A theoretical study on the optical absorption of green fluorescent protein chromophore in solutions

References

• Shimomura O, Johnson FH. Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan. Aequorea. J Cell Comp Physiol. 1962;59:223–239.
   PubMedGoogle Scholar
• Paige JS, Wu KY, Jaffrey SR. RNA mimics of green fluorescent protein. Science. 2011;333:642–646.
   PubMed Web of Science ®Google Scholar
• Höfer K, Langejürgen LV, Jäschke A. Universal aptamer-based real-time monitoring of enzymatic RNA synthesis. J Am Chem Soc. 2013;135:13692–13694.
   PubMed Web of Science ®Google Scholar
• Song W, Strack RL, Svensen N, et al. Plug-and-play fluorophores extend the spectral properties of spinach. J Am Chem Soc. 2014;136:1198–1201.
   PubMed Web of Science ®Google Scholar
• Ward WW, Prentice HJ, Roth AF, et al. Spectral perturbations of the aequorea green fluorescent protein. Photochem Photobiol. 1982;35:803–808.
   Web of Science ®Google Scholar
• Niwa H, Inouye S, Hirano T, et al. Chemical nature of the light emitter of the Aequorea green fluorescent protein. Proc Nat Acad Sci USA. 1996;:13617–13622.
   PubMed Web of Science ®Google Scholar
• Tsien RY. The green fluorescent protein. Annu Rev Biochem. 1998;67:509–544.
   PubMed Web of Science ®Google Scholar
• Bell AF, He X, Wachter RM, et al. Probing the ground state structure of the green fluorescent protein chromophore using Raman spectroscopy. Biochemistry. 2000;39:4423–4431.
   PubMed Web of Science ®Google Scholar
• Yampolsky IV, Remington SJ, Martynov VI, et al. Synthesis and properties of the chromophore of the asFP595 chromoprotein from Anemonia sulcata. Biochemistry. 2005;44:5788–5793.
   PubMed Web of Science ®Google Scholar
• Dong J, Solntsev KM, Tolbert LM. Solvatochromism of the green fluorescence protein chromophore and its derivatives. J Am Chem Soc. 2006;128:12038–12039.
   PubMed Web of Science ®Google Scholar
• Das AK, Hasegawa J, Miyahara T, et al. Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study. J Comput Chem. 2003;24:1421–1431.
   PubMed Web of Science ®Google Scholar
• Hasegawa J, Fujimoto K, Swerts B, et al. Excited states of GFP chromophore and active site studied by the SAC-CI method: effect of protein-environment and mutations. J Comput Chem. 2007;28:2443–2452.
   PubMed Web of Science ®Google Scholar
• Uppsten M, Durbeej B. Quantum chemical comparison of vertical, adiabatic, and 0–0 excitation energies: The PYP and GFP chromophores. J Comput Chem. 2012;33:1892–1901.
   PubMed Web of Science ®Google Scholar
• Filippi C, Zaccheddu M, Buda F. Absorption spectrum of the green fluorescent protein chromophore: A difficult case for ab initio methods? J Chem Theory Comput. 2009;5:2074–2087.
   PubMed Web of Science ®Google Scholar
• Marques MAL, López X, Varsano D, et al. Time-dependent density-functional approach for biological chromophores: the case of the green fluorescent protein. Phys Rev Lett. 2003;90:258101.
   PubMed Web of Science ®Google Scholar
• Helms V, Winstead C, Langhoff PW. Low-lying electronic excitations of the green fluorescent protein chromophore. J Mol Struct (Theochem). 2000;506:179–189.
   Web of Science ®Google Scholar
• Send R, Kaila VRI, Sundholm D. Benchmarking the approximate second-order coupled-cluster method on biochromophores. J Chem Theory Comput. 2011;7:2473–2484.
   PubMed Web of Science ®Google Scholar
• Steindal AH, Olsen JMH, Ruud K, et al. A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein. Phys Chem Chem Phys. 2012;14:5440–5451.
   PubMed Web of Science ®Google Scholar
• Schwabe T, Beerepoot MTP, Olsen JMH, et al. Analysis of computational models for an accurate study of electronic excitations in GFP. Phys Chem Chem Phys. 2015;17:2582–2588.
   PubMed Web of Science ®Google Scholar
• Harczuk I, Murugan NA, Vahtras O, Ågren H. Studies of pH-sensitive optical properties of the deGFP1 green fluorescent protein using a unique polarizable force field. J Chem Theory Comput. 2014;10:3492–3502.
   PubMed Web of Science ®Google Scholar
• Voityuk AA, Michel-Beyerle M-E, Rösch N. Protonation effects on the chromophore of green fluorescent protein. Quantum chemical study of the absorption spectrum. Chem Phys Lett. 1997;272:162–167.
   Web of Science ®Google Scholar
• Voityuk AA, Michel-Beyerle M-E, Rösch N. Quantum chemical modeling of structure and absorption spectra of the chromophore in green fluorescent proteins. Chem Phys. 1998;231:13–25.
   Web of Science ®Google Scholar
• Voityuk AA, Kummer AD, Michel-Beyerle M-E, Rösch N. Absorption spectra of the GFP chromophore in solution: comparison of theoretical and experimental results. Chem Phys. 2001;269:83–91.
   Web of Science ®Google Scholar
• Nemukhin A, Topol IA, Burt SK. Electronic excitations of the chromophore from the fluorescent protein as FP595 in solutions. J Chem Theory Comput. 2006;2:292–299.
   PubMed Web of Science ®Google Scholar
• Nemukhin AV, Gigoenko BL, Savitsky AP. Computer modeling of the structure and spectra of fluorescent proteins. Acta Naturae. 2009;2:33–43.
   Google Scholar
• Polyakov IV, Grigorenko BL, Epifanovsky EM, et al. Potential energy landscape of the electronic states of the GFP chromophore in different protonation forms: electronic transition energies and conical intersections. J Chem Theory Comput. 2010;6:2377–2387.
   PubMed Web of Science ®Google Scholar
• Bravaya KB, Grigorenko BL, Nemukhin AV, et al. Quantum chemistry behind bioimaging: insights from ab Initio studies of fluorescent proteins and their chromophores. Acc Chem Res. 2012;45:265–275.
   PubMed Web of Science ®Google Scholar
• Zuev D, Bravaya KB, Makarova MV, Krylov AI. Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins. J Chem Phys. 2011;135:194304.
   PubMed Web of Science ®Google Scholar
• Bravaya KB. M. G. Khrenova, Grigorenko BL, et al., Effect of protein environment on electronically excited and ionized states of the green fluorescent protein chromophore. J Phys Chem B. 2011;115:8296–8303.
   PubMed Web of Science ®Google Scholar
• Ghosh D, Acharya A, Tiwari SC, et al. Toward understanding the redox properties of model chromophores from the green fluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects. J Phys Chem B. 2012;116:12398–12405.
   PubMed Web of Science ®Google Scholar
• Lazzari-Dean J, Krylov AI, Bravaya KB. The effects of resonance delocalization and the extent of π system on ionization energies of model fluorescent proteins chromophores. Int J Quam Chem. 2015;115:1258–1264.
   Web of Science ®Google Scholar
• Martin ME, Negri F, Olivucci M. Origin, nature, and fate of the fluorescent state of the green fluorescent protein chromophore at the CASPT2//CASSCF resolution. J Am Chem Soc. 2004;126:5452–5464.
   PubMed Web of Science ®Google Scholar
• Sinicropi A, Anduniow T, Férre N, Basosi R, Olivucci M. Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level. J Am Chem Soc. 2005;127:11534–11535.
   PubMed Web of Science ®Google Scholar
• Petrone A, Caruso P, Tenuta S, Rega N. On the optical absorption of the anionic GFP chromophore in vacuum, solution, and protein. Phys Chem Chem Phys. 2013;15:20536–20544.
   PubMed Web of Science ®Google Scholar
• Xie D, Zeng J. Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions. J Comput Chem. 2005;26:1487–1496.
   PubMed Web of Science ®Google Scholar
• Zhang L, Xie D, Zeng J. Electronic excitations of green fluorescent proteins: Modeling solvatochromatic shifts of chromophore model compounds in solutions. J. Theor. Comp. Chem. 2006;5:375–390.
   Web of Science ®Google Scholar
• Yan W, Zhang L, Xie D, et al. Electronic excitations of green fluorescent proteins: modeling solvatochromatic shifts of red fluorescent protein chromophore model compound in aqueous solutions. J Phys Chem B. 2007;111:14055–14063.
   PubMed Web of Science ®Google Scholar
• Yokogawa D, Sato H, Sakaki S. New generation of the reference interaction site model self-consistent field method: introduction of spatial electron density distribution to the solvation theory. J Chem Phys. 2007;126:244504.
   PubMed Web of Science ®Google Scholar
• Yokogawa D, Sato H, Sakaki S. Analytical energy gradient for reference interaction site model self-consistent field explicitly including spatial electron density distribution. J Chem Phys. 2009;131:214504.
   PubMed Web of Science ®Google Scholar
• Sato H. A modern solvation theory: quantum chemistry and statistical chemistry. Phys Chem Chem Phys. 2013;15:7450–7465.
   PubMed Web of Science ®Google Scholar
• Wada T, Nakano H, Sato H. Solvatochromic shift of brooker’s merocyanine: Hartree-Fock exchange in time dependent density functional calculation and hydrogen bonding effect. J Chem Theory Comput. 2014;10:4535–4547.
   PubMed Web of Science ®Google Scholar
• Chandler D, Andersen HC. Optimized cluster expansions for classical fluids. II. Theory of molecular liquids. J Chem Phys. 1972;57:1930–1931.
   Web of Science ®Google Scholar
• Hirata F, Rossky PJ. An extended rism equation for molecular polar fluids. Chem Phys Lett. 1981;83:329–334.
   Web of Science ®Google Scholar
• Hirata F, editor. Molecular theory of solvation. Dordrecht: Kluwer; 2003.
   Google Scholar
• Marenich AV, Cramer CJ, Truhlar DG. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B. 2009;113:6378–6396.
   PubMed Web of Science ®Google Scholar
• Frisch MJ, Trucks GW, Schlegel HB, et al. Gaussian 09, Revision D.01. Wallingford (CT): Gaussian Inc.; 2009.
   Google Scholar
• Schmidt MW, Baldridge KK, Boatz JA, et al. General Atomic and Molecular Electronic Structure System. J Comput Chem. 1993;14:1347–1363.
   Web of Science ®Google Scholar
• Nielsen SB, Lapierre A, Andersen JU, et al. Absorption spectrum of the green fluorescent protein chromophore anion in vacuo. Phys Rev Lett. 2001;87:228102.
   PubMed Web of Science ®Google Scholar
• Forbes MW, Jockusch RA. Deactivation pathways of an isolated green fluorescent protein model chromophore studied by electronic action spectroscopy. J Am Chem Soc. 2009;131:17038–17039.
   PubMed Web of Science ®Google Scholar
• Chingin K, Balabin RM, Frankevich V, et al. 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. Int J Mass Spectrom. 2011;306:241–245.
   Web of Science ®Google Scholar
• Bhaskaran-Nair K, Valiev M, Deng SHM, et al. Probing microhydration effect on the electronic structure of the GFP chromophore anion: Photoelectron spectroscopy and theoretical investigations. J Chem Phys. 2015;143:224301.
   PubMed Web of Science ®Google Scholar