(Q34546748)

2 August 2017

title

Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin (English)

1 reference

2 August 2017

Hiroshi C Watanabe

1

1 reference

2 August 2017

Yoshiharu Mori

2

1 reference

2 August 2017

Takashi Tada

3

1 reference

2 August 2017

Shozo Yokoyama

4

1 reference

2 August 2017

Takahisa Yamato

5

1 reference

2 August 2017

publication date

1 January 2010

1 reference

2 August 2017

1 reference

2 August 2017

volume

6

1 reference

2 August 2017

page(s)

67-68

1 reference

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

2 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Crystal structure of squid rhodopsin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

A novel spectral tuning in the short wavelength-sensitive (SWS1 and SWS2) pigments of bluefin killifish (Lucania goodei)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Computational photochemistry of retinal proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Origin and consequences of steric strain in the rhodopsin binding pocket

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Scalable molecular dynamics with NAMD

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Time-resolved photointermediate changes in rhodopsin glutamic acid 181 mutants.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

QM/MM study of energy storage and molecular rearrangements due to the primary event in vision

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Retinal counterion switch in the photoactivation of the G protein-coupled receptor rhodopsin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Relative orientation between the beta-ionone ring and the polyene chain for the chromophore of rhodopsin in native membranes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Function of extracellular loop 2 in rhodopsin: glutamic acid 181 modulates stability and absorption wavelength of metarhodopsin II.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Studies on the structure of the G-protein-coupled receptor rhodopsin including the putative G-protein binding site in unactivated and activated forms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Conformation and orientation of the retinyl chromophore in rhodopsin: a critical evaluation of recent NMR data on the basis of theoretical calculations results in a minimum energy structure consistent with all experimental data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Comparative protein modelling by satisfaction of spatial restraints

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Improved sensitivity of profile searches through the use of sequence weights and gap excision.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Stereochemical quality of protein structure coordinates

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Studies on cephalopod rhodopsin: photoisomerization of the chromophore

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Visual-pigment spectra: implications of the protonation of the retinal Schiff base

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Probing and modeling the absorption of retinal protein chromophores in vacuo.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Color-changing mutation in the E-F loop of proteorhodopsin

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Calculating absorption shifts for retinal proteins: computational challenges.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Structure, spectroscopy, and spectral tuning of the gas-phase retinal chromophore: the beta-ionone "handle" and alkyl group effect.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

The role of Glu181 in the photoactivation of rhodopsin

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Absorption of schiff-base retinal chromophores in vacuo

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Ground and excited state CASPT2 geometry optimizations of small organic molecules

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

Observations of light-induced structural changes of retinal within rhodopsin

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032607

On the mechanism of wavelength regulation in visual pigments

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21297892

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Anion-induced wavelength regulation of absorption maxima of Schiff bases of retinal

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21297892

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Spectral tuning of photoactive yellow protein

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21297892

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.2142/BIOPHYSICS.6.67

1 reference

2 August 2017

1 reference

2 August 2017

1 reference