(Q36915183)

17 August 2017

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K. (English)

1 reference

17 August 2017

Shuhua Ma

1

1 reference

17 August 2017

Lakshmi S Devi-Kesavan

series ordinal

2

1 reference

17 August 2017

Jiali Gao

series ordinal

3

1 reference

17 August 2017

language of work or name

English

0 references

publication date

13 October 2007

1 reference

Journal of the American Chemical Society

17 August 2017

1 reference

17 August 2017

129

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17 August 2017

44

1 reference

17 August 2017

13633-13645

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Mechanisms and free energies of enzymatic reactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

MEROPS: the peptidase database

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

How enzymes work: analysis by modern rate theory and computer simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Exploration of the P1 SAR of aldehyde cathepsin K inhibitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Selective inhibition of the collagenolytic activity of human cathepsin K by altering its S2 subsite specificity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Uracil-DNA glycosylase acts by substrate autocatalysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Expression of cathepsin K in lung epithelial cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Canonical dynamics: Equilibrium phase-space distributions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Design of potent and selective human cathepsin K inhibitors that span the active site

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Crystal structure of human osteoclast cathepsin K complex with E-64

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Crystal structure of human cathepsin K complexed with a potent inhibitor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Structure of chymopapain at 1.7 A resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Pycnodysostosis, a lysosomal disease caused by cathepsin K deficiency

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Proteolytic activity of human osteoclast cathepsin K. Expression, purification, activation, and substrate identification

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Cathepsin K, but not cathepsins B, L, or S, is abundantly expressed in human osteoclasts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Molecular cloning of a possible cysteine proteinase predominantly expressed in osteoclasts.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Molecular cloning of human cDNA for cathepsin K: novel cysteine proteinase predominantly expressed in bone

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Linkage of pycnodysostosis to chromosome 1q21 by homozygosity mapping

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Human cathepsin O2, a novel cysteine protease highly expressed in osteoclastomas and ovary molecular cloning, sequencing and tissue distribution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Current problems in mechanistic studies of serine and cysteine proteinases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Structure of papain refined at 1.65 A resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

On the size of the active site in proteases. I. Papain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Mapping the active site of papain with the aid of peptide substrates and inhibitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

A protein engineering study of the role of aspartate 158 in the catalytic mechanism of papain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Contribution of the glutamine 19 side chain to transition-state stabilization in the oxyanion hole of papain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Binding of chloromethyl ketone substrate analogues to crystalline papain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

S3 to S3' subsite specificity of recombinant human cathepsin K and development of selective internally quenched fluorescent substrates

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Revised definition of substrate binding sites of papain-like cysteine proteases

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Structural determinants of specificity in the cysteine protease cruzain

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Curious structure in "canonical" alanine-based peptides

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Human cathepsin O2, a matrix protein-degrading cysteine protease expressed in osteoclasts. Functional expression of human cathepsin O2 in Spodoptera frugiperda and characterization of the enzyme

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Contributions to the S'-subsite specificity of papain

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Semicarbazone-based inhibitors of cathepsin K, are they prodrugs for aldehyde inhibitors?

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Exploration of the P2-P3 SAR of aldehyde cathepsin K inhibitors

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Probing cathepsin K activity with a selective substrate spanning its active site.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Insight into the catalysis of hydrolysis of four newly synthesized substrates by papain: a proton inventory study

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

QM/MM study of the active site of free papain and of the NMA-papain complex.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2556303

Hydrolysis of acyl-activated thiol esters. Acid catalysis and acid inhibition

4 September 2018

1 reference

12 December 2020

KINETICS OF PAPAIN-CATALYZED HYDROLYSIS OF ALPHA-N-BENZOYL-L-ARGININE ETHYL ESTER AND ALPHA-N-BENZOYL-L-ARGININAMIDE

1 reference

12 December 2020

Structure of actinidin, after refinement at 1.7 A resolution

1 reference

12 December 2020

Catalytic mechanism in papain family of cysteine peptidases

1 reference

12 December 2020

Computer simulation and analysis of the reaction pathway of triosephosphate isomerase

1 reference

12 December 2020

The specificity of the S1' subsite of cysteine proteases

1 reference

12 December 2020

Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction

1 reference

12 December 2020

A combined QM/MM study of the nucleophilic addition reaction of methanethiolate and N-methylacetamide

1 reference

12 December 2020

Structural and Functional Roles of Asparagine 175 in the Cysteine Protease Papain

1 reference

12 December 2020

On the active site of proteases. 3. Mapping the active site of papain; specific peptide inhibitors of papain

1 reference

12 December 2020

Structure of actinidin: Details of the polypeptide chain conformation and active site from an electron density map at 2·8 Å resolution

1 reference

12 December 2020

Simulation of the enzyme reaction mechanism of malate dehydrogenase

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA074222+

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

17935329

1 reference