1 reference

Europe PubMed Central

13 August 2017

1 reference

Europe PubMed Central

13 August 2017

1 reference

Europe PubMed Central

13 August 2017

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