GFP family: structural insights into spectral tuning.

Proteins homologous to green fluorescent protein (GFP) span most of the visible spectrum, offering indispensable tools for live cell imaging. Structural transformations, such as posttranslational autocatalytic and photo-induced modifications, chromophore isomerization, and rearrangements in its environment underlie the unique capacity of these proteins to tune their own optical characteristics. A better understanding of optical self-tuning mechanisms would assist in the engineering of more precisely adapted variants and in expanding the palette of GFP-like proteins to the near-infrared region. The latest advances in this field shed light upon multiple features of protein posttranslational chemistry, and establish some important basic principles about the interplay of structure and spectral properties in the GFP family.

[1]  Atsushi Miyawaki,et al.  Photo-induced peptide cleavage in the green-to-red conversion of a fluorescent protein. , 2003, Molecular cell.

[2]  A. Miyawaki,et al.  Ultrafast excited-state dynamics of the photoswitchable protein Dronpa. , 2007, Journal of the American Chemical Society.

[3]  V. Martynov,et al.  Chromophore structure of the kindling fluorescent protein asFP595 from Anemonia sulcata. , 2007, Journal of the American Chemical Society.

[4]  Konstantin A Lukyanov,et al.  A colourless green fluorescent protein homologue from the non-fluorescent hydromedusa Aequorea coerulescens and its fluorescent mutants. , 2003, The Biochemical journal.

[5]  J. Wiedenmann,et al.  Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Takeharu Nagai,et al.  Cyan-emitting and orange-emitting fluorescent proteins as a donor/acceptor pair for fluorescence resonance energy transfer. , 2004, The Biochemical journal.

[7]  Robert E Campbell,et al.  Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins. , 2007, Biochemistry.

[8]  Roger Y. Tsien,et al.  Crystal Structure of the Aequorea victoria Green Fluorescent Protein , 1996, Science.

[9]  V. I. Martynov,et al.  Photoconversion of the Chromophore of a Fluorescent Protein from Dendronephthya sp. , 2004, Biochemistry (Moscow).

[10]  R. Tsien,et al.  Evolution of new nonantibody proteins via iterative somatic hypermutation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[11]  B. Vallone,et al.  Chromophore-protein interactions in the anthozoan green fluorescent protein asFP499. , 2006, Biophysical journal.

[12]  P. Selvin.  Fluorescence resonance energy transfer. , 1995, Methods in enzymology.

[13]  Richard N. Day,et al.  Fluorescent protein spectra. , 2001, Journal of cell science.

[14]  J. Tainer,et al.  The case of the missing ring: radical cleavage of a carbon-carbon bond and implications for GFP chromophore biosynthesis. , 2007, Journal of the American Chemical Society.

[15]  B. I. Maksimov,et al.  A Purple-blue Chromoprotein from Goniopora tenuidens Belongs to the DsRed Subfamily of GFP-like Proteins* , 2003, Journal of Biological Chemistry.

[16]  S. Boxer,et al.  Dynamic Stokes shift in green fluorescent protein variants , 2007, Proceedings of the National Academy of Sciences.

[17]  Roger Y. Tsien,et al.  Improved green fluorescence , 1995, Nature.

[18]  Peter Dedecker,et al.  Photo-induced protonation/deprotonation in the GFP-like fluorescent protein Dronpa: mechanism responsible for the reversible photoswitching , 2006, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[19]  Nathan C Shaner,et al.  Novel chromophores and buried charges control color in mFruits. , 2006, Biochemistry.

[20]  R Y Tsien,et al.  Wavelength mutations and posttranslational autoxidation of green fluorescent protein. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[21]  V. Pletnev,et al.  Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 Å , 2007, Russian Journal of Bioorganic Chemistry.

[22]  R. Tsien,et al.  The Fluorescent Toolbox for Assessing Protein Location and Function , 2006, Science.

[23]  S J Remington,et al.  Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Yuichiro Hori,et al.  [Crystal structure of the Aequorea victoria green fluorescent protein]. , 2007, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[25]  Atsushi Miyawaki,et al.  Semi‐rational engineering of a coral fluorescent protein into an efficient highlighter , 2005, EMBO reports.

[26]  Konstantin A Lukyanov,et al.  Common pathway for the red chromophore formation in fluorescent proteins and chromoproteins. , 2004, Chemistry & biology.

[27]  N. Pletneva,et al.  Structure and reactivity of the chromophore of a GFP-like chromoprotein from Condylactis gigantea. , 2006, Biochemistry.

[28]  Konstantin A Lukyanov,et al.  Far-red fluorescent proteins evolved from a blue chromoprotein from Actinia equina. , 2005, The Biochemical journal.

[29]  K. Lukyanov,et al.  Diversity and evolution of the green fluorescent protein family , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[30]  S. Lukyanov,et al.  GFP‐like chromoproteins as a source of far‐red fluorescent proteins , 2001, FEBS letters.

[31]  S. Lukyanov,et al.  GFP-like proteins as ubiquitous metazoan superfamily: evolution of functional features and structural complexity. , 2004, Molecular biology and evolution.

[32]  John A Tainer,et al.  Structural evidence for an enolate intermediate in GFP fluorophore biosynthesis. , 2006, Journal of the American Chemical Society.

[33]  Marco A Mena,et al.  Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library , 2006, Nature Biotechnology.

[34]  Robert E Campbell,et al.  Hue-shifted monomeric variants of Clavularia cyan fluorescent protein: identification of the molecular determinants of color and applications in fluorescence imaging , 2008 .

[35]  S. Boxer,et al.  Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 2. Unusual photophysical properties. , 2007, Biochemistry.

[36]  Patrick S Daugherty,et al.  Evolutionary optimization of fluorescent proteins for intracellular FRET , 2005, Nature Biotechnology.

[37]  Mark A Rizzo,et al.  An improved cyan fluorescent protein variant useful for FRET , 2004, Nature Biotechnology.

[38]  O. Hoegh‐Guldberg,et al.  The 2.2 A crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation. , 2003, Structure.

[39]  Atsushi Miyawaki,et al.  Crystallographic evidence for water-assisted photo-induced peptide cleavage in the stony coral fluorescent protein Kaede. , 2007, Journal of molecular biology.

[40]  S J Remington,et al.  Crystal structure and photodynamic behavior of the blue emission variant Y66H/Y145F of green fluorescent protein. , 1997, Biochemistry.

[41]  S. Remington.  Fluorescent proteins: maturation, photochemistry and photophysics. , 2006, Current opinion in structural biology.

[42]  Christian Eggeling,et al.  Structure and mechanism of the reversible photoswitch of a fluorescent protein. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Atsushi Miyawaki,et al.  Structural Characterization of a Blue Chromoprotein and Its Yellow Mutant from the Sea Anemone Cnidopus Japonicus* , 2006, Journal of Biological Chemistry.

[44]  Lars V. Schäfer,et al.  Photoswitching of the fluorescent protein asFP595: mechanism, proton pathways, and absorption spectra. , 2007, Angewandte Chemie.

[45]  K. Burgess,et al.  Syntheses of highly fluorescent GFP-chromophore analogues. , 2008, Journal of the American Chemical Society.

[46]  S. Lukyanov,et al.  Chromophore Environment Provides Clue to “Kindling Fluorescent Protein” Riddle* , 2003, The Journal of Biological Chemistry.

[47]  Peter Dedecker,et al.  Reversible single-molecule photoswitching in the GFP-like fluorescent protein Dronpa. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  K K Baldridge,et al.  The structure of the chromophore within DsRed, a red fluorescent protein from coral. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[49]  G. Patterson,et al.  Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. , 1997, Biophysical journal.

[50]  J. Rossjohn,et al.  The 1.7 A crystal structure of Dronpa: a photoswitchable green fluorescent protein. , 2006, Journal of molecular biology.

[51]  V. Verkhusha,et al.  Innovation: Photoactivatable fluorescent proteins. , 2005, Nature reviews. Molecular cell biology.

[52]  S. Lukyanov,et al.  Synthesis and properties of the chromophore of the asFP595 chromoprotein from Anemonia sulcata. , 2005, Biochemistry.

[53]  K. Solntsev,et al.  Solvatochromism of the green fluorescence protein chromophore and its derivatives. , 2006, Journal of the American Chemical Society.

[54]  Hetal N. Patel,et al.  Oxidative chemistry in the GFP active site leads to covalent cross-linking of a modified leucine side chain with a histidine imidazole: implications for the mechanism of chromophore formation. , 2005, Biochemistry.

[55]  J. Tainer,et al.  Defining the role of arginine 96 in green fluorescent protein fluorophore biosynthesis. , 2005, Biochemistry.

[56]  P. Tonge,et al.  An alternate proton acceptor for excited-state proton transfer in green fluorescent protein: rewiring GFP. , 2008, Journal of the American Chemical Society.

[57]  A. Miyawaki,et al.  Competition between energy and proton transfer in ultrafast excited-state dynamics of an oligomeric fluorescent protein red Kaede. , 2006, The journal of physical chemistry. B.

[58]  G Ulrich Nienhaus,et al.  Optimized and far-red-emitting variants of fluorescent protein eqFP611. , 2008, Chemistry & biology.

[59]  J. Rossjohn,et al.  Variations on the GFP Chromophore , 2005, Journal of Biological Chemistry.

[60]  K. Lukyanov,et al.  Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis , 2002, BMC Biochemistry.

[61]  J. Tainer,et al.  Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[62]  S. Lukyanov,et al.  Natural Animal Coloration Can Be Determined by a Nonfluorescent Green Fluorescent Protein Homolog* , 2000, The Journal of Biological Chemistry.

[63]  Christian Eggeling,et al.  Structural basis for reversible photoswitching in Dronpa , 2007, Proceedings of the National Academy of Sciences.

[64]  V. Verkhusha,et al.  Photoactivatable fluorescent proteins , 2005, Nature Reviews Molecular Cell Biology.

[65]  S. Boxer,et al.  Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 1. Mutagenesis and structural studies. , 2007, Biochemistry.

[66]  S. Lukyanov,et al.  Fluorescent proteins from nonbioluminescent Anthozoa species , 1999, Nature Biotechnology.

[67]  S J Remington,et al.  Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Chromophore aspartate oxidation-decarboxylation in the green-to-red conversion of a fluorescent protein from Zoanthus sp. 2. , 2007, Biochemistry.

[69]  R. Wachter,et al.  Chromogenic cross-link formation in green fluorescent protein. , 2007, Accounts of chemical research.

[70]  Konstantin A Lukyanov,et al.  zFP538, a yellow-fluorescent protein from Zoanthus, contains a novel three-ring chromophore. , 2005, Biochemistry.

[71]  A. Miyawaki,et al.  Light-dependent regulation of structural flexibility in a photochromic fluorescent protein , 2008, Proceedings of the National Academy of Sciences.

[72]  M. Davidson,et al.  Advances in fluorescent protein technology , 2011, Journal of Cell Science.

[73]  G. Orlovsky,et al.  The kindling fluorescent protein: a transient photoswitchable marker. , 2006, Physiology.

[74]  Sean C. Smith,et al.  A structural basis for the pH-dependent increase in fluorescence efficiency of chromoproteins. , 2007, Journal of molecular biology.

[75]  Konstantin A Lukyanov,et al.  The first mutant of the Aequorea victoria green fluorescent protein that forms a red chromophore. , 2008, Biochemistry.

[76]  Robert E Campbell,et al.  Structural basis for reversible photobleaching of a green fluorescent protein homologue , 2007, Proceedings of the National Academy of Sciences.

[77]  X. Shu,et al.  Kindling fluorescent protein from Anemonia sulcata: dark-state structure at 1.38 A resolution. , 2005, Biochemistry.

[78]  Alexander Wlodawer,et al.  The structural basis for spectral variations in green fluorescent protein , 1997, Nature Structural Biology.

[79]  D. Shcherbo,et al.  Bright far-red fluorescent protein for whole-body imaging , 2007, Nature Methods.

[80]  P. Tonge,et al.  Author ' s personal copy Crystal Structure and Raman Studies of dsFP 483 , a Cyan Fluorescent Protein from Discosoma striata , 2008 .

[81]  S J Remington,et al.  Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein. , 1998, Structure.

[82]  Crystal structures of amFP486, a cyan fluorescent protein from Anemonia majano, and variants , 2005 .

[83]  P. Chou,et al.  Ortho green fluorescence protein synthetic chromophore; excited-state intramolecular proton transfer via a seven-membered-ring hydrogen-bonding system. , 2007, Journal of the American Chemical Society.

[84]  J. Hofkens,et al.  Photoconversion in the red fluorescent protein from the sea anemone Entacmaea quadricolor: is cis-trans isomerization involved? , 2006, Journal of the American Chemical Society.

[85]  K. Solntsev,et al.  The meta-green fluorescent protein chromophore. , 2007, Journal of the American Chemical Society.

[86]  R. Ranganathan,et al.  The structural basis for red fluorescence in the tetrameric GFP homolog DsRed , 2000, Nature Structural Biology.

[87]  Mark Prescott,et al.  The 2.0-Å Crystal Structure of eqFP611, a Far Red Fluorescent Protein from the Sea Anemone Entacmaea quadricolor* , 2003, Journal of Biological Chemistry.

[88]  A. Miyawaki,et al.  Regulated Fast Nucleocytoplasmic Shuttling Observed by Reversible Protein Highlighting , 2004, Science.

[89]  R. Tsien,et al.  Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein , 2004, Nature Biotechnology.

[90]  J. Rossjohn,et al.  Amino acid substitutions around the chromophore of the chromoprotein Rtms5 influence polypeptide cleavage. , 2006, Biochemical and biophysical research communications.

[91]  Hetal N. Patel,et al.  Base Catalysis of Chromophore Formation in Arg96 and Glu222 Variants of Green Fluorescent Protein* , 2005, Journal of Biological Chemistry.