(Q35228068)

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Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra

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scholarly article

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Europe PubMed Central

PubMed publication ID

7 August 2017

Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra (English)

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Europe PubMed Central

PubMed publication ID

7 August 2017

infrared spectroscopy

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based on heuristic

inferred from title

quantum mechanics

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6

object named as

Marcus Elstner

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

7

object named as

Qiang Cui

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Europe PubMed Central

PubMed publication ID

7 August 2017

author name string

Puja Goyal

1

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Europe PubMed Central

PubMed publication ID

7 August 2017

Nilanjan Ghosh

2

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Europe PubMed Central

PubMed publication ID

7 August 2017

Prasad Phatak

3

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Europe PubMed Central

PubMed publication ID

7 August 2017

Maike Clemens

4

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Europe PubMed Central

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7 August 2017

Michael Gaus

5

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7 August 2017

language of work or name

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publication date

6 September 2011

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Europe PubMed Central

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7 August 2017

Journal of the American Chemical Society

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Europe PubMed Central

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7 August 2017

133

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Europe PubMed Central

PubMed publication ID

7 August 2017

38

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

14981-14997

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Proton-coupled electron transfer in cytochrome oxidase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Charges in the hydrophobic interior of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Directional proton transfer in membrane proteins achieved through protonated protein-bound water molecules: a proton diode

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Cytochrome c oxidase: exciting progress and remaining mysteries

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Structures and spectral signatures of protonated water networks in bacteriorhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Quantum structure of the intermolecular proton bond

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Structural changes in the L photointermediate of bacteriorhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Calculated proton uptake on anaerobic reduction of cytochrome C oxidase: is the reaction electroneutral?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Proton binding within a membrane protein by a protonated water cluster

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Quantum statistics and classical mechanics: real time correlation functions from ring polymer molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Crystal structure of the L intermediate of bacteriorhodopsin: evidence for vertical translocation of a water molecule during the proton pumping cycle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Simultaneous monitoring of light-induced changes in protein side-group protonation, chromophore isomerization, and backbone motion of bacteriorhodopsin by time-resolved Fourier-transform infrared spectroscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

pKa calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

What are the dielectric "constants" of proteins and how to validate electrostatic models?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Protonation reactions and their coupling in bacteriorhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Structure of bacteriorhodopsin at 1.55 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

In situ determination of transient pKa changes of internal amino acids of bacteriorhodopsin by using time-resolved attenuated total reflection Fourier-transform infrared spectroscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Thermal motions in bacteriorhodopsin at different hydration levels studied by neutron scattering: correlation with kinetics and light-induced conformational changes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

"Strong" hydrogen bonds in chemistry and biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Titration of aspartate-85 in bacteriorhodopsin: what it says about chromophore isomerization and proton release

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

A linkage of the pKa's of asp-85 and glu-204 forms part of the reprotonation switch of bacteriorhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Thermal motions and function of bacteriorhodopsin in purple membranes: effects of temperature and hydration studied by neutron scattering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Glutamic Acid 204 is the Terminal Proton Release Group at the Extracellular Surface of Bacteriorhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Functions of a New Photoreceptor Membrane

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

27 July 2018

Role of Arg82 in the early steps of the bacteriorhodopsin proton-pumping cycle.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Microscopic pKa analysis of Glu286 in cytochrome c oxidase (Rhodobacter sphaeroides): toward a calibrated molecular model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Potential proton-release channels in bacteriorhodopsin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Active internal waters in the bacteriorhodopsin photocycle. A comparative study of the L and M intermediates at room and cryogenic temperatures by infrared spectroscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Optimized atomic radii for protein continuum electrostatics solvation forces.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Energy transduction: proton transfer through the respiratory complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Spectral signatures of hydrated proton vibrations in water clusters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Grand canonical Monte Carlo simulations of water in protein environments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Quantum corrections to classical time-correlation functions: hydrogen bonding and anharmonic floppy modes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

26 September 2018

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

15 November 2018

A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions

1 reference

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15 November 2018

How Does a Membrane Protein Achieve a Vectorial Proton Transfer Via Water Molecules?

1 reference

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15 November 2018

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178665

15 November 2018

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1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

12 December 2020

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Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy

1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

12 December 2020

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Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The melting temperature of the most common models of water

1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

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based on heuristic

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1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

SCC-DFTB: what is the proper degree of self-consistency?

1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

12 December 2020

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pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications

1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

12 December 2020

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On the applicability of centroid and ring polymer path integral molecular dynamics for vibrational spectroscopy

1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

12 December 2020

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Spectral Signatures of the Pentagonal Water Cluster in Bacteriorhodopsin

1 reference

https://pubmed.ncbi.nlm.nih.gov/21761868

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based on heuristic

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Solvent mobility and the protein 'glass' transition

1 reference

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Glutamate-194 to cysteine mutation inhibits fast light-induced proton release in bacteriorhodopsin

1 reference

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based on heuristic

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Identifiers

10.1021/JA201568S

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

ResearchGate publication ID

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