(Q37353692)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19405533%20AND%20SRC:MED&resulttype=core&format=json

27 January 2020

title

Long-distance proton transfer with a break in the bacteriorhodopsin active site (English)

1 reference

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27 January 2020

4

1 reference

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27 January 2020

Jeremy C Smith

6

1 reference

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27 January 2020

Ana-Nicoleta Bondar

8

1 reference

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27 January 2020

9

Marcus Elstner

1 reference

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27 January 2020

author name string

Prasad Phatak

1

1 reference

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27 January 2020

Jan S Frähmcke

2

1 reference

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27 January 2020

Marius Wanko

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19405533%20AND%20SRC:MED&resulttype=core&format=json

27 January 2020

Paul Strodel

5

1 reference

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27 January 2020

Sándor Suhai

7

1 reference

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27 January 2020

language of work or name

English

0 references

publication date

1 May 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19405533%20AND%20SRC:MED&resulttype=core&format=json

Journal of the American Chemical Society

27 January 2020

published in

1 reference

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27 January 2020

volume

131

1 reference

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27 January 2020

issue

20

1 reference

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27 January 2020

page(s)

7064-7078

1 reference

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

27 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Structures and spectral signatures of protonated water networks in 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=2746972

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Color Tuning in Rhodopsins: The Mechanism for the Spectral Shift between Bacteriorhodopsin and Sensory Rhodopsin 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=2746972

Is there an excitonic interaction or antenna system in 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=2746972

Proton binding within a membrane protein by a protonated water cluster

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of 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=2746972

Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Infrared methods for monitoring the protonation state of carboxylic amino acids in the photocycle of 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=2746972

Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Tight Asp-85--Thr-89 association during the pump switch of 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=2746972

Structural alterations for proton translocation in the M state of wild-type 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=2746972

Molecular dynamics study of the nature and origin of retinal's twisted structure in 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=2746972

Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 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=2746972

Structure of bacteriorhodopsin at 1.55 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=2746972

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Kinetic and thermodynamic study of the bacteriorhodopsin photocycle over a wide pH range

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Electron diffraction studies of light-induced conformational changes in the Leu-93 --> Ala bacteriorhodopsin mutant.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

VMD: visual molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Glutamic Acid 204 is the Terminal Proton Release Group at the Extracellular Surface of 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=2746972

Replacement of leucine-93 by alanine or threonine slows down the decay of the N and O intermediates in the photocycle of bacteriorhodopsin: implications for proton uptake and 13-cis-retinal----all-trans-retinal reisomerization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Determination of retinal chromophore structure in bacteriorhodopsin with resonance Raman spectroscopy

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

CD spectrum of bacteriorhodopsin: Best evidence against exciton model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Electron paramagnetic resonance study of structural changes in the O photointermediate of bacteriorhodopsin

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Fourier transform infrared spectra of a late intermediate of the bacteriorhodopsin photocycle suggest transient protonation of Asp-212.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Partitioning of free energy gain between the photoisomerized retinal and the protein in bacteriorhodopsin

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

The tertiary structural changes in bacteriorhodopsin occur between M states: X-ray diffraction and Fourier transform infrared spectroscopy

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

The two pKa's of aspartate-85 and control of thermal isomerization and proton release in the arginine-82 to lysine mutant of bacteriorhodopsin.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Kinetic and spectroscopic evidence for an irreversible step between deprotonation and reprotonation of the Schiff base in the bacteriorhodopsin photocycle

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Temperature and pH sensitivity of the O(640) intermediate of the bacteriorhodopsin photocycle

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Calculating absorption shifts for retinal proteins: computational challenges.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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=2746972

Crystal structures of acid blue and alkaline purple forms of 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=2746972

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=2746972

The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal-mode 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=2746972

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=2746972

Calculation of proton transfers in Bacteriorhodopsin bR and M intermediates

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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=2746972

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=2746972

Molecular mechanism of spectral tuning in sensory rhodopsin II.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Time-resolved FT-IR spectroscopic investigation of the pH-dependent proton transfer reactions in the E194Q mutant of 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=2746972

A model-independent approach to assigning bacteriorhodopsin's intramolecular reactions to photocycle intermediates

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746972

Protein conformational changes in the bacteriorhodopsin photocycle

3 December 2018

1 reference

12 December 2020

Chromophore distortions in the bacteriorhodopsin photocycle: evolution of the H-C14-C15-H dihedral angle measured by solid-state NMR

1 reference

12 December 2020

Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy

1 reference

12 December 2020

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

1 reference

12 December 2020

Tuning of Retinal Twisting in Bacteriorhodopsin Controls the Directionality of the Early Photocycle Steps

1 reference

12 December 2020

Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method

1 reference

12 December 2020

Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements

1 reference

12 December 2020

Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins.

1 reference

12 December 2020

Relationship of retinal configuration and internal proton transfer at the end of the bacteriorhodopsin photocycle

1 reference

12 December 2020

Bacteriorhodopsin's intramolecular proton-release pathway consists of a hydrogen-bonded network

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA809767V

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19405533%20AND%20SRC:MED&resulttype=core&format=json

release_jhbzbmjugfefredvrlipbtmxyy

27 January 2020

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/jhbzbmjugfefredvrlipbtmxyy

24 November 2022

mapped directly with Wikidata item

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19405533%20AND%20SRC:MED&resulttype=core&format=json

27 January 2020

PubMed publication ID

19405533

1 reference