1
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Riedl M, Renger T, Seibt J. Theory of 2D electronic spectroscopy of water soluble chlorophyll-binding protein (WSCP): Signatures of Chl b derivate. J Chem Phys 2024; 160:184114. [PMID: 38726933 DOI: 10.1063/5.0200876] [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: 01/29/2024] [Accepted: 04/21/2024] [Indexed: 06/29/2024] Open
Abstract
We investigate how electronic excitations and subsequent dissipative dynamics in the water soluble chlorophyll-binding protein (WSCP) are connected to features in two-dimensional (2D) electronic spectra, thereby comparing results from our theoretical approach with experimental data from the literature. Our calculations rely on third-order response functions, which we derived from a second-order cumulant expansion of the dissipative dynamics involving the partial ordering prescription, assuming a fast vibrational relaxation in the potential energy surfaces of excitons. Depending on whether the WSCP complex containing a tetrameric arrangement of pigments composed of two dimers with weak excitonic coupling between them binds the chlorophyll variant Chl a or Chl b, the resulting linear absorption and circular dichroism spectra and particularly the 2D spectra exhibit substantial differences in line shapes. These differences between Chl a WSCP and Chl b WSCP cannot be explained by the slightly modified excitonic couplings within the two variants. In the case of Chl a WSCP, the assumption of equivalent dimer subunits facilitates a reproduction of substantial features from the experiment by the calculations. In contrast, for Chl b WSCP, we have to assume that the sample, in addition to Chl b dimers, contains a small but distinct fraction of chemically modified Chl b pigments. The existence of such Chl b derivates has been proposed by Pieper et al. [J. Phys. Chem. B 115, 4042 (2011)] based on low-temperature absorption and hole-burning spectroscopy. Here, we provide independent evidence.
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Affiliation(s)
- Michael Riedl
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Joachim Seibt
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
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2
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Zazubovich V, Jankowiak R. High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes. Int J Mol Sci 2024; 25:3850. [PMID: 38612659 PMCID: PMC11011720 DOI: 10.3390/ijms25073850] [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: 02/23/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Photosystem I (PSI) is one of the two main pigment-protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI3), PSI3 mutants, and PSI3-IsiA18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure-function relationship. We will focus on the so-called "red antenna states" of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI3 and PSI3-IsiA18 supercomplexes allowed us to make inferences about EET from the IsiA18 ring to the PSI3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA18 ring to the PSI3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.
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Affiliation(s)
- Valter Zazubovich
- Department of Physics, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
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3
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Perrett S, Chatrchyan V, Buckup T, van Thor JJ. Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography. J Chem Phys 2024; 160:100901. [PMID: 38456527 DOI: 10.1063/5.0188888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities of XFELs advance, we anticipate that a new range of coherent control and structural Raman measurements will become achievable. Shorter optical and x-ray pulse durations and increasingly more exotic pulse regimes are becoming available at free electron lasers. Moreover, with high repetition enabled by the superconducting technology of European XFEL (EuXFEL) and Linac Coherent Light Source (LCLS-II) , it will be possible to improve the signal-to-noise ratio of the light-induced differences, allowing for the observation of vibronic motion on the sub-Angstrom level. To predict and assign this coherent motion, which is measurable with a structural technique, new theoretical approaches must be developed. In this paper, we present a theoretical density matrix approach to model the various population and coherent dynamics of a system, which considers molecular system parameters and excitation conditions. We emphasize the use of the Wigner transform of the time-dependent density matrix, which provides a phase space representation that can be directly compared to the experimental positional displacements measured in a TR-SFX experiment. Here, we extend the results from simple models to include more realistic schemes that include large relaxation terms. We explore a variety of pulse schemes using multiple model systems using realistic parameters. An open-source software package is provided to perform the density matrix simulation and Wigner transformations. The open-source software allows us to define any arbitrary level schemes as well as any arbitrary electric field in the interaction Hamiltonian.
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Affiliation(s)
- Samuel Perrett
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Viktoria Chatrchyan
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität, D-69120 Heidelberg, Germany
| | - Tiago Buckup
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität, D-69120 Heidelberg, Germany
| | - Jasper J van Thor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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4
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Cherepanov DA, Neverov KV, Obukhov YN, Maleeva YV, Gostev FE, Shelaev IV, Aybush AV, Kritsky MS, Nadtochenko VA. Femtosecond Dynamics of Excited States of Chlorophyll Tetramer in Water-Soluble Chlorophyll-Binding Protein BoWSCP. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1580-1595. [PMID: 38105026 DOI: 10.1134/s0006297923100139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 12/19/2023]
Abstract
The paper reports on the absorption dynamics of chlorophyll a in a symmetric tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP. It was measured by a broadband femtosecond laser pump-probe spectroscopy within the range from 400 to 750 nm and with a time resolution of 20 fs-200 ps. When BoWSCP was excited in the region of the Soret band at a wavelength of 430 nm, nonradiative intramolecular conversion S3→S1 was observed with a characteristic time of 83 ± 9 fs. When the complex was excited in the region of the Qy band at 670 nm, relaxation transition between two excitonic states of the chlorophyll dimer was observed in the range of 105 ± 10 fs. Absorption spectra of the excited singlet states S1 and S3 of chlorophyll a were obtained. The delocalization of the excited state between exciton-coupled Chl molecules in BoWSCP tetramer changed in time and depended on the excitation energy. When BoWSCP is excited in the Soret band region, an ultrafast photochemical reaction is observed. This could result from the reduction of tryptophan in the vicinity of chlorophyll.
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Affiliation(s)
- Dmitry A Cherepanov
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
- Belozersky Research Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Konstantin V Neverov
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yuriy N Obukhov
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Yulia V Maleeva
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Feodor E Gostev
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Ivan V Shelaev
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
- Belozersky Research Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Arseny V Aybush
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Michail S Kritsky
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Victor A Nadtochenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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5
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Seibt J, Lindorfer D, Renger T. Signatures of intramolecular vibrational and vibronic Q[Formula: see text]-Q[Formula: see text] coupling effects in absorption and CD spectra of chlorophyll dimers. PHOTOSYNTHESIS RESEARCH 2023; 156:19-37. [PMID: 36040654 PMCID: PMC10070234 DOI: 10.1007/s11120-022-00946-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
An electron-vibrational coupling model that includes the vibronic (non-adiabatic) coupling between the Q[Formula: see text] and Q[Formula: see text] transitions of chlorophyll (Chl), created by Reimers and coworkers (Scientific Rep. 3, 2761, 2013) is extended here to chlorophyll dimers with interchlorophyll excitonic coupling. The model is applied to a Chl a dimer of the water-soluble chlorophyll binding protein (WSCP). As for isolated chlorophyll, the vibronic coupling is found to have a strong influence on the high-frequency vibrational sideband in the absorption spectrum, giving rise to a band splitting. In contrast, in the CD spectrum the interplay of vibronic coupling and static disorder leads to a strong suppression of the vibrational sideband in excellent agreement with the experimental data. The conservative nature of the CD spectrum in the low-energy region is found to be caused by a delicate balance of the intermonomer excitonic coupling between the purely electronic Q[Formula: see text] transition and the Q[Formula: see text] transition involving intramolecular vibrational excitations on one hand and the coupling to higher-energy electronic transitions on the other hand.
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Affiliation(s)
- Joachim Seibt
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria.
| | - Dominik Lindorfer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria
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6
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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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7
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Friedl C, Fedorov DG, Renger T. Towards a quantitative description of excitonic couplings in photosynthetic pigment-protein complexes: quantum chemistry driven multiscale approaches. Phys Chem Chem Phys 2022; 24:5014-5038. [PMID: 35142765 PMCID: PMC8865841 DOI: 10.1039/d1cp03566e] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A structure-based quantitative calculation of excitonic couplings between photosynthetic pigments has to describe the dynamical polarization of the protein/solvent environment of the pigments, giving rise to reaction field and screening effects. Here, this challenging problem is approached by combining the fragment molecular orbital (FMO) method with the polarizable continuum model (PCM). The method is applied to compute excitonic couplings between chlorophyll a (Chl a) pigments of the water-soluble chlorophyll-binding protein (WSCP). By calibrating the vacuum dipole strength of the 0–0 transition of the Chl a chromophores according to experimental data, an excellent agreement between calculated and experimental linear absorption and circular dichroism spectra of WSCP is obtained. The effect of the mutual polarization of the pigment ground states is calculated to be very small. The simple Poisson-Transition-charge-from-Electrostatic-potential (Poisson-TrEsp) method is found to accurately describe the screening part of the excitonic coupling, obtained with FMO/PCM. Taking into account that the reaction field effects of the latter method can be described by a scalar constant leads to an improvement of Poisson-TrEsp that is expected to provide the basis for simple and realistic calculations of optical spectra and energy transfer in photosynthetic light-harvesting complexes. In addition, we present an expression for the estimation of Huang–Rhys factors of high-frequency pigment vibrations from experimental fluorescence line-narrowing spectra that takes into account the redistribution of oscillator strength by the interpigment excitonic coupling. Application to WSCP results in corrected Huang–Rhys factors that are less than one third of the original values obtained by the standard electronic two-state analysis that neglects the above redistribution. These factors are important for the estimation of the dipole strength of the 0–0 transition of the chromophores and for the development of calculation schemes for the spectral density of the exciton-vibrational coupling. The importance of reaction field and screening effects on the excitonic couplings is demonstrated, and from quantum-chemical calculations a single scaling factor is derived that can be used to improve simple models based on the Poisson equation.![]()
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Affiliation(s)
- Christian Friedl
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
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8
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Reimers JR, Rätsep M, Freiberg A. Asymmetry in the Q y Fluorescence and Absorption Spectra of Chlorophyll a Pertaining to Exciton Dynamics. Front Chem 2020; 8:588289. [PMID: 33344415 PMCID: PMC7738624 DOI: 10.3389/fchem.2020.588289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
Significant asymmetry found between the high-resolution Qy emission and absorption spectra of chlorophyll-a is herein explained, providing basic information needed to understand photosynthetic exciton transport and photochemical reactions. The Qy spectral asymmetry in chlorophyll has previously been masked by interference in absorption from the nearby Qx transition, but this effect has recently been removed using extensive quantum spectral simulations or else by analytical inversion of absorption and magnetic circular dichroism data, allowing high-resolution absorption information to be accurately determined from fluorescence-excitation spectra. To compliment this, here, we measure and thoroughly analyze the high-resolution differential fluorescence line narrowing spectra of chlorophyll-a in trimethylamine and in 1-propanol. The results show that vibrational frequencies often change little between absorption and emission, yet large changes in line intensities are found, this effect also being strongly solvent dependent. Among other effects, the analysis in terms of four basic patterns of Duschinsky-rotation matrix elements, obtained using CAM-B3LYP calculations, predicts that a chlorophyll-a molecule excited into a specific vibrational level, may, without phase loss or energy relaxation, reemit the light over a spectral bandwidth exceeding 1,000 cm−1 (0.13 eV) to influence exciton-transport dynamics.
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Affiliation(s)
- Jeffrey R Reimers
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Margus Rätsep
- Institute of Physics, University of Tartu, Tartu, Estonia
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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9
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Chaillet M, Lengauer F, Adolphs J, Müh F, Fokas AS, Cole DJ, Chin AW, Renger T. Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment. J Phys Chem Lett 2020; 11:10306-10314. [PMID: 33227205 PMCID: PMC7751012 DOI: 10.1021/acs.jpclett.0c03123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Inhomogeneous broadening of optical lines of the Fenna-Matthews-Olson (FMO) light-harvesting protein is investigated by combining a Monte Carlo sampling of low-energy conformational substates of the protein with a quantum chemical/electrostatic calculation of local transition energies (site energies) of the pigments. The good agreement between the optical spectra calculated for the inhomogeneous ensemble and the experimental data demonstrates that electrostatics is the dominant contributor to static disorder in site energies. Rotamers of polar amino acid side chains are found to cause bimodal distribution functions of site energy shifts, which can be probed by hole burning and single-molecule spectroscopy. When summing over the large number of contributions, the resulting distribution functions of the site energies become Gaussians, and the correlations in site energy fluctuations at different sites practically average to zero. These results demonstrate that static disorder in the FMO protein is in the realm of the central limit theorem of statistics.
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Affiliation(s)
- Marten
L. Chaillet
- Bijvoet
Centre for Biomolecular Research, University
of Utrecht, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Florian Lengauer
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Julian Adolphs
- Leibniz
Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Frank Müh
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Alexander S. Fokas
- TCM
Group, Cavendish Laboratory, 19 J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Alex W. Chin
- Centre
National de la Recherce Scientifique, Institute des Nanosciences de
Paris, Sorbonne Université, Paris, France
| | - Thomas Renger
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
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10
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Khmelnitskiy A, Toporik H, Mazor Y, Jankowiak R. On the Red Antenna States of Photosystem I Mutants from Cyanobacteria Synechocystis PCC 6803. J Phys Chem B 2020; 124:8504-8515. [DOI: 10.1021/acs.jpcb.0c05201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton Khmelnitskiy
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Hila Toporik
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Yuval Mazor
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
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11
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Prabahar V, Afriat-Jurnou L, Paluy I, Peleg Y, Noy D. New homologues of Brassicaceae water-soluble chlorophyll proteins shed light on chlorophyll binding, spectral tuning, and molecular evolution. FEBS J 2019; 287:991-1004. [PMID: 31549491 DOI: 10.1111/febs.15068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/02/2019] [Accepted: 09/18/2019] [Indexed: 01/06/2023]
Abstract
Type-II water-soluble chlorophyll (Chl) proteins (WSCPs) of Brassicaceae are promising models for understanding how protein sequence and structure affect Chl binding and spectral tuning in photosynthetic Chl-protein complexes. However, to date, their use has been limited by the small number of known WSCPs, which also limited understanding their physiological roles. To overcome these limitations, we performed a phylogenetic analysis to compile a more comprehensive and complete set of natural type-II WSCP homologues. The identified homologues were heterologously expressed in Escherichia coli, purified, tested for assembly with chlorophylls, and spectroscopically characterized. The analyses led to the discovery of previously unrecognized type-IIa and IIb subclass WSCPs, as well as of a new subclass that did not bind chlorophylls. Further analysis by ancestral sequence reconstruction yielded sequences of putative ancestors of the three subclasses, which were subsequently recombinantly expressed in E. coli, purified and characterized. Combining the phylogenetic and spectroscopic data with molecular structural information revealed distinct Chl-binding motifs, and identified residues critically impacting spectral tuning. The distinct Chl-binding properties of the WSCP archetypes suggest that the non-Chl-binding subclass evolved from a Chl-binding ancestor that most likely lost its Chl-binding capacity upon localization in the plant tissues with low Chl content. This dual evolutionary trajectory is consistent with WSCPs association with the Kunitz-type protease inhibitors superfamily, and indications of their inhibitory activity in response to various forms of stress in plants. These findings suggest new directions for exploring the physiological roles of WSCPs and the correlation, if any, between Chl-binding and protease inhibition functionality.
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Affiliation(s)
| | - Livnat Afriat-Jurnou
- Migal-Galilee Research Institute, Kiryat Shmona, Israel.,Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
| | - Irina Paluy
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Dror Noy
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
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12
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Zazubovich V, Jankowiak R. How Well Does the Hole-Burning Action Spectrum Represent the Site-Distribution Function of the Lowest-Energy State in Photosynthetic Pigment-Protein Complexes? J Phys Chem B 2019; 123:6007-6013. [PMID: 31265294 DOI: 10.1021/acs.jpcb.9b03806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the first time, we combined Monte Carlo and nonphotochemical hole burning (NPHB) master equation approaches to allow for ultrahigh-resolution (<0.005 cm-1, smaller than the typical homogeneous line widths at 5 K) simulations of the NPHB spectra of dimers and trimers of interacting pigments. These simulations reveal significant differences between the zero-phonon hole (ZPH) action spectrum and the site-distribution function (SDF) of the lowest-energy state. The NPHB of the lowest-energy pigment, following the excitation energy transfer (EET) from the higher-energy pigments which are excited directly, results in the shifts of all excited states. These shifts affect the ZPH action spectra and EET times derived from the widths of the spectral holes burned in the donor-dominated regions. The effect is present for a broad variety of realistic antihole functions, and it is maximal at relatively low values of interpigment coupling (V ≤ 5 cm-1) where the use of the Förster approximation is justified. These findings need to be considered in interpreting various optical spectra of photosynthetic pigment-protein complexes for which SDFs (describing the inhomogeneous broadening) are often obtained directly from the ZPH action spectra. Water-soluble chlorophyll-binding protein (WSCP) was considered as an example.
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Affiliation(s)
- Valter Zazubovich
- Department of Physics , Concordia University , 7141 Sherbrooke Street West , Montreal H4B 1R6 , Quebec , Canada
| | - Ryszard Jankowiak
- Department of Chemistry , Kansas State University , Manhattan , Kansas 66506 , United States
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13
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Adolphs J, Maier F, Renger T. Wavelength-Dependent Exciton-Vibrational Coupling in the Water-Soluble Chlorophyll Binding Protein Revealed by Multilevel Theory of Difference Fluorescence Line-Narrowing. J Phys Chem B 2018; 122:8891-8899. [PMID: 30183300 DOI: 10.1021/acs.jpcb.8b08410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the most powerful line-narrowing techniques used to unravel the homogeneous lineshapes of inhomogeneously broadened systems is difference fluorescence line-narrowing spectroscopy. When this spectroscopy was applied to multichromophoric systems so far, the spectra were analyzed by an effective two-level system approach, composed of the electronic ground state and the lowest exciton state. An effective Huang-Rhys factor was assigned for the coupling of this state to the vibrations. Here, we extend this approach by including a multilevel line shape theory, which takes into account the excitonic coupling between pigments and thereby the effect of the delocalization of the excited states explicitly. In this way, it becomes possible to extract the spectral density of the local exciton-vibrational coupling. The theory is applied to the recombinant water-soluble chlorophyll binding protein reconstituted with chlorophyll a or b and reveals a significant decrease of the Huang-Rhys factor of the local exciton-vibrational coupling with decreasing transition energy of the chlorophylls. This decrease could be due to the increase in steric interactions reducing the flexibility of the environment and red-shifting the site energy of the pigments.
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Affiliation(s)
- Julian Adolphs
- Institute for Theoretical Physics , Johannes Kepler University Linz , Altenberger Strasse 69 , 4040 Linz , Austria
| | - Franziska Maier
- Institute for Theoretical Physics , Johannes Kepler University Linz , Altenberger Strasse 69 , 4040 Linz , Austria
| | - Thomas Renger
- Institute for Theoretical Physics , Johannes Kepler University Linz , Altenberger Strasse 69 , 4040 Linz , Austria
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14
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Khmelnitskiy A, Saer RG, Blankenship RE, Jankowiak R. Excitonic Energy Landscape of the Y16F Mutant of the Chlorobium tepidum Fenna-Matthews-Olson (FMO) Complex: High Resolution Spectroscopic and Modeling Studies. J Phys Chem B 2018; 122:3734-3743. [PMID: 29554425 DOI: 10.1021/acs.jpcb.7b11763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We report high-resolution (low-temperature) absorption, emission, and nonresonant/resonant hole-burned (HB) spectra and results of excitonic calculations using a non-Markovian reduced density matrix theory (with an improved algorithm for parameter optimization in heterogeneous samples) obtained for the Y16F mutant of the Fenna-Matthews-Olson (FMO) trimer from the green sulfur bacterium Chlorobium tepidum. We show that the Y16F mutant is a mixture of FMO complexes with three independent low-energy traps (located near 817, 821, and 826 nm), in agreement with measured composite emission and HB spectra. Two of these traps belong to mutated FMO subpopulations characterized by significantly modified low-energy excitonic states. Hamiltonians for the two major subpopulations (Sub821 and Sub817) provide new insight into extensive changes induced by the single-point mutation in the vicinity of BChl 3 (where tyrosine Y16 was replaced with phenylalanine F16). The average decay time(s) from the higher exciton state(s) in the Y16F mutant depends on frequency and occurs on a picosecond time scale.
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Affiliation(s)
| | - Rafael G Saer
- Departments of Biology and Chemistry , Washington University in St. Louis , Saint Louis , Missouri 63130 , United States
| | - Robert E Blankenship
- Departments of Biology and Chemistry , Washington University in St. Louis , Saint Louis , Missouri 63130 , United States
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15
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Tiwari V, Jonas DM. Electronic energy transfer through non-adiabatic vibrational-electronic resonance. II. 1D spectra for a dimer. J Chem Phys 2018; 148:084308. [DOI: 10.1063/1.5003193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vivek Tiwari
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
| | - David M. Jonas
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
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16
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Levenberg A, Shafiei G, Lujan MA, Giannacopoulos S, Picorel R, Zazubovich V. Probing Energy Landscapes of Cytochrome b 6f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent. J Phys Chem B 2017; 121:9848-9858. [PMID: 28956922 DOI: 10.1021/acs.jpcb.7b07686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In non-photochemical spectral hole burning (NPHB) and spectral hole recovery experiments, cytochrome b6f protein exhibits behavior that is almost independent of the deuteration of the buffer/glycerol glassy matrix containing the protein, apart from some differences in heat dissipation. On the other hand, strong dependence of the hole burning properties on sample preparation procedures was observed and attributed to a large increase of the electron-phonon coupling and shortening of the excited-state lifetime occurring when n-dodecyl β-d-maltoside (DM) is used as a detergent instead of n-octyl β-d-glucopyranoside (OGP). The data was analyzed assuming that the tunneling parameter distribution or barrier distribution probed by NPHB and encoded into the spectral holes contains contributions from two nonidentical components with accidentally degenerate excited state λ-distributions. Both components likely reflect protein dynamics, although with some small probability one of them (with larger md2) may still represent the dynamics involving specifically the -OH groups of the water/glycerol solvent. Single proton tunneling in the water/glycerol solvent environment or in the protein can be safely excluded as the origin of observed NPHB and hole recovery dynamics. The intensity dependence of the hole growth kinetics in deuterated samples likely reflects differences in heat dissipation between protonated and deuterated samples. These differences are most probably due to the higher interface thermal resistivity between (still protonated) protein and deuterated water/glycerol outside environment.
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Affiliation(s)
- Alexander Levenberg
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Golia Shafiei
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Maria A Lujan
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005, 50059 Zaragoza, Spain
| | - Steven Giannacopoulos
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005, 50059 Zaragoza, Spain
| | - Valter Zazubovich
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
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17
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Zhang HD, Qiao Q, Xu RX, Yan Y. Solvent-induced polarization dynamics and coherent two-dimensional spectroscopy: Dissipaton equation of motion approach. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Dinh TC, Renger T. Lineshape theory of pigment-protein complexes: How the finite relaxation time of nuclei influences the exciton relaxation-induced lifetime broadening. J Chem Phys 2016; 145:034105. [DOI: 10.1063/1.4958322] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thanh-Chung Dinh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
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19
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Challenges facing an understanding of the nature of low-energy excited states in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1627-1640. [PMID: 27372198 DOI: 10.1016/j.bbabio.2016.06.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 01/09/2023]
Abstract
While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.
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The lowest-energy chlorophyll of photosystem II is adjacent to the peripheral antenna: Emitting states of CP47 assigned via circularly polarized luminescence. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1580-1593. [PMID: 27342201 DOI: 10.1016/j.bbabio.2016.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 11/22/2022]
Abstract
The identification of low-energy chlorophyll pigments in photosystem II (PSII) is critical to our understanding of the kinetics and mechanism of this important enzyme. We report parallel circular dichroism (CD) and circularly polarized luminescence (CPL) measurements at liquid helium temperatures of the proximal antenna protein CP47. This assembly hosts the lowest-energy chlorophylls in PSII, responsible for the well-known "F695" fluorescence band of thylakoids and PSII core complexes. Our new spectra enable a clear identification of the lowest-energy exciton state of CP47. This state exhibits a small but measurable excitonic delocalization, as predicated by its CD and CPL. Using structure-based simulations incorporating the new spectra, we propose a revised set of site energies for the 16 chlorophylls of CP47. The significant difference from previous analyses is that the lowest-energy pigment is assigned as Chl 612 (alternately numbered Chl 11). The new assignment is readily reconciled with the large number of experimental observations in the literature, while the most common previous assignment for the lowest energy pigment, Chl 627(29), is shown to be inconsistent with CD and CPL results. Chl 612(11) is near the peripheral light-harvesting system in higher plants, in a lumen-exposed region of the thylakoid membrane. The low-energy pigment is also near a recently proposed binding site of the PsbS protein. This result consequently has significant implications for our understanding of the kinetics and regulation of energy transfer in PSII.
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