1
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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 2024:10.1038/s41589-024-01626-0. [PMID: 38831036 DOI: 10.1038/s41589-024-01626-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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2
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Toutounji M. Empirical asymmetric phonon sideband due to phonons in the protein matrix present in photosynthetic complexes: Time-domain response theory. BIOPHYSICAL REPORTS 2024; 4:100146. [PMID: 38375357 PMCID: PMC10875334 DOI: 10.1016/j.bpr.2024.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024]
Abstract
The phonon spectral density plays a key role in probing the dynamical and spectral behavior of molecular aggregates. One may utilize the intimate connection between the one-phonon profile and the phonon spectral density to extract a plausible form of the spectral density of media with rich structure using advanced optical spectroscopy. The excitonic transition is normally accompanied by a broad, asymmetric phonon-side band due to the coupling to the phonons in the surrounding protein matrix present in photosynthetic complexes. The asymmetry in the one-phonon profile of a homogeneous absorption spectrum and other experiments performed on photosynthetic bacterial reaction centers (BRCs) led the Small group to employ a half-Gaussian distribution function on the red side and half-Lorentzian distribution function on the blue side of the absorption lineshape to account for the one-phonon profile asymmetrical shape and relaxation effects contributing to spectroscopy and dynamics of BRCs at hand. Different research groups successfully employed the theory of Small to simulate their photosynthetic spectral data so they could calculate the homogeneous absorption and hole-burned spectra of photosynthetic complexes. Although this report does not directly use the formulae of homogeneous absorption, hole-burning, and fluorescence line-narrowed spectra of BRCs, and photosynthetic complexes, developed by Hayes-Small, it builds on their idea of the phonon sideband asymmetric shape in deriving an accurate and computationally efficient linear electronic transition dipole moment time correlation function. Besides the compelling tractability and efficiency of this correlation function, it accounts for excitonic coupling and eliminates all the inconsistencies arising in the Hayes-Small theory.
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Affiliation(s)
- Mohamad Toutounji
- College of Science, Department of Chemistry, UAE University, Al-Ain, UAE
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3
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Zheng Y, Zhou Y, Zhang D, Ning J, Tang F, Zheng C. Effects of the excitation wavelength and temperature on the zero-phonon emission line of Cr:YAG. APPLIED OPTICS 2024; 63:322-326. [PMID: 38227224 DOI: 10.1364/ao.506308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/30/2023] [Indexed: 01/17/2024]
Abstract
In this work, a detailed study was conducted of the temperature and excitation wavelength-dependent photoluminescence (PL) spectra of the chromium-doped yttrium aluminum garnet (Cr:YAG) transparent ceramic. Focusing on the two sets of zero-phonon lines (ZPLs) of the 2 E→4 A 2 transition in this material, the PL spectra are discovered to evolve significantly with respect to temperature and be highly dependent on the excitation wavelength. Compared to the continuous variation behavior with temperature, an increase in the excitation wavelength leads to a blueshift of the peak position within the regions of 450 nm to 465 nm, 465 nm to 490 nm, and 490 nm to 500 nm, and a sharp change in the PL position at the excitation wavelengths of 465 nm and 490 nm. The electron-phonon coupling (EPC) effect is believed to be more sensitive to the excitation wavelength. Different excitation wavelengths involve different electronic levels participating in the light emission processes, which explains the evolution behavior of the PL peak position with respect to the excitation wavelength. Moreover, the emergence of weak peaks next to the ZPLs at particular temperatures and excitation wavelengths is also observed. This work compares the influence of the temperature and excitation wavelength to the PL properties of the Cr:YAG transparent ceramic, which promotes an advanced understanding of the luminescence behavior of the Cr:YAG transparent ceramics.
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4
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Gustin I, Kim CW, McCamant DW, Franco I. Mapping electronic decoherence pathways in molecules. Proc Natl Acad Sci U S A 2023; 120:e2309987120. [PMID: 38015846 PMCID: PMC10710033 DOI: 10.1073/pnas.2309987120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.
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Affiliation(s)
- Ignacio Gustin
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Chang Woo Kim
- Department of Chemistry, Chonnam National University, Gwangju61186, South Korea
| | - David W. McCamant
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Ignacio Franco
- Department of Chemistry, University of Rochester, Rochester, NY14627
- Department of Physics, University of Rochester, Rochester, NY14627
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5
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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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6
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Zhu R, Ruan M, Li H, Leng X, Zou J, Wang J, Chen H, Wang Z, Weng Y. Vibrational and vibronic coherences in the energy transfer process of light-harvesting complex II revealed by two-dimensional electronic spectroscopy. J Chem Phys 2022; 156:125101. [DOI: 10.1063/5.0082280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The presence of quantum coherence in light-harvesting complex II (LHCII) as a mechanism to understand the efficiency of the light-harvesting function in natural photosynthetic systems is still debated due to its structural complexity and weak-amplitude coherent oscillations. Here, we revisit the coherent dynamics and clarify different types of coherences in the energy transfer processes of LHCII using a joint method of the high-S/N transient grating and two-dimensional electronic spectroscopy. We find that the electronic coherence decays completely within 50 fs at room temperature. The vibrational coherences of chlorophyll a dominate over oscillations within 1 ps, whereas a low-frequency mode of 340 cm−1 with a vibronic mixing character may participate in vibrationally assisted energy transfer between chlorophylls a. Our results may suggest that vibronic mixing is relevant for rapid energy transfer processes among chlorophylls in LHCII.
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Affiliation(s)
- Ruidan Zhu
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meixia Ruan
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Li
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Leng
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiading Zou
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayu Wang
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailong Chen
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Zhuan Wang
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuxiang Weng
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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7
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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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8
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Du M, Qin M, Cui H, Wang C, Xu Y, Ma X, Yi X. Role of Spatially Correlated Fluctuations in Photosynthetic Excitation Energy Transfer with an Equilibrium and a Nonequilibrium Initial Bath. J Phys Chem B 2021; 125:6417-6430. [PMID: 34105973 DOI: 10.1021/acs.jpcb.1c02041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transfer of excitation energy in photosynthetic light-harvesting complexes has inspired growing interest for its scientific and engineering significance. Recent experimental findings have suggested that spatially correlated environmental fluctuations may account for the existence of long-lived quantum coherent energy transfer observed even at physiological temperature. In this paper, we investigate the effects of spatial correlations on the excitation energy transfer dynamics by including a nonequilibrium initial bath in a simulated donor-acceptor model. The initial bath state, which is assumed to be either equilibrium or nonequilibrium, is expanded in powers of coupling strength within the polaron formalism of a quantum master equation. The spatial correlations of bath fluctuations strongly influence the decay of coherence in the dynamics. The role of a nonequilibrium initial bath is also influenced by spatial correlations and becomes the most conspicuous for certain degrees of spatial correlations from which we propose a picture that the spatial correlations of bath fluctuations open up new energy transfer pathways, playing a role of protecting coherence. Besides, we apply the polaron master equation approach to study the dynamics in a two-site subsystem of the FMO complex and provide a practical example that shows the versatility of this approach.
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Affiliation(s)
- Min Du
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Ming Qin
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.,Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
| | - Haitao Cui
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.,Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
| | - Chunyang Wang
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Yuqing Xu
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xiaoguang Ma
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xuexi Yi
- Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
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9
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Reinot T, Jassas M, Kell A, Casazza AP, Santabarbara S, Jankowiak R. On wavelength-dependent exciton lifetime distributions in reconstituted CP29 antenna of the photosystem II and its site-directed mutants. J Chem Phys 2021; 154:085101. [PMID: 33639775 DOI: 10.1063/5.0038217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To provide more insight into the excitonic structure and exciton lifetimes of the wild type (WT) CP29 complex of photosystem II, we measured high-resolution (low temperature) absorption, emission, and hole burned spectra for the A2 and B3 mutants, which lack chlorophylls a612 and b614 (Chls), respectively. Experimental and modeling results obtained for the WT CP29 and A2/B3 mutants provide new insight on the mutation-induced changes at the molecular level and shed more light on energy transfer dynamics. Simulations of the A2 and B3 optical spectra, using the second-order non-Markovian theory, and comparison with improved fits of WT CP29 optical spectra provide more insight into their excitonic structure, mutation induced changes, and frequency-dependent distributions of exciton lifetimes (T1). A new Hamiltonian obtained for WT CP29 reveals that deletion of Chls a612 or b614 induces changes in the site energies of all remaining Chls. Hamiltonians obtained for A2 and B3 mutants are discussed in the context of the energy landscape of chlorophylls, excitonic structure, and transfer kinetics. Our data suggest that the lowest exciton states in A2 and B3 mutants are contributed by a611(57%), a610(17%), a615(15%) and a615(58%), a611(20%), a612(15%) Chls, respectively, although other compositions of lowest energy states are also discussed. Finally, we argue that the calculated exciton decay times are consistent with both the hole-burning and recent transient absorption measurements. Wavelength-dependent T1 distributions offer more insight into the interpretation of kinetic traces commonly described by discrete exponentials in global analysis/global fitting of transient absorption experiments.
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Affiliation(s)
- Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Mahboobe Jassas
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Adam Kell
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Anna Paola Casazza
- Istituto di Biologia e Biotecnologia Agraria, C.N.R., Via Bassini 15, 20133 Milano, Italy
| | - Stefano Santabarbara
- Photosynthesis Research Unit, Centro Studi sulla Biologia Cellulare e Molecolare delle Piante, C.N.R., Milano, Italy
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
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10
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Sosa ML, Wong CY. Revealing the evolving mixture of molecular aggregates during organic film formation using simulations of in situ absorbance. J Chem Phys 2020; 153:214902. [PMID: 33291921 DOI: 10.1063/5.0020788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In this work, we introduce a method for modeling the evolving absorbance spectrum of an organic molecule, pseudoisocyanine (PIC), measured during the process of molecular aggregation. Despite being historically considered a J-aggregate, we find that the absorbance spectrum of PIC cannot be adequately modeled using solely J-aggregates either during molecular aggregation or in the final dry film. The collection of absorbance spectra during solution-casting is particularly difficult since a distribution of aggregates with various sizes and structures can coexist. Here, spectra measured during film formation are fit to a weighted sum of simulated spectra of two aggregate species, revealing the combinations of Coulombic coupling values, Huang-Rhys parameters, and aggregate sizes that provide good fits to measured spectra. The peak intensity ratios and relative peak positions are highly sensitive to the aggregate structure, and fitting only these features enables the rapid comparison of aggregate combinations. We find that the spectra of PIC aggregates cannot be modeled using the Huang-Rhys factor of the PIC monomer, as is typically assumed, leading us to consider models that utilize independent Huang-Rhys factors for each aggregate species. This method of fitting only the key spectral features allows an experimental spectrum to be modeled within 1 h-2 h when using a single Huang-Rhys factor, making the simulation of a series of in situ measurements during aggregation computationally feasible.
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Affiliation(s)
- Morgan L Sosa
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
| | - Cathy Y Wong
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
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11
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Reppert M. Delocalization Effects in Chlorophyll Fluorescence: Nonperturbative Line Shape Analysis of a Vibronically Coupled Dimer. J Phys Chem B 2020; 124:10024-10033. [PMID: 33138372 DOI: 10.1021/acs.jpcb.0c05789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Non-adiabatic vibrational/electronic (vibronic) interactions in photosynthetic pigment/protein complexes (PPCs) have recently attracted considerable interest as a potential source for long-lived dynamic coherence and optimized light harvesting. The analysis of such effects is limited, however, by the complexity of the vibrational spectrum of biological pigments such as chlorophyll (Chl) molecules, which often makes numerical calculations prohibitively expensive and complicates the interpretation of experimental spectroscopic data. This work contributes to both challenges by using numerically exact computational methods to systematically examine vibronic mixing effects in the low-temperature fluorescence spectra of a Chl dimer possessing a full complement of local vibrations, using parameters extracted from experimental data. The results highlight the varying roles local vibrations can play in energy-transfer dynamics, both enhancing delocalization through vibronic resonance and, conversely, inducing dynamic localization by acting as a "self-bath" for local electronic transitions. In the specific context of line-narrowed fluorescence, the results indicate that, while low-frequency features are strongly suppressed by delocalization, high-frequency modes are likely to be dynamically localized in the parameter regime relevant to most photosynthetic complexes.
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Affiliation(s)
- Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2050, United States
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12
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Gorka M, Cherepanov DA, Semenov AY, Golbeck JH. Control of electron transfer by protein dynamics in photosynthetic reaction centers. Crit Rev Biochem Mol Biol 2020; 55:425-468. [PMID: 32883115 DOI: 10.1080/10409238.2020.1810623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Trehalose and glycerol are low molecular mass sugars/polyols that have found widespread use in the protection of native protein states, in both short- and long-term storage of biological materials, and as a means of understanding protein dynamics. These myriad uses are often attributed to their ability to form an amorphous glassy matrix. In glycerol, the glass is formed only at cryogenic temperatures, while in trehalose, the glass is formed at room temperature, but only upon dehydration of the sample. While much work has been carried out to elucidate a mechanistic view of how each of these matrices interact with proteins to provide stability, rarely have the effects of these two independent systems been directly compared to each other. This review aims to compile decades of research on how different glassy matrices affect two types of photosynthetic proteins: (i) the Type II bacterial reaction center from Rhodobacter sphaeroides and (ii) the Type I Photosystem I reaction center from cyanobacteria. By comparing aggregate data on electron transfer, protein structure, and protein dynamics, it appears that the effects of these two distinct matrices are remarkably similar. Both seem to cause a "tightening" of the solvation shell when in a glassy state, resulting in severely restricted conformational mobility of the protein and associated water molecules. Thus, trehalose appears to be able to mimic, at room temperature, nearly all of the effects on protein dynamics observed in low temperature glycerol glasses.
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Affiliation(s)
- Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - 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, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.,Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
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13
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Yan Y, Liu Y, Xing T, Shi Q. Theoretical study of excitation energy transfer and nonlinear spectroscopy of photosynthetic light‐harvesting complexes using the nonperturbative reduced dynamics method. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1498] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yaming Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Physical Science Laboratory Huairou National Comprehensive Science Center Beijing China
| | - Yanying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Physical Science Laboratory Huairou National Comprehensive Science Center Beijing China
| | - Tao Xing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Physical Science Laboratory Huairou National Comprehensive Science Center Beijing China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Physical Science Laboratory Huairou National Comprehensive Science Center Beijing China
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14
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Pieper J, Artene P, Rätsep M, Pajusalu M, Freiberg A. Evaluation of Electron–Phonon Coupling and Spectral Densities of Pigment–Protein Complexes by Line-Narrowed Optical Spectroscopy. J Phys Chem B 2018; 122:9289-9301. [DOI: 10.1021/acs.jpcb.8b05220] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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15
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Jassas M, Chen J, Khmelnitskiy A, Casazza AP, Santabarbara S, Jankowiak R. Structure-Based Exciton Hamiltonian and Dynamics for the Reconstituted Wild-type CP29 Protein Antenna Complex of the Photosystem II. J Phys Chem B 2018; 122:4611-4624. [DOI: 10.1021/acs.jpcb.8b00032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Rätsep M, Timpmann K, Kawakami T, Wang-Otomo ZY, Freiberg A. Spectrally Selective Spectroscopy of Native Ca-Containing and Ba-Substituted LH1-RC Core Complexes from Thermochromatium tepidum. J Phys Chem B 2017; 121:10318-10326. [PMID: 29058423 DOI: 10.1021/acs.jpcb.7b07841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The LH1-RC core complex from the thermophilic photosynthetic purple sulfur bacterium Thermochromatium tepidum has recently attracted interest of many researchers because of its several unique properties, such as increased robustness against environmental hardships and the much red-shifted near-infrared absorption spectrum of the LH1 antenna exciton polarons. The known near-atomic-resolution crystal structure of the complex well supported this attention. Yet several mechanistic aspects of the complex prominence remained to be understood. In this work, samples of the native, Ca2+-containing core complexes were investigated along with those destabilized by Ba2+ substitution, using various spectrally selective steady-state and picosecond time-resolved spectroscopic techniques at physiological and cryogenic temperatures. As a result, the current interpretation of exciton spectra of the complex was significantly clarified. Specifically, by evaluating the homogeneous and inhomogeneous compositions of the spectra, we showed that there is little to no effect of cation substitution on the dynamic or kinetic properties of antenna excitons. Reasons of the extra red shift of absorption/fluorescence spectra observed in the Ca-LH1-RC and not in the Ba-LH1-RC complex should thus be searched in subtle structural differences following the inclusion of different cations into the core complex scaffold.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia
| | | | | | - Arvi Freiberg
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu , Riia 23, 51010 Tartu, Estonia
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17
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Pieper J, Rätsep M, Golub M, Schmitt FJ, Artene P, Eckert HJ. Excitation energy transfer in phycobiliproteins of the cyanobacterium Acaryochloris marina investigated by spectral hole burning. PHOTOSYNTHESIS RESEARCH 2017; 133:225-234. [PMID: 28560566 DOI: 10.1007/s11120-017-0396-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/06/2017] [Indexed: 06/07/2023]
Abstract
The cyanobacterium Acaryochloris marina developed two types of antenna complexes, which contain chlorophyll-d (Chl d) and phycocyanobilin (PCB) as light-harvesting pigment molecules, respectively. The latter membrane-extrinsic complexes are denoted as phycobiliproteins (PBPs). Spectral hole burning was employed to study excitation energy transfer and electron-phonon coupling in PBPs. The data reveal a rich spectral substructure with a total of four low-energy electronic states whose absorption bands peak at 633, 644, 654, and at about 673 nm. The electronic states at ~633 and 644 nm can be tentatively attributed to phycocyanin (PC) and allophycocyanin (APC), respectively. The remaining low-energy electronic states including the terminal emitter at 673 nm may be associated with different isoforms of PC, APC, or the linker protein. Furthermore, the hole burning data reveal a large number of excited state vibrational frequencies, which are characteristic for the chromophore PCB. In summary, the results are in good agreement with the low-energy level structure of PBPs and electron-phonon coupling parameters reported by Gryliuk et al. (BBA 1837:1490-1499, 2014) based on difference fluorescence line-narrowing experiments.
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Affiliation(s)
- Jörg Pieper
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia.
| | - Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia
| | - Maksym Golub
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia
| | - Franz-Josef Schmitt
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University Berlin, Berlin, Germany
| | - Petrica Artene
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia
| | - Hann-Jörg Eckert
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University Berlin, Berlin, Germany
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18
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Hutchison CD, van Thor JJ. Populations and coherence in femtosecond time resolved X-ray crystallography of the photoactive yellow protein. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1276726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Jasper J. van Thor
- Molecular Biophysics, Imperial College London, South Kensington Campus, London, UK
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19
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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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20
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Reinot T, Chen J, Kell A, Jassas M, Robben KC, Zazubovich V, Jankowiak R. On the Conflicting Estimations of Pigment Site Energies in Photosynthetic Complexes: A Case Study of the CP47 Complex. ANALYTICAL CHEMISTRY INSIGHTS 2016; 11:35-48. [PMID: 27279733 PMCID: PMC4892206 DOI: 10.4137/aci.s32151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/10/2016] [Accepted: 04/26/2016] [Indexed: 01/14/2023]
Abstract
We focus on problems with elucidation of site energies
(E0n) for photosynthetic complexes (PSCs) in order to raise some genuine concern regarding the conflicting estimations propagating in the literature. As an example, we provide a stern assessment of the site energies extracted from fits to optical spectra of the widely studied CP47 antenna complex of photosystem II from spinach, though many general comments apply to other PSCs as well. Correct values of
E0n for chlorophyll (Chl) a in CP47 are essential for understanding its excitonic structure, population dynamics, and excitation energy pathway(s). To demonstrate this, we present a case study where simultaneous fits of multiple spectra (absorption, emission, circular dichroism, and nonresonant hole-burned spectra) show that several sets of parameters can fit the spectra very well. Importantly, we show that variable emission maxima (690–695 nm) and sample-dependent bleaching in nonresonant hole-burning spectra reported in literature could be explained, assuming that many previously studied CP47 samples were a mixture of intact and destabilized proteins. It appears that the destabilized subpopulation of CP47 complexes could feature a weakened hydrogen bond between the 131-keto group of Chl29 and the PsbH protein subunit, though other possibilities cannot be entirely excluded, as discussed in this work. Possible implications of our findings are briefly discussed.
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Affiliation(s)
- Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Jinhai Chen
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Adam Kell
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Mahboobe Jassas
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Kevin C Robben
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | | | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, KS, USA.; Department of Physics, Kansas State University, Manhattan, KS, USA
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21
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Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
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Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
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22
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Jurinovich S, Viani L, Prandi IG, Renger T, Mennucci B. Towards an ab initio description of the optical spectra of light-harvesting antennae: application to the CP29 complex of photosystem II. Phys Chem Chem Phys 2016; 17:14405-16. [PMID: 25872495 DOI: 10.1039/c4cp05647g] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light-harvesting pigment-protein complexes (PPC) represent the fundamental units through which the photosynthetic organisms absorb sunlight and funnel the energy to the reaction centre for carrying out the primary energy conversion reactions of photosynthesis. Here we apply a multiscale computational strategy to a specific PPC present in the photosystem II of plants and algae (CP29) to investigate in what detail should the environment effects due to protein and membrane/solvent be included for an accurate description of optical spectra. We find that a refinement of the crystal structure is needed before any meaningful quantum chemical calculations of pigment transition energies can be performed. For this purpose we apply classical molecular dynamics simulations of the PPC within its natural environment and we perform ab initio computations of the exciton Hamiltonian of the complex, including the environment either implicitly by the polarizable continuum model (PCM) or explicitly using the polarizable QM/MM methodology (MMPol). However, PCM essentially leads to an unspecific redshift of all transition energies, and MMPol is able to reveal site-specific changes in the optical properties of the pigments. Based on the latter and the excitonic couplings obtained within a polarizable QM/MM methodology, optical spectra are calculated, which are in good qualitative agreement with experimental data. A weakness of the approach is however found in the overestimation of the fluctuations of the excitonic parameters of the pigments along the MD trajectory. An explanation for such a finding in terms of the limits of the force fields commonly used for protein cofactors is presented and discussed.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 3, I-56124 Pisa, Italy.
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23
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Rätsep M, Pajusalu M, Linnanto JM, Freiberg A. Subtle spectral effects accompanying the assembly of bacteriochlorophylls into cyclic light harvesting complexes revealed by high-resolution fluorescence spectroscopy. J Chem Phys 2015; 141:155102. [PMID: 25338912 DOI: 10.1063/1.4897637] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have observed that an assembly of the bacteriochloropyll a molecules into B850 and B875 groups of cyclic bacterial light-harvesting complexes LH2 and LH1, respectively, results an almost total loss of the intra-molecular vibronic structure in the fluorescence spectrum, and simultaneously, an essential enhancement of its phonon sideband due to electron-phonon coupling. While the suppression of the vibronic coupling in delocalized (excitonic) molecular systems is predictable, as also confirmed by our model calculations, a boost of the electron-phonon coupling is rather unexpected. The latter phenomenon is explained by exciton self-trapping, promoted by mixing the molecular exciton states with charge transfer states between the adjacent chromophores in the tightly packed B850 and B875 arrangements. Similar, although less dramatic trends were noted for the light-harvesting complexes containing chlorophyll pigments.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | - Mihkel Pajusalu
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | | | - Arvi Freiberg
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia and Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
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24
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Etinski M, Petković M, Ristić MM, Marian CM. Electron–Vibrational Coupling and Fluorescence Spectra of Tetra-, Penta-, and Hexacoordinated Chlorophylls c1 and c2. J Phys Chem B 2015; 119:10156-69. [DOI: 10.1021/acs.jpcb.5b05079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mihajlo Etinski
- Faculty
of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Milena Petković
- Faculty
of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Miroslav M. Ristić
- Faculty
of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Christel M. Marian
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
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25
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Rancova O, Jankowiak R, Abramavicius D. Probing environment fluctuations by two-dimensional electronic spectroscopy of molecular systems at temperatures below 5 K. J Chem Phys 2015; 142:212428. [DOI: 10.1063/1.4918584] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Olga Rancova
- Department of Theoretical Physics, Vilnius University, Sauletekio al 9-III, 10222 Vilnius, Lithuania
| | - Ryszard Jankowiak
- Department of Chemistry and Department of Physics, Kansas State University, 213 CBC Building Manhattan, Kansas 66506-0401, USA
| | - Darius Abramavicius
- Department of Theoretical Physics, Vilnius University, Sauletekio al 9-III, 10222 Vilnius, Lithuania
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26
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Najafi M, Herascu N, Shafiei G, Picorel R, Zazubovich V. Conformational Changes in Pigment–Protein Complexes at Low Temperatures—Spectral Memory and a Possibility of Cooperative Effects. J Phys Chem B 2015; 119:6930-40. [PMID: 25985255 DOI: 10.1021/acs.jpcb.5b02845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mehdi Najafi
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Nicoleta Herascu
- 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
| | - 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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27
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Reppert M, Kell A, Pruitt T, Jankowiak R. Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers. J Chem Phys 2015; 142:094111. [DOI: 10.1063/1.4913685] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mike Reppert
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Adam Kell
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Thomas Pruitt
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
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28
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29
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Vrandecic K, Rätsep M, Wilk L, Rusevich L, Golub M, Reppert M, Irrgang KD, Kühlbrandt W, Pieper J. Protein dynamics tunes excited state positions in light-harvesting complex II. J Phys Chem B 2015; 119:3920-30. [PMID: 25664910 DOI: 10.1021/jp5112873] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Light harvesting and excitation energy transfer in photosynthesis are relatively well understood at cryogenic temperatures up to ∼100 K, where crystal structures of several photosynthetic complexes including the major antenna complex of green plants (LHC II) are available at nearly atomic resolution. The situation is much more complex at higher or even physiological temperatures, because the spectroscopic properties of antenna complexes typically undergo drastic changes above ∼100 K. We have addressed this problem using a combination of quasielastic neutron scattering (QENS) and optical spectroscopy on native LHC II and mutant samples lacking the Chl 2/Chl a 612 pigment molecule. Absorption difference spectra of the Chl 2/Chl a 612 mutant of LHC II reveal pronounced changes of spectral position and their widths above temperatures as low as ∼80 K. The complementary QENS data indicate an onset of conformational protein motions at about the same temperature. This finding suggests that excited state positions in LHC II are affected by protein dynamics on the picosecond time scale. In more detail, this means that at cryogenic temperatures the antenna complex is trapped in certain protein conformations. At higher temperature, however, a variety of conformational substates with different spectral position may be thermally accessible. At the same time, an analysis of the widths of the absorption difference spectra of Chl 2/Chl a 612 reveals three different reorganization energies or Huang-Rhys factors in different temperature ranges, respectively. These findings imply that (dynamic) pigment-protein interactions fine-tune electronic energy levels and electron-phonon coupling of LHC II for efficient excitation energy transfer at physiological temperatures.
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Affiliation(s)
- Kamarniso Vrandecic
- Institute of Physics, University of Tartu , Ravila 14C, 50411 Tartu, Estonia
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30
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Jurinovich S, Viani L, Curutchet C, Mennucci B. Limits and potentials of quantum chemical methods in modelling photosynthetic antennae. Phys Chem Chem Phys 2015; 17:30783-92. [DOI: 10.1039/c5cp00986c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A critical overview of quantum chemical approaches to simulate the light-harvesting process in photosynthetic antennae is presented together with a perspective on the developments that need to be introduced to reach a quantitative predictive power.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale
- University of Pisa
- 56124 Pisa
- Italy
| | - Lucas Viani
- Dipartimento di Chimica e Chimica Industriale
- University of Pisa
- 56124 Pisa
- Italy
- Institute for Fluid Dynamics
| | - Carles Curutchet
- Departament de Fisicoquímica
- Facultat de Farmàcia
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- University of Pisa
- 56124 Pisa
- Italy
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31
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Pajusalu M, Kunz R, Rätsep M, Timpmann K, Köhler J, Freiberg A. Unified analysis of ensemble and single-complex optical spectral data from light-harvesting complex-2 chromoproteins for gaining deeper insight into bacterial photosynthesis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052709. [PMID: 26651725 DOI: 10.1103/physreve.92.052709] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 05/15/2023]
Abstract
Bacterial light-harvesting pigment-protein complexes are very efficient at converting photons into excitons and transferring them to reaction centers, where the energy is stored in a chemical form. Optical properties of the complexes are known to change significantly in time and also vary from one complex to another; therefore, a detailed understanding of the variations on the level of single complexes and how they accumulate into effects that can be seen on the macroscopic scale is required. While experimental and theoretical methods exist to study the spectral properties of light-harvesting complexes on both individual complex and bulk ensemble levels, they have been developed largely independently of each other. To fill this gap, we simultaneously analyze experimental low-temperature single-complex and bulk ensemble optical spectra of the light-harvesting complex-2 (LH2) chromoproteins from the photosynthetic bacterium Rhodopseudomonas acidophila in order to find a unique theoretical model consistent with both experimental situations. The model, which satisfies most of the observations, combines strong exciton-phonon coupling with significant disorder, characteristic of the proteins. We establish a detailed disorder model that, in addition to containing a C_{2}-symmetrical modulation of the site energies, distinguishes between static intercomplex and slow conformational intracomplex disorders. The model evaluations also verify that, despite best efforts, the single-LH2-complex measurements performed so far may be biased toward complexes with higher Huang-Rhys factors.
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Affiliation(s)
- Mihkel Pajusalu
- Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu, Estonia
| | - Ralf Kunz
- Experimental Physics IV and Bayreuth Institute for Macromolecular Research, University of Bayreuth, 95440 Bayreuth, Germany
| | - Margus Rätsep
- Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu, Estonia
| | - Jürgen Köhler
- Experimental Physics IV and Bayreuth Institute for Macromolecular Research, University of Bayreuth, 95440 Bayreuth, Germany
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
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32
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Zazubovich V. Fluorescence Line Narrowing and Δ-FLN Spectra in the Presence of Excitation Energy Transfer between Weakly Coupled Chromophores. J Phys Chem B 2014; 118:13535-43. [DOI: 10.1021/jp509056z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valter Zazubovich
- Department of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal H4B 1R6, Quebec, Canada
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33
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Gall A, Pascal AA, Robert B. Vibrational techniques applied to photosynthesis: Resonance Raman and fluorescence line-narrowing. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:12-8. [PMID: 25268562 DOI: 10.1016/j.bbabio.2014.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/12/2014] [Accepted: 09/22/2014] [Indexed: 11/25/2022]
Abstract
Resonance Raman spectroscopy may yield precise information on the conformation of, and the interactions assumed by, the chromophores involved in the first steps of the photosynthetic process. Selectivity is achieved via resonance with the absorption transition of the chromophore of interest. Fluorescence line-narrowing spectroscopy is a complementary technique, in that it provides the same level of information (structure, conformation, interactions), but in this case for the emitting pigment(s) only (whether isolated or in an ensemble of interacting chromophores). The selectivity provided by these vibrational techniques allows for the analysis of pigment molecules not only when they are isolated in solvents, but also when embedded in soluble or membrane proteins and even, as shown recently, in vivo. They can be used, for instance, to relate the electronic properties of these pigment molecules to their structure and/or the physical properties of their environment. These techniques are even able to follow subtle changes in chromophore conformation associated with regulatory processes. After a short introduction to the physical principles that govern resonance Raman and fluorescence line-narrowing spectroscopies, the information content of the vibrational spectra of chlorophyll and carotenoid molecules is described in this article, together with the experiments which helped in determining which structural parameter(s) each vibrational band is sensitive to. A selection of applications is then presented, in order to illustrate how these techniques have been used in the field of photosynthesis, and what type of information has been obtained. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Andrew Gall
- Institute of Biology and Technology Saclay, CEA, UMR 8221 CNRS, 91191 Gif/Yvette, France
| | - Andrew A Pascal
- Institute of Biology and Technology Saclay, CEA, UMR 8221 CNRS, 91191 Gif/Yvette, France
| | - Bruno Robert
- Institute of Biology and Technology Saclay, CEA, UMR 8221 CNRS, 91191 Gif/Yvette, France.
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Lin C, Reppert M, Feng X, Jankowiak R. Modeling of fluorescence line-narrowed spectra in weakly coupled dimers in the presence of excitation energy transfer. J Chem Phys 2014; 141:035101. [PMID: 25053340 DOI: 10.1063/1.4887083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work describes simple analytical formulas to describe the fluorescence line-narrowed (FLN) spectra of weakly coupled chromophores in the presence of excitation energy transfer (EET). Modeling studies for dimer systems (assuming low fluence and weak coupling) show that the FLN spectra (including absorption and emission spectra) calculated for various dimers using our model are in good agreement with spectra calculated by: (i) the simple convolution method and (ii) the more rigorous treatment using the Redfield approach [T. Renger and R. A. Marcus, J. Chem. Phys. 116, 9997 (2002)]. The calculated FLN spectra in the presence of EET of all three approaches are very similar. We argue that our approach provides a simplified and computationally more efficient description of FLN spectra in the presence of EET. This method also has been applied to FLN spectra obtained for the CP47 antenna complex of Photosystem II reported by Neupane et al. [J. Am. Chem. Soc. 132, 4214 (2010)], which indicated the presence of uncorrelated EET between pigments contributing to the two lowest energy (overlapping) exciton states, each mostly localized on a single chromophore. Calculated and experimental FLN spectra for CP47 complex show very good qualitative agreement.
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Affiliation(s)
- Chen Lin
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Mike Reppert
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Ximao Feng
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
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35
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Müh F, Lindorfer D, Schmidt am Busch M, Renger T. Towards a structure-based exciton Hamiltonian for the CP29 antenna of photosystem II. Phys Chem Chem Phys 2014; 16:11848-63. [PMID: 24603694 DOI: 10.1039/c3cp55166k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The exciton Hamiltonian pertaining to the first excited states of chlorophyll (Chl) a and b pigments in the minor light-harvesting complex CP29 of plant photosystem II is determined based on the recent crystal structure at 2.8 Å resolution applying a combined quantum chemical/electrostatic approach as used earlier for the major light-harvesting complex LHCII. Two electrostatic methods for the calculation of the local transition energies (site energies), referred to as the Poisson-Boltzmann/quantum chemical (PBQC) and charge density coupling (CDC) method, which differ in the way the polarizable environment of the pigments is described, are compared and found to yield comparable results, when tested against fits of measured optical spectra (linear absorption, linear dichroism, circular dichroism, and fluorescence). The crystal structure shows a Chl a/b ratio of 2.25, whereas a ratio between 2.25 and 3.0 can be estimated from the simulation of experimental spectra. Thus, it is possible that up to one Chl b is lost in CP29 samples. The lowest site energy is found to be located at Chl a604 close to neoxanthin. This assignment is confirmed by the simulation of wild-type-minus-mutant difference spectra of reconstituted CP29, where a tyrosine residue next to Chl a604 is modified in the mutant. Nonetheless, the terminal emitter domain (TED), i.e. the pigments contributing mostly to the lowest exciton state, is found at the Chl a611-a612-a615 trimer due to strong excitonic coupling between these pigments, with the largest contributions from Chls a611 and a612. A major difference between CP29 and LHCII is that Chl a610 is not the energy sink in CP29, which is presumably to a large extent due to the replacement of a lysine residue with alanine close to the TED.
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Affiliation(s)
- Frank Müh
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria.
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36
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Excitation energy transfer and electron-vibrational coupling in phycobiliproteins of the cyanobacterium Acaryochloris marina investigated by site-selective spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1490-9. [PMID: 24560813 DOI: 10.1016/j.bbabio.2014.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/26/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
In adaption to its specific environmental conditions, the cyanobacterium Acaryochloris marina developed two different types of light-harvesting complexes: chlorophyll-d-containing membrane-intrinsic complexes and phycocyanobilin (PCB) - containing phycobiliprotein (PBP) complexes. The latter complexes are believed to form a rod-shaped structure comprising three homo-hexamers of phycocyanin (PC), one hetero-hexamer of phycocyanin and allophycocyanin (APC) and probably a linker protein connecting the PBPs to the reaction centre. Excitation energy transfer and electron-vibrational coupling in PBPs have been investigated by selectively excited fluorescence spectra. The data reveal a rich spectral substructure with a total of five low-energy electronic states with fluorescence bands at 635nm, 645nm, 654nm, 659nm and a terminal emitter at about 673 nm. The electronic states at ~635 and 645 nm are tentatively attributed to PC and APC, respectively, while an apparent heterogeneity among PC subunits may also play a role. The other fluorescence bands may be associated with three different isoforms of the linker protein. Furthermore, a large number of vibrational features can be identified for each electronic state with intense phonon sidebands peaking at about 31 to 37cm⁻¹, which are among the highest phonon frequencies observed for photosynthetic antenna complexes. The corresponding Huang-Rhys factors S fall in the range between 0.98 (terminal emitter), 1.15 (APC), and 1.42 (PC). Two characteristic vibronic lines at about 1580 and 1634cm⁻¹ appear to reflect CNH⁺ and CC stretching modes of the PCB chromophore, respectively. The exact phonon and vibrational frequencies vary with electronic state implying that the respective PCB chromophores are bound to different protein environments. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.
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37
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Kell A, Feng X, Reppert M, Jankowiak R. On the Shape of the Phonon Spectral Density in Photosynthetic Complexes. J Phys Chem B 2013; 117:7317-23. [DOI: 10.1021/jp405094p] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Mike Reppert
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Ryszard Jankowiak
- Faculty
of Applied Physics and
Mathematics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
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38
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Lin C, Renge I, Jankowiak R. Fluorescence line-narrowing difference spectra: Dependence of Huang–Rhys factor on excitation wavelength. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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Feng X, Pan X, Li M, Pieper J, Chang W, Jankowiak R. Spectroscopic Study of the Light-Harvesting CP29 Antenna Complex of Photosystem II—Part I. J Phys Chem B 2013; 117:6585-92. [DOI: 10.1021/jp4004328] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ximao Feng
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United
States
| | - Xiaowei Pan
- National Laboratory
of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Mei Li
- National Laboratory
of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Tartu, Estonia
| | - Wenrui Chang
- National Laboratory
of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United
States
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk,
Poland
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40
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Feng X, Kell A, Pieper J, Jankowiak R. Modeling of Optical Spectra of the Light-Harvesting CP29 Antenna Complex of Photosystem II—Part II. J Phys Chem B 2013; 117:6593-602. [DOI: 10.1021/jp4004278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ximao Feng
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United
States
| | - Adam Kell
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United
States
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Tartu, Estonia
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United
States
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk,
Poland
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41
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Kolli A, O'Reilly EJ, Scholes GD, Olaya-Castro A. The fundamental role of quantized vibrations in coherent light harvesting by cryptophyte algae. J Chem Phys 2013; 137:174109. [PMID: 23145719 DOI: 10.1063/1.4764100] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The influence of fast vibrations on energy transfer and conversion in natural molecular aggregates is an issue of central interest. This article shows the important role of high-energy quantized vibrations and their non-equilibrium dynamics for energy transfer in photosynthetic systems with highly localized excitonic states. We consider the cryptophyte antennae protein phycoerythrin 545 and show that coupling to quantized vibrations, which are quasi-resonant with excitonic transitions is fundamental for biological function as it generates non-cascaded transport with rapid and wider spatial distribution of excitation energy. Our work also indicates that the non-equilibrium dynamics of such vibrations can manifest itself in ultrafast beating of both excitonic populations and coherences at room temperature, with time scales in agreement with those reported in experiments. Moreover, we show that mechanisms supporting coherent excitonic dynamics assist coupling to selected modes that channel energy to preferential sites in the complex. We therefore argue that, in the presence of strong coupling between electronic excitations and quantized vibrations, a concrete and important advantage of quantum coherent dynamics is precisely to tune resonances that promote fast and effective energy distribution.
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Affiliation(s)
- Avinash Kolli
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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42
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Acharya K, Neupane B, Zazubovich V, Sayre RT, Picorel R, Seibert M, Jankowiak R. Site energies of active and inactive pheophytins in the reaction center of Photosystem II from Chlamydomonas reinhardtii. J Phys Chem B 2012; 116:3890-9. [PMID: 22397491 DOI: 10.1021/jp3007624] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is widely accepted that the primary electron acceptor in various Photosystem II (PSII) reaction center (RC) preparations is pheophytin a (Pheo a) within the D1 protein (Pheo(D1)), while Pheo(D2) (within the D2 protein) is photochemically inactive. The Pheo site energies, however, have remained elusive, due to inherent spectral congestion. While most researchers over the past two decades placed the Q(y)-states of Pheo(D1) and Pheo(D2) bands near 678-684 and 668-672 nm, respectively, recent modeling [Raszewski et al. Biophys. J. 2005, 88, 986 - 998; Cox et al. J. Phys. Chem. B 2009, 113, 12364 - 12374] of the electronic structure of the PSII RC reversed the assignment of the active and inactive Pheos, suggesting that the mean site energy of Pheo(D1) is near 672 nm, whereas Pheo(D2) (~677.5 nm) and Chl(D1) (~680 nm) have the lowest energies (i.e., the Pheo(D2)-dominated exciton is the lowest excited state). In contrast, chemical pigment exchange experiments on isolated RCs suggested that both pheophytins have their Q(y) absorption maxima at 676-680 nm [Germano et al. Biochemistry 2001, 40, 11472 - 11482; Germano et al. Biophys. J. 2004, 86, 1664 - 1672]. To provide more insight into the site energies of both Pheo(D1) and Pheo(D2) (including the corresponding Q(x) transitions, which are often claimed to be degenerate at 543 nm) and to attest that the above two assignments are most likely incorrect, we studied a large number of isolated RC preparations from spinach and wild-type Chlamydomonas reinhardtii (at different levels of intactness) as well as the Chlamydomonas reinhardtii mutant (D2-L209H), in which the active branch Pheo(D1) is genetically replaced with chlorophyll a (Chl a). We show that the Q(x)-/Q(y)-region site energies of Pheo(D1) and Pheo(D2) are ~545/680 nm and ~541.5/670 nm, respectively, in good agreement with our previous assignment [Jankowiak et al. J. Phys. Chem. B 2002, 106, 8803 - 8814]. The latter values should be used to model excitonic structure and excitation energy transfer dynamics of the PSII RCs.
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Affiliation(s)
- K Acharya
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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43
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Herascu N, Ahmouda S, Picorel R, Seibert M, Jankowiak R, Zazubovich V. Effects of the Distributions of Energy or Charge Transfer Rates on Spectral Hole Burning in Pigment–Protein Complexes at Low Temperatures. J Phys Chem B 2011; 115:15098-109. [DOI: 10.1021/jp208142k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicoleta Herascu
- Department of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6 Canada
| | - Somaya Ahmouda
- Department of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6 Canada
| | - Rafael Picorel
- Estacion Experimental Aula Dei (CSIC), Avda. Montañana, 50059 Zaragoza, Spain
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Michael Seibert
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Valter Zazubovich
- Department of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6 Canada
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44
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Feng X, Neupane B, Acharya K, Zazubovich V, Picorel R, Seibert M, Jankowiak R. Spectroscopic Study of the CP43′ Complex and the PSI–CP43′ Supercomplex of the Cyanobacterium Synechocystis PCC 6803. J Phys Chem B 2011; 115:13339-49. [DOI: 10.1021/jp206054b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ximao Feng
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Bhanu Neupane
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Khem Acharya
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal, Quebec, Canada
| | - Rafael Picorel
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Estación Experimental de Aula Dei (CSIC), Zaragoza, Spain
| | - Michael Seibert
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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45
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Neupane B, Dang NC, Kelley RF, Wasielewski MR, Jankowiak R. Low-Temperature Frequency Domain Study of Excitation Energy Transfer in Ethynyl-Linked Chlorophyll Trefoils and Aggregates. J Phys Chem B 2011; 115:10391-9. [DOI: 10.1021/jp2027252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bhanu Neupane
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Nhan C. Dang
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Richard F. Kelley
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael R. Wasielewski
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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46
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Real-time vibrational dynamics in chlorophyll a studied with a few-cycle pulse laser. Biophys J 2011; 101:995-1003. [PMID: 21843492 DOI: 10.1016/j.bpj.2011.07.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 07/12/2011] [Accepted: 07/14/2011] [Indexed: 11/20/2022] Open
Abstract
We use a 6.8-fs laser as the light source for broad-band femtosecond pump-probe real-time vibrational spectroscopy to investigate both electronic relaxation and vibrational dynamics of the Q(y)-band of Chl-a at 293 K. More than 25 vibrational modes coupled to the Q(y) transition are observed. Eleven of them have been clarified predominantly due to the excited state, and six of them are concluded to be nearly exclusively resulting from the ground-state wave-packet motion. Moreover, thanks to the broad-band detection over 5000 cm⁻¹, the modulated signals due to the excited state vibrational coherence are observed on both sides of the 0-0 transition with equal separation. The corresponding nonlinear process has been studied using a three-level model, from which the probe wavelength dependence of the phase of the periodic modulation can be calculated. The probe wavelength dependence of the vibrational amplitude is interpreted in terms of the interaction between the "pump" or "laser," Stokes, and anti-Stokes field intermediated by the molecular vibrations. In addition, an excited state absorption peak at ~709 nm has been observed. To the best of our knowledge, this is the first study of broad-band real-time vibrational spectroscopy in Chl-a.
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47
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Theiss C, Schmitt FJ, Pieper J, Nganou C, Grehn M, Vitali M, Olliges R, Eichler HJ, Eckert HJ. Excitation energy transfer in intact cells and in the phycobiliprotein antennae of the chlorophyll d containing cyanobacterium Acaryochloris marina. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1473-1487. [PMID: 21396735 DOI: 10.1016/j.jplph.2011.02.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 02/04/2011] [Accepted: 02/07/2011] [Indexed: 05/30/2023]
Abstract
The cyanobacterium Acaryochloris marina is unique because it mainly contains Chlorophyll d (Chl d) in the core complexes of PS I and PS II instead of the usually dominant Chl a. Furthermore, its light harvesting system has a structure also different from other cyanobacteria. It has both, a membrane-internal chlorophyll containing antenna and a membrane-external phycobiliprotein (PBP) complex. The first one binds Chl d and is structurally analogous to CP43. The latter one has a rod-like structure consisting of three phycocyanin (PC) homohexamers and one heterohexamer containing PC and allophycocyanin (APC). In this paper, we give an overview on the investigations of excitation energy transfer (EET) in this PBP-light-harvesting system and of charge separation in the photosystem II (PS II) reaction center of A. marina performed at the Technische Universität Berlin. Due to the unique structure of the PBP antenna in A. marina, this EET occurs on a much shorter overall time scale than in other cyanobacteria. We also briefly discuss the question of the pigment composition in the reaction center (RC) of PS II and the nature of the primary donor of the PS II RC.
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Affiliation(s)
- Christoph Theiss
- Institute of Optics and Atomic Physics, Technische Universität Berlin, Strasse des 17. Juni 135, Berlin, Germany.
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48
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Shaller AD, Wang W, Li A, Moyna G, Han JJ, Helms GL, Li ADQ. Sequence-Controlled Oligomers Fold into Nanosolenoids and Impart Unusual Optical Properties. Chemistry 2011; 17:8350-62. [DOI: 10.1002/chem.201100612] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Indexed: 11/10/2022]
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49
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Jankowiak R, Reppert M, Zazubovich V, Pieper J, Reinot T. Site Selective and Single Complex Laser-Based Spectroscopies: A Window on Excited State Electronic Structure, Excitation Energy Transfer, and Electron–Phonon Coupling of Selected Photosynthetic Complexes. Chem Rev 2011; 111:4546-98. [DOI: 10.1021/cr100234j] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Mike Reppert
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal H4B1R6 Quebec, Canada
| | - Jörg Pieper
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University of Berlin, Germany
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | - Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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50
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Herascu N, Najafi M, Amunts A, Pieper J, Irrgang KD, Picorel R, Seibert M, Zazubovich V. Parameters of the protein energy landscapes of several light-harvesting complexes probed via spectral hole growth kinetics measurements. J Phys Chem B 2011; 115:2737-47. [PMID: 21391534 DOI: 10.1021/jp108775y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The parameters of barrier distributions on the protein energy landscape in the excited electronic state of the pigment/protein system have been determined by means of spectral hole burning for the lowest-energy pigments of CP43 core antenna complex and CP29 minor antenna complex of spinach Photosystem II (PS II) as well as of trimeric and monomeric LHCII complexes transiently associated with the pea Photosystem I (PS I) pool. All of these complexes exhibit sixty to several hundred times lower spectral hole burning yields as compared with molecular glassy solids previously probed by means of the hole growth kinetics measurements. Therefore, the entities (groups of atoms), which participate in conformational changes in protein, appear to be significantly larger and heavier than those in molecular glasses. No evidence of a small (∼1 cm(-1)) spectral shift tier of the spectral diffusion dynamics has been observed. Therefore, our data most likely reflect the true barrier distributions of the intact protein and not those related to the interface or surrounding host. Possible applications of the barrier distributions as well as the assignments of low-energy states of CP29 and LHCII are discussed in light of the above results.
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Affiliation(s)
- Nicoleta Herascu
- Department of Physics, Concordia University, Montreal, Quebec, Canada
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