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Kerfeld CA, Sutter M. Orange carotenoid proteins: structural understanding of evolution and function. Trends Biochem Sci 2024; 49:819-828. [PMID: 38789305 DOI: 10.1016/j.tibs.2024.04.010] [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: 01/26/2024] [Revised: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024]
Abstract
Cyanobacteria uniquely contain a primitive water-soluble carotenoprotein, the orange carotenoid protein (OCP). Nearly all extant cyanobacterial genomes contain genes for the OCP or its homologs, implying an evolutionary constraint for cyanobacteria to conserve its function. Genes encoding the OCP and its two constituent structural domains, the N-terminal domain, helical carotenoid proteins (HCPs), and its C-terminal domain, are found in the most basal lineages of extant cyanobacteria. These three carotenoproteins exemplify the importance of the protein for carotenoid properties, including protein dynamics, in response to environmental changes in facilitating a photoresponse and energy quenching. Here, we review new structural insights for these carotenoproteins and situate the role of the protein in what is currently understood about their functions.
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Affiliation(s)
- 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.
| | - 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
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Salvadori G, Mennucci B. Analogies and Differences in the Photoactivation Mechanism of Bathy and Canonical Bacteriophytochromes Revealed by Multiscale Modeling. J Phys Chem Lett 2024; 15:8078-8084. [PMID: 39087732 PMCID: PMC11376688 DOI: 10.1021/acs.jpclett.4c01823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Bacteriophytochromes are light-sensing biological machines that switch between two photoreversible states, Pr and Pfr. Their relative stability is opposite in canonical and bathy bacteriophytochromes, but in both cases the switch between them is triggered by the photoisomerization of an embedded bilin chromophore. We applied an integrated multiscale strategy of excited-state QM/MM nonadiabatic dynamics and (QM/)MM molecular dynamics simulations with enhanced sampling techniques to the Agrobacterium fabrum bathy phytochrome and compared the results with those obtained for the canonical phytochrome Deinococcus radiodurans. Contrary to what recently suggested, we found that photoactivation in both phytochromes is triggered by the same hula-twist motion of the bilin chromophore. However, only in the bathy phytochrome, the bilin reaches the final rotated structure already in the first intermediate. This allows a reorientation of the binding pocket in a microsecond time scale, which can propagate through the entire protein causing the spine to tilt.
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Affiliation(s)
- Giacomo Salvadori
- Institute for Computational Biomedicine (INM-9/IAS-5), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, 56124 Pisa, Italy
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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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Pedraza-González L, Accomasso D, Cupellini L, Granucci G, Mennucci B. Ultrafast excited-state dynamics of Luteins in the major light-harvesting complex LHCII. Photochem Photobiol Sci 2024; 23:303-314. [PMID: 38151602 DOI: 10.1007/s43630-023-00518-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/23/2023] [Indexed: 12/29/2023]
Abstract
Carotenoid pigments are known to present a functional versatility when bound to light-harvesting complexes. This versatility originates from a strong correlation between a complex electronic structure and a flexible geometry that is easily tunable by the surrounding protein environment. Here, we investigated how the different L1 and L2 sites of the major trimeric light-harvesting complex (LHCII) of green plants tune the electronic structure of the two embedded luteins, and how this reflects on their ultrafast dynamics upon excitation. By combining molecular dynamics and quantum mechanics/molecular mechanics calculations, we found that the two luteins feature a different conformation around the second dihedral angle in the lumenal side. The s-cis preference of the lutein in site L2 allows for a more planar geometry of the π -conjugated backbone, which results in an increased degree of delocalization and a reduced excitation energy, explaining the experimentally observed red shift. Despite these remarkable differences, according to surface hopping simulations the two luteins present analogous ultrafast dynamics upon excitation: the bright S 2 state quickly decays (in ∼ 50 fs) to the dark intermediate S x , eventually ending up in the S 1 state. Furthermore, by employing two different theoretical approaches (i.e., Förster theory and an excitonic version of surface hopping), we investigated the experimentally debated energy transfer between the two luteins. With both approaches, no evident energy transfer was observed in the ultrafast timescale.
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Affiliation(s)
- Laura Pedraza-González
- 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
| | - Giovanni Granucci
- 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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Accomasso D, Londi G, Cupellini L, Mennucci B. The nature of carotenoid S* state and its role in the nonphotochemical quenching of plants. Nat Commun 2024; 15:847. [PMID: 38286840 PMCID: PMC11258248 DOI: 10.1038/s41467-024-45090-9] [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: 07/15/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
In plants, light-harvesting complexes serve as antennas to collect and transfer the absorbed energy to reaction centers, but also regulate energy transport by dissipating the excitation energy of chlorophylls. This process, known as nonphotochemical quenching, seems to be activated by conformational changes within the light-harvesting complex, but the quenching mechanisms remain elusive. Recent spectroscopic measurements suggest the carotenoid S* dark state as the quencher of chlorophylls' excitation. By investigating lutein embedded in different conformations of CP29 (a minor antenna in plants) via nonadiabatic excited state dynamics simulations, we reveal that different conformations of the complex differently stabilize the lutein s-trans conformer with respect to the dominant s-cis one. We show that the s-trans conformer presents the spectroscopic signatures of the S* state and rationalize its ability to accept energy from the closest excited chlorophylls, providing thus a relationship between the complex's conformation and the nonphotochemical quenching.
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Affiliation(s)
- Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124, Pisa, Italy.
- Faculty of Chemistry, University of Warsaw, 02-093, Warsaw, Poland.
| | - Giacomo Londi
- 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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