Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes (Q42144097)

17 October 2017

Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes (English)

1 reference

17 October 2017

13

1 reference

Nicole Frankenberg-Dinkel

17 October 2017

4

David von Stetten

0 references

11

Nicole Frankenberg-Dinkel

0 references

Tilman Lamparter

14

Francisco Velazquez Escobar

Tilman Lamparter

0 references

Francisco Velazquez Escobar

2

0 references

Steve Kaminski

Steve Kaminski

3

0 references

Patrick Scheerer

Patrick Scheerer

8

0 references

Peter Hildebrandt

Peter Hildebrandt

16

0 references

Patrick Piwowarski

9

Patrick Piwowarski

1 reference

17 October 2017

Johannes Salewski

1

1 reference

17 October 2017

Anke Keidel

5

1 reference

17 October 2017

Yvonne Rippers

6

1 reference

17 October 2017

Norbert Michael

7

1 reference

17 October 2017

Franz Bartl

10

1 reference

17 October 2017

Simone Ringsdorf

12

1 reference

17 October 2017

Tilman Lamparter

14

1 reference

17 October 2017

Maria Andrea Mroginski

15

1 reference

17 October 2017

language of work or name

English

0 references

publication date

19 April 2013

1 reference

Journal of Biological Chemistry

17 October 2017

1 reference

17 October 2017

288

1 reference

17 October 2017

23

1 reference

17 October 2017

16800-16814

1 reference

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

17 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Solid-state NMR spectroscopy to probe photoactivation in canonical phytochromes.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Bathy phytochromes in rhizobial soil bacteria

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Protein annotation and modelling servers at University College London

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Features and development of Coot

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Light-induced conformational changes of the chromophore and the protein in phytochromes: bacterial phytochromes as model systems.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Phytochrome three-dimensional structures and functions

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

A brief history of phytochromes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: reconciling structural and spectroscopic data by QM/MM calculations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

CHARMM: the biomolecular simulation program

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Distinct classes of red/far-red photochemistry within the phytochrome superfamily

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

The fungal phytochrome FphA from Aspergillus nidulans.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

The structure of a complete phytochrome sensory module in the Pr ground state

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

FTIR study of the photoinduced processes of plant phytochrome phyA using isotope-labeled bilins and density functional theory calculations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Mutational analysis of Deinococcus radiodurans bacteriophytochrome reveals key amino acids necessary for the photochromicity and proton exchange cycle of phytochromes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

The chromophore structures of the Pr States in plant and bacterial phytochromes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Quantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-C-phycocyanin

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

High resolution structure of Deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

29 May 2018

QM/MM studies of enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Scalable molecular dynamics with NAMD

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

SWISS-MODEL: An automated protein homology-modeling server

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

The pair of bacteriophytochromes from Agrobacterium tumefaciens are histidine kinases with opposing photobiological properties

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Phytochrome from Agrobacterium tumefaciens has unusual spectral properties and reveals an N-terminal chromophore attachment site

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Phytochrome ancestry: sensors of bilins and light.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Protein secondary structure prediction based on position-specific scoring matrices

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Eukaryotic phytochromes: light-regulated serine/threonine protein kinases with histidine kinase ancestry

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

A cyanobacterial phytochrome two-component light sensory system.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Errors in protein structures

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Resonance Raman analysis of the Pr and Pfr forms of phytochrome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Basic local alignment search tool

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Fourier transform resonance Raman spectroscopy of phytochrome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Molecular cloning of a novel phytochrome gene of the moss Ceratodon purpureus which encodes a putative light-regulated protein kinase

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

A prokaryotic phytochrome.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Chemical inhomogeneity in the ultrafast dynamics of the DXCF cyanobacteriochrome Tlr0924.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Solid-state NMR spectroscopic study of chromophore-protein interactions in the Pr ground state of plant phytochrome A.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Femtosecond photodynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. 2. reverse dynamics.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Photophysical diversity of two novel cyanobacteriochromes with phycocyanobilin chromophores: photochemistry and dark reversion kinetics

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Structure of the chromophore binding pocket in the Pr state of plant phytochrome phyA.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Characterization of the covalent and noncovalent adducts of Agp1 phytochrome assembled with biliverdin and phycocyanobilin by circular dichroism and flash photolysis.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Domain interaction in cyanobacterial phytochromes as a prerequisite for spectral integrity.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Homologous expression of a bacterial phytochrome. The cyanobacterium Fremyella diplosiphon incorporates biliverdin as a genuine, functional chromophore.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Highly conserved residues Asp-197 and His-250 in Agp1 phytochrome control the proton affinity of the chromophore and Pfr formation.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Assembly of synthetic locked chromophores with agrobacterium phytochromes Agp1 and Agp2.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

The Aspergillus nidulans phytochrome FphA represses sexual development in red light

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Light-induced proton release of phytochrome is coupled to the transient deprotonation of the tetrapyrrole chromophore

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Biochemical and spectroscopic characterization of the bacterial phytochrome of Pseudomonas aeruginosa

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Phytochrome Cph1 from the cyanobacterium Synechocystis PCC6803. Purification, assembly, and quaternary structure.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Disruption of a Synechocystis sp. PCC 6803 gene with partial similarity to phytochrome genes alters growth under changing light qualities.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675613

Density-functional thermochemistry. III. The role of exact exchange

17 August 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M113.457531

PROCHECK: a program to check the stereochemical quality of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M113.457531

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M113.457531

Chromophore Heterogeneity and Photoconversion in Phytochrome Crystals and Solution Studied by Resonance Raman Spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M113.457531

QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M113.457531

Raman Spectra of the Phycoviolobilin Cofactor in Phycoerythrocyanin Calculated by QM/MM Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M113.457531

Protonation State and Structural Changes of the Tetrapyrrole Chromophore during the Pr→ PfrPhototransformation of Phytochrome: A Resonance Raman Spectroscopic Study†

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M113.457531

Elucidating photoinduced structural changes in phytochromes by the combined application of resonance Raman spectroscopy and theoretical methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M113.457531

21 January 2018

Identifiers

DOI

10.1074/JBC.M113.457531

1 reference

17 October 2017

1 reference

17 October 2017

PubMed publication ID

23603902

1 reference