(Q40143952)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

title

Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

Cláudio M. Soares

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

author name string

Baptista AM

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

language of work or name

English

0 references

publication date

1 June 1999

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

volume

76

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

page(s)

2978-2998

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

LINKED FUNCTIONS AND RECIPROCAL EFFECTS IN HEMOGLOBIN: A SECOND LOOK.

8 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c3: structural basis for functional cooperativity

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Crystal structure of cytochrome c3 from Desulfovibrio desulfuricans Norway at 1.7 A resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Classical electrostatics in biology and chemistry

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Refined structure of cytochrome c3 at 1.8 A resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Calculations of electrostatic interactions in biological systems and in solutions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Complex formation between methionine and a heme peptide from cytochrome c

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Free energy via molecular simulation: applications to chemical and biomolecular systems

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

The nature of protein dipole moments: experimental and calculated permanent dipole of alpha-chymotrypsin.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

WHAT IF: a molecular modeling and drug design program

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Electrostatic interactions in macromolecules: theory and applications

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Electrostatic Energy and Macromolecular Function

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Redox bohr-effects in the cytochrome system of mitochondria

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Growth yields and growth rates of Desulfovibrio vulgaris (Marburg) growing on hydrogen plus sulfate and hydrogen plus thiosulfate as the sole energy sources

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Prediction of pH-dependent properties of proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Energetics of charge-charge interactions in proteins.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

A thermodynamic model for the cooperative functional properties of the tetraheme cytochrome c3 from Desulfovibrio gigas.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Protein control of iron-sulfur cluster redox potentials

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Electrostatic effects in macromolecules: fundamental concepts and practical modeling.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Cytochrome c3 from Desulfovibrio gigas: crystal structure at 1.8 A resolution and evidence for a specific calcium-binding site

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Regulation of the redox order of four hemes by pH in cytochrome c3 from D. vulgaris Miyazaki F.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

NMR studies of electron transfer mechanisms in a protein with interacting redox centres: Desulfovibrio gigas cytochrome c3.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

The dielectric constant of a folded protein

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Electrostatic effects of charge perturbations introduced by metal oxidation in proteins. A theoretical analysis

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Decomposition of the Free Energy of a System in Terms of Specific Interactions

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300269

Isolation and characterization of Desulfovibrio growing on hydrogen plus sulfate as the sole energy source

2 December 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Control of the redox potential in c-type cytochromes: importance of the entropic contribution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Monte Carlo sampling methods using Markov chains and their applications

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Redox-Bohr effect in electron/proton energy transduction: cytochrome c 3 coupled to hydrogenase works as a 'proton thruster' in Desulfovibrio vulgaris

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Comparative redox and pK a calculations on cytochrome c 3 from several Desulfovibrio species using continuum electrostatic methods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Structure analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 1.9 A resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Equation of State Calculations by Fast Computing Machines

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

7 January 2021

Free energy simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Structure of the tetraheme cytochrome from Desulfovibrio desulfuricans ATCC 27774: X-ray diffraction and electron paramagnetic resonance studies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Assignment of the redox potentials to the four haems in Desulfovibrio vulgaris cytochrome c 3 by 2D-NMR

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Replacement of Lysine 45 by Uncharged Residues Modulates the Redox-Bohr Effect in Tetraheme Cytochromec3ofDesulfovibrio vulgaris(Hildenborough)†

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Theoretical studies on the redox-Bohr effect in cytochrome c 3 from Desulfovibrio vulgaris Hildenborough

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Homotropic and heterotropic cooperativity in the tetrahaem cytochrome c3 from Desulfovibrio vulgaris

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

NMR studies of cooperativity in the tetrahaem cytochrome c3 from Desulfovibrio vulgaris

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

On the calculation of pKas in proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977452-7

Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/10354425

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(99)77452-7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10354425%20AND%20SRC:MED&resulttype=core&format=json

8 December 2019

1 reference