1
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Fujimoto KJ, Tsuzuki YA, Inoue K, Yanai T. Molecular Mechanisms behind Circular Dichroism Spectral Variations between Channelrhodopsin and Heliorhodopsin Dimers. J Phys Chem Lett 2024; 15:5788-5794. [PMID: 38780133 PMCID: PMC11145647 DOI: 10.1021/acs.jpclett.4c00879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Channelrhodopsin (ChR) and heliorhodopsin (HeR) are microbial rhodopsins with similar structures but different circular dichroism (CD) spectra: ChR shows biphasic negative and positive bands, whereas HeR shows a single positive band. We explored the physicochemical factors underlying these differences through computational methods. Using the exciton model based on first-principles computations, we obtained the CD spectra of ChR and HeR. The obtained spectra indicate that the protein dimer structures and the quantum mechanical treatment of the retinal chromophore and its interacting amino acids are crucial for accurately reproducing the experimental spectra. Further calculations revealed that the sign of the excitonic coupling was opposite between the ChR and HeR dimers, which was attributed to the contrasting second term of the orientation factor between the two retinal chromophores. These findings demonstrate that slight variations in the intermolecular orientation of the two chromophores can result in significant differences in the CD spectral shape.
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Affiliation(s)
- Kazuhiro J. Fujimoto
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Aichi 464-8601, Japan
- Department
of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Yuta A. Tsuzuki
- Department
of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Keiichi Inoue
- The
Institute for Solid State Physics, The University
of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Takeshi Yanai
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Aichi 464-8601, Japan
- Department
of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Aichi 464-8601, Japan
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2
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Sherefedin U, Belay A, Gudishe K, Kebede A, Kumela AG, Asemare S. Photophysical Properties of Sinapic Acid and Ferulic Acid and Their Binding Mechanism with Caffeine. J Fluoresc 2024:10.1007/s10895-024-03689-7. [PMID: 38592595 DOI: 10.1007/s10895-024-03689-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/23/2024] [Indexed: 04/10/2024]
Abstract
Sinapic acid (SA) and ferulic acid (FA) are bioactive compounds used in the food, pharmaceutical, and cosmetic industries due to their antioxidant properties. In this work, we studied the photophysical properties of SA and FA in different solvents and concentrations and their interactions with caffeine (CF), using ultraviolet-visible (UV-Vis), fluorescence spectroscopy and Fourier transform infrared (FTIR) spectroscopy. The findings show that the quantum yield, fluorescence lifetime, radiative decay rates, and non-radiative decay rates of SA and FA are influenced by the concentrations and solvent polarity. The interaction between SA and FA with CF was also studied using UV-Vis and fluorescence spectroscopy. The results indicate that the CF quenched the fluorescence intensity of SA and FA by static quenching due to the formation of a non-fluorescent complex. The van't Hoff equation suggests that the van der Waals forces and hydrogen bonds force were responsible for the interaction between SA and CF, as indicated by a negative change in enthalpy (Δ H o < 0) and a negative change in entropy (Δ S o < 0). On the other hand, the interaction between FA and CF was primarily controlled by electrostatic force, as indicated by a negative change in enthalpy (Δ H o < 0) and a positive change in entropy (Δ S o > 0). The negative change in Gibbs free energy (Δ G o ) indicates that both compounds underwent a spontaneous binding process.
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Affiliation(s)
- Umer Sherefedin
- Department of Applied Physics, School of Applied Sciences, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
| | - Abebe Belay
- Department of Applied Physics, School of Applied Sciences, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
| | - Kusse Gudishe
- Department of Applied Physics, School of Applied Natural and Computational Sciences, Jinka University, P.O. Box 165, Jinka, Ethiopia
- Department of Applied Physics, College of Natural and Computational Sciences, Mekdela Amba University, Tullu Awulia, P.O. Box 32, Amhara, Ethiopia
| | - Alemu Kebede
- Department of Applied Physics, School of Applied Sciences, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
| | - Alemayehu Getahun Kumela
- Department of Applied Physics, School of Applied Sciences, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
- Department of Applied Physics, School of Applied Natural and Computational Sciences, Jinka University, P.O. Box 165, Jinka, Ethiopia
- Department of Applied Physics, College of Natural and Computational Sciences, Mekdela Amba University, Tullu Awulia, P.O. Box 32, Amhara, Ethiopia
| | - Semahegn Asemare
- Department of Applied Physics, School of Applied Sciences, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
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3
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Rolczynski BS, Díaz SA, Kim YC, Mathur D, Klein WP, Medintz IL, Melinger JS. Determining interchromophore effects for energy transport in molecular networks using machine-learning algorithms. Phys Chem Chem Phys 2023; 25:3651-3665. [PMID: 36648290 DOI: 10.1039/d2cp04960k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nature uses chromophore networks, with highly optimized structural and energetic characteristics, to perform important chemical functions. Due to its modularity, predictable aggregation characteristics, and established synthetic protocols, structural DNA nanotechnology is a promising medium for arranging chromophore networks with analogous structural and energetic controls. However, this high level of control creates a greater need to know how to optimize the systems precisely. This study uses the system's modularity to produce variations of a coupled 14-Site chromophore network. It uses machine-learning algorithms and spectroscopy measurements to reveal the energy-transport roles of these Sites, paying particular attention to the cooperative and inhibitive effects they impose on each other for transport across the network. The physical significance of these patterns is contextualized, using molecular dynamics simulations and energy-transport modeling. This analysis yields insights about how energy transfers across the Donor-Relay and Relay-Acceptor interfaces, as well as the energy-transport pathways through the homogeneous Relay segment. Overall, this report establishes an approach that uses machine-learning methods to understand, in fine detail, the role that each Site plays in an optoelectronic molecular network.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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4
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Manian A, Hudson RJ, Ramkissoon P, Smith TA, Russo SP. Interexcited State Photophysics I: Benchmarking Density Functionals for Computing Nonadiabatic Couplings and Internal Conversion Rate Constants. J Chem Theory Comput 2023; 19:271-292. [PMID: 36490305 DOI: 10.1021/acs.jctc.2c00888] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the first benchmarking study of nonadiabatic matrix coupling elements (NACMEs) calculated using different density functionals. Using the S1 → S0 transition in perylene solvated in toluene as a case study, we calculate the photophysical properties and corresponding rate constants for a variety of density functionals from each rung of Jacob's ladder. The singlet photoluminescence quantum yield (sPLQY) is taken as a measure of accuracy, measured experimentally here as 0.955. Important quantum chemical parameters such as geometries, absorption, emission, and adiabatic energies, NACMEs, Hessians, and transition dipole moments were calculated for each density functional basis set combination (data set) using density functional theory based multireference configuration interaction (DFT/MRCI) and compared to experiment where possible. We were able to derive simple relations between the TDDFT and DFT/MRCI photophysical properties; with semiempirical damping factors of ∼0.843 ± 0.017 and ∼0.954 ± 0.064 for TDDFT transition dipole moments and energies to DFT/MRCI level approximations, respectively. NACMEs were dominated by out-of-plane derivative components belonging to the center-most ring atoms with weaker contributions from perturbations along the transverse and longitudinal axes. Calculated theoretical spectra compared well to both experiment and literature, with fluorescence lifetimes between 7.1 and 12.5 ns, agreeing within a factor of 2 with experiment. Internal conversion (IC) rates were then calculated and were found to vary wildly between 106-1016 s-1 compared with an experimental rate of the order 107 s-1. Following further testing by mixing data sets, we found a strong dependence on the method used to obtain the Hessian. The 5 characterized data sets ranked in order of most promising are PBE0/def2-TZVP, ωB97XD/def2-TZVP, HCTH407/TZVP, PBE/TZVP, and PBE/def2-TZVP.
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Affiliation(s)
- Anjay Manian
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne3000, Australia
| | - Rohan J Hudson
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville3010, Australia
| | - Pria Ramkissoon
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville3010, Australia
| | - Trevor A Smith
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville3010, Australia
| | - Salvy P Russo
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne3000, Australia
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5
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Fujimoto KJ, Minoda T, Yanai T. Spectral Tuning Mechanism of Photosynthetic Light-Harvesting Complex II Revealed by Ab Initio Dimer Exciton Model. J Phys Chem B 2021; 125:10459-10470. [PMID: 34521196 DOI: 10.1021/acs.jpcb.1c04457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Excited states of two kinds of bacteriochlorophyll (BChl) aggregates, B850 and B800, in photosynthetic light-harvesting complex II (LH2) are theoretically investigated by developing and using an extended exciton model considering efficiently evaluated excitonic coupling. Our exciton model based on dimer fragmentation is shown to reproduce the experimental absorption spectrum of LH2 with good accuracy, entailing their different redshifts originating from aggregations of B850 and B800. The systematic analysis has been performed on the spectra by quantitatively decomposing their spectral shift energies into the contributions of various effects: structural distortion, electrostatic, excitonic coupling, and charge-transfer (CT) effects. Our results show that the spectral redshift of B800 is mainly attributed to its electrostatic interaction with the protein environment, while that of B850 arises from the marked effect of the excitonic coupling between BChl units. The interchromophore CT excitation also plays a key role in the spectral redshift of B850. This CT effect can be effectively described using our dimer model. This suited characterization reveals that the pronounced CT effect originates from the characteristics of B850 that has closely spaced BChls as dimers. We highlight the importance of the refinement of the crystal structure with the use of quantum chemical methods for prediction of the spectrum.
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Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Takumi Minoda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Takeshi Yanai
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
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6
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Excitation energy transfer kinetics of trimeric, monomeric and subunit-depleted Photosystem I from Synechocystis PCC 6803. Biochem J 2021; 478:1333-1346. [PMID: 33687054 DOI: 10.1042/bcj20210021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 01/16/2023]
Abstract
Photosystem I is the most efficient photosynthetic enzyme with structure and composition highly conserved among all oxygenic phototrophs. Cyanobacterial Photosystem I is typically associated into trimers for reasons that are still debated. Almost universally, Photosystem I contains a number of long-wavelength-absorbing 'red' chlorophylls (Chls), that have a sizeable effect on the excitation energy transfer and trapping. Here we present spectroscopic comparison of trimeric Photosystem I from Synechocystis PCC 6803 with a monomeric complex from the ΔpsaL mutant and a 'minimal' monomeric complex ΔFIJL, containing only subunits A, B, C, D, E, K and M. The quantum yield of photochemistry at room temperature was the same in all complexes, demonstrating the functional robustness of this photosystem. The monomeric complexes had a reduced far-red absorption and emission equivalent to the loss of 1.5-2 red Chls emitting at 710-715 nm, whereas the longest-wavelength emission at 722 nm was not affected. The picosecond fluorescence kinetics at 77 K showed spectrally and kinetically distinct red Chls in all complexes and equilibration times of up to 50 ps. We found that the red Chls are not irreversible traps at 77 K but can still transfer excitations to the reaction centre, especially in the trimeric complexes. Structure-based Förster energy transfer calculations support the assignment of the lowest-energy state to the Chl pair B37/B38 and the trimer-specific red Chl emission to Chls A32/B7 located at the monomer-monomer interface. These intermediate-energy red Chls facilitate energy migration from the lowest-energy states to the reaction centre.
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7
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Fujimoto KJ, Inoue K. Excitonic coupling effect on the circular dichroism spectrum of sodium-pumping rhodopsin KR2. J Chem Phys 2020; 153:045101. [DOI: 10.1063/5.0013642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Kazuhiro J. Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8581, Japan
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8
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Kusano S, Ichikura Y, Fujimoto KJ, Konishi S, Yamada Y, Hayashida O. Exciton-coupled Circular Dichroism-based Glucose and Galactose Selective Sensing in Aqueous Media with an Anthracene-appended Benzoxaborole Dimer. CHEM LETT 2020. [DOI: 10.1246/cl.200244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Shuhei Kusano
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Yuma Ichikura
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Kazuhiro J. Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Sae Konishi
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Yuji Yamada
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Osamu Hayashida
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
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9
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Fiedor L, Dudkowiak A, Pilch M. The origin of the dark S 1 state in carotenoids: a comprehensive model. J R Soc Interface 2019; 16:20190191. [PMID: 31480924 DOI: 10.1098/rsif.2019.0191] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In carotenoids, by analogy to polyenes, the symmetry of the π-electron system is often invoked to explain their peculiar electronic features, in particular the inactivity of the S0 → S1 transition in one-photon excitation. In this review, we verify whether the molecular symmetry of carotenoids and symmetry of their π-electron system are supported in experimental and computational studies. We focus on spectroscopic techniques which are sensitive to the electron density distribution, including the X-ray crystallography, electronic absorption, two-photon techniques, circular dichroism, nuclear magnetic resonance, Stark and vibrational spectroscopies, and on this basis we seek for the origin of inactivity of the S1 state. We come across no experimental and computational evidence for the symmetry effects and the existence of symmetry restrictions on the electronic states of carotenoids. They do not possess an inversion centre and the C2h symmetry approximation of carotenoid structure is by no means justified. In effect, the application of symmetry rules (and notification) to the electronic states of carotenoids in this symmetry group may lead to a wrong interpretation of experimental data. This conclusion together with the results summarized in the review allows us to advance a consistent model that explains the inactivity of the S0 → S1 transition. Within this model, S1 is never accessible from S0 due to the negative synergy of (i) the contributions of double excitations of very low probability, which elevate S1 energy, and (ii) a non-verticality of the S0 → S1 transition, due to the breaking of Born-Oppenheimer approximation. Certainly, our simple model requires a further experimental and theoretical verification.
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Affiliation(s)
- Leszek Fiedor
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Kraków, Poland
| | - Alina Dudkowiak
- Faculty of Technical Physics, Poznan University of Technology, Piotrowo 3, 60965 Poznan, Poland
| | - Mariusz Pilch
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Kraków, Poland.,Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30387 Kraków, Poland
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10
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Tridgett M, Moore-Kelly C, Duprey JLHA, Iturbe LO, Tsang CW, Little HA, Sandhu SK, Hicks MR, Dafforn TR, Rodger A. Linear dichroism of visible-region chromophores using M13 bacteriophage as an alignment scaffold. RSC Adv 2018; 8:29535-29543. [PMID: 30713683 PMCID: PMC6333254 DOI: 10.1039/c8ra05475d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/12/2018] [Indexed: 11/22/2022] Open
Abstract
It is a challenge within the field of biomimetics to recreate the properties of light-harvesting antennae found in plants and photosynthetic bacteria. Attempts to recreate these biological structures typically rely on the alignment of fluorescent moieties via attachment to an inert linear scaffold, e.g. DNA, RNA or amyloid fibrils, to enable Förster resonance energy transfer (FRET) between attached chromophores. While there has been some success in this approach, refinement of the alignment of the chromophores is often limited, which may limit the efficiency of energy transfer achieved. Here we demonstrate how linear dichroism spectroscopy may be used to ascertain the overall alignment of chromophores bound to the M13 bacteriophage, a model linear scaffold, and demonstrate how this may be used to distinguish between lack of FRET efficiency due to chromophore separation, and chromophore misalignment. This approach will allow the refinement of artificial light-harvesting antennae in a directed fashion.
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Affiliation(s)
- Matthew Tridgett
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Charles Moore-Kelly
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Jean-Louis H A Duprey
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Lorea Orueta Iturbe
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Chi W Tsang
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Haydn A Little
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Sandeep K Sandhu
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Matthew R Hicks
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Alison Rodger
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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11
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Bricker WP, Banal JL, Stone MB, Bathe M. Molecular model of J-aggregated pseudoisocyanine fibers. J Chem Phys 2018; 149:024905. [PMID: 30007374 DOI: 10.1063/1.5036656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Aggregated cyanines form ordered supramolecular structures with the potential to transport energy efficiently over long distances, a hallmark of photosynthetic light-harvesting complexes. In concentrated aqueous solution, pseudoisocyanine (PIC) spontaneously forms fibers with a chiral J-band red-shifted 1600 cm-1 from the monomeric 0-0 transition. A cryogenic transmission electron microscopy analysis of these fibers show an average fiber width of 2.89 nm, although the molecular-level structure of the aggregate is currently unknown. To determine a molecular model for these PIC fibers, the calculated spectra and dynamics using a Frenkel exciton model are compared to experiment. A chiral aggregate model in which the PIC monomers are neither parallel nor orthogonal to the long axis of the fiber is shown to replicate the experimental spectra most closely. This model can be physically realized by the sequential binding of PIC dimers and monomers to the ends of the fiber. These insights into the molecular aggregation model for aqueous PIC can also be applied to other similar cyanine-based supramolecular complexes with the potential for long-range energy transport, a key building block for the rational design of novel excitonic systems.
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Affiliation(s)
- William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Matthew B Stone
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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12
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Whittemore TJ, White TA, Turro C. New Ligand Design Provides Delocalization and Promotes Strong Absorption throughout the Visible Region in a Ru(II) Complex. J Am Chem Soc 2017; 140:229-234. [PMID: 29260869 DOI: 10.1021/jacs.7b09389] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The new Ru(II)-anthraquinone complex [Ru(bpy)2(qdpq)](PF6)2 (Ru-qdpq; bpy = 2,2'-bipyridine; qdpq = 2,3-di(2-pyridyl)naphtho[2,3-f]quinoxaline-7,12-quinone) possesses a strong 1MLCT Ru → qdpq absorption with a maximum at 546 nm that tails into the near-IR and is significantly red-shifted relative to that of the related complex [Ru(bpy)2(qdppz)](PF6)2 (Ru-qdppz; qdppz = naphtho[2,3-a]dipyrido[3,2-h:2',3'-f]phenazine-5,18-dione), with λmax = 450 nm. Ru-qdppz possesses electronically isolated proximal and distal qdppz-based excited states; the former is initially generated and decays to the latter, which repopulates the ground state with τ = 362 ps. In contrast, excitation of Ru-qdpq results in the population of a relatively long-lived (τ = 19 ns) Ru(dπ) → qdpq(π*) 3MLCT excited state where the promoted electron is delocalized throughout the qdpq ligand. Ultrafast spectroscopy, used together with steady-state absorption, electrochemistry, and DFT calculations, indicates that the unique coordination modes of the qdpq and qdppz ligands impart substantially different electronic communication throughout the quinone-containing ligand, affecting the excited state and electron transfer properties of these molecules. These observations create a pathway to synthesize complexes with red-shifted absorptions that possess long-lived, redox-active excited states that are useful for various applications, including solar energy conversion and photochemotherapy.
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Affiliation(s)
- Tyler J Whittemore
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - Travis A White
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - Claudia Turro
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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13
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Fujimoto KJ, Balashov SP. Vibronic coupling effect on circular dichroism spectrum: Carotenoid–retinal interaction in xanthorhodopsin. J Chem Phys 2017. [DOI: 10.1063/1.4977045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Kazuhiro J. Fujimoto
- Faculty of Pharmaceutical Sciences, Hokuriku University, Ho-3 Kanagawa-machi, Kanazawa 920-1181, Japan
| | - Sergei P. Balashov
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
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14
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López-Tarifa P, Liguori N, van den Heuvel N, Croce R, Visscher L. Coulomb couplings in solubilised light harvesting complex II (LHCII): challenging the ideal dipole approximation from TDDFT calculations. Phys Chem Chem Phys 2017; 19:18311-18320. [DOI: 10.1039/c7cp03284f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the coulomb coupling interactions of natural chromophores in the solubilised light harvesting complex II (LHCII) using DFT quantum chemistry calculations.
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Affiliation(s)
- P. López-Tarifa
- Amsterdam Center for Multiscale Modeling
- Dep. Theoretical Chemistry
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Nicoletta Liguori
- Laboratory of Biophysics of Photosynthesis
- Dep. Physics and Astronomy
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Naudin van den Heuvel
- Van 't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- The Netherlands
| | - Roberta Croce
- Laboratory of Biophysics of Photosynthesis
- Dep. Physics and Astronomy
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling
- Dep. Theoretical Chemistry
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
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15
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Tsargorodska A, Cartron ML, Vasilev C, Kodali G, Mass OA, Baumberg JJ, Dutton PL, Hunter CN, Törmä P, Leggett GJ. Strong Coupling of Localized Surface Plasmons to Excitons in Light-Harvesting Complexes. NANO LETTERS 2016; 16:6850-6856. [PMID: 27689237 PMCID: PMC5135229 DOI: 10.1021/acs.nanolett.6b02661] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/28/2016] [Indexed: 05/24/2023]
Abstract
Gold nanostructure arrays exhibit surface plasmon resonances that split after attaching light harvesting complexes 1 and 2 (LH1 and LH2) from purple bacteria. The splitting is attributed to strong coupling between the localized surface plasmon resonances and excitons in the light-harvesting complexes. Wild-type and mutant LH1 and LH2 from Rhodobacter sphaeroides containing different carotenoids yield different splitting energies, demonstrating that the coupling mechanism is sensitive to the electronic states in the light harvesting complexes. Plasmon-exciton coupling models reveal different coupling strengths depending on the molecular organization and the protein coverage, consistent with strong coupling. Strong coupling was also observed for self-assembling polypeptide maquettes that contain only chlorins. However, it is not observed for monolayers of bacteriochlorophyll, indicating that strong plasmon-exciton coupling is sensitive to the specific presentation of the pigment molecules.
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Affiliation(s)
- Anna Tsargorodska
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K.
| | - Michaël L. Cartron
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Cvetelin Vasilev
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Goutham Kodali
- The
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 10104, United States
| | - Olga A. Mass
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jeremy J. Baumberg
- Cavendish
Laboratory, Dept. of Physics, University
of Cambridge, J. J. Thomson
Ave, Cambridge, CB3 0HE, U.K.
| | - P. Leslie Dutton
- The
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 10104, United States
| | - C. Neil Hunter
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Päivi Törmä
- COMP Centre
of Excellence, Department of Applied Physics, Aalto University, School of Science,
P.O. Box 15100, 00076 Aalto, Finland
| | - Graham J. Leggett
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K.
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16
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Chiang HK, Chu LK. Wavelength-dependent photocycle activity of xanthorhodopsin in the visible region. Biochem Biophys Rep 2016; 7:347-352. [PMID: 28955925 PMCID: PMC5613640 DOI: 10.1016/j.bbrep.2016.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/10/2016] [Accepted: 07/12/2016] [Indexed: 12/02/2022] Open
Abstract
Xanthorhodopsin (xR) is a dual-chromophore proton-pump photosynthetic protein comprising one retinal Schiff base and one light-harvesting antenna salinixanthin (SX). The excitation wavelength-dependent transient population of the intermediate M demonstrates that the excitation of the retinal at 570 nm leads to the highest photocycle activity and the excitations of SX at 460 and 430 nm reduce the activity to ca. 37% relatively, suggesting an energy transfer pathway from the S2 state of the SX to the S1 state of the retinal and a quick internal vibrational relaxation in the S2 state of SX prior to the energy transfer from SX to retinal. Energy transfer efficiency from the salinixanthin (SX) to the retinal is ca. 37%. Energy transfer efficiency is not dependent on wavelength at 486–430 nm. Energy transfer from the S2 state of SX to the S2 state of retinal is less accessible.
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17
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DiSpirito AA, Semrau JD, Murrell JC, Gallagher WH, Dennison C, Vuilleumier S. Methanobactin and the Link between Copper and Bacterial Methane Oxidation. Microbiol Mol Biol Rev 2016; 80:387-409. [PMID: 26984926 PMCID: PMC4867365 DOI: 10.1128/mmbr.00058-15] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu(2+) to Cu(1+). In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs.
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Affiliation(s)
- Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - J Colin Murrell
- Earth and Life Systems Alliance, School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Warren H Gallagher
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, USA
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Stéphane Vuilleumier
- Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
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18
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Synthesis, Crystal Structures, and DFT Calculations of Three New Cyano(phenylsulfonyl)indoles and a Key Synthetic Precursor Compound. CRYSTALS 2015. [DOI: 10.3390/cryst5030376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Horibe T, Qian P, Hunter CN, Hashimoto H. Stark absorption spectroscopy on the carotenoids bound to B800-820 and B800-850 type LH2 complexes from a purple photosynthetic bacterium, Phaeospirillum molischianum strain DSM120. Arch Biochem Biophys 2015; 572:158-166. [PMID: 25536050 DOI: 10.1016/j.abb.2014.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 11/16/2022]
Abstract
Stark absorption spectroscopy was applied to clarify the structural differences between carotenoids bound to the B800-820 and B800-850 LH2 complexes from a purple photosynthetic bacterium Phaeospirillum (Phs.) molischianum DSM120. The former complex is produced when the bacteria are grown under stressed conditions of low temperature and dim light. These two LH2 complexes bind carotenoids with similar composition, 10% lycopene and 80% rhodopin, each with the same number of conjugated CC double bonds (n=11). Quantitative classical and semi-quantum chemical analyses of Stark absorption spectra recorded in the carotenoid absorption region reveal that the absolute values of the difference dipole moments |Δμ| have substantial differences (2 [D/f]) for carotenoids bound to either B800-820 or B800-850 complexes. The origin of this striking difference in the |Δμ| values was analyzed using the X-ray crystal structure of the B800-850 LH2 complex from Phs. molischianum DSM119. Semi-empirical molecular orbital calculations predict structural deformations of the major carotenoid, rhodopin, bound within the B800-820 complex. We propose that simultaneous rotations around neighboring CC and CC bonds account for the differences in the 2 [D/f] of the |Δμ| value. The plausible position of the rotation is postulated to be located around C21-C24 bonds of rhodopin.
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Affiliation(s)
- Tomoko Horibe
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Hideki Hashimoto
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan; The Osaka City University Advanced Research Institute for Natural Science and Technology (OCARINA), 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.
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20
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Synthesis, Crystal and Molecular Structure Studies and DFT Calculations of Phenyl Quinoline-2-Carboxylate and 2-Methoxyphenyl Quinoline-2-Carboxylate; Two New Quinoline-2 Carboxylic Derivatives. CRYSTALS 2015. [DOI: 10.3390/cryst5010100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Baral BS, Bandow NL, Vorobev A, Freemeier BC, Bergman BH, Herdendorf TJ, Fuentes N, Ellias L, Turpin E, Semrau JD, DiSpirito AA. Mercury binding by methanobactin from Methylocystis strain SB2. J Inorg Biochem 2014; 141:161-169. [DOI: 10.1016/j.jinorgbio.2014.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 01/08/2023]
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22
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Rancova O, Sulskus J, Abramavicius D. Insight into the Structure of Photosynthetic LH2 Aggregate from Spectroscopy Simulations. J Phys Chem B 2012; 116:7803-14. [DOI: 10.1021/jp302817p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Olga Rancova
- Department of Theoretical
Physics, Vilnius University, Saulėtekio
al. 9-III, LT-10222
Vilnius, Lithuania
| | - Juozas Sulskus
- Department of Theoretical
Physics, Vilnius University, Saulėtekio
al. 9-III, LT-10222
Vilnius, Lithuania
| | - Darius Abramavicius
- Department of Theoretical
Physics, Vilnius University, Saulėtekio
al. 9-III, LT-10222
Vilnius, Lithuania
- State
Key Laboratory of Supramolecular
Structure and Materials, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
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23
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You ZQ, Hsu CP. Ab inito study on triplet excitation energy transfer in photosynthetic light-harvesting complexes. J Phys Chem A 2011; 115:4092-100. [PMID: 21410281 DOI: 10.1021/jp200200x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the triplet energy transfer (TET) for photosynthetic light-harvesting complexes, the bacterial light-harvesting complex II (LH2) of Rhodospirillum molischianum and Rhodopseudomonas acidophila, and the peridinin-chlorophyll a protein (PCP) from Amphidinium carterae. The electronic coupling factor was calculated with the recently developed fragment spin difference scheme (You and Hsu, J. Chem. Phys. 2010, 133, 074105), which is a general computational scheme that yields the overall coupling under the Hamiltonian employed. The TET rates were estimated based on the couplings obtained. For all light-harvesting complexes studied, there exist nanosecond triplet energy transfer from the chlorophylls to the carotenoids. This result supports a direct triplet quenching mechanism for the photoprotection function of carotenoids. The TET rates are similar for a broad range of carotenoid triplet state energy, which implies a general and robust TET quenching role for carotenoids in photosynthesis. This result is also consistent with the weak dependence of TET kinetics on the type or the number of π conjugation lengths in the carotenoids and their analogues reported in the literature. We have also explored the possibility of forming triplet excitons in these complexes. In B850 of LH2 or the peridinin cluster in PCP, it is unlikely to have triplet exciton since the energy differences of any two neighboring molecules are likely to be much larger than their TET couplings. Our results provide theoretical limits to the possible photophysics in the light-harvesting complexes.
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Affiliation(s)
- Zhi-Qiang You
- Taiwan International Graduate Program, Academia Sinica, 128 Section 2 Academia Road, Nankang, Taipei 11529, Taiwan
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24
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Olbrich C, Kleinekathöfer U. Time-dependent atomistic view on the electronic relaxation in light-harvesting system II. J Phys Chem B 2011; 114:12427-37. [PMID: 20809619 DOI: 10.1021/jp106542v] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aiming at a better understanding of the molecular details in light absorption during photosynthesis, spatial and temporal correlation functions as well as spectral densities have been determined. At the focus of the present study are the light-harvesting II complexes of the purple bacterium Rhodospirillum molischianum. The calculations are based on a time-dependent combination of molecular dynamics simulations and quantum chemistry methods. Using a 12 ps long trajectory, different quantum chemical methods have been compared to each other. Furthermore, several approaches to determine the couplings between the individual chromophores have been tested. Correlations between energy gap fluctuations of different individual pigments are analyzed but found to be negligible. From the energy gap fluctuations, spectral densities are extracted which serve as input for calculations of optical properties and exciton dynamics. To this end, the spectral densities are tested by determining the linear absorption of the complete two-ring system. One important difference from earlier studies is given by the severely extended length of the trajectory along which the quantum chemical calculations have been performed. Due to this extension, more accurate and reliable data have been obtained in the low frequency regime which is important in the dynamics of electronic relaxation.
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Affiliation(s)
- Carsten Olbrich
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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25
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Excited-state properties of the 16 kDa red carotenoid protein from Arthrospira maxima. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:30-5. [DOI: 10.1016/j.bbabio.2010.08.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 08/21/2010] [Accepted: 08/24/2010] [Indexed: 10/19/2022]
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26
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Belay A. Measurement of integrated absorption cross-section, oscillator strength and number density of caffeine in coffee beans by integrated absorption coefficient technique. Food Chem 2010. [DOI: 10.1016/j.foodchem.2009.12.052] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Georgakopoulou S, Möller D, Sachs N, Herrmann H, Aebi U. Near-UV circular dichroism reveals structural transitions of vimentin subunits during intermediate filament assembly. J Mol Biol 2008; 386:544-53. [PMID: 19136013 DOI: 10.1016/j.jmb.2008.12.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 12/19/2008] [Accepted: 12/19/2008] [Indexed: 10/21/2022]
Abstract
In vitro assembly of vimentin intermediate filaments (IFs) proceeds from soluble, reconstituted tetrameric complexes to mature filaments in three distinct stages: (1) within the first seconds after initiation of assembly, tetramers laterally associate into unit-length filaments (ULFs), on average 17 nm wide; (2) for the next few minutes, ULFs grow by longitudinal annealing into short, immature filaments; (3) almost concomitant with elongation, these immature filaments begin to radially compact, yielding approximately 11-nm-wide IFs at around 15 min. The near-UV CD signal of soluble tetramers exhibits two main peaks at 285 and 278 nm, which do not change during ULF formation. In contrast, the CD signal of mature IFs exhibits two major changes: (1) the 278-nm band, denoting the transition of the tyrosines from the ground state to the first vibrational mode of the excited state, is lost; (2) a red-shifted band appears at 291 nm, indicating the emergence of a new electronic species. These changes take place independently and at different time scales. The 278-nm signal disappears within the first minute of assembly, compatible with increased rigidity of the tyrosines during elongation of the ULFs. The rise of the 291-nm band has a lifetime of approximately 13 min and denotes the generation of phenolates by deprotonation of the tyrosines' hydroxyl group after they relocalize into a negatively charged environment. The appearance of such tyrosine-binding "pockets" in the assembling filaments highlights an essential part of the molecular rearrangements characterizing the later stages of the assembly process, including the radial compaction.
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Affiliation(s)
- Sofia Georgakopoulou
- M. E. Müller Institute for Structural Biology, University of Basel, Switzerland.
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28
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Temperature-induced dissociation reaction and dynamics of light-harvesting complex II isolated from purple photosynthetic bacterium Rps. palustris. CHINESE SCIENCE BULLETIN 2008. [DOI: 10.1007/s11434-007-0159-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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García-Martín A, Pazur A, Wilhelm B, Silber M, Robert B, Braun P. The Role of Aromatic Phenylalanine Residues in Binding Carotenoid to Light-Harvesting Model and Wild-Type Complexes. J Mol Biol 2008; 382:154-66. [DOI: 10.1016/j.jmb.2008.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2008] [Revised: 06/29/2008] [Accepted: 07/02/2008] [Indexed: 10/21/2022]
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30
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Feng J, Li X, Liu Y. Effects of pH on the peripheral light-harvesting antenna complex for Rhodopseudomonas palustris. SCIENCE IN CHINA. SERIES C, LIFE SCIENCES 2008; 51:760-766. [PMID: 18677604 DOI: 10.1007/s11427-008-0093-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 05/21/2008] [Indexed: 05/26/2023]
Abstract
In this work steady-state absorption spectroscopy, circular dichroism spectroscopy and sub-microsecond time-resolved absorption spectroscopy were used to investigate the effect of pH on the structures and functions of LH2 complex for Rhodopseudomonas palustris. The results revealed that: (1) B800 Bchla was gradually transformed to free pigments absorbing around 760 nm on the minutes timescale upon the induction of strong acidic pH, and subsequently there disappeared the CD signal for Q(y) band of B800 in the absence of B800. In addition, Carotenoids changed with the similar tendency to B850 BChl. (2) The introduction of strong basic pH gave rise to no significant changes for B800 Bchla, while B850 BChla experienced remarkable spectral blue-shift from 852 to 837 nm. Similar phenomenon was seen for the CD signal for Q(y) band of B850. Carotenoids displayed strong and pH-independent CD signals in the visible range. (3) In the case of both physiological and basic pH, broad and asymmetrical positive T( n ) <-- T(1) transient absorption appeared following the pulsed photo-excitation of Car at 532 nm. By contrast, the featureless and weak positive signal was observed on the sub-microsecond timescale in the acidic pH environment. The aforementioned experimental results indicated that acidic pH-induced removal of B800 Bchla prevented the generation of the carotenoid triplet state ((3)Car), which is known to be essential for the photo-protection function. Nevertheless, carotenoids can still perform this important physiological role under the basic pH condition, where the spectral blue shift of B850 exerts little effect on the overall structure of the cyclic aggregate, therefore favoring the formation of carotenoid triplet state.
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Affiliation(s)
- Juan Feng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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31
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Harvey PD, Stern C, Gros CP, Guilard R. Comments on the through-space singlet energy transfers and energy migration (exciton) in the light harvesting systems. J Inorg Biochem 2007; 102:395-405. [PMID: 18160130 DOI: 10.1016/j.jinorgbio.2007.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 09/20/2007] [Accepted: 09/30/2007] [Indexed: 10/22/2022]
Abstract
Recent findings on the photophysical investigations of several cofacial bisporphyrin dyads for through space singlet and triplet energy transfers raised several serious questions about the mechanism of the energy transfers and energy migration in the light harvesting devices, notably LH II, in the heavily studied purple photosynthetic bacteria. The key issue is that for simple cofacial or slipped dyads with controlled geometry using rigid spacers or spacers with limited flexibilities, the fastest possible rates for singlet energy transfer for three examples are in the 10 x 10(9)s(-1) (i.e. just in the 100 ps time scale) for donor-acceptor distances approaching 3.5-3.6 A. The reported time scale for energy transfers between different bacteriochlorophylls, notably B800*-->B850, is in the picosecond time scale despite the long Mg...Mg separation of approximately 18 A. Such a short rate drastically contrasts with the well accepted Förster theory. This article reviews the modern knowledge of the structure, bacteriochlorophyll a transition moments, and photophysical processes and dynamics in LH II, and compares these parameters with the recently investigated model bisporphyrin dyads build upon octa-etio-porphyrin chromophores and rigid and semi-rigid spacers. The recently discovered role of the rhodopin glucoside residue called carotenoid will be commented as the possible relay for energy transfer, including the possibility of uphill processes at room temperature. In this context, the concept of energy migration, called exciton, may also be affected by relays and uphill processes. Also, it is becoming more and more apparent that the presence of an irreversible electron transfer reaction at the reaction center, i.e. electron transfer from the special pair to the phyophytin macrocycle and so on, renders the rates for energy transfer and migration more rapid precluding all possibility of back transfers.
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Affiliation(s)
- Pierre D Harvey
- Département de Chimie, Université de Sherbrooke, Sherbrooke, PQ, Canada J1K 2R1.
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32
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Georgakopoulou S, van der Zwan G, Bassi R, van Grondelle R, van Amerongen H, Croce R. Understanding the changes in the circular dichroism of light harvesting complex II upon varying its pigment composition and organization. Biochemistry 2007; 46:4745-54. [PMID: 17402710 DOI: 10.1021/bi062031y] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we modeled the circular dichroism (CD) spectrum of LHCII, the main light harvesting antenna of photosystem II of higher plants. Excitonic calculations are performed for a monomeric subunit, taken from the crystal structure of trimeric LHCII from spinach [Liu, Z. F., Yan, H. C., Wang, K. B., Kuang, T. Y., Zhang, J. P., Gui, L. L., An, X. M., and Chang, W. R. (2004) Nature 428, 287-292]. All of the major features of the CD spectrum above 450 nm are satisfactorily reproduced, and possible orientations of the Chl and carotenoid transition dipole moments are identified. The obtained modeling parameters are used to simulate the CD spectra of two complexes with altered pigment composition: a mutant lacking Chls a 611-612 and a complex lacking the carotenoid neoxanthin. By removing the relevant pigment(s) from the structure, we are able to reproduce their spectra, which implies that the alteration does not disturb the overall structure. The CD spectrum of trimeric LHCII shows a reversed relative intensity of the two negative bands around 470 and 490 nm as compared to monomeric LHCII. The simulations reproduce this reversal, indicating that it is mainly due to interactions between chromophores in different monomeric subunits, and the trimerization does not induce observable changes in the monomeric structure. Our simulated spectrum resembles one of two different trimeric CD spectra reported in literature. We argue that the differences in the experimental trimeric CD spectra are caused by changes in the strength of the monomer-monomer interactions due to the differences in detergents used for the purification of the complexes.
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Affiliation(s)
- Sofia Georgakopoulou
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, c/o ITC, Via Sommarive 18 38050 Povo (Trento), Italy
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33
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Balashov SP, Imasheva ES, Lanyi JK. Induced chirality of the light-harvesting carotenoid salinixanthin and its interaction with the retinal of xanthorhodopsin. Biochemistry 2006; 45:10998-1004. [PMID: 16953586 PMCID: PMC2528006 DOI: 10.1021/bi061098i] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In xanthorhodopsin, a retinal protein-carotenoid complex of Salinibacter ruber, the carotenoid salinixanthin functions as a light-harvesting antenna in supplying additional excitation energy for retinal isomerization and proton transport. Another retinal protein, archaerhodopsin, has been shown to contain a carotenoid, bacterioruberin, but without an antenna function. We report here that the binding site confers a chiral geometry on salinixanthin in xanthorhodopsin and confirm that the same is true for bacterioruberin in archaerhodopsin. Cell membranes containing these rhodopsins exhibit CD spectra with sharp positive bands in the visible region where the carotenoids absorb, and in the case of xanthorhodopsin a negative band at 536 nm, as well as bands in the UV region. The carotenoid in ethanol has very weak optical activity in the visible region of the spectrum. Denaturation of the opsin upon deprotonation of the Schiff base at pH 12.5 eliminates the induced CD bands in both proteins. In one of these proteins, but not in the other, the carotenoid binding site depends entirely on the retinal. Hydrolysis of the retinal Schiff base of xanthorhodopsin with hydroxylamine eliminates the induced CD bands of salinixanthin. In contrast, hydrolysis of the Schiff base in archaerhodopsin does not abolish the CD bands of bacterioruberin. Thus, consistent with its antenna function, the carotenoid binding site interacts closely with the retinal only in xanthorhodopsin, and this interaction is the major source of the CD bands. In this protein, protonation of the counterion with a decrease in pH from 8 to 5 causes significant changes in the CD spectrum. The observed spectral features suggest that binding of salinixanthin in xanthorhodopsin involves the cyclohexenone ring of the carotenoid and its conformational heterogeneity is restricted.
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Affiliation(s)
- Sergei P Balashov
- Department of Physiology and Biophysics, University of California, D340 Medical Science I, Irvine, California 92697, USA.
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Papagiannakis E, van Stokkum IHM, Vengris M, Cogdell RJ, van Grondelle R, Larsen DS. Excited-State Dynamics of Carotenoids in Light-Harvesting Complexes. 1. Exploring the Relationship between the S1 and S* States. J Phys Chem B 2006; 110:5727-36. [PMID: 16539518 DOI: 10.1021/jp054633h] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dispersed transient absorption spectra collected at variable excitation intensities in combination with time-resolved signals were used to explore the underlying connectivity of the electronic excited-state manifold of the carotenoid rhodopin glucoside in the light-harvesting 2 complex isolated from Rhodopseudomonas acidophila. We find that the S state, which was recently identified as an excited state in carotenoids bound in bacterial light-harvesting complexes, exhibits a different response to the increase of excitation intensity than the S(1) state, which suggests that the models used so far to describe the excited states of carotenoids are incomplete. We propose two new models that can describe both the time-resolved and the intensity-dependent data; the first postulates that S(1) and S* are not populated in parallel after the decay of the initially excited S(2) state but instead result from the excitation of distinct ground-state subpopulations. The second model introduces a resonantly enhanced light-induced transition during excitation, which promotes population to higher-lying excited states that favors the formation of S* over S(1). Multiwavelength target analysis of the time-resolved and excitation-intensity dependence measurements were used to characterize the involved states and their responses. We show that both proposed models adequately fit the measured data, although it is not possible to determine which model is most apt. The physical origins and implications of both models are explored.
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Affiliation(s)
- Emmanouil Papagiannakis
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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Georgakopoulou S, van Grondelle R, van der Zwan G. Explaining the Visible and Near-Infrared Circular Dichroism Spectra of Light-Harvesting 1 Complexes from Purple Bacteria: A Modeling Study. J Phys Chem B 2006; 110:3344-53. [PMID: 16494349 DOI: 10.1021/jp051794c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we investigate the origin and characteristics of the circular dichroism (CD) spectrum of various light-harvesting 1 (LH1) complexes. The near-infrared (NIR) CD signal of these core antennae is strongly nonconservative, and the nature of this nonconservativity is under examination in this paper. So far, on the basis of the high-resolution structures of LH2, we have been able to model the absorption and CD spectra in the bacteriochlorophyll (BChl) Q(Y) and Q(X) regions of LH2 (Georgakopoulou et al., Biophys. J. 2002, 82, 2184-2197), as well as in the carotenoid region (Georgakopoulou et al., Biophys. J. 2004, 87, 3010-3022). We proceed by applying the same modeling method in order to reproduce the LH1 spectra. We assume a ring of dimers in a perfect circular arrangement with 16-fold symmetry, and account for all excitonic interactions within the ring. Because LH1 complexes exhibit Q(Y) and Q(X) CD signals of very low intensity, higher transitions can easily affect these regions. Therefore, we expand the model and take into account also the Soret and carotenoid transitions. We can now understand the shape of the absorption and CD spectra and contemplate the structure of the LH1 complex. The latter is similar to LH2 in that it is a very symmetric ring dominated by excitonic interactions. The larger number of symmetry and the bigger diameter of LH1, combined with small rotations of the BChl transition dipole moments, are responsible for the display of CD signals that are very low in intensity. The interaction of the Q(Y) with the carotenoid transitions results in complete loss of the conservativity. Interaction energies between all the pigments in the ring are calculated, and their values are in good accordance with what is reported in the literature.
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Affiliation(s)
- Sofia Georgakopoulou
- Department of Biophysics and Physics of Complex Systems, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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Georgakopoulou S, van der Zwan G, Olsen JD, Hunter CN, Niederman RA, van Grondelle R. Investigation of the Effects of Different Carotenoids on the Absorption and CD Signals of Light Harvesting 1 Complexes. J Phys Chem B 2006; 110:3354-61. [PMID: 16494350 DOI: 10.1021/jp0517955] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Absorption and circular dichroism (CD) spectra of light-harvesting (LH)1 complexes from the purple bacteria Rhodobacter (Rba.) sphaeroides and Rhodospirillum (Rsp.) rubrum are presented. The complexes exhibit very low intensity, highly nonconservative, near-infrared (NIR) CD spectra. Absorption and CD spectra from several mutant and reconstituted LH1 complexes, with the carotenoid neurosporene and the precursor phytoene replacing the wild-type (WT) carotenoids, are also examined. The experiments show that the position of the carotenoid bands as well as the bacteriochlorophyll (BChl)/carotenoid ratio affect the NIR CD spectra: bluer bands and larger ratios make the NIR CD signal more conservative. Modeling results that support this finding are presented. This study, combined with the theoretical approach of the companion paper, where modeling of such complexes is presented and discussed in detail, provide a complete explanation of the origin of the nonconservative NIR CD spectra of LH1 and B820.
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Affiliation(s)
- Sofia Georgakopoulou
- Department of Biophysics and Physics of Complex Systems, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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