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Grechishnikova G, Wat JH, de Cordoba N, Miyake E, Phadkule A, Srivastava A, Savikhin S, Slipchenko L, Huang L, Reppert M. Controlling Vibronic Coupling in Chlorophyll Proteins: The Effects of Excitonic Delocalization and Vibrational Localization. J Phys Chem Lett 2024; 15:9456-9465. [PMID: 39250712 DOI: 10.1021/acs.jpclett.4c01826] [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: 09/11/2024]
Abstract
Vibrational-electronic (vibronic) coupling plays a critical role in excitation energy transfer in molecular aggregates and pigment-protein complexes (PPCs). But the interplay between excitonic delocalization and vibronic interactions is complex, often leaving even qualitative questions as to what conceptual framework (e.g., Redfield versus Förster theory) should be used to interpret experimental results. To shed light on this issue, we report here on the interplay between excitonic delocalization and vibronic coupling in site-directed mutants of the water-soluble chlorophyll protein (WSCP), as reflected in 77 K fluorescence spectra. Experimentally, we find that in PPCs where excitonic delocalization is disrupted (either by mutagenesis or heterodimer formation), the relative intensity of the vibrational sideband (VSB) in fluorescence spectra is suppressed by up to 37% compared to that of the native protein. Numerical simulations reveal that this effect results from the localization of high-frequency vibrations in the coupled system; while excitonic delocalization suppresses the purely electronic transition due to H-aggregate-like dipole-dipole interference, high-frequency vibrations are unaffected, leading to a relative enhancement of the VSB. By comparing VSB intensities of PPCs both in the presence and absence of excitonic delocalization, we extract a set of "local" Huang-Rhys (HR) factors for Chl a in WSCP. More generally, our results suggest a significant role for geometric effects in controlling energy-transfer rates (which depend sensitively on absorption/fluorescence line shapes) in molecular aggregates and PPCs.
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Affiliation(s)
- Galina Grechishnikova
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jacob H Wat
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nicolas de Cordoba
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ethan Miyake
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lyudmila Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Libai Huang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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2
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Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat Chem Biol 2024; 20:906-915. [PMID: 38831036 PMCID: PMC11213709 DOI: 10.1038/s41589-024-01626-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
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Affiliation(s)
- Nathan M Ennist
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Shunzhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison A Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | | | | | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Anthony V Sica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ash Sueh Hua
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arundhati P Deshmukh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Avi Z Swartz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ralph A Cacho
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Novy
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Luo L, Martin AP, Tandoh EK, Chistoserdov A, Slipchenko LV, Savikhin S, Xu W. Impact of Peripheral Hydrogen Bond on Electronic Properties of the Primary Acceptor Chlorophyll in the Reaction Center of Photosystem I. Int J Mol Sci 2024; 25:4815. [PMID: 38732034 PMCID: PMC11084960 DOI: 10.3390/ijms25094815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Photosystem I (PS I) is a photosynthetic pigment-protein complex that absorbs light and uses the absorbed energy to initiate electron transfer. Electron transfer has been shown to occur concurrently along two (A- and B-) branches of reaction center (RC) cofactors. The electron transfer chain originates from a special pair of chlorophyll a molecules (P700), followed by two chlorophylls and one phylloquinone in each branch (denoted as A-1, A0, A1, respectively), converging in a single iron-sulfur complex Fx. While there is a consensus that the ultimate electron donor-acceptor pair is P700+A0-, the involvement of A-1 in electron transfer, as well as the mechanism of the very first step in the charge separation sequence, has been under debate. To resolve this question, multiple groups have targeted electron transfer cofactors by site-directed mutations. In this work, the peripheral hydrogen bonds to keto groups of A0 chlorophylls have been disrupted by mutagenesis. Four mutants were generated: PsaA-Y692F; PsaB-Y667F; PsaB-Y667A; and a double mutant PsaA-Y692F/PsaB-Y667F. Contrary to expectations, but in agreement with density functional theory modeling, the removal of the hydrogen bond by Tyr → Phe substitution was found to have a negligible effect on redox potentials and optical absorption spectra of respective chlorophylls. In contrast, Tyr → Ala substitution was shown to have a fatal effect on the PS I function. It is thus inferred that PsaA-Y692 and PsaB-Y667 residues have primarily structural significance, and their ability to coordinate respective chlorophylls in electron transfer via hydrogen bond plays a minor role.
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Affiliation(s)
- Lujun Luo
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA; (L.L.)
| | - Antoine P. Martin
- Department of Physics, Purdue University, West Lafayette, IN 47907, USA
| | - Elijah K. Tandoh
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA; (L.L.)
| | - Andrei Chistoserdov
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | | | - Sergei Savikhin
- Department of Physics, Purdue University, West Lafayette, IN 47907, USA
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA; (L.L.)
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Ahad S, Lin C, Reppert M. PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations. J Chem Phys 2024; 160:154111. [PMID: 38639311 DOI: 10.1063/5.0198443] [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: 01/18/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter's capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna-Matthews-Olson protein, and ring deformation in photosystems I and II.
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Affiliation(s)
- S Ahad
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - C Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - M Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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5
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Slipchenko LV. Detangling Solvatochromic Effects by the Effective Fragment Potential Method. J Phys Chem A 2024; 128:656-669. [PMID: 38193780 DOI: 10.1021/acs.jpca.3c06194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Understanding molecular interactions in complex systems opens avenues for the efficient design of new materials with target properties. Energy decomposition methods provide a means to obtain a detailed picture of intermolecular interactions. This work introduces a molecular modeling approach for decomposing the solvatochromic shifts of the electronic excited states into the contributions of the individual molecular fragments of the environment surrounding the chromophore. The developed approach is implemented for the QM/EFP (quantum mechanics/effective fragment potential) model that provides a rigorous first-principles-based description of the electronic states of the chromophores in complex polarizable environments. On the example of two model systems, water pentamer and hydrated uracil, we show how the decomposition of the solvatochromic shifts into the contributions of individual solvent water molecules provides a detailed picture of the intermolecular interactions in the ground and excited states of these systems. The analysis also demonstrates the nonadditivity of solute-solvent interactions and the significant contribution of solute polarization to the total values of solvatochromic shifts.
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Affiliation(s)
- Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
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Abstract
Biological pigment-protein complexes (PPCs) exhibit a remarkable ability to tune the optical properties of biological excitons (bioexcitons) through specific pigment-protein interactions. While such fine-tuning allows natural systems (e.g., photosynthetic proteins) to carry out their native functions with near-optimal performance, native function itself is often suboptimal for applications such as biofuel production or quantum technology development. This perspective offers a look at near-term prospects for the rational reoptimization of PPC bioexcitons for new functions using site-directed mutagenesis. The primary focus is on the "structure-spectrum" challenge of understanding the relationships between structural features and spectroscopic properties. While recent examples demonstrate that site-directed mutagenesis can be used to tune nearly all key bioexciton parameters (e.g., site energies, interpigment couplings, and electronic-vibrational interactions), critical challenges remain before we achieve truly rational design of bioexciton properties.
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Affiliation(s)
- Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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7
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Cignoni E, Cupellini L, Mennucci B. Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes. J Chem Theory Comput 2023; 19:965-977. [PMID: 36701385 PMCID: PMC9933434 DOI: 10.1021/acs.jctc.2c01044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Indexed: 01/27/2023]
Abstract
We propose a machine learning (ML)-based strategy for an inexpensive calculation of excitonic properties of light-harvesting complexes (LHCs). The strategy uses classical molecular dynamics simulations of LHCs in their natural environment in combination with ML prediction of the excitonic Hamiltonian of the embedded aggregate of pigments. The proposed ML model can reproduce the effects of geometrical fluctuations together with those due to electrostatic and polarization interactions between the pigments and the protein. The training is performed on the chlorophylls of the major LHC of plants, but we demonstrate that the model is able to extrapolate well beyond the initial training set. Moreover, the accuracy in predicting the effects of the environment is tested on the simulation of the small changes observed in the absorption spectra of the wild-type and a mutant of a minor LHC.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124Pisa, Italy
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Ciuti S, Agostini A, Barbon A, Bortolus M, Paulsen H, Di Valentin M, Carbonera D. Magnetophotoselection in the Investigation of Excitonically Coupled Chromophores: The Case of the Water-Soluble Chlorophyll Protein. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123654. [PMID: 35744779 PMCID: PMC9227413 DOI: 10.3390/molecules27123654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/01/2022]
Abstract
A magnetophotoselection (MPS) investigation of the photoexcited triplet state of chlorophyll a both in a frozen organic solvent and in a protein environment, provided by the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum, is reported. The MPS experiment combines the photoselection achieved by exciting with linearly polarized light with the magnetic selection of electron paramagnetic resonance (EPR) spectroscopy, allowing the determination of the relative orientation of the optical transition dipole moment and the zero-field splitting tensor axes in both environments. We demonstrate the robustness of the proposed methodology for a quantitative description of the excitonic interactions among pigments. The orientation of the optical transition dipole moments determined by the EPR analysis in WSCP, identified as an appropriate model system, are in excellent agreement with those calculated in the point-dipole approximation. In addition, MPS provides information on the electronic properties of the triplet state, localized on a single chlorophyll a pigment of the protein cluster, in terms of orientation of the zero-field splitting tensor axes in the molecular frame.
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Affiliation(s)
- Susanna Ciuti
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
| | - Alessandro Agostini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Antonio Barbon
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
| | - Harald Paulsen
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim Becher-Weg 7, 55128 Mainz, Germany;
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
- Correspondence: (M.D.V.); (D.C.); Tel.: +39-0498275139 (M.D.V.); +39-0498275144 (D.C.)
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.C.); (A.A.); (A.B.); (M.B.)
- Correspondence: (M.D.V.); (D.C.); Tel.: +39-0498275139 (M.D.V.); +39-0498275144 (D.C.)
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