The flexibility of a distant loop modulates active site motion and product release in ribonuclease A. (Q42551075)

2 November 2017

The flexibility of a distant loop modulates active site motion and product release in ribonuclease A. (English)

1 reference

2 November 2017

Eric D Watt

2

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author name string

Nicolas Doucet

series ordinal

1

1 reference

PMCID

2741010

2 November 2017

J Patrick Loria

series ordinal

3

1 reference

PMCID

2741010

2 November 2017

language of work or name

English

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publication date

1 August 2009

1 reference

2 November 2017

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2 November 2017

48

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2 November 2017

30

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2 November 2017

7160-7168

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Limits to Catalysis by Ribonuclease A.

2 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

The mechanism of rate-limiting motions in enzyme function.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Conformational dynamics in loop swap mutants of homologous fibronectin type III domains

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

The dynamic energy landscape of dihydrofolate reductase catalysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Intrinsic dynamics of an enzyme underlies catalysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Computational modeling of the catalytic reaction in triosephosphate isomerase.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

The role of dynamics in enzyme activity

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

The crystal structure of eosinophil cationic protein in complex with 2',5'-ADP at 2.0 A resolution reveals the details of the ribonucleolytic active site

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 Å resolution

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Three-dimensional crystal structure of human eosinophil cationic protein (RNase 3) at 1.75 A resolution

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Crystal structures of ribonuclease A complexes with 5'-diphosphoadenosine 3'-phosphate and 5'-diphosphoadenosine 2'-phosphate at 1.7 A resolution

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

The CD4 determinant for downregulation by HIV-1 Nef directly binds to Nef. Mapping of the Nef binding surface by NMR.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Engineering ribonuclease A: production, purification and characterization of wild-type enzyme and mutants at Gln11.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

13C NMR studies of the molecular dynamics of selectively 13C-enriched ribonuclease complexes.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Conformational States of Bovine Pancreatic Ribonuclease A Observed by Normal and Partially Relaxed Carbon 13 Nuclear Magnetic Resonance

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Structure of phosphate-free ribonuclease A refined at 1.26 .ANG

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Solution conformations of the B-loop fragments of human transforming growth factor alpha and epidermal growth factor by 1H nuclear magnetic resonance and restrained molecular dynamics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

A hybrid of bovine pancreatic ribonuclease and human angiogenin: an external loop as a module controlling substrate specificity?

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Converting trypsin to chymotrypsin: the role of surface loops

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Segmental movement: definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

A comparison of the structures of apo dogfish M4 lactate dehydrogenase and its ternary complexes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Correlation proton magnetic resonance studies at 250 MHz of bovine pancreatic ribonuclease. II. pH and inhibitor-induced conformational transitions affecting histidine-48 and one tyrosine residue of ribonuclease A

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Engineering the substrate specificity of Staphylococcus aureus Sortase A. The beta6/beta7 loop from SrtB confers NPQTN recognition to SrtA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Enzyme dynamics along the reaction coordinate: critical role of a conserved residue

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Temperature Dependence of the Backbone Dynamics of Ribonuclease A in the Ground State and Bound to the Inhibitor 5‘-Phosphothymidine (3‘-5‘)Pyrophosphate Adenosine 3‘-Phosphate

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Catalysis by ribonuclease A is limited by the rate of substrate association.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Triosephosphate isomerase catalysis is diffusion controlled. Appendix: Analysis of triose phosphate equilibria in aqueous solution by 31P NMR.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2741010

Pervasive conformational fluctuations on microsecond time scales in a fibronectin type III domain

16 August 2018

1 reference

12 December 2020

Evidence for flexibility in the function of ribonuclease A

1 reference

12 December 2020

A 31P NMR study of the association of uridine-3′-monophosphate to ribonuclease A

1 reference

12 December 2020

Ribonuclease A: carbon-13 nuclear magnetic resonance assignments, binding sites, and conformational flexibility

1 reference

12 December 2020

Relaxation Spectra of Ribonuclease. V. The Interaction of Ribonuclease with Cytidylyl-3':5'-cytidine1

1 reference

12 December 2020

Some spectrophotometric and polarimetric experiments with ribonuclease

1 reference

12 December 2020

Relaxation Spectra of Ribonuclease. IV. The Interaction of Ribonuclease with Cytidine 2':3'-Cyclic Phosphate1

1 reference

12 December 2020

Relaxation Spectra of Ribonuclease. III. Further Investigation of the Interaction of Ribonuclease and Cytidine 3'-Phosphate

1 reference

12 December 2020

Relaxation Spectra of Ribonuclease. II. Isomerization of Ribonuclease at Neutral pH Values

1 reference

12 December 2020

Characterization of the transition state of functional enzyme dynamics

1 reference

12 December 2020

Differential multiple-quantum relaxation arising from cross-correlated time-modulation of isotropic chemical shifts

1 reference

12 December 2020

Sequence-specific dynamics modulate recognition specificity in WW domains

1 reference

12 December 2020

Equilibrium Measurements of the Binding of Cytidine 3'-Phosphate to Ribonuclease1

1 reference

12 December 2020

The occupancy of two distinct conformations by active-site histidine-119 in crystals of ribonuclease is modulated by pH

1 reference

12 December 2020

Identifiers

DOI

10.1021/BI900830G

1 reference

2 November 2017

1 reference

2 November 2017

1 reference

PMCID

2741010