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Title: Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies

Authors:
; ; ; ; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1368287
Resource Type:
Journal Article
Journal Name:
Chemical Science
Additional Journal Information:
Journal Volume: 8; Journal Issue: 6; Journal ID: ISSN 2041-6520
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Baloban, Mikhail, Shcherbakova, Daria M., Pletnev, Sergei, Pletnev, Vladimir Z., Lagarias, J. Clark, and Verkhusha, Vladislav V. Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. United States: N. p., 2017. Web. doi:10.1039/C7SC00855D.
Baloban, Mikhail, Shcherbakova, Daria M., Pletnev, Sergei, Pletnev, Vladimir Z., Lagarias, J. Clark, & Verkhusha, Vladislav V. Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. United States. doi:10.1039/C7SC00855D.
Baloban, Mikhail, Shcherbakova, Daria M., Pletnev, Sergei, Pletnev, Vladimir Z., Lagarias, J. Clark, and Verkhusha, Vladislav V. Sun . "Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies". United States. doi:10.1039/C7SC00855D.
@article{osti_1368287,
title = {Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies},
author = {Baloban, Mikhail and Shcherbakova, Daria M. and Pletnev, Sergei and Pletnev, Vladimir Z. and Lagarias, J. Clark and Verkhusha, Vladislav V.},
abstractNote = {},
doi = {10.1039/C7SC00855D},
journal = {Chemical Science},
issn = {2041-6520},
number = 6,
volume = 8,
place = {United States},
year = {2017},
month = {1}
}

Works referenced in this record:

High Resolution Structure of Deinococcus Bacteriophytochrome Yields New Insights into Phytochrome Architecture and Evolution
journal, February 2007

  • Wagner, Jeremiah R.; Zhang, Junrui; Brunzelle, Joseph S.
  • Journal of Biological Chemistry, Vol. 282, Issue 16
  • DOI: 10.1074/jbc.M611824200

Origins of Fluorescence in Evolved Bacteriophytochromes
journal, September 2014

  • Bhattacharya, Shyamosree; Auldridge, Michele E.; Lehtivuori, Heli
  • Journal of Biological Chemistry, Vol. 289, Issue 46
  • DOI: 10.1074/jbc.M114.589739

Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence
journal, December 2015

  • Rumyantsev, Konstantin A.; Shcherbakova, Daria M.; Zakharova, Natalia I.
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep18348

Harnessing phytochrome's glowing potential
journal, November 2004

  • Fischer, A. J.; Lagarias, J. C.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 50
  • DOI: 10.1073/pnas.0407645101

Structures of cyanobacteriochromes from phototaxis regulators AnPixJ and TePixJ reveal general and specific photoconversion mechanism
journal, December 2012

  • Narikawa, R.; Ishizuka, T.; Muraki, N.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 3
  • DOI: 10.1073/pnas.1212098110

A Second Conserved GAF Domain Cysteine Is Required for the Blue/Green Photoreversibility of Cyanobacteriochrome Tlr0924 from Thermosynechococcus elongatus
journal, July 2008

  • Rockwell, Nathan C.; Njuguna, Stephanie Lane; Roberts, Laurel
  • Biochemistry, Vol. 47, Issue 27
  • DOI: 10.1021/bi800088t

A Near-Infrared BiFC Reporter for In Vivo Imaging of Protein-Protein Interactions
journal, August 2013


Multiple Roles of a Conserved GAF Domain Tyrosine Residue in Cyanobacterial and Plant Phytochromes
journal, November 2005

  • Fischer, Amanda J.; Rockwell, Nathan C.; Jang, Abigail Y.
  • Biochemistry, Vol. 44, Issue 46
  • DOI: 10.1021/bi051633z

Structure-guided Engineering Enhances a Phytochrome-based Infrared Fluorescent Protein
journal, December 2011

  • Auldridge, Michele E.; Satyshur, Kenneth A.; Anstrom, David M.
  • Journal of Biological Chemistry, Vol. 287, Issue 10
  • DOI: 10.1074/jbc.M111.295121

Phytochrome Structure and Signaling Mechanisms
journal, June 2006


A naturally monomeric infrared fluorescent protein for protein labeling in vivo
journal, June 2015

  • Yu, Dan; Baird, Michelle A.; Allen, John R.
  • Nature Methods, Vol. 12, Issue 8
  • DOI: 10.1038/nmeth.3447

Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome
journal, July 2013

  • Piatkevich, Kiryl D.; Subach, Fedor V.; Verkhusha, Vladislav V.
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3153

ARP / wARP and molecular replacement
journal, September 2001

  • Perrakis, Anastassis; Harkiolaki, Maria; Wilson, Keith S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 10
  • DOI: 10.1107/S0907444901014007

PROCHECK: a program to check the stereochemical quality of protein structures
journal, April 1993

  • Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.
  • Journal of Applied Crystallography, Vol. 26, Issue 2
  • DOI: 10.1107/S0021889892009944

Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes
journal, January 2016

  • Stepanenko, Olesya V.; Baloban, Mikhail; Bublikov, Grigory S.
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep18750

Engineering of bacterial phytochromes for near-infrared imaging, sensing, and light-control in mammals
journal, January 2013

  • Piatkevich, Kiryl D.; Subach, Fedor V.; Verkhusha, Vladislav V.
  • Chemical Society Reviews, Vol. 42, Issue 8
  • DOI: 10.1039/c3cs35458j

Structure of a Bacteriophytochrome and Light-Stimulated Protomer Swapping with a Gene Repressor
journal, August 2012


Molecular Basis of Spectral Diversity in Near-Infrared Phytochrome-Based Fluorescent Proteins
journal, November 2015


Bacteriophytochromes are photochromic histidine kinases using a biliverdin chromophore
journal, December 2001

  • Bhoo, Seong-Hee; Davis, Seth J.; Walker, Joseph
  • Nature, Vol. 414, Issue 6865
  • DOI: 10.1038/414776a

Near-infrared fluorescent proteins for multicolor in vivo imaging
journal, June 2013

  • Shcherbakova, Daria M.; Verkhusha, Vladislav V.
  • Nature Methods, Vol. 10, Issue 8
  • DOI: 10.1038/nmeth.2521

Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome
journal, May 2009


A Photo-Labile Thioether Linkage to Phycoviolobilin Provides the Foundation for the Blue/Green Photocycles in DXCF-Cyanobacteriochromes
journal, January 2013


A clearer vision for in vivo imaging
journal, April 2001

  • Weissleder, Ralph
  • Nature Biotechnology, Vol. 19, Issue 4
  • DOI: 10.1038/86684

Bright and stable near-infrared fluorescent protein for in vivo imaging
journal, July 2011

  • Filonov, Grigory S.; Piatkevich, Kiryl D.; Ting, Li-Min
  • Nature Biotechnology, Vol. 29, Issue 8
  • DOI: 10.1038/nbt.1918

The Biliverdin Chromophore Binds Covalently to a Conserved Cysteine Residue in the N-Terminus of Agrobacterium Phytochrome Agp1
journal, March 2004

  • Lamparter, Tilman; Carrascal, Montserrat; Michael, Norbert
  • Biochemistry, Vol. 43, Issue 12
  • DOI: 10.1021/bi035693l

Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction
journal, September 2008

  • Yang, X.; Kuk, J.; Moffat, K.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 38
  • DOI: 10.1073/pnas.0806718105

A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome
journal, November 2005

  • Wagner, Jeremiah R.; Brunzelle, Joseph S.; Forest, Katrina T.
  • Nature, Vol. 438, Issue 7066
  • DOI: 10.1038/nature04118

Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion
journal, July 2007

  • Yang, X.; Stojkovic, E. A.; Kuk, J.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 30
  • DOI: 10.1073/pnas.0701737104

The phytofluors: a new class of fluorescent protein probes
journal, November 1997


Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors
journal, November 2005

  • Karniol, Baruch; Wagner, Jeremiah R.; Walker, Joseph M.
  • Biochemical Journal, Vol. 392, Issue 1
  • DOI: 10.1042/BJ20050826

Biliprotein maturation: the chromophore attachment: Biliprotein chromophore attachment
journal, February 2008


Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011

  • Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911001314

Bacterial phytochromes: More than meets the light
journal, January 2011

  • Auldridge, Michele E.; Forest, Katrina T.
  • Critical Reviews in Biochemistry and Molecular Biology, Vol. 46, Issue 1
  • DOI: 10.3109/10409238.2010.546389

Fluorescence quantum yield of oxazine and carbazine laser dyes
journal, November 1981


Mutational Analysis of Deinococcus radiodurans Bacteriophytochrome Reveals Key Amino Acids Necessary for the Photochromicity and Proton Exchange Cycle of Phytochromes
journal, January 2008

  • Wagner, Jeremiah R.; Zhang, Junrui; von Stetten, David
  • Journal of Biological Chemistry, Vol. 283, Issue 18
  • DOI: 10.1074/jbc.M709355200

Bacteriophytochromes in anoxygenic photosynthetic bacteria
journal, July 2008


On the Origin of Heme Absorption Band Shifts and Associated Protein Structural Relaxation in Myoglobin following Flash Photolysis
journal, April 1997

  • Franzen, Stefan; Boxer, Steven G.
  • Journal of Biological Chemistry, Vol. 272, Issue 15
  • DOI: 10.1074/jbc.272.15.9655

Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes
journal, June 2011

  • Rockwell, N. C.; Martin, S. S.; Feoktistova, K.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 29
  • DOI: 10.1073/pnas.1107844108

Fluorescence quantum yield and photochemistry of bacteriophytochrome constructs
journal, January 2011

  • Toh, K. C.; Stojković, Emina A.; van Stokkum, Ivo H. M.
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 25
  • DOI: 10.1039/c1cp00050k

A Brief History of Phytochromes
journal, April 2010


Signal amplification and transduction in phytochrome photosensors
journal, April 2014

  • Takala, Heikki; Björling, Alexander; Berntsson, Oskar
  • Nature, Vol. 509, Issue 7499
  • DOI: 10.1038/nature13310

Defining the Bilin Lyase Domain:  Lessons from the Extended Phytochrome Superfamily
journal, November 2000

  • Wu, Shu-Hsing; Lagarias, J. Clark
  • Biochemistry, Vol. 39, Issue 44
  • DOI: 10.1021/bi001123z

Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging
journal, August 2016

  • Shcherbakova, Daria M.; Baloban, Mikhail; Emelyanov, Alexander V.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12405

MOLREP an Automated Program for Molecular Replacement
journal, December 1997


Fluorescence Properties of the Chromophore-Binding Domain of Bacteriophytochrome from Deinococcus radiodurans
journal, April 2013

  • Lehtivuori, Heli; Rissanen, Ilona; Takala, Heikki
  • The Journal of Physical Chemistry B, Vol. 117, Issue 38
  • DOI: 10.1021/jp312061b