(Q42536182)

1 November 2017

Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study (English)

1 reference

1 November 2017

Roux B

1

1 reference

1 November 2017

Nina M

series ordinal

2

1 reference

1 November 2017

Pomès R

series ordinal

3

1 reference

1 November 2017

Smith JC

series ordinal

4

1 reference

1 November 2017

language of work or name

English

0 references

publication date

1 August 1996

1 reference

1 November 2017

1 reference

1 November 2017

71

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1 November 2017

2

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1 November 2017

670-681

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Protein catalysis of the retinal subpicosecond photoisomerization in the primary process of bacteriorhodopsin photosynthesis.

1 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Experimental evidence for secondary protein-chromophore interactions at the Schiff base linkage in bacteriorhodopsin: Molecular mechanism for proton pumping

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Molecular dynamics study of the proton pump cycle of bacteriorhodopsin

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Structure and dynamics of bacteriorhodopsin. Comparison of simulation and experiment.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Environmental effects on the protonation states of active site residues in bacteriorhodopsin

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Evidence for a bound water molecule next to the retinal Schiff base in bacteriorhodopsin and rhodopsin: a resonance Raman study of the Schiff base hydrogen/deuterium exchange

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Buried waters and internal cavities in monomeric proteins

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Structure and Fluctuations of Bacteriorhodopsin in the Purple Membrane: A Molecular Dynamics Study

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its G36S mutant

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

On the mechanism of hydrogen-deuterium exchange in bacteriorhodopsin

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Acid-base equilibrium of the Schiff base in bacteriorhodopsin.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Dark-adapted bacteriorhodopsin contains 13-cis, 15-syn and all-trans, 15-anti retinal Schiff bases

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Water and proteins. II. The location and dynamics of water in protein systems and its relation to their stability and properties

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Rhodopsin-like protein from the purple membrane of Halobacterium halobium

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Functions of a New Photoreceptor Membrane

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Structure and hydration of purple membranes in different conditions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Bacteriorhodopsin mutants containing single tyrosine to phenylalanine substitutions are all active in proton translocation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Replacement of aspartic acid-96 by asparagine in bacteriorhodopsin slows both the decay of the M intermediate and the associated proton movement

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Aspartic acid-96 is the internal proton donor in the reprotonation of the Schiff base of bacteriorhodopsin

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Aspartic acids 96 and 85 play a central role in the function of bacteriorhodopsin as a proton pump

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Structure-function studies on bacteriorhodopsin. X. Individual substitutions of arginine residues by glutamine affect chromophore formation, photocycle, and proton translocation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Role of aspartate-96 in proton translocation by bacteriorhodopsin.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Solid-state 13C and 15N NMR study of the low pH forms of bacteriorhodopsin

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Solid-state 13C NMR study of tyrosine protonation in dark-adapted bacteriorhodopsin

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Protonation state of Asp (Glu)-85 regulates the purple-to-blue transition in bacteriorhodopsin mutants Arg-82----Ala and Asp-85----Glu: the blue form is inactive in proton translocation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Bacteriorhodopsin mutants containing single substitutions of serine or threonine residues are all active in proton translocation.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Vibrational spectroscopy of bacteriorhodopsin mutants. Evidence that Thr-46 and Thr-89 form part of a transient network of hydrogen bonds

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Water is required for proton transfer from aspartate-96 to the bacteriorhodopsin Schiff base

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Internal water molecules and H‐bonding in biological macromolecules: A review of structural features with functional implications

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Detection of a water molecule in the active-site of bacteriorhodopsin: hydrogen bonding changes during the primary photoreaction.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Free energy simulations: the meaning of the individual contributions from a component analysis.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Solid-state 13C NMR studies of retinal in bacteriorhodopsin

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1233524

Water molecules and exchangeable hydrogen ions at the active centre of bacteriorhodopsin localized by neutron diffraction. Elements of the proton pathway?

1 December 2018

1 reference

12 December 2020

Vibrational spectroscopy of bacteriorhodopsin mutants: light-driven proton transport involves protonation changes of aspartic acid residues 85, 96, and 212

1 reference

12 December 2020

Molecular dynamics study of bacteriorhodopsin and artificial pigments

1 reference

12 December 2020

Light-driven protonation changes of internal aspartic acids of bacteriorhodopsin: an investigation by static and time-resolved infrared difference spectroscopy using [4-13C]aspartic acid labeled purple membrane

1 reference

12 December 2020

Interaction of aspartate-85 with a water molecule and the protonated Schiff base in the L intermediate of bacteriorhodopsin: a Fourier-transform infrared spectroscopic study

1 reference

12 December 2020

Solid-state 13C NMR of the retinal chromophore in photointermediates of bacteriorhodopsin: characterization of two forms of M

1 reference

12 December 2020

Can the stability of protein mutants be predicted by free energy calculations?

1 reference

12 December 2020

10.1016/S0006-3495(96)79267-6

Identifiers

DOI

1 reference

1 November 2017

1 reference

1 November 2017

PubMed publication ID

8842206

1 reference