(Q33943496)

30 July 2017

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes (English)

1 reference

30 July 2017

4

Darrin M York

1 reference

30 July 2017

Elena Formoso

1

0 references

Jon M Matxain

object named as

Jon M Matxain

series ordinal

2

0 references

author name string

Xabier Lopez

series ordinal

3

1 reference

PubMed ID

20455590

30 July 2017

language of work or name

English

0 references

publication date

1 June 2010

1 reference

Journal of Physical Chemistry B

30 July 2017

1 reference

30 July 2017

114

1 reference

30 July 2017

7371-7382

1 reference

30 July 2017

21

1 reference

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

30 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Ribonuclease a: revealing structure-function relationships with semisynthesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Pentavalent Organo-Vanadates as Transition State Analogues for Phosphoryl Transfer Reactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

CHARMM: the biomolecular simulation program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Influence of naturally-occurring 5â ²-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: An X-ray crystallographic study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Dynamics of RNase-A and S-Protein: A Molecular Dynamics Simulation of the Transition Toward a Folding Intermediate

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Atomic resolution structures of ribonuclease A at six pH values

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Contribution of the active site histidine residues of ribonuclease A to nucleic acid binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Excavating an active site: the nucleobase specificity of ribonuclease A

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Canonical dynamics: Equilibrium phase-space distributions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Three-dimensional structure of the complexes of ribonuclease A with 2',5'-CpA and 3',5'-d(CpA) in aqueous solution, as obtained by NMR and restrained molecular dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Interaction of substrate uridyl 3',5'-adenosine with ribonuclease A: a molecular dynamics study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Bovine pancreatic ribonuclease A as a model of an enzyme with multiple substrate binding sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Active site of RNase: neutron diffraction study of a complex with uridine vanadate, a transition-state analog

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

The mechanism of action of ribonuclease

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Active site dynamics of ribonuclease

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

The eosinophilic leukocyte: structure and function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Insights into current limitations of density functional theory.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Replacement of His12 or His119 of bovine pancreatic ribonuclease A with acidic amino acid residues for the modification of activity and stability

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

X-ray structure of a ribonuclease A-uridine vanadate complex at 1.3 A resolution.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Protein-water interactions in ribonuclease A and angiogenin: a molecular dynamics study.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Hydrolysis of cyclic phosphates by ribonuclease A: a computational study using a simplified ab initio quantum model.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

In vitro studies on selective inhibition of tumor cell growth by seminal ribonuclease.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2892782

Evidence for flexibility in the function of ribonuclease A

29 October 2018

1 reference

12 December 2020

Energetics of Catalysis by Ribonucleases: Fate of the 2',3'-Cyclic Phosphodiester Intermediate

1 reference

12 December 2020

1 reference

12 December 2020

Structure of the crystalline complex of deoxycytidylyl-3',5'-guanosine (3',5'-dCpdG) cocrystallized with ribonuclease at 1.9 A resolution

1 reference

12 December 2020

[13C]Methylated ribonuclease A. 13C NMR studies of the interaction of lysine 41 with active site ligands

1 reference

12 December 2020

The Active Site and Mechanism of Action of Bovine Pancreatic Ribonuclease

1 reference

12 December 2020

Characterization of the transition state of functional enzyme dynamics

1 reference

12 December 2020

Mechanism and binding sites in the ribonuclease reaction. II. Kinetic studies on the first step of the reaction

1 reference

12 December 2020

Site-directed mutagenesis of bovine pancreatic ribonuclease: lysine-41 and aspartate-121

1 reference

12 December 2020

Ribonuclease A mutant His119 Asn: the role of histidine in catalysis

1 reference

12 December 2020

Isolation and characterization of angiogenin, an angiogenic protein from human carcinoma cells

1 reference

12 December 2020

Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP909004Y

1 reference

30 July 2017

1 reference

30 July 2017

1 reference

PubMed ID

20455590