(Q47407220)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

title

Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Vivek Sharma

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Edina Rosta

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

author name string

Markus Kaukonen

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Peter R Rich

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

language of work or name

English

0 references

publication date

13 November 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

2 April 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

volume

114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

issue

48

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

page(s)

E10339-E10348

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

Mitochondrial cytochrome c oxidase: catalysis, coupling and controversies

2 April 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Redox-induced activation of the proton pump in the respiratory complex I.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Structural Changes and Proton Transfer in Cytochrome c Oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The subunit composition and function of mammalian cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Structural studies on bovine heart cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Yeast cytochrome c oxidase: a model system to study mitochondrial forms of the haem-copper oxidase superfamily

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopy

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Redox-Dependent Conformational Changes in Cytochrome c Oxidase Suggest a Gating Mechanism for Proton Uptake

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Cytochrome c oxidase: exciting progress and remaining mysteries

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Diversity of the heme-copper superfamily in archaea: insights from genomics and structural modeling.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The proton pumping pathway of bovine heart cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Sequence analysis of the cbb3 oxidases and an atomic model for the Rhodobacter sphaeroides enzyme.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Scalable molecular dynamics with NAMD

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

FTIR detection of protonation/deprotonation of key carboxyl side chains caused by redox change of the Cu(A)-heme a moiety and ligand dissociation from the heme a3-Cu(B) center of bovine heart cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Structure and dynamics of hydronium in the ion channel gramicidin A.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

VMD: visual molecular dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The superfamily of heme-copper respiratory oxidases

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Possible proton relay pathways in cytochrome c oxidase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The effect of pH on redox titrations of haem a in cyanide-liganded cytochrome-c oxidase: experimental and modelling studies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Redox bohr-effects in the cytochrome system of mitochondria

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Involvement of intramitochondrial protons in redox reactions of cytochromea

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Proton pump coupled to cytochrome c oxidase in mitochondria

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

New perspectives on proton pumping in cellular respiration.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Reaction mechanism of cytochrome c oxidase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

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

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Computational study of the activated O(H) state in the catalytic mechanism of cytochrome c oxidase.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

IR signatures of the metal centres of bovine cytochrome c oxidase: assignments and redox-linkage

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Exploring the possible role of Glu286 in CcO by electrostatic energy computations combined with molecular dynamics.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Effective pumping proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Functions of the hydrophilic channels in protonmotive cytochrome c oxidase.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The superfamily of heme-copper oxygen reductases: types and evolutionary considerations.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The mechanism for proton pumping in cytochrome c oxidase from an electrostatic and quantum chemical perspective

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Effect of the damping function in dispersion corrected density functional theory.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Kinetic gating of the proton pump in cytochrome c oxidase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5715751

Possible mechanism of proton transfer through peptide groups in the H-pathway of the bovine cytochrome c oxidase

1 December 2018

1 reference

12 December 2020

CHARMM-GUI: a web-based graphical user interface for CHARMM

1 reference

12 December 2020

Assignment of the CO-sensitive carboxyl group in mitochondrial forms of cytochrome c oxidase using yeast mutants

1 reference

12 December 2020

Charge parameterization of the metal centers in cytochromecoxidase

1 reference

12 December 2020

Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity.

1 reference

12 December 2020

Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

1 reference

12 December 2020

Climbing the Density Functional Ladder: Nonempirical Meta–Generalized Gradient Approximation Designed for Molecules and Solids

1 reference

12 December 2020

Spectroelectrochemical study of the cytochrome a site in carbon monoxide inhibited cytochrome c oxidase

1 reference

12 December 2020

Mutations in the putative H-channel in the cytochrome c oxidase from Rhodobacter sphaeroides show that this channel is not important for proton conduction but reveal modulation of the properties of heme a

1 reference

12 December 2020

Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pKA and conformation

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1708628114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29133387%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

PubMed publication ID

29133387

1 reference