Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations (Q33907934)

29 July 2017

Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations (English)

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29 July 2017

B Isralewitz

1

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29 July 2017

S Izrailev

series ordinal

2

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29 July 2017

K Schulten

series ordinal

3

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29 July 2017

language of work or name

English

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publication date

1 December 1997

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29 July 2017

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29 July 2017

73

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2972-2979

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6

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describes a project that uses

29 July 2017

molecular dynamics simulation

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Reconstructing potential energy functions from simulated force-induced unbinding processes

inferred from title

cites work

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Molecular dynamics study of unbinding of the avidin-biotin complex

5 July 2018

1 reference

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Dynamic strength of molecular adhesion bonds

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Knowledge-based protein secondary structure assignment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Analysis of conformational changes in bacteriorhodopsin upon retinal removal

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Electron-crystallographic refinement of the structure of bacteriorhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Two light-transducing membrane proteins: bacteriorhodopsin and the mammalian rhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Mechanism of light-dependent proton translocation by bacteriorhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Adhesion forces between individual ligand-receptor pairs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

A collision gradient method to determine the immersion depth of nitroxides in lipid bilayers: application to spin-labeled mutants of bacteriorhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Biological applications of optical forces

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Site of attachment of retinal in bacteriorhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Reversible Dissociation of the Purple Complex in Bacteriorhodopsin and Identification of 13-cis and all-trans-Retinal as its Chromophores

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Light-dependent reaction of bacteriorhodopsin with hydroxylamine in cell suspensions of Halobacterium halobium: demonstration of an apo-membrane.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Structure-function studies on bacteriorhodopsin. V. Effects of amino acid substitutions in the putative helix F.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Studies of rhodopsin and bacteriorhodopsin using modified retinals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Aspartic acid substitutions affect proton translocation by bacteriorhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Bacteriorhodopsin, a membrane protein that uses light to translocate protons

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Structure-function studies on bacteriorhodopsin. IX. Substitutions of tryptophan residues affect protein-retinal interactions in bacteriorhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Structure-function studies on bacteriorhodopsin. VIII. Substitutions of the membrane-embedded prolines 50, 91, and 186: the effects are determined by the substituting amino acids.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Basic local alignment search tool

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

The retinylidene Schiff base counterion in bacteriorhodopsin.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Wild-type and mutant bacteriorhodopsins D85N, D96N, and R82Q: purification to homogeneity, pH dependence of pumping, and electron diffraction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Locations of Arg-82, Asp-85, and Asp-96 in helix C of bacteriorhodopsin relative to the aqueous boundaries

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

A unifying concept for ion translocation by retinal proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Proton transfer and energy coupling in the bacteriorhodopsin photocycle

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Hydrophobic amino acids in the retinal-binding pocket of bacteriorhodopsin.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Long-range effects on the retinal chromophore of bacteriorhodopsin caused by surface carboxyl group modification.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Effects of detergent micelles on the recombination reaction of opsin and 11-cis-retinal.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Arrangement of rhodopsin transmembrane α-helices

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Retinal Binding during Folding and Assembly of the Membrane Protein Bacteriorhodopsin†

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181203

Refolding of an integral membrane protein. Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments

29 October 2018

1 reference

12 December 2020

Regeneration of rhodopsin and bacteriorhodopsin. The role of retinal analogues as inhibitors

1 reference

12 December 2020

Denaturation and renaturation of bacteriorhodopsin in detergents and lipid-detergent mixtures

1 reference

12 December 2020

Effect of variation of retinal polyene side-chain length on formation and function of bacteriorhodopsin analogue pigments

1 reference

12 December 2020

Mechanism of vitamin A movement between rod outer segments, interphotoreceptor retinoid-binding protein, and liposomes

1 reference

12 December 2020

Structural studies on transmembrane proteins. 1. Model study using bacteriorhodopsin mutants containing single cysteine residues

1 reference

12 December 2020

Membrane protein folding and oligomerization: the two-stage model

1 reference

12 December 2020

Solubility of retinoids in water

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12 December 2020

Molecular dynamics study of bacteriorhodopsin and artificial pigments

1 reference

12 December 2020

The role of water in retinal complexation to bacterio-opsin

1 reference

12 December 2020

Reconstitution of bacteriorhodopsin

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12 December 2020

Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin

1 reference

12 December 2020

10.1016/S0006-3495(97)78326-7

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DOI

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29 July 2017

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29 July 2017

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