(Q37309585)

19 August 2017

Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps (English)

1 reference

19 August 2017

5

1 reference

19 August 2017

M Hoffmann

3

0 references

author name string

P H König

1

1 reference

19 August 2017

N Ghosh

2

1 reference

19 August 2017

M Elstner

4

1 reference

19 August 2017

Th Frauenheim

6

1 reference

19 August 2017

Q Cui

7

1 reference

19 August 2017

language of work or name

English

0 references

publication date

1 January 2006

1 reference

Journal of Physical Chemistry A

19 August 2017

1 reference

19 August 2017

110

1 reference

19 August 2017

2

1 reference

19 August 2017

548-563

1 reference

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

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Redox-driven membrane-bound proton pumps

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Cytochrome c oxidase: 25 years of the elusive proton pump

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Glycerol facilitator GlpF and the associated aquaporin family of channels

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

A perspective on enzyme catalysis.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

A computer simulation study of the hydrated proton in a synthetic proton channel

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Liquid-vapor oscillations of water in hydrophobic nanopores

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Computer simulations of enzyme catalysis: methods, progress, and insights

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Impact of enzyme motion on activity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Molecular dynamics simulation of proton transport through the influenza A virus M2 channel

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Quantum mechanical methods for enzyme kinetics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Control of the selectivity of the aquaporin water channel family by global orientational tuning

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Water conduction through the hydrophobic channel of a carbon nanotube

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

A combined molecular dynamics and diffusion model of single proton conduction through gramicidin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Cellular and molecular biology of the aquaporin water channels

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Proton and electron transfer in bacterial reaction centers

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Marcus rate theory applied to enzymatic proton transfer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

The pore dimensions of gramicidin A.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Refined structure of human carbonic anhydrase II at 2.0 A resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Computer simulation of the initial proton transfer step in human carbonic anhydrase I

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Molecular mechanisms for proton transport in membranes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Structural bases of hydrogen tunneling in enzymes: progress and puzzles

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Dynamic water networks in cytochrome C oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Proton transfer in carbonic anhydrase measured by equilibrium isotope exchange

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Molecular Dynamics Simulations of the Gramicidin Channel

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Role of histidine 64 in the catalytic mechanism of human carbonic anhydrase II studied with a site-specific mutant

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Structure and dynamics of a proton wire: a theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Key role of electrostatic interactions in bacteriorhodopsin proton transfer

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

A molecular switch and proton wire synchronize the active sites in thiamine enzymes

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Structural determinants of proton blockage in aquaporins

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Grand canonical Monte Carlo simulations of water in protein environments.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Mechanism of primary proton transfer in bacteriorhodopsin

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

The mechanism of proton exclusion in aquaporin channels

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Electrostatic study of the proton pumping mechanism in bovine heart cytochrome C oxidase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Molecular basis of proton blockage in aquaporins

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Water-gated mechanism of proton translocation by cytochrome c oxidase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728601

A Critical Evaluation of Different QM/MM Frontier Treatments with SCC-DFTB as the QM Method

2 September 2018

1 reference

12 December 2020

Molecular dynamics simulations of human carbonic anhydrase II: insight into experimental results and the role of solvation

1 reference

12 December 2020

Proton translocation by bacteriorhodopsin and heme-copper oxidases

1 reference

12 December 2020

Binding of Human Carbonic Anhydrase to Human Hemoglobin

1 reference

12 December 2020

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

1 reference

12 December 2020

The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel

1 reference

12 December 2020

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

1 reference

12 December 2020

Intermittent Permeation of Cylindrical Nanopores by Water

1 reference

12 December 2020

Transport in proton conductors for fuel-cell applications: simulations, elementary reactions, and phenomenology

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP052328Q

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

16405327

1 reference