Photophysics and Dihedral Freedom of the Chromophore in Yellow, Blue, and Green Fluorescent Protein

Green fluorescent protein (GFP) and GFP-like fluorescent proteins owe their photophysical properties to an autocatalytically formed intrinsic chromophore. According to quantum mechanical calculations, the excited state of chromophore model systems has significant dihedral freedom, which may lead to fluorescence quenching intersystem crossing. Molecular dynamics simulations with freely rotating chromophoric dihedrals were performed on green, yellow, and blue fluorescent proteins in order to model the dihedral freedom available to the chromophore in the excited state. Most current theories suggest that a restriction in the rotational freedom of the fluorescent protein chromophore will lead to an increase in fluorescence brightness and/or quantum yield. According to our calculations, the dihedral freedom of the systems studied (BFP > A5 > YFP > GFP) increases in the inverse order to the quantum yield. In all simulations, the chromophore undergoes a negatively correlated hula twist (also known as a bottom hula twist mechanism).

• Publication year

  2008

• Venue

  Journal of Physical Chemistry B

• Publication date

  2008-12-09

• Fields of study

  Biology, Medicine, Physics, Chemistry

• Identifiers
  DOI 10.1021/jp806285sPMID 19067572PMCID 2671006
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Bull. Chem. Soc. Jpn. への投稿のすすめ

  2011cited by this paper
• Meta and para effects in the ultrafast excited-state dynamics of the green fluorescent protein chromophores.

  2008cited by this paper
• Syntheses of highly fluorescent GFP-chromophore analogues.

  2008cited by this paper
• The Role of the Tight-Turn, Broken Hydrogen Bonding, Glu222 and Arg96 in the Post-translational Green Fluorescent Protein Chromophore Formation.

  2008cited by this paper
• Light-dependent regulation of structural flexibility in a photochromic fluorescent protein

  2008cited by this paper
• Structural basis for reversible photoswitching in Dronpa

  2007cited by this paper
• 1.8 A bright-state structure of the reversibly switchable fluorescent protein Dronpa guides the generation of fast switching variants.

  2007cited by this paper
• Structural rearrangements near the chromophore influence the maturation speed and brightness of DsRed variants.

  2007cited by this paper
• Advances in fluorescent protein technology

  2007cited by this paper
• Dynamic Stokes shift in green fluorescent protein variants

  2007cited by this paper
• Ultrafast excited-state dynamics of the photoswitchable protein Dronpa.

  2007cited by this paper
• Chromogenic cross-link formation in green fluorescent protein.

  2007cited by this paper
• Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function

  2007cited by this paper
• Blue fluorescent protein from the calcium‐sensitive photoprotein aequorin: Catalytic properties for the oxidation of coelenterazine as an oxygenase

  2006cited by this paper
• Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library

  2006cited by this paper
• The Role of the Protein Matrix in Green Fluorescent Protein Fluorescence

  2006cited by this paper
• The kindling fluorescent protein: a transient photoswitchable marker.

  2006cited by this paper
• Photoconversion in the red fluorescent protein from the sea anemone Entacmaea quadricolor: is cis-trans isomerization involved?

  2006cited by this paper
• Cyan fluorescent protein: molecular dynamics, simulations, and electronic absorption spectrum.

  2005cited by this paper
• The 2.1A crystal structure of the far-red fluorescent protein HcRed: inherent conformational flexibility of the chromophore.

  2005cited by this paper
• Fluorescent proteins as a toolkit for in vivo imaging.

  2005cited by this paper
• A guide to choosing fluorescent proteins

  2005cited by this paper
• Excited-state structure determination of the green fluorescent protein chromophore.

  2005cited by this paper
• Understanding GFP chromophore biosynthesis: controlling backbone cyclization and modifying post-translational chemistry.

  2005cited by this paper
• Enhancement of the fluorescence of the blue fluorescent proteins by high pressure or low temperature.

  2005cited by this paper
• Solvent effects on the vibrational activity and photodynamics of the green fluorescent protein chromophore: a quantum-chemical study.

  2005cited by this paper
• Structure and mechanism of the reversible photoswitch of a fluorescent protein.

  2005cited by this paper
• Selective fluorescence recovery after bleaching of single E2GFP proteins induced by two-photon excitation.

  2005cited by this paper
• The photophysics of green fluorescent protein: influence of the key amino acids at positions 65, 203, and 222.

  2005cited by this paper
• Structural and spectral response of Aequorea victoria green fluorescent proteins to chromophore fluorination.

  2005cited by this paper
• Kindling fluorescent protein from Anemonia sulcata: dark-state structure at 1.38 A resolution.

  2005cited by this paper
• Optical absorption of the blue fluorescent protein: a first-principles study.

  2005cited by this paper
• Building and breeding molecules to spy on cells and tumors

  2005cited by this paper
• Variations on the GFP Chromophore

  2005cited by this paper
• Glowing Genes: A Revolution In Biotechnology

  2005cited by this paper
• IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW，Thompson RW，et al//Proc Natl Acad Sci U S A

  2005cited by this paper
• CRC handbook of organic photochemistry and photobiology

  2004cited by this paper
• Uncovering the hidden ground state of green fluorescent protein

  2004cited by this paper
• Role of protein in the primary step of the photoreaction of yellow protein

  2004cited by this paper
• The crystal structure of the Y66L variant of green fluorescent protein supports a cyclization-oxidation-dehydration mechanism for chromophore maturation.

  2004cited by this paper
• Conical intersection dynamics in solution: the chromophore of Green Fluorescent Protein.

  2004cited by this paper
• Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein

  2004cited by this paper
• A new harvest of fluorescent proteins

  2004cited by this paper
• Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures

  2003cited by this paper
• Fluorescent derivatives of the GFP chromophore give a new insight into the GFP fluorescence process.

  2003cited by this paper
• The 2.2 A crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation.

  2003cited by this paper
• The 2.0-Å Crystal Structure of eqFP611, a Far Red Fluorescent Protein from the Sea Anemone Entacmaea quadricolor*

  2003cited by this paper
• The Cambridge Structural Database: a quarter of a million crystal structures and rising.

  2002cited by this paper
• Crystal Structure of Venus, a Yellow Fluorescent Protein with Improved Maturation and Reduced Environmental Sensitivity*

  2002cited by this paper
• Fully flexible low-mode docking: application to induced fit in HIV integrase.

  2001cited by this paper
• The Protein Data Bank

  2000cited by this paper
• Shedding light on the dark and weakly fluorescent states of green fluorescent proteins.

  1999cited by this paper
• Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein.

  1998cited by this paper
• Crystal structure and photodynamic behavior of the blue emission variant Y66H/Y145F of green fluorescent protein.

  1997cited by this paper
• Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein.

  1997cited by this paper
• The structural basis for spectral variations in green fluorescent protein

  1997cited by this paper
• Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer.

  1996cited by this paper
• Crystal Structure of the Aequorea victoria Green Fluorescent Protein

  1996cited by this paper
• The molecular structure of green fluorescent protein

  1996cited by this paper
• Chemical nature of the light emitter of the Aequorea green fluorescent protein.

  1996cited by this paper
• Wavelength mutations and posttranslational autoxidation of green fluorescent protein.

  1994cited by this paper
• Chemical structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein.

  1993cited by this paper

• Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials

  2025cites this paper
• A twisted chromophore powers a turn-on fluorescent protein chloride sensor.

  2025cites this paper
• Photoinduced chromophore dissociation resulting in aggregation-induced red fluorescence

  2025cites this paper
• Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains.

  2025cites this paper
• Fluorescent Sensor for the Visualization of Amino Acid Neurotransmitters in Neurons Based on an SNAr Reaction.

  2025cites this paper
• Different Patterns of Pd-Promoted C-H Bond Activation in (Z)-4-Hetarylidene-5(4H)-Oxazolones and Consequences in Photophysical Properties

  2024cites this paper
• Fluorogenesis: Inducing Fluorescence in a Non-Fluorescent Protein Through Photoinduced Chromophore Transfer of a Genetically Encoded Chromophore

  2023cites this paper
• Ultrafast Excited State Relaxation of a Model Green Fluorescent Protein Chromophore: Femtosecond Fluorescence and Transient Absorption Study

  2022cites this paper
• Steric and Electronic Origins of Fluorescence in GFP and GFP-like Proteins.

  2022cites this paper
• Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing

  2022cites this paper
• Pressure and temperature dependence of fluorescence anisotropy of green fluorescent protein

  2022cites this paper
• Prediction of fluorophore brightness in designed mini fluorescence activating proteins

  2021cites this paper
• Fluorescent Orthopalladated Complexes of 4-Aryliden-5(4H)-oxazolones from the Kaede Protein: Synthesis and Characterization

  2021cites this paper
• Disentangling Chromophore States in a Reversibly Switchable Green Fluorescent Protein: Mechanistic Insights from NMR Spectroscopy.

  2021cites this paper
• FPredX: Interpretable models for the prediction of spectral maxima, brightness, and oligomeric states of fluorescent proteins

  2021cites this paper
• Simultaneous analyses of fluorescence decay and anisotropy decay in green fluorescent protein dimer from jellyfish Clytia gregaria: FRET and Molecular dynamics simulation

  2021cites this paper
• Fluorescent Protein Variants Generated by Reassembly between Skeleton and Chromophore

  2021cites this paper
• Fluorescent Proteins Filters, Mirrors and Wavelengths

  2020cites this paper
• Unraveling the Effect on Luminescent Properties by Postsynthetic Covalent and Noncovalent Grafting of gfp Chromophore Analogues in Nanoscale MOF-808.

  2020cites this paper
• Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry ( MERCURY )

  2020cites this paper
• Structure‐guided evolution of Green2 toward photostability and quantum yield enhancement by F145Y substitution

  2020cites this paper
• Inspecting fluctuation and coordination around chromophore inside green fluorescent protein from water to nonpolar solvent

  2019cites this paper
• Inverted solvatochromic Stokes shift in GFP-like chromophores with extended conjugation

  2018cites this paper
• Femtosecond Time-Resolved Raman Spectroscopy Reveals Structural Evidence for meta Effect in Stilbenols.

  2018cites this paper
• Orthopalladation of GFP-Like Fluorophores Through C-H Bond Activation: Scope and Photophysical Properties

  2018cites this paper
• Ultrafast trans-cis photoisomerization of the neutral chromophore in green fluorescent proteins: Surface-hopping dynamics simulation.

  2018cites this paper
• High-Content Reporter Assays.

  2018cites this paper
• On the mechanism of non-radiative decay of blue fluorescent protein chromophore: New insight from the excited-state molecular dynamics simulations and potential energy calculations.

  2017cites this paper
• Mispacking and the Fitness Landscape of the Green Fluorescent Protein Chromophore Milieu.

  2017cites this paper
• Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?

  2017cites this paper
• Increasing the Quantum Yield of Red Fluorescent Proteins Using Rational Design

  2016influential citation
• Fluorescent Proteins: The Show Must go on!

  2016cites this paper
• Emission shaping in fluorescent proteins: role of electrostatics and π-stacking.

  2016cites this paper
• Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein.

  2016cites this paper
• Brighter Red Fluorescent Proteins by Rational Design of Triple-Decker Motif.

  2016cites this paper
• GREEN FLUORESCENT PROTEIN AS AN ANALYTICAL TOOL IN PROCESS ANALYTICAL TECHNOLOGY

  2016cites this paper
• Excited-State Intramolecular Proton Transfer in a Blue Fluorescence Chromophore Induces Dual Emission.

  2016cites this paper
• Hidden photoinduced reactivity of the blue fluorescent protein mKalama1.

  2015cites this paper
• Smaller 145th residue makes fluorescent protein non-fluorescent: Fluorescence lifetimes of enhanced yellow fluorescent protein (eYFP) Y145 mutants and H148 mutants

  2015cites this paper
• Ultrasensitive detection of aliphatic nitro-organics based on “turn-on” fluorescent sensor array

  2015cites this paper
• Structural Flexibility and Oxygen Diffusion Pathways in Monomeric Fluorescent Proteins

  2014influential citation
• Towards the realization of ab initio dynamics at the speed of molecular mechanics: simulations with interpolated diabatic Hamiltonian.

  2014cites this paper
• Non-adiabatic dynamics of isolated green fluorescent protein chromophore anion.

  2014cites this paper
• Exploring the active site structure of a photoreceptor protein by Raman optical activity.

  2013cites this paper
• Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation.

  2013cites this paper
• Excitation energy migration in yellow fluorescent protein (citrine) layers adsorbed on modified gold surfaces

  2013cites this paper
• Probing the Dynamics of Red Fluorescent Protein Variants using NMR Spectroscopy: How Directed Development Affected Protein Dynamics

  2013cites this paper
• Étude théorique de l’extinction de fluorescence des protéines fluorescentes : champ de forces, mécanisme moléculaire et modèle cinétique

  2012cites this paper
• Intramolecular hydrogen bonding plays a crucial role in the photophysics and photochemistry of the GFP chromophore.

  2012cites this paper
• Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%

  2012cites this paper
• A theoretical study on photomagnetic fluorescent protein chromophore coupled diradicals and their possible applications.

  2012cites this paper
• Interpolated mechanics-molecular mechanics study of internal rotation dynamics of the chromophore unit in blue fluorescent protein and its variants.

  2012cites this paper
• Gas-phase infrared spectrum of the anionic GFP-chromophore

  2012cites this paper
• First‐principles simulations of two photon absorption spectra of dynamic structural chromophores in green fluorescent protein

  2012cites this paper
• Primary Photophysical Processes in Chromoproteins

  2011cites this paper
• Synthesis and Optical Properties of Two-Photon Absorbing GFP-type Probes

  2011cites this paper
• Excited state relaxation dynamics of model green fluorescent protein chromophore analogs: evidence for cis-trans isomerism.

  2011cites this paper
• Absorption of the green fluorescent protein chromophore anion in the gas phase studied by a combination of FTICR mass spectrometry with laser-induced photodissociation spectroscopy

  2011cites this paper
• Excited State Dynamics of the Green Fluorescent Protein on the Nanosecond Time Scale.

  2011cites this paper
• Photofragmentation of and electron photodetachment from a GFP model chromophore in a quadrupole ion trap

  2011cites this paper
• An OFF-ON fluorescent probe for Zn2+ based on a GFP-inspired imidazolone derivative attached to a 1,10-phenanthroline moiety.

  2011cites this paper
• Proton transfer events in GFP.

  2011cites this paper
• Green fluorescent protein: A perspective

  2011cites this paper
• Function and structure of GFP-like proteins in the protein data bank.

  2011cites this paper
• Fluorescence Lifetime of Fluorescent Proteins

  2011cites this paper
• Potential Energy Landscape of the Electronic States of the GFP Chromophore in Different Protonation Forms: Electronic Transition Energies and Conical Intersections.

  2010cites this paper
• Topochemistry and photomechanical effects in crystals of green fluorescent protein-like chromophores: effects of hydrogen bonding and crystal packing.

  2010cites this paper
• Twisted intramolecular charge transfer in a model green fluorescent protein luminophore analog

  2010cites this paper
• The N-arylamino conjugation effect in the photochemistry of fluorescent protein chromophores and aminostilbenes.

  2010cites this paper
• On the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins.

  2010cites this paper
• Photophysics and Spectroscopy of Fluorophores in the Green Fluorescent Protein Family

  2010cites this paper
• Spectroscopy of gas-phase (bio)-molecular ions

  2010cites this paper
• Intrinsic dynamics in ECFP and Cerulean control fluorescence quantum yield.

  2009cites this paper
• Conical intersections, charge localization, and photoisomerization pathway selection in a minimal model of a degenerate monomethine dye.

  2009cites this paper
• Computer Modeling of the Structure and Spectra of Fluorescent Proteins

  2009cites this paper
• Traitement des interactions électrostatiques dans les systèmes moléculaires - Etude par simulation numérique de protéines fluorescentes

  2009influential citation
• GFP: from jellyfish to the Nobel prize and beyond.

  2009cites this paper
• A diabatic three-state representation of photoisomerization in the green fluorescent protein chromophore.

  2009cites this paper
• Excited state reactions in fluorescent proteins.

  2009cites this paper
• Excited state dynamics in the green fluorescent protein

  2009cites this paper