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Bergeler M, Mizuno H, Fron E, Harvey JN. QM/MM-Based Calculations of Absorption and Emission Spectra of LSSmOrange Variants. J Phys Chem B 2016; 120:12454-12465. [DOI: 10.1021/acs.jpcb.6b09815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maike Bergeler
- Department
of Chemistry, Quantum Chemistry and Physical Chemistry
Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology
Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Hideaki Mizuno
- Department
of Chemistry, Quantum Chemistry and Physical Chemistry
Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology
Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Eduard Fron
- Department
of Chemistry, Quantum Chemistry and Physical Chemistry
Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology
Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Jeremy N. Harvey
- Department
of Chemistry, Quantum Chemistry and Physical Chemistry
Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology
Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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2
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Peccati F, Solans-Monfort X, Sodupe M. The role of charge transfer in the photophysics of dithiophene-based (NIADs) fluorescent markers for amyloid-β detection. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1934-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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3
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Armengol P, Gelabert R, Moreno M, Lluch JM. Chromophore interactions leading to different absorption spectra in mNeptune1 and mCardinal red fluorescent proteins. Phys Chem Chem Phys 2016; 18:16964-76. [PMID: 27294977 DOI: 10.1039/c6cp01297c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Extensive MD simulations combined with QM/MM calculations have been performed on mNeptune1 and mCardinal red fluorescent proteins to establish the reasons behind the red shift of the excitation wavelength of mCardinal with respect to mNeptune1. In both cases, it is seen that Arg197 stabilizes the chromophore but cannot be described as stabilizing preferentially the excited state because of the anchor point of the interaction. The interactions of the linking bonds to the α-helix of both proteins to the chromophore have been analyzed. It has been found that, besides the presence of a strategically placed residue Gln41 in mCardinal, solvation water molecules play an active role in the energetics of the stabilization of the excited state, which is preferentially stabilized in the case of mCardinal in contrast to mNeptune1.
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Affiliation(s)
- Pau Armengol
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Miquel Moreno
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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4
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Bose S, Chakrabarty S, Ghosh D. Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant. J Phys Chem B 2016; 120:4410-20. [DOI: 10.1021/acs.jpcb.6b03723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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5
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Randino C, Gelabert R, Moreno M, Lluch JM, Piatkevich KD. Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein. Phys Chem Chem Phys 2015; 17:29363-73. [PMID: 26473582 DOI: 10.1039/c5cp04428f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Classical molecular dynamics (MD) simulations are carried out for the recently developed TagRFP675 fluorescent protein (FP), which is specifically designed to fully absorb and emit in the near infrared (NIR) region of the electromagnetic spectrum. Since the X-ray data of TagRFP675 reveal that the chromophore exists in both the cis and trans configuration and it can also be neutral (protonated) or anionic (deprotonated) depending on the pH of the media, a total of 8 molecular dynamic simulations have been run to simulate all the possible states of the chromophore. Time-dependent DFT (TDDFT) single point calculations are performed at selected points along the simulation to theoretically mimic the absorption spectrum of the protein. Our simulations compare well (within the expected error of the computational method) with the experimental results. Our theoretical procedure allows for an analysis of the molecular orbitals involved in the lowest energy electronic excitations of the chromophore and, more interestingly, for a full analysis of the H-bond interactions between the chromophore and its surrounding residues and solvent (water) molecules. This study does not support the hypothesis, exclusively based on the analysis of X-ray data, that the isomerization of nearby residues provokes the rearrangement of the hydrogen bonds in the chromophore's immediate environment leading to the observed red shift of the absorption bands at higher pHs. Instead, we attribute this shift mainly to the superposition of bands of the neutral and anionic chromophores that are expected to coexist at almost the full range of pHs experimentally analyzed. An additional factor that could contribute to this shift is the experimentally observed increase of the cis configuration of the chromophore at higher pHs.
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Affiliation(s)
- Carlos Randino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Miquel Moreno
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Kiryl D Piatkevich
- Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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6
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Peccati F, Hernando J, Blancafort L, Solans-Monfort X, Sodupe M. Disaggregation-induced fluorescence enhancement of NIAD-4 for the optical imaging of amyloid-β fibrils. Phys Chem Chem Phys 2015; 17:19718-25. [DOI: 10.1039/c5cp02728d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence enhancement of the NIAD-4 marker upon interaction with amyloid-β fibrils arises from the disaggregation of the oligomers that spontaneously form in aqueous solution.
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Affiliation(s)
- Francesca Peccati
- Departament de Química
- Universitat Autònoma de Barcelona
- 08193 Bellaterra
- Spain
| | - Jordi Hernando
- Departament de Química
- Universitat Autònoma de Barcelona
- 08193 Bellaterra
- Spain
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi i Departament de Química
- Campus Montilivi
- Universitat de Girona
- Girona
- Spain
| | | | - Mariona Sodupe
- Departament de Química
- Universitat Autònoma de Barcelona
- 08193 Bellaterra
- Spain
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7
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Nadal-Ferret M, Gelabert R, Moreno M, Lluch JM. How Does the Environment Affect the Absorption Spectrum of the Fluorescent Protein mKeima? J Chem Theory Comput 2013; 9:1731-42. [DOI: 10.1021/ct301003t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marc Nadal-Ferret
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Ricard Gelabert
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Miquel Moreno
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - José M. Lluch
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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8
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Fron E, Van der Auweraer M, Moeyaert B, Michiels J, Mizuno H, Hofkens J, Adam V. Revealing the excited-state dynamics of the fluorescent protein Dendra2. J Phys Chem B 2013; 117:2300-13. [PMID: 23356883 DOI: 10.1021/jp309219m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Green-to-red photoconversion is a reaction that occurs in a limited number of fluorescent proteins and that is currently mechanistically debated. In this contribution, we report on our investigation of the photoconvertible fluorescent protein Dendra2 by employing a combination of pump-probe, up-conversion and single photon timing spectroscopic techniques. Our findings indicate that upon excitation of the neutral green state an excited state proton transfer proceeds with a time constant of 3.4 ps between the neutral green and the anionic green states. In concentrated solution we detected resonance energy transfer (25 ps time constant) between green and red monomers. The time-resolved emission spectra suggest also the formation of a super-red species, first observed for DsRed (a red fluorescent protein from the corallimorph species Discosoma) and consistent with peculiar structural details present in both proteins.
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Affiliation(s)
- Eduard Fron
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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9
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A time-dependent DFT/molecular dynamics study of the proton-wire responsible for the red fluorescence in the LSSmKate2 protein. Theor Chem Acc 2013. [DOI: 10.1007/s00214-012-1327-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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