Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein (Q33664368)

28 July 2017

title

Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein (English)

1 reference

28 July 2017

2

Jarek Juraszek

1 reference

28 July 2017

Jocelyne Vreede

1

1 reference

28 July 2017

Peter G Bolhuis

series ordinal

3

1 reference

28 July 2017

language of work or name

English

0 references

publication date

26 January 2010

1 reference

Proceedings of the National Academy of Sciences of the United States of America

28 July 2017

published in

1 reference

28 July 2017

volume

107

1 reference

28 July 2017

issue

6

1 reference

28 July 2017

page(s)

2397-2402

1 reference

Rapid equilibrium sampling initiated from nonequilibrium data

28 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Conformational changes in the N-terminal region of photoactive yellow protein: a time-resolved diffusion study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Role of a conserved salt bridge between the PAS core and the N-terminal domain in the activation of the photoreceptor photoactive yellow protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

GROMACS: fast, flexible, and free

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

How well can simulation predict protein folding kinetics and thermodynamics?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Reaction coordinates and rates from transition paths

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Predicting the signaling state of photoactive yellow protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Time-resolved resonance raman structural studies of the pB' intermediate in the photocycle of photoactive yellow protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Deuterium isotope effects in the photocycle transitions of the photoactive yellow protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Active site mutants implicate key residues for control of color and light cycle kinetics of photoactive yellow protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Primary structure of a photoactive yellow protein from the phototrophic bacterium Ectothiorhodospira halophila, with evidence for the mass and the binding site of the chromophore

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Transient proton uptake and release is associated with the photocycle of the photoactive yellow protein from the purple phototrophic bacterium Ectothiorhodospira halophila

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Photoactive yellow protein from the purple phototrophic bacterium, Ectothiorhodospira halophila. Quantum yield of photobleaching and effects of temperature, alcohols, glycerol, and sucrose on kinetics of photobleaching and recovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

Protonation/deprotonation reactions triggered by photoactivation of photoactive yellow protein from Ectothiorhodospira halophila

21 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

The solution structure of a transient photoreceptor intermediate: Delta25 photoactive yellow protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Initial steps of signal generation in photoactive yellow protein revealed with femtosecond mid-infrared spectroscopy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Protonation of the chromophore in the photoactive yellow protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Automatic method for identifying reaction coordinates in complex systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Obtaining reaction coordinates by likelihood maximization

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Extensions to the likelihood maximization approach for finding reaction coordinates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Controlled reduction of the humidity induces a shortcut recovery reaction in the photocycle of photoactive yellow protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Structural changes during the photocycle of photoactive yellow protein monitored by ultraviolet resonance raman spectra of tyrosine and tryptophan

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Distinguishing chromophore structures of photocycle intermediates of the photoreceptor PYP by transient fluorescence and energy transfer

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Dynamics of protein and chromophore structural changes in the photocycle of photoactive yellow protein monitored by time-resolved optical rotatory dispersion

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Rate constant and reaction coordinate of Trp-cage folding in explicit water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Markovian milestoning with Voronoi tessellations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0908754107

Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823881

30 October 2018

Identifiers

DOI

10.1073/PNAS.0908754107

1 reference

28 July 2017

0 references

1 reference

28 July 2017

1 reference