1
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Chrupková P, van Stokkum IHM, Friedrich T, Moldenhauer M, Budisa N, Tseng HW, Polívka T, Cherepanov DA, Maksimov EG, Kloz M. Raman Vibrational Signatures of Excited States of Echinenone in the Orange Carotenoid Protein (OCP) and Implications for its Photoactivation Mechanism. J Mol Biol 2024; 436:168625. [PMID: 38797429 DOI: 10.1016/j.jmb.2024.168625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024]
Abstract
In this study, the vibrational characteristics of optically excited echinenone in various solvents and the Orange Carotenoid Protein (OCP) in red and orange states are systematically investigated through steady-state and time-resolved spectroscopy techniques. Time-resolved experiments, employing both Transient Absorption (TA) and Femtosecond Stimulated Raman Spectroscopy (FSRS), reveal different states in the OCP photoactivation process. The time-resolved studies indicate vibrational signatures of exited states positioned above the S1 state during the initial 140 fs of carotenoid evolution in OCP, an absence of a vibrational signature for the relaxed S1 state of echinenone in OCP, and more robust signatures of a highly excited ground state (GS) in OCP. Differences in S1 state vibration population signatures between OCP and solvents are attributed to distinct conformations of echinenone in OCP and hydrogen bonds at the keto group forming a short-lived intramolecular charge transfer (ICT) state. The vibrational dynamics of the hot GS in OCP show a more pronounced red shift of ground state CC vibration compared to echinenone in solvents, thus suggesting an unusually hot form of GS. The study proposes a hypothesis for the photoactivation mechanism of OCP, emphasizing the high level of vibrational excitation in longitudinal stretching modes as a driving force. In conclusion, the comparison of vibrational signatures reveals unique dynamics of energy dissipation in OCP, providing insights into the photoactivation mechanism and highlighting the impact of the protein environment on carotenoid behavior. The study underscores the importance of vibrational analysis in understanding the intricate processes involved in early phase OCP photoactivation.
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Affiliation(s)
- Petra Chrupková
- The Extreme Light Infrastructure ERIC, ELI Beamlines Facility, Za Radnicí 835, Dolní Břežany, Czech Republic; University of South Bohemia in České Budějovice, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Ivo H M van Stokkum
- Vrije Universiteit, Department of Physics and Astronomy, Faculty of Sciences, De Boelelaan 1081, 1081HV Amsterdam, the Netherlands
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Marcus Moldenhauer
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Nediljko Budisa
- University of Manitoba, Department of Chemistry, 144 Dysart Rd, 360 Parker Building, Winnipeg, MB R3T 2N2, Canada
| | - Hsueh-Wei Tseng
- University of Manitoba, Department of Chemistry, 144 Dysart Rd, 360 Parker Building, Winnipeg, MB R3T 2N2, Canada
| | - Tomáš Polívka
- University of South Bohemia in České Budějovice, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 142432 Moscow, Russian Federation; Lomonosov Moscow State University, A.N. Belozersky Institute of Physical-Chemical Biology, 119991 Moscow, Russian Federation
| | - Eugene G Maksimov
- Lomonosov Moscow State University, Faculty of Biology, Vorobyovy Gory 1-12, Moscow 119991, Russian Federation
| | - Miroslav Kloz
- The Extreme Light Infrastructure ERIC, ELI Beamlines Facility, Za Radnicí 835, Dolní Břežany, Czech Republic.
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2
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Liguori N, van Stokkum IH, Muzzopappa F, Kennis JTM, Kirilovsky D, Croce R. The Orange Carotenoid Protein Triggers Cyanobacterial Photoprotection by Quenching Bilins via a Structural Switch of Its Carotenoid. J Am Chem Soc 2024; 146:21913-21921. [PMID: 39058977 PMCID: PMC11311238 DOI: 10.1021/jacs.4c06695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
Cyanobacteria were the first microorganisms that released oxygen into the atmosphere billions of years ago. To do it safely under intense sunlight, they developed strategies that prevent photooxidation in the photosynthetic membrane, by regulating the light-harvesting activity of their antenna complexes-the phycobilisomes-via the orange-carotenoid protein (OCP). This water-soluble protein interacts with the phycobilisomes and triggers nonphotochemical quenching (NPQ), a mechanism that safely dissipates overexcitation in the membrane. To date, the mechanism of action of OCP in performing NPQ is unknown. In this work, we performed ultrafast spectroscopy on a minimal NPQ system composed of the active domain of OCP bound to the phycobilisome core. The use of this system allowed us to disentangle the signal of the carotenoid from that of the bilins. Our results demonstrate that the binding to the phycobilisomes modifies the structure of the ketocarotenoid associated with OCP. We show that this molecular switch activates NPQ, by enabling excitation-energy transfer from the antenna pigments to the ketocarotenoid.
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Affiliation(s)
- Nicoletta Liguori
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ivo H.M. van Stokkum
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Fernando Muzzopappa
- Institute
for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette ,France
| | - John T. M. Kennis
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Diana Kirilovsky
- Institute
for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette ,France
| | - Roberta Croce
- Department
of Physics and Astronomy and Institute for Lasers, Life and Biophotonics,
Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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3
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Khanna A, Shedge SV, Zuehlsdorff TJ, Isborn CM. Calculating absorption and fluorescence spectra for chromophores in solution with ensemble Franck-Condon methods. J Chem Phys 2024; 161:044121. [PMID: 39077907 DOI: 10.1063/5.0217080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Accurately modeling absorption and fluorescence spectra for molecules in solution poses a challenge due to the need to incorporate both vibronic and environmental effects, as well as the necessity of accurate excited state electronic structure calculations. Nuclear ensemble approaches capture explicit environmental effects, Franck-Condon methods capture vibronic effects, and recently introduced ensemble-Franck-Condon approaches combine the advantages of both methods. In this study, we present and analyze simulated absorption and fluorescence spectra generated with combined ensemble-Franck-Condon approaches for three chromophore-solvent systems and compare them to standard ensemble and Franck-Condon spectra, as well as to the experiment. Employing configurations obtained from ground and excited state ab initio molecular dynamics, three combined ensemble-Franck-Condon approaches are directly compared to each other to assess the accuracy and relative computational time. We find that the approach employing an average finite-temperature Franck-Condon line shape generates spectra nearly identical to the direct summation of an ensemble of Franck-Condon spectra at one-fourth of the computational cost. We analyze how the spectral simulation method, as well as the level of electronic structure theory, affects spectral line shapes and associated Stokes shifts for 7-nitrobenz-2-oxa-1,3-diazol-4-yl and Nile red in dimethyl sulfoxide and 7-methoxy coumarin-4-acetic acid in methanol. For the first time, our studies show the capability of combined ensemble-Franck-Condon methods for both absorption and fluorescence spectroscopy and provide a powerful tool for simulating linear optical spectra.
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Affiliation(s)
- Ajay Khanna
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
| | - Sapana V Shedge
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
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4
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Myers CA, Lu SY, Shedge S, Pyuskulyan A, Donahoe K, Khanna A, Shi L, Isborn CM. Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol. J Phys Chem B 2024; 128:5685-5699. [PMID: 38832562 DOI: 10.1021/acs.jpcb.4c01401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. The strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.
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Affiliation(s)
- Christopher A Myers
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Shao-Yu Lu
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Sapana Shedge
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Arthur Pyuskulyan
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Katherine Donahoe
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Ajay Khanna
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
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5
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Arcidiacono A, Cignoni E, Mazzeo P, Cupellini L, Mennucci B. Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning. J Phys Chem A 2024; 128:3646-3658. [PMID: 38683801 PMCID: PMC11089512 DOI: 10.1021/acs.jpca.4c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/03/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024]
Abstract
Solvatochromism occurs in both homogeneous solvents and more complex biological environments, such as proteins. While in both cases the solvatochromic effects report on the surroundings of the chromophore, their interpretation in proteins becomes more complicated not only because of structural effects induced by the protein pocket but also because the protein environment is highly anisotropic. This is particularly evident for highly conjugated and flexible molecules such as carotenoids, whose excitation energy is strongly dependent on both the geometry and the electrostatics of the environment. Here, we introduce a machine learning (ML) strategy trained on quantum mechanics/molecular mechanics calculations of geometrical and electrochromic contributions to carotenoids' excitation energies. We employ this strategy to compare solvatochromism in protein and solvent environments. Despite the important specifities of the protein, ML models trained on solvents can faithfully predict excitation energies in the protein environment, demonstrating the robustness of the chosen descriptors.
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Affiliation(s)
- Amanda Arcidiacono
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Edoardo Cignoni
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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6
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Sauer PV, Cupellini L, Sutter M, Bondanza M, Domínguez Martin MA, Kirst H, Bína D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polívka7 T, Mennucci B, Kerfeld CA. Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. SCIENCE ADVANCES 2024; 10:eadk7535. [PMID: 38578996 PMCID: PMC10997198 DOI: 10.1126/sciadv.adk7535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.
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Affiliation(s)
- Paul V. Sauer
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - María Agustina Domínguez Martin
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henning Kirst
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Bína
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | | | - Basil J. Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Tomáš Polívka7
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Thermo Fisher Scientific, Eindhoven, Netherlands
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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7
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Chukhutsina VU, Hutchison CDM, van Thor JJ. The Carbonyl Group in β2 of the Carotenoid Tunes the Photocycle Kinetics in Orange Carotenoid Protein. J Mol Biol 2024; 436:168463. [PMID: 38307159 DOI: 10.1016/j.jmb.2024.168463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
Adaptation to rapid environmental changes is crucial for maintaining optimal photosynthetic efficiency and is ultimately key to the survival of all photosynthetic organisms. Like most of them, cyanobacteria protect their photosynthetic apparatus against rapidly increasing light intensities by nonphotochemical quenching (NPQ). In cyanobacteria, NPQ is controlled by Orange Carotenoid Protein (OCP) photocycle. OCP is the only known photoreceptor that uses carotenoid for its light activation. How carotenoid drives and controls this unique photoactivation process is still unknown. However, understanding and potentially controlling the OCP photocycle may open up new possibilities for improving photosynthetic biomass. Here we investigate the effect of the carbonyl group in the β2 ring of the carotenoid on the OCP photocycle. We report microsecond to minute OCP light activation kinetics and Arrhenius plots of the two OCP forms: Canthaxanthin-bound OCP (OCPCAN) and echinenone-bound OCP (OCPECH). The difference between the two carotenoids is the presence of a carbonyl group in the β2-ring located in the N-terminal domain of the protein. A combination of temperature-dependent spectroscopy, flash photolysis, and pump-probe transient absorption allows us to report the previously unresolved OCP intermediate associated primarily with the absorption bleach (OCPB). OCPB dominates the photokinetics in the μs to subms time range for OCPCAN and in the μs to ms range for OCPECH. We show that in OCPCAN the OCP photocycle steps are always faster than in OCPECH: from 2 to almost 20 times depending on the step. These results suggest that the presence of the carbonyl group in the β2-ring of the carotenoid accelerates the OCP photocycle.
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Affiliation(s)
- Volha U Chukhutsina
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
| | | | - Jasper J van Thor
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
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8
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Stadnichuk IN, Krasilnikov PM. Relationship between non-photochemical quenching efficiency and the energy transfer rate from phycobilisomes to photosystem II. PHOTOSYNTHESIS RESEARCH 2024; 159:177-189. [PMID: 37328680 DOI: 10.1007/s11120-023-01031-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023]
Abstract
The chromophorylated PBLcm domain of the ApcE linker protein in the cyanobacterial phycobilisome (PBS) serves as a bottleneck for Förster resonance energy transfer (FRET) from the PBS to the antennal chlorophyll of photosystem II (PS II) and as a redirection point for energy distribution to the orange protein ketocarotenoid (OCP), which is excitonically coupled to the PBLcm chromophore in the process of non-photochemical quenching (NPQ) under high light conditions. The involvement of PBLcm in the quenching process was first directly demonstrated by measuring steady-state fluorescence spectra of cyanobacterial cells at different stages of NPQ development. The time required to transfer energy from the PBLcm to the OCP is several times shorter than the time it takes to transfer energy from the PBLcm to the PS II, ensuring quenching efficiency. The data obtained provide an explanation for the different rates of PBS quenching in vivo and in vitro according to the half ratio of OCP/PBS in the cyanobacterial cell, which is tens of times lower than that realized for an effective NPQ process in solution.
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Affiliation(s)
- Igor N Stadnichuk
- K.A. Timiryazev Institute of Plant Physiology, RAS, Botanicheskaya 35, 127726, Moscow, Russia.
| | - Pavel M Krasilnikov
- Biological Faculty of M.V., Lomonosov State University, Lenin Hills 12, 119991, Moscow, Russia
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9
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
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10
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Tsoraev GV, Bukhanko AY, Mamchur AA, Yaroshevich IA, Sluchanko NN, Tseng HW, Moldenhauer M, Budisa N, Friedrich T, Maksimov EG. Intrinsic tryptophan fluorescence quenching by iodine in non-canonical amino acid reveals alteration of the hydrogen bond network in the photoactive orange carotenoid protein. Biochem Biophys Res Commun 2023; 683:149119. [PMID: 37862781 DOI: 10.1016/j.bbrc.2023.10.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
The Orange Carotenoid Protein (OCP) regulates cyanobacterial photosynthetic activity through photoactivation in intense light. A hydrogen bonding network involving the keto-carotenoid oxygen and Y201 and W288 residues prevents the spontaneous activation of dark-adapted OCP. To investigate the role of the hydrogen bonds in OCP photocycling, we introduced non-canonical amino acids near the keto-carotenoid, particularly iodine at the meta-position of Y201. This modification significantly increased the yield of red OCP photoproducts, albeit with a shorter lifetime. Changes in tryptophan fluorescence during photocycling influenced by the presence of iodine near W288 revealed interactions between Y201 and W288 in the absence of the carotenoid in the C-domain. We propose that upon the relaxation of red states, a ternary complex with the carotenoid is formed. Analysis of spectral signatures and interaction energies indicates that the specific iodo-tyrosine configuration enhances interactions between the carotenoid and W288.
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Affiliation(s)
- Georgy V Tsoraev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Hsueh-Wei Tseng
- Technical University of Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Marcus Moldenhauer
- Technical University of Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Thomas Friedrich
- Technical University of Berlin, Institute of Chemistry PC 14, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Eugene G Maksimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
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11
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Pes F, Polack É, Mazzeo P, Dusson G, Stamm B, Lipparini F. A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born-Oppenheimer Molecular Dynamics. J Phys Chem Lett 2023; 14:9720-9726. [PMID: 37879072 PMCID: PMC10626629 DOI: 10.1021/acs.jpclett.3c02098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023]
Abstract
This Letter introduces the so-called Quasi Time-Reversible scheme based on Grassmann extrapolation (QTR G-Ext) of density matrices for an accurate calculation of initial guesses in Born-Oppenheimer Molecular Dynamics (BOMD) simulations. The method shows excellent results on four large molecular systems that are representative of real-life production applications, ranging from 21 to 94 atoms simulated with Kohn-Sham (KS) density functional theory surrounded with a classical environment with 6k to 16k atoms. Namely, it clearly reduces the number of self-consistent field iterations while at the same time achieving energy-conserving simulations, resulting in a considerable speed-up of BOMD simulations even when tight convergence of the KS equations is required.
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Affiliation(s)
- Federica Pes
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Étienne Polack
- CERMICS, École des Ponts and Inria Paris, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Valée, France
| | - Patrizia Mazzeo
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Geneviève Dusson
- Laboratoire
de Mathématiques de Besançon, UMR CNRS 6623, Université de Franche-Comté, 16 route de Gray, 25030 Besançon, France
| | - Benjamin Stamm
- Institute
of Applied Analysis and Numerical Simulation, University of Stuttgart, 70569 Stuttgart, Germany
| | - Filippo Lipparini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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12
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Arcidiacono A, Accomasso D, Cupellini L, Mennucci B. How orange carotenoid protein controls the excited state dynamics of canthaxanthin. Chem Sci 2023; 14:11158-11169. [PMID: 37860660 PMCID: PMC10583711 DOI: 10.1039/d3sc02662k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Orange Carotenoid Protein (OCP) is a ketocarotenoid-binding protein essential for photoprotection in cyanobacteria. The main steps of the photoactivated conversion which converts OCP from its resting state to the active one have been extensively investigated. However, the initial photochemical event in the ketocarotenoid which triggers the large structural changes finally leading to the active state is still not understood. Here we employ QM/MM surface hopping nonadiabatic dynamics to investigate the excited-state decay of canthaxanthin in OCP, both in the ultrafast S2 to S1 internal conversion and the slower decay leading back to the ground state. For the former step we show the involvement of an additional excited state, which in the literature has been often named the SX state, and we characterize its nature. For the latter step, we reveal an excited state decay characterized by multiple timescales, which are related to the ground-state conformational heterogeneity of the ketocarotenoid. We assigned the slowly decaying population to the so-called S* state. Finally, we identify a minor decay pathway involving double-bond photoisomerization, which could be the initial trigger to photoactivation of OCP.
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Affiliation(s)
- Amanda Arcidiacono
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Davide Accomasso
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
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13
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Han MH, Yang HW, Yoon J, Villafani Y, Song JY, Pan CH, Park K, Cho Y, Song JJ, Kim SJ, Park YI, Park J. Color-Tuning Mechanism of the Lit Form of Orange Carotenoid Protein. Mol Cells 2023; 46:513-525. [PMID: 37587751 PMCID: PMC10440265 DOI: 10.14348/molcells.2023.2186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.
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Affiliation(s)
- Man-Hyuk Han
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Department of Biological Sciences, KI for the BioCentury, KAIST, Daejeon 34141, Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Jungmin Yoon
- Department of Biological Sciences, KI for the BioCentury, KAIST, Daejeon 34141, Korea
| | - Yvette Villafani
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Cheol Ho Pan
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea
| | - Youngmoon Cho
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, KI for the BioCentury, KAIST, Daejeon 34141, Korea
| | - Seung Joong Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Quantum Intelligence Corp., Seoul 07326, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Jiyong Park
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
- Department of Chemistry, KAIST, Daejeon 34141, Korea
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14
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Guan J, Lu Y, Sen K, Abdul Nasir J, Desmoutier AW, Hou Q, Zhang X, Logsdail AJ, Dutta G, Beale AM, Strange RW, Yong C, Sherwood P, Senn HM, Catlow CRA, Keal TW, Sokol AA. Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220234. [PMID: 37211033 PMCID: PMC10200352 DOI: 10.1098/rsta.2022.0234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/23/2023]
Abstract
Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
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Affiliation(s)
- Jingcheng Guan
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Jamal Abdul Nasir
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | | | - Qing Hou
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Institute of Photonic Chips, University of Shanghai for Science of Technology, Shanghai 201512, People’s Republic of China
| | - Xingfan Zhang
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Andrew J. Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Gargi Dutta
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Department of Physics, Balurghat College, Balurghat 733101, West Bengal, India
| | - Andrew M. Beale
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK
| | - Hans M. Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - C. Richard A. Catlow
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Thomas W. Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Alexey A. Sokol
- Department of Chemistry, University College London, London WC1H 0AJ, UK
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15
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Pishchalnikov RY, Yaroshevich IA, Zlenko DV, Tsoraev GV, Osipov EM, Lazarenko VA, Parshina EY, Chesalin DD, Sluchanko NN, Maksimov EG. The role of the local environment on the structural heterogeneity of carotenoid β-ionone rings. PHOTOSYNTHESIS RESEARCH 2023; 156:3-17. [PMID: 36063303 DOI: 10.1007/s11120-022-00955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Our analysis of the X-ray crystal structure of canthaxanthin (CAN) showed that its ketolated β-ionone rings can adopt two energetically equal, but structurally distinct puckers. Quantum chemistry calculations revealed that the potential energy surface of the β-ionone ring rotation over the plane of the conjugated π-system in carotenoids depends on the pucker state of the β-ring. Considering different pucker states and β-ionone ring rotation, we found six separate local minima on the potential energy surface defining the geometry of the keto-β-ionone ring-two cis and one trans orientation for each of two pucker states. We observed a small difference in energy and no difference in relative orientation for the cis-minima, but a pronounced difference for the position of trans-minimum in alternative pucker configurations. An energetic advantage of β-ionone ring rotation from a specific pucker type can reach up to 8 kJ/mol ([Formula: see text]). In addition, we performed the simulation of linear absorption of CAN in hexane and in a unit cell of the CAN crystal. The electronic energies of [Formula: see text] transition were estimated both for the CAN monomer and in the CAN crystal. The difference between them reached [Formula: see text], which roughly corresponds to the energy gap between A and B pucker states predicted by theoretical estimations. Finally, we have discussed the importance of such effects for biological systems whose local environment determines conformational mobility, and optical/functional characteristics of carotenoid.
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Affiliation(s)
- Roman Y Pishchalnikov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str., 38, Moscow, Russia, 119991.
| | - Igor A Yaroshevich
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Dmitry V Zlenko
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
- A.N. Severtsov Institute of Ecology and Evolution (IEE), RAS, Moscow, Russia, 117071
| | - Georgy V Tsoraev
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Evgenii M Osipov
- Laboratory for Biocrystallography, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Vladimir A Lazarenko
- National Research Center "Kurchatov Institute", 1 Akademika Kurchatova Pl., Moscow, Russia, 123182
| | - Evgenia Yu Parshina
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Denis D Chesalin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str., 38, Moscow, Russia, 119991
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia, 119071
| | - Eugene G Maksimov
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
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16
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Deepika C, Wolf J, Roles J, Ross I, Hankamer B. Sustainable Production of Pigments from Cyanobacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 183:171-251. [PMID: 36571616 DOI: 10.1007/10_2022_211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pigments are intensely coloured compounds used in many industries to colour other materials. The demand for naturally synthesised pigments is increasing and their production can be incorporated into circular bioeconomy approaches. Natural pigments are produced by bacteria, cyanobacteria, microalgae, macroalgae, plants and animals. There is a huge unexplored biodiversity of prokaryotic cyanobacteria which are microscopic phototrophic microorganisms that have the ability to capture solar energy and CO2 and use it to synthesise a diverse range of sugars, lipids, amino acids and biochemicals including pigments. This makes them attractive for the sustainable production of a wide range of high-value products including industrial chemicals, pharmaceuticals, nutraceuticals and animal-feed supplements. The advantages of cyanobacteria production platforms include comparatively high growth rates, their ability to use freshwater, seawater or brackish water and the ability to cultivate them on non-arable land. The pigments derived from cyanobacteria and microalgae include chlorophylls, carotenoids and phycobiliproteins that have useful properties for advanced technical and commercial products. Development and optimisation of strain-specific pigment-based cultivation strategies support the development of economically feasible pigment biorefinery scenarios with enhanced pigment yields, quality and price. Thus, this chapter discusses the origin, properties, strain selection, production techniques and market opportunities of cyanobacterial pigments.
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Affiliation(s)
- Charu Deepika
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Juliane Wolf
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - John Roles
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ian Ross
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ben Hankamer
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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17
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Chukhutsina VU, Baxter JM, Fadini A, Morgan RM, Pope MA, Maghlaoui K, Orr CM, Wagner A, van Thor JJ. Light activation of Orange Carotenoid Protein reveals bicycle-pedal single-bond isomerization. Nat Commun 2022; 13:6420. [PMID: 36307413 PMCID: PMC9616832 DOI: 10.1038/s41467-022-34137-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Orange Carotenoid protein (OCP) is the only known photoreceptor which uses carotenoid for its activation. It is found exclusively in cyanobacteria, where it functions to control light-harvesting of the photosynthetic machinery. However, the photochemical reactions and structural dynamics of this unique photosensing process are not yet resolved. We present time-resolved crystal structures at second-to-minute delays under bright illumination, capturing the early photoproduct and structures of the subsequent reaction intermediates. The first stable photoproduct shows concerted isomerization of C9'-C8' and C7'-C6' single bonds in the bicycle-pedal (s-BP) manner and structural changes in the N-terminal domain with minute timescale kinetics. These are followed by a thermally-driven recovery of the s-BP isomer to the dark state carotenoid configuration. Structural changes propagate to the C-terminal domain, resulting, at later time, in the H-bond rupture of the carotenoid keto group with protein residues. Solution FTIR and UV/Vis spectroscopy support the single bond isomerization of the carotenoid in the s-BP manner and subsequent thermal structural reactions as the basis of OCP photoreception.
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Affiliation(s)
- Volha U. Chukhutsina
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - James M. Baxter
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Alisia Fadini
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Rhodri M. Morgan
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Matthew A. Pope
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Karim Maghlaoui
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Christian M. Orr
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE UK
| | - Armin Wagner
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE UK
| | - Jasper J. van Thor
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
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18
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Mondragón-Solórzano G, Sandoval-Lira J, Nochebuena J, Cisneros GA, Barroso-Flores J. Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of Blastochloris viridis' Light Harvesting 1-Reaction Center Complex. J Chem Theory Comput 2022; 18:4555-4564. [PMID: 35767461 PMCID: PMC10408377 DOI: 10.1021/acs.jctc.2c00497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Various photosynthetic organisms have evolved to absorb light in different regions of the visible light spectrum, thus adapting to the various lighting conditions available on Earth. While most of these autotrophic organisms absorb wavelengths around the 700-800 nm region, some are capable of red-shifted absorptions above this range, but none as remarkably as Blastochloris viridis whose main absorption is observed at 1015 nm, approximately 220 nm (0.34 eV) lower in energy than their main constituent pigments, BChl-b, whose main absorption is observed at 795 nm. The structure of its light harvesting 1-reaction center was recently elucidated by cryo-EM; however, the electronic structure details behind this red-shifted absorption remain unattended. We used hybrid quantum mechanics/molecular mechanics (QM/MM) calculations to optimize one of the active centers and performed classical molecular dynamics (MD) simulations to sample conformations beyond the optimized structure. We did excited state calculations with the time-dependent density functional theory method at the CAM-B3LYP/cc-pVDZ level of theory. We reproduced the near IR absorption by sequentially modifying the number of components involved in our systems using representative structures from the calculated MD ensemble. Natural transition orbital analysis reveals the participation of the BChl-b fragments to the main transition in the native structure and the structures obtained from the QM/MM and MD simulations. H-bonding pigment-protein interactions play a role on the conformation stabilization and orientation; however, the bacteriochlorin ring conformations and the exciton delocalization are the most relevant factors to explain the red-shifting phenomenon.
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Affiliation(s)
- Gustavo Mondragón-Solórzano
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM. Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano. Toluca de Lerdo 50200, México
- Instituto de Química. Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
| | - Jacinto Sandoval-Lira
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM. Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano. Toluca de Lerdo 50200, México
- Instituto de Química. Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
- Departamento de Ingeniería Ambiental, Instituto Tecnológico Superior de San Martín Texmelucan, TecNM, Camino a la Barranca de Pesos, C.P. 74120 San Martín Texmelucan, Puebla, México
| | - Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75801, United States
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75801, United States
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75801, United States
| | - Joaquín Barroso-Flores
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM. Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano. Toluca de Lerdo 50200, México
- Instituto de Química. Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
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19
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Church JR, Amoyal GS, Borin VA, Adam S, Olsen JMH, Schapiro I. Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry. Chemistry 2022; 28:e202200139. [PMID: 35307890 PMCID: PMC9325082 DOI: 10.1002/chem.202200139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Indexed: 11/11/2022]
Abstract
Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean's depth which tunes their maximum absorption: blue‐absorbing proteorhodopsin (BPR) and green‐absorbing proteorhodopsin (GPR). This blue/green color‐shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C14−C15 bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts.
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Affiliation(s)
- Jonathan R Church
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Gil S Amoyal
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | | | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
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20
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Cignoni E, Slama V, Cupellini L, Mennucci B. The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol. J Chem Phys 2022; 156:120901. [DOI: 10.1063/5.0086275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Slama
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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21
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Polack É, Dusson G, Stamm B, Lipparini F. Grassmann Extrapolation of Density Matrices for Born-Oppenheimer Molecular Dynamics. J Chem Theory Comput 2021; 17:6965-6973. [PMID: 34623810 PMCID: PMC8582259 DOI: 10.1021/acs.jctc.1c00751] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 01/16/2023]
Abstract
Born-Oppenheimer molecular dynamics (BOMD) is a powerful but expensive technique. The main bottleneck in a density functional theory BOMD calculation is the solution to the Kohn-Sham (KS) equations that requires an iterative procedure that starts from a guess for the density matrix. Converged densities from previous points in the trajectory can be used to extrapolate a new guess; however, the nonlinear constraint that an idempotent density needs to satisfy makes the direct use of standard linear extrapolation techniques not possible. In this contribution, we introduce a locally bijective map between the manifold where the density is defined and its tangent space so that linear extrapolation can be performed in a vector space while, at the same time, retaining the correct physical properties of the extrapolated density using molecular descriptors. We apply the method to real-life, multiscale, polarizable QM/MM BOMD simulations, showing that sizeable performance gains can be achieved, especially when a tighter convergence to the KS equations is required.
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Affiliation(s)
- Étienne Polack
- Laboratoire
de Mathématiques de Besançon, UMR CNRS 6623, Université
Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Geneviève Dusson
- Laboratoire
de Mathématiques de Besançon, UMR CNRS 6623, Université
Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Benjamin Stamm
- Department
of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany
| | - Filippo Lipparini
- Dipartimento
di Chimica e Chimica Industriale, Univeristà
di Pisa, Via G. Moruzzi
13, I-56124 Pisa, Italy
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22
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UV Excitation of Carotenoid Binding Proteins OCP and HCP: Excited‐State Dynamics and Product Formation. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Lokstein H, Renger G, Götze JP. Photosynthetic Light-Harvesting (Antenna) Complexes-Structures and Functions. Molecules 2021; 26:molecules26113378. [PMID: 34204994 PMCID: PMC8199901 DOI: 10.3390/molecules26113378] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Chlorophylls and bacteriochlorophylls, together with carotenoids, serve, noncovalently bound to specific apoproteins, as principal light-harvesting and energy-transforming pigments in photosynthetic organisms. In recent years, enormous progress has been achieved in the elucidation of structures and functions of light-harvesting (antenna) complexes, photosynthetic reaction centers and even entire photosystems. It is becoming increasingly clear that light-harvesting complexes not only serve to enlarge the absorption cross sections of the respective reaction centers but are vitally important in short- and long-term adaptation of the photosynthetic apparatus and regulation of the energy-transforming processes in response to external and internal conditions. Thus, the wide variety of structural diversity in photosynthetic antenna “designs” becomes conceivable. It is, however, common for LHCs to form trimeric (or multiples thereof) structures. We propose a simple, tentative explanation of the trimer issue, based on the 2D world created by photosynthetic membrane systems.
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Affiliation(s)
- Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 12116 Prague, Czech Republic
- Correspondence:
| | - Gernot Renger
- Max-Volmer-Laboratorium, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Jan P. Götze
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany;
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24
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Yaroshevich IA, Maksimov EG, Sluchanko NN, Zlenko DV, Stepanov AV, Slutskaya EA, Slonimskiy YB, Botnarevskii VS, Remeeva A, Gushchin I, Kovalev K, Gordeliy VI, Shelaev IV, Gostev FE, Khakhulin D, Poddubnyy VV, Gostev TS, Cherepanov DA, Polívka T, Kloz M, Friedrich T, Paschenko VZ, Nadtochenko VA, Rubin AB, Kirpichnikov MP. Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein. Commun Biol 2021; 4:539. [PMID: 33972665 PMCID: PMC8110590 DOI: 10.1038/s42003-021-02022-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion. Yaroshevich et al. present a chemical reaction mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP). They find that photoactivation critically involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. This study suggests the role of charge-transfer states during OCP photoconversion.
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Affiliation(s)
- Igor A Yaroshevich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Eugene G Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia. .,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Zlenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey V Stepanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Slutskaya
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yury B Slonimskiy
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Viacheslav S Botnarevskii
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.,Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan V Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Fedor E Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Timofey S Gostev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Moscow, Russia
| | - Tomáš Polívka
- Institute of Physics, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Kloz
- ELI-Beamlines, Institute of Physics, Praha, Czech Republic
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC14, Berlin, Germany
| | | | - Victor A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Andrew B Rubin
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P Kirpichnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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25
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Spectral Features of Canthaxanthin in HCP2. A QM/MM Approach. Molecules 2021; 26:molecules26092441. [PMID: 33922133 PMCID: PMC8122715 DOI: 10.3390/molecules26092441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 11/17/2022] Open
Abstract
The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some of these paralogs have been reported to act as singlet oxygen quenchers, their distinct functional roles remain unclear. One of these paralogs (HCP2) exclusively binds canthaxanthin (CAN) and its crystal structure has been recently characterized. Its absorption spectrum is significantly red-shifted, in comparison to the protein in solution, due to a dimerization where the two carotenoids are closely placed, favoring an electronic coupling interaction. Both the crystal and solution spectra are red-shifted by more than 50 nm when compared to canthaxanthin in solution. Using molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) studies of HCP2, we aim to simulate these shifts as well as obtain insight into the environmental and coupling effects of carotenoid-protein interactions.
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26
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Maity S, Daskalakis V, Elstner M, Kleinekathöfer U. Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II. Phys Chem Chem Phys 2021; 23:7407-7417. [PMID: 33876100 DOI: 10.1039/d1cp01011e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light-Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born-Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. To the best of our knowledge, this is the first theoretical attempt on this large complex system is ever made to accurately simulate the spectral density. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
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27
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Mascoli V, Liguori N, Cupellini L, Elias E, Mennucci B, Croce R. Uncovering the interactions driving carotenoid binding in light-harvesting complexes. Chem Sci 2021; 12:5113-5122. [PMID: 34163750 PMCID: PMC8179543 DOI: 10.1039/d1sc00071c] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/14/2021] [Indexed: 11/25/2022] Open
Abstract
Carotenoids are essential constituents of plant light-harvesting complexes (LHCs), being involved in protein stability, light harvesting, and photoprotection. Unlike chlorophylls, whose binding to LHCs is known to require coordination of the central magnesium, carotenoid binding relies on weaker intermolecular interactions (such as hydrogen bonds and van der Waals forces), whose character is far more elusive. Here we addressed the key interactions responsible for carotenoid binding to LHCs by combining molecular dynamics simulations and polarizable quantum mechanics/molecular mechanics calculations on the major LHC, LHCII. We found that carotenoid binding is mainly stabilized by van der Waals interactions with the surrounding chlorophyll macrocycles rather than by hydrogen bonds to the protein, the latter being more labile than predicted from structural data. Furthermore, the interaction network in the binding pockets is relatively insensitive to the chemical structure of the embedded carotenoid. Our results are consistent with a number of experimental data and challenge the role played by specific interactions in the assembly of pigment-protein complexes.
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Affiliation(s)
- Vincenzo Mascoli
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Nicoletta Liguori
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Lorenzo Cupellini
- Department of Chemistry, University of Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Eduard Elias
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Benedetta Mennucci
- Department of Chemistry, University of Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Roberta Croce
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
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28
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Marrazzini G, Giovannini T, Scavino M, Egidi F, Cappelli C, Koch H. Multilevel Density Functional Theory. J Chem Theory Comput 2021; 17:791-803. [PMID: 33449681 PMCID: PMC7880574 DOI: 10.1021/acs.jctc.0c00940] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
Following recent
developments in multilevel embedding methods,
we introduce a novel density matrix-based multilevel approach within
the framework of density functional theory (DFT). In this multilevel
DFT, the system is partitioned in an active and an inactive fragment,
and all interactions are retained between the two parts. The decomposition
of the total system is performed upon the density matrix. The orthogonality
between the two parts is maintained by solving the Kohn–Sham
equations in the MO basis for the active part only, while keeping
the inactive density matrix frozen. This results in the reduction
of computational cost. We outline the theory and implementation and
discuss the differences and similarities with state-of-the-art DFT
embedding methods. We present applications to aqueous solutions of
methyloxirane and glycidol.
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Affiliation(s)
- Gioia Marrazzini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Marco Scavino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Henrik Koch
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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29
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Bondanza M, Cupellini L, Faccioli P, Mennucci B. Molecular Mechanisms of Activation in the Orange Carotenoid Protein Revealed by Molecular Dynamics. J Am Chem Soc 2020; 142:21829-21841. [PMID: 33332967 PMCID: PMC7775743 DOI: 10.1021/jacs.0c10461] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Light-harvesting
in photosynthesis is accompanied by photoprotective
processes. In cyanobacteria, the photoprotective role is played by
a specialized complex, the orange carotenoid protein, which is activated
by strong blue-green light. This photoactivation involves a unique
series of structural changes which terminate with an opening of the
complex into two separate domains, one of which acts as a quencher
for the light-harvesting complexes. Many experimental studies have
tried to reveal the molecular mechanisms through which the energy
absorbed by the carotenoid finally leads to the large conformational
change of the complex. Here, for the first time, these mechanisms
are revealed by simulating at the atomistic level the whole dynamics
of the complex through an effective combination of enhanced sampling
techniques. On the basis of our findings, we can conclude that the
carotenoid does not act as a spring that, releasing its internal strain,
induces the dissociation, as was previously proposed, but as a “latch”
locking together the two domains. The photochemically triggered displacement
of the carotenoid breaks this balance, allowing the complex to dissociate.
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Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Pietro Faccioli
- Physics Department, Trento University, Via Sommarive 14, 38128 Povo, Trento, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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30
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Pigni NB, Clark KL, Beck WF, Gascón JA. Spectral Signatures of Canthaxanthin Translocation in the Orange Carotenoid Protein. J Phys Chem B 2020; 124:11387-11395. [PMID: 33287537 DOI: 10.1021/acs.jpcb.0c08756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The orange carotenoid protein (OCP) is involved in the photoprotective processes in cyanobacteria via nonphotochemical quenching. Triggered by blue-green light absorption, the carotenoid chromophore undergoes translocation, displacing around 12 Å from the C-terminal domain (CTD) to the N-terminal domain (NTD). The detailed molecular rearrangements that occur within the carotenoid and the protein during this process remain largely elusive. By using a combination of molecular dynamics, well-tempered metadynamics, and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations, we were able to mimic the translocation of the carotenoid from the inactive OCPO and obtain metastable red-shifted states in the photoactivation mechanism, replicating the λmax values of reference experimental spectra. In addition, our simulations give insight into the structure of the red-shifted form of the inactive state of OCP.
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Affiliation(s)
- Natalia B Pigni
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States.,Instituto de Ciencia y Tecnología de Alimentos Córdoba (ICYTAC-CONICET), Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - Kevin L Clark
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Warren F Beck
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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31
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Lambros E, Lipparini F, Cisneros GA, Paesani F. A Many-Body, Fully Polarizable Approach to QM/MM Simulations. J Chem Theory Comput 2020; 16:7462-7472. [PMID: 33213149 PMCID: PMC8131112 DOI: 10.1021/acs.jctc.0c00932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum-mechanical contributions (e.g., exchange-repulsion and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Using the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit two-body and three-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 two-body and three-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | | | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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32
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Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP. Sci Rep 2020; 10:15564. [PMID: 32968135 PMCID: PMC7512017 DOI: 10.1038/s41598-020-72383-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/31/2020] [Indexed: 11/18/2022] Open
Abstract
The Orange Carotenoid Protein (OCP) is a water-soluble protein that governs photoprotection in many cyanobacteria. The 35 kDa OCP is structurally and functionally modular, consisting of an N-terminal effector domain (NTD) and a C-terminal regulatory domain (CTD); a carotenoid spans the two domains. The CTD is a member of the ubiquitous Nuclear Transport Factor-2 (NTF2) superfamily (pfam02136). With the increasing availability of cyanobacterial genomes, bioinformatic analysis has revealed the existence of a new family of proteins, homologs to the CTD, the C-terminal domain-like carotenoid proteins (CCPs). Here we purify holo-CCP2 directly from cyanobacteria and establish that it natively binds canthaxanthin (CAN). We use small-angle X-ray scattering (SAXS) to characterize the structure of this carotenoprotein in two distinct oligomeric states. A single carotenoid molecule spans the two CCPs in the dimer. Our analysis with X-ray footprinting-mass spectrometry (XFMS) identifies critical residues for carotenoid binding that likely contribute to the extreme red shift (ca. 80 nm) of the absorption maximum of the carotenoid bound by the CCP2 dimer and a further 10 nm shift in the tetramer form. These data provide the first structural description of carotenoid binding by a protein consisting of only an NTF2 domain.
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33
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Maksimov EG, Protasova EA, Tsoraev GV, Yaroshevich IA, Maydykovskiy AI, Shirshin EA, Gostev TS, Jelzow A, Moldenhauer M, Slonimskiy YB, Sluchanko NN, Friedrich T. Probing of carotenoid-tryptophan hydrogen bonding dynamics in the single-tryptophan photoactive Orange Carotenoid Protein. Sci Rep 2020; 10:11729. [PMID: 32678150 PMCID: PMC7366913 DOI: 10.1038/s41598-020-68463-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/25/2020] [Indexed: 01/07/2023] Open
Abstract
The photoactive Orange Carotenoid Protein (OCP) plays a key role in cyanobacterial photoprotection. In OCP, a single non-covalently bound keto-carotenoid molecule acts as a light intensity sensor, while the protein is responsible for forming molecular contacts with the light-harvesting antenna, the fluorescence of which is quenched by OCP. Activation of this physiological interaction requires signal transduction from the photoexcited carotenoid to the protein matrix. Recent works revealed an asynchrony between conformational transitions of the carotenoid and the protein. Intrinsic tryptophan (Trp) fluorescence has provided valuable information about the protein part of OCP during its photocycle. However, wild-type OCP contains five Trp residues, which makes extraction of site-specific information impossible. In this work, we overcame this problem by characterizing the photocycle of a fully photoactive OCP variant (OCP-3FH) with only the most critical tryptophan residue (Trp-288) in place. Trp-288 is of special interest because it forms a hydrogen bond to the carotenoid's keto-oxygen to keep OCP in its dark-adapted state. Using femtosecond pump-probe fluorescence spectroscopy we analyzed the photocycle of OCP-3FH and determined the formation rate of the very first intermediate suggesting that generation of the recently discovered S* state of the carotenoid in OCP precedes the breakage of the hydrogen bonds. Therefore, following Trp fluorescence of the unique photoactive OCP-3FH variant, we identified the rate of the H-bond breakage and provided novel insights into early events accompanying photoactivation of wild-type OCP.
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Affiliation(s)
- Eugene G. Maksimov
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia ,0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Elena A. Protasova
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Georgy V. Tsoraev
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Igor A. Yaroshevich
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anton I. Maydykovskiy
- 0000 0001 2342 9668grid.14476.30Department of Quantum Electronics, Faculty of Physics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Evgeny A. Shirshin
- 0000 0001 2342 9668grid.14476.30Department of Quantum Electronics, Faculty of Physics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Timofey S. Gostev
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | - Marcus Moldenhauer
- 0000 0001 2292 8254grid.6734.6Technical University of Berlin, Institute of Chemistry PC 14, Straße des des 17. Juni 135, 10623 Berlin, Germany
| | - Yury B. Slonimskiy
- 0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Nikolai N. Sluchanko
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia ,0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Thomas Friedrich
- 0000 0001 2292 8254grid.6734.6Technical University of Berlin, Institute of Chemistry PC 14, Straße des des 17. Juni 135, 10623 Berlin, Germany
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Khan T, Dominguez-Martin MA, Šímová I, Fuciman M, Kerfeld CA, Polívka T. Excited-State Properties of Canthaxanthin in Cyanobacterial Carotenoid-Binding Proteins HCP2 and HCP3. J Phys Chem B 2020; 124:4896-4905. [DOI: 10.1021/acs.jpcb.0c03137] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tuhin Khan
- Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Maria Agustina Dominguez-Martin
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ivana Šímová
- Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Marcel Fuciman
- Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Cheryl A. Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tomáš Polívka
- Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
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Bondanza M, Nottoli M, Cupellini L, Lipparini F, Mennucci B. Polarizable embedding QM/MM: the future gold standard for complex (bio)systems? Phys Chem Chem Phys 2020; 22:14433-14448. [DOI: 10.1039/d0cp02119a] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We provide a perspective of the induced dipole formulation of polarizable QM/MM, showing how efficient implementations will enable their application to the modeling of dynamics, spectroscopy, and reactivity in complex biosystems.
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Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
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Adamec F, Farci D, Bína D, Litvín R, Khan T, Fuciman M, Piano D, Polívka T. Photophysics of deinoxanthin, the keto-carotenoid bound to the main S-layer unit of Deinococcus radiodurans. Photochem Photobiol Sci 2020; 19:495-503. [DOI: 10.1039/d0pp00031k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An ultrafast transient absorption experiment on the SDBC, which binds the carotenoid deinoxanthin, reveals a non-specific binding site that loosely binds the carotenoid, but protects the carotenoid from the outer environment.
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Affiliation(s)
- František Adamec
- Institute of Physics
- Faculty of Science
- University of South Bohemia
- České Budějovice
- Czech Republic
| | - Domenica Farci
- Department of Plant Physiology
- Warsaw University of Life Sciences - SGGW
- Warsaw
- Poland
| | - David Bína
- Institute of Chemistry
- Faculty of Science
- University of South Bohemia
- Czech Republic
- Biology Centre
| | - Radek Litvín
- Institute of Chemistry
- Faculty of Science
- University of South Bohemia
- Czech Republic
- Biology Centre
| | - Tuhin Khan
- Institute of Physics
- Faculty of Science
- University of South Bohemia
- České Budějovice
- Czech Republic
| | - Marcel Fuciman
- Institute of Physics
- Faculty of Science
- University of South Bohemia
- České Budějovice
- Czech Republic
| | - Dario Piano
- Department of Plant Physiology
- Warsaw University of Life Sciences - SGGW
- Warsaw
- Poland
- Laboratory of Photobiology and Plant Physiology
| | - Tomáš Polívka
- Institute of Physics
- Faculty of Science
- University of South Bohemia
- České Budějovice
- Czech Republic
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