1
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Sokolov M, Hoffmann DS, Dohmen PM, Krämer M, Höfener S, Kleinekathöfer U, Elstner M. Non-adiabatic molecular dynamics simulations provide new insights into the exciton transfer in the Fenna-Matthews-Olson complex. Phys Chem Chem Phys 2024; 26:19469-19496. [PMID: 38979564 DOI: 10.1039/d4cp02116a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
A trajectory surface hopping approach, which uses machine learning to speed up the most time-consuming steps, has been adopted to investigate the exciton transfer in light-harvesting systems. The present neural networks achieve high accuracy in predicting both Coulomb couplings and excitation energies. The latter are predicted taking into account the environment of the pigments. Direct simulation of exciton dynamics through light-harvesting complexes on significant time scales is usually challenging due to the coupled motion of nuclear and electronic degrees of freedom in these rather large systems containing several relatively large pigments. In the present approach, however, we are able to evaluate a statistically significant number of non-adiabatic molecular dynamics trajectories with respect to exciton delocalization and exciton paths. The formalism is applied to the Fenna-Matthews-Olson complex of green sulfur bacteria, which transfers energy from the light-harvesting chlorosome to the reaction center with astonishing efficiency. The system has been studied experimentally and theoretically for decades. In total, we were able to simulate non-adiabatically more than 30 ns, sampling also the relevant space of parameters within their uncertainty. Our simulations show that the driving force supplied by the energy landscape resulting from electrostatic tuning is sufficient to funnel the energy towards site 3, from where it can be transferred to the reaction center. However, the high efficiency of transfer within a picosecond timescale can be attributed to the rather unusual properties of the BChl a molecules, resulting in very low inner and outer-sphere reorganization energies, not matched by any other organic molecule, e.g., used in organic electronics. A comparison with electron and exciton transfer in organic materials is particularly illuminating, suggesting a mechanism to explain the comparably high transfer efficiency.
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Affiliation(s)
- Monja Sokolov
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - David S Hoffmann
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - Philipp M Dohmen
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Mila Krämer
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - Sebastian Höfener
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | | | - Marcus Elstner
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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2
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Cappelletti D, Barbieri M, Aliprandi A, Maggini M, Đorđević L. Self-assembled π-conjugated chromophores: preparation of one- and two-dimensional nanostructures and their use in photocatalysis. NANOSCALE 2024; 16:9153-9168. [PMID: 38639760 PMCID: PMC11097008 DOI: 10.1039/d4nr00383g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024]
Abstract
Photocatalytic systems have attracted research interest as a clean approach to generate energy from abundant sunlight. In this context, developing efficient and robust photocatalytic structures is crucial. Recently, self-assembled organic chromophores have entered the stage as alternatives to both molecular systems and (in)organic semiconductors. Nanostructures made of self-assembled π-conjugated dyes offer, on the one hand, molecular customizability to tune their optoelectronic properties and activities and on the other hand, provide benefits from heterogeneous catalysis that include ease of separation, recyclability and improved photophysical properties. In this contribution, we present recent achievements in constructing supramolecular photocatalytic systems made of chromophores for applications in water splitting, H2O2 evolution, CO2 reduction, or environmental remediation. We discuss strategies that can be used to prepare ordered photocatalytic systems with an emphasis on the effect of packing between the dyes and the resulting photocatalytic activity. We further showcase supramolecular strategies that allow interfacing the organic nanostructures with co-catalysts, molecules, polymers, and (in)organic materials. The principles discussed here are the foundation for the utilization of these self-assembled materials in photocatalysis.
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Affiliation(s)
- David Cappelletti
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Marianna Barbieri
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Alessandro Aliprandi
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Michele Maggini
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Luka Đorđević
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
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3
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Götze JP, Maity S, Kleinekathöfer U. Incoherent Energy Transfer between the Baseplate and FMO Protein Explored at Ideal Geometries. J Phys Chem B 2023; 127:7829-7838. [PMID: 37691433 DOI: 10.1021/acs.jpcb.3c02568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The Förster resonance energy transfer (FRET) between the Fenna-Matthews-Olson (FMO) protein complex and the chlorosomal baseplate (CBP) is investigated by using an idealized model. This simplified model is based on crystal structure and molecular dynamics conformations. Some of the further input, such as the transition dipole moments, was extracted from earlier molecular-level simulations. The resulting model mimics the effects of the relative position between the CBP and the FMO complex on the corresponding FRET efficiency under ideal conditions, involving about 1.3 billion FRET calculations per investigated model. In this idealized model and employing some approximations, it is found that FRET efficiency is almost completely independent of the FMO trimer orientation (displacement, distance, and rotation), despite FMO and CBP being highly structured complexes. Even removing individual FMO BChl triples will only reduce the FRET efficiency by up to 8.6%. An FMO containing only the least efficient BChl triple will retain about 25% of the FRET efficiency of a full FMO complex. In addition to its proposed function as an energetic funnel, FMO is thus identified to act as a highly robust spatial funnel for CBP excitation harvesting, independent of the mutual CBP-FMO orientation.
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Affiliation(s)
- Jan P Götze
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Sayan Maity
- School of Science, Constructor University, Campusring 1, 28759 Bremen, Germany
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4
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Ress L, Malý P, Landgraf JB, Lindorfer D, Hofer M, Selby J, Lambert C, Renger T, Brixner T. Time-resolved circular dichroism of excitonic systems: theory and experiment on an exemplary squaraine polymer. Chem Sci 2023; 14:9328-9349. [PMID: 37712031 PMCID: PMC10498725 DOI: 10.1039/d3sc01674a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023] Open
Abstract
Experimental and theoretical foundations for femtosecond time-resolved circular dichroism (TRCD) spectroscopy of excitonic systems are presented. In this method, the system is pumped with linearly polarized light and the signal is defined as the difference between the transient absorption spectrum probed with left and with right circularly polarized light. We present a new experimental setup with a polarization grating as key element to generate circularly polarized pulses. Herein the positive (negative) first order of the diffracted light is left-(right-)circularly polarized and serves as a probe pulse in a TRCD experiment. The grating is capable of transferring ultrashort broadband pulses ranging from 470 nm to 720 nm into two separate beams with opposite ellipticity. By applying a specific chopping scheme we can switch between left and right circular polarizations and detect transient absorption (TA) and TRCD spectra on a shot-to-shot basis simultaneously. We perform experiments on a squaraine polymer, investigating excitonic dynamics, and we develop a general theory for TRCD experiments of excitonically coupled systems that we then apply to describe the experimental data in this particular example. At a magic angle of 54.7° between the pump-pulse polarization and the propagation direction of the probe pulse, the TRCD and TA signals become particularly simple to analyze, since the orientational average over random orientations of complexes factorizes into that of the interaction with the pump and the probe pulse, and the intrinsic electric quadrupole contributions to the TRCD signal average to zero for isotropic samples. Application of exciton theory to linear absorption and to linear circular dichroism spectra of squaraine polymers reveals the presence of two fractions of polymer conformations, a dominant helical conformation with close interpigment distances that are suggested to lead to short-range contributions to site energy shifts and excitonic couplings of the squaraine molecules, and a fraction of unfolded random coils. Theory demonstrates that TRCD spectra of selectively excited helices can resolve state populations that are practically invisible in TA spectroscopy due to the small dipole strength of these states. A qualitative interpretation of TRCD and TA spectra in the spectral window investigated experimentally is offered. The 1 ps time component found in these spectra is related to the slow part of exciton relaxation obtained between states of the helix in the low-energy half of the exciton manifold. The dominant 140 ps time constant reflects the decay of excited states to the electronic ground state.
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Affiliation(s)
- Lea Ress
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Pavel Malý
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
- Faculty of Mathematics and Physics, Charles University Ke Karlovu 5 121 16 Praha 2 Czech Republic
| | - Jann B Landgraf
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Universität Freiburg Georges-Köhler-Allee 105 79110 Freiburg Germany
| | - Dominik Lindorfer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz Altenberger Str. 69 4040 Linz Austria
| | - Michael Hofer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz Altenberger Str. 69 4040 Linz Austria
| | - Joshua Selby
- Institut für Organische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Christoph Lambert
- Institut für Organische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz Altenberger Str. 69 4040 Linz Austria
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
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5
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Lyratzakis A, Meier-Credo J, Langer JD, Tsiotis G. Insights into the sulfur metabolism of Chlorobaculum tepidum by label-free quantitative proteomics. Proteomics 2023; 23:e2200138. [PMID: 36790022 DOI: 10.1002/pmic.202200138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 01/20/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023]
Abstract
Chlorobaculum tepidum is an anaerobic green sulfur bacterium which oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. It can also oxidize sulfide to produce extracellular S0 globules, which can be further oxidized to sulfate and used as an electron donor. Here, we performed label-free quantitative proteomics on total cell lysates prepared from different metabolic states, including a sulfur production state (10 h post-incubation [PI]), the beginning of sulfur consumption (20 h PI), and the end of sulfur consumption (40 h PI), respectively. We observed an increased abundance of the sulfide:quinone oxidoreductase (Sqr) proteins in 10 h PI indicating a sulfur production state. The periplasmic thiosulfate-oxidizing Sox enzymes and the dissimilatory sulfite reductase (Dsr) subunits showed an increased abundance in 20 h PI, corresponding to the sulfur-consuming state. In addition, we found that the abundance of the heterodisulfide-reductase and the sulfhydrogenase operons was influenced by electron donor availability and may be associated with sulfur metabolism. Further, we isolated and analyzed the extracellular sulfur globules in the different metabolic states to study their morphology and the sulfur cluster composition, yielding 58 previously uncharacterized proteins in purified globules. Our results show that C. tepidum regulates the cellular levels of enzymes involved in sulfur metabolism in response to the availability of reduced sulfur compounds.
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Affiliation(s)
| | - Jakob Meier-Credo
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Julian D Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Georgios Tsiotis
- Department of Chemistry, University of Crete, Voutes Campus, Heraklion, Greece
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6
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Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium Chlorobaculum tepidum. Proc Natl Acad Sci U S A 2023; 120:e2216734120. [PMID: 36693097 PMCID: PMC9945994 DOI: 10.1073/pnas.2216734120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Light energy absorption and transfer are very important processes in photosynthesis. In green sulfur bacteria light is absorbed primarily by the chlorosomes and its energy is transferred via the Fenna-Matthews-Olson (FMO) proteins to a homodimeric reaction center (RC). Here, we report the cryogenic electron microscopic structure of the intact FMO-RC apparatus from Chlorobaculum tepidum at 2.5 Å resolution. The FMO-RC apparatus presents an asymmetric architecture and contains two FMO trimers that show different interaction patterns with the RC core. Furthermore, the two permanently bound transmembrane subunits PscC, which donate electrons to the special pair, interact only with the two large PscA subunits. This structure fills an important gap in our understanding of the transfer of energy from antenna to the electron transport chain of this RC and the transfer of electrons from reduced sulfur compounds to the special pair.
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Chen JH, Wang W, Wang C, Kuang T, Shen JR, Zhang X. Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:223-234. [PMID: 36125941 DOI: 10.1111/jipb.13367] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/19/2022] [Indexed: 06/15/2023]
Abstract
The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.
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Affiliation(s)
- Jing-Hua Chen
- College of Life Science, Zhejiang University, Hangzhou, 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Weiwei Wang
- College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Chen Wang
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Tingyun Kuang
- Key Laboratory of Photobiology, Institute of Botany, Photosynthesis Research Center, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jian-Ren Shen
- Key Laboratory of Photobiology, Institute of Botany, Photosynthesis Research Center, the Chinese Academy of Sciences, Beijing, 100093, China
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Xing Zhang
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, 310058, China
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8
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Götze JP, Anders F, Petry S, Felix Witte J, Lokstein H. Spectral Characterization of the Main Pigments in the Plant Photosynthetic Apparatus by Theory and Experiment. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Górecki M, Lipparini F, Albano G, Jávorfi T, Hussain R, Siligardi G, Pescitelli G, Di Bari L. Electronic Circular Dichroism Imaging (ECDi) Casts a New Light on the Origin of Solid-State Chiroptical Properties. Chemistry 2021; 28:e202103632. [PMID: 34935206 DOI: 10.1002/chem.202103632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/05/2022]
Abstract
Solid-state ECD (ss-ECD) spectra of a model microcrystalline solid, finasteride, dispersed into a KCl pellet were recorded by using the synchrotron radiation source at the Diamond B23 beamline. Scanning a surface of 36 mm2 with a step of 0.5 mm, we measured a set of ECD imaging (ECDi) spectra very different from each other and from the ss-ECD recorded with a bench-top instrument (1 cm2 area). This is due to the anisotropic part of the ECD (ACD), which averages to zero in solution or on a large number of randomly oriented crystallites, but can otherwise be extremely large. Two-way singular value decomposition (SVD) analysis, through experimental and simulated TDDFT spectra, disclosed that the measured and theoretical principal components are in line with each other. This finding demonstrates that the observed isotropic ss-ECD spectrum is governed by the anisotropy of locally oriented crystals. It also introduces a new quality for ss-ECD measurements and opens a new future for probing and mapping chiral materials in the solid state such as active pharmaceutical ingredients (APIs).
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Affiliation(s)
- Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy
| | - Gianluigi Albano
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy.,Present address: Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", via Edoardo Orabona 4, 70126, Bari, Italy
| | - Tamás Jávorfi
- Diamond Light Source, Ltd., Chilton, Didcot, Oxfordshire, OX11 0DE, UK
| | - Rohanah Hussain
- Diamond Light Source, Ltd., Chilton, Didcot, Oxfordshire, OX11 0DE, UK
| | | | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy
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10
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Chen JH, Wu H, Xu C, Liu XC, Huang Z, Chang S, Wang W, Han G, Kuang T, Shen JR, Zhang X. Architecture of the photosynthetic complex from a green sulfur bacterium. Science 2021; 370:370/6519/eabb6350. [PMID: 33214250 DOI: 10.1126/science.abb6350] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/09/2020] [Indexed: 01/09/2023]
Abstract
The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from Chlorobaculum tepidum The GsbRC binds considerably fewer (bacterio)chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs.
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Affiliation(s)
- Jing-Hua Chen
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Hangjun Wu
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Caihuang Xu
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Xiao-Chi Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Zihui Huang
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Shenghai Chang
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Guangye Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China. .,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 700-8530 Okayama, Japan
| | - Xing Zhang
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China. .,Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, 310058 Zhejiang, China.,Zhejiang Laboratory for System and Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121 Zhejiang, China
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11
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Abstract
Photosynthetic membranes are typically densely packed with proteins, and this is crucial for their function in efficient trapping of light energy. Despite being crowded with protein, the membranes are fluid systems in which proteins and smaller molecules can diffuse. Fluidity is also crucial for photosynthetic function, as it is essential for biogenesis, electron transport, and protein redistribution for functional regulation. All photosynthetic membranes seem to maintain a delicate balance between crowding, order, and fluidity. How does this work in phototrophic bacteria? In this review, we focus on two types of intensively studied bacterial photosynthetic membranes: the chromatophore membranes of purple bacteria and the thylakoid membranes of cyanobacteria. Both systems are distinct from the plasma membrane, and both have a distinctive protein composition that reflects their specialized roles. Chromatophores are formed from plasma membrane invaginations, while thylakoid membranes appear to be an independent intracellular membrane system. We discuss the techniques that can be applied to study the organization and dynamics of these membrane systems, including electron microscopy techniques, atomic force microscopy, and many variants of fluorescence microscopy. We go on to discuss the insights that havebeen acquired from these techniques, and the role of membrane dynamics in the physiology of photosynthetic membranes. Membrane dynamics on multiple timescales are crucial for membrane function, from electron transport on timescales of microseconds to milliseconds to regulation and biogenesis on timescales of minutes to hours. We emphasize the open questions that remain in the field.
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Affiliation(s)
- Conrad W. Mullineaux
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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12
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Greening C, Lithgow T. Formation and function of bacterial organelles. Nat Rev Microbiol 2020; 18:677-689. [PMID: 32710089 DOI: 10.1038/s41579-020-0413-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 01/28/2023]
Abstract
Advances in imaging technologies have revealed that many bacteria possess organelles with a proteomically defined lumen and a macromolecular boundary. Some are bound by a lipid bilayer (such as thylakoids, magnetosomes and anammoxosomes), whereas others are defined by a lipid monolayer (such as lipid bodies), a proteinaceous coat (such as carboxysomes) or have a phase-defined boundary (such as nucleolus-like compartments). These diverse organelles have various metabolic and physiological functions, facilitating adaptation to different environments and driving the evolution of cellular complexity. This Review highlights that, despite the diversity of reported organelles, some unifying concepts underlie their formation, structure and function. Bacteria have fundamental mechanisms of organelle formation, through which conserved processes can form distinct organelles in different species depending on the proteins recruited to the luminal space and the boundary of the organelle. These complex subcellular compartments provide evolutionary advantages as well as enabling metabolic specialization, biogeochemical processes and biotechnological advances. Growing evidence suggests that the presence of organelles is the rule, rather than the exception, in bacterial cells.
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Affiliation(s)
- Chris Greening
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
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13
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Akhtar P, Nowakowski PJ, Wang W, Do TN, Zhao S, Siligardi G, Garab G, Shen JR, Tan HS, Lambrev PH. Spectral tuning of light-harvesting complex II in the siphonous alga Bryopsis corticulans and its effect on energy transfer dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148191. [PMID: 32201306 DOI: 10.1016/j.bbabio.2020.148191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 12/17/2022]
Abstract
Light-harvesting complex II (LHCII) from the marine green macroalga Bryopsis corticulans is spectroscopically characterized to understand the structural and functional changes resulting from adaptation to intertidal environment. LHCII is homologous to its counterpart in land plants but has a different carotenoid and chlorophyll (Chl) composition. This is reflected in the steady-state absorption, fluorescence, linear dichroism, circular dichroism and anisotropic circular dichroism spectra. Time-resolved fluorescence and two-dimensional electronic spectroscopy were used to investigate the consequences of this adaptive change in the pigment composition on the excited-state dynamics. The complex contains additional Chl b spectral forms - absorbing at around 650 nm and 658 nm - and lacks the red-most Chl a forms compared with higher-plant LHCII. Similar to plant LHCII, energy transfer between Chls occurs on timescales from under hundred fs (mainly from Chl b to Chl a) to several picoseconds (mainly between Chl a pools). However, the presence of long-lived, weakly coupled Chl b and Chl a states leads to slower exciton equilibration in LHCII from B. corticulans. The finding demonstrates a trade-off between the enhanced absorption of blue-green light and the excitation migration time. However, the adaptive change does not result in a significant drop in the overall photochemical efficiency of Photosystem II. These results show that LHCII is a robust adaptable system whose spectral properties can be tuned to the environment for optimal light harvesting.
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Affiliation(s)
- Parveen Akhtar
- Biological Research Centre, Szeged, Hungary; ELI-ALPS, ELI Nonprofit Ltd., Szeged, Hungary
| | - Paweł J Nowakowski
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Wenda Wang
- Photosynthesis Research Centre, Chinese Academy of Sciences, Beijing, China
| | - Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Songhao Zhao
- Photosynthesis Research Centre, Chinese Academy of Sciences, Beijing, China
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Győző Garab
- Biological Research Centre, Szeged, Hungary; Department of Physics, Faculty of Science, University of Ostrava, Czech Republic
| | - Jian-Ren Shen
- Photosynthesis Research Centre, Chinese Academy of Sciences, Beijing, China; Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore.
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14
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Kaliakin DS, Nakata H, Kim Y, Chen Q, Fedorov DG, Slipchenko LV. FMOxFMO: Elucidating Excitonic Interactions in the Fenna-Matthews-Olson Complex with the Fragment Molecular Orbital Method. J Chem Theory Comput 2020; 16:1175-1187. [PMID: 31841349 DOI: 10.1021/acs.jctc.9b00621] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to study Förster resonance energy transfer (FRET), the fragment molecular orbital (FMO) method is extended to compute electronic couplings between local excitations via the excited state transition density model, enabling efficient calculations of nonlocal excitations in a large molecular system and overcoming the previous limitation of being able to compute only local excitations. The results of these simple but accurate models are validated against full quantum calculations without fragmentation. The developed method is applied to a very important photosynthetic pigment-protein complex, the Fenna-Matthews-Olson complex (FMOc), that is responsible for the energy transfer from a chlorosome to the reaction center in the green sulfur bacteria. Absorption and circular dichroism spectra of FMOc are simulated, and the role of the molecular environment on the excitations is revealed.
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Affiliation(s)
- Danil S Kaliakin
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Hiroya Nakata
- Research Institute for Advanced Materials and Devices , Kyocera , 5-3 Hikaridai-3 , Seika-cho Soraku-gun, Kyoto 619-0237 , Japan
| | - Yongbin Kim
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Qifeng Chen
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat) , National Institute of Advanced Industrial Science and Technology (AIST) , Central 2, Umezono 1-1-1 , Tsukuba 305-8568 , Japan
| | - Lyudmila V Slipchenko
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
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15
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Jassas M, Goodson C, Blankenship RE, Jankowiak R, Kell A. On Excitation Energy Transfer within the Baseplate BChl a-CsmA Complex of Chloroflexus aurantiacus. J Phys Chem B 2019; 123:9786-9791. [PMID: 31660744 DOI: 10.1021/acs.jpcb.9b08043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, a hybrid approach combining solid-state NMR spectroscopy and cryo-electron microscopy showed that the baseplate in green sulfur bacterium Chlorobaculum tepidum is a 2D lattice of BChl a-CsmA dimers [Nielsen, J. T.; et al., Nat. Commun. 2016, 7, 12454-12465]. While the existence of the BChl a-CsmA subunit was previously known, the proposed orientations of the BChl a pigments had only been elucidated from spectral data up to this point. Regarding the electronic structure of the baseplate, two models have been proposed. 2D electronic spectroscopy data were interpreted as revealing that at least four excitonically coupled BChl a might be in close contact. Conversely, spectral hole burning data suggested that the lowest energy state was localized, yet additional states are sometimes observed because of the presence of the Fenna-Matthews-Olson (FMO) antenna protein. To solve this conundrum, this work studies the chlorosome-baseplate complex from Chloroflexus aurantiacus, which does not contain the FMO protein. The results confirm that in both C. tepidum and C. aurantiacus, excitation energy is transferred to a localized low-energy trap state near 818 nm with similar rates, most likely via exciton hopping.
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Affiliation(s)
| | - Carrie Goodson
- Departments of Biology and Chemistry , Washington University in Saint Louis , Saint Louis , Missouri 63130 , United States
| | - Robert E Blankenship
- Departments of Biology and Chemistry , Washington University in Saint Louis , Saint Louis , Missouri 63130 , United States
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16
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Macroorganisation and flexibility of thylakoid membranes. Biochem J 2019; 476:2981-3018. [DOI: 10.1042/bcj20190080] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
Abstract
The light reactions of photosynthesis are hosted and regulated by the chloroplast thylakoid membrane (TM) — the central structural component of the photosynthetic apparatus of plants and algae. The two-dimensional and three-dimensional arrangement of the lipid–protein assemblies, aka macroorganisation, and its dynamic responses to the fluctuating physiological environment, aka flexibility, are the subject of this review. An emphasis is given on the information obtainable by spectroscopic approaches, especially circular dichroism (CD). We briefly summarise the current knowledge of the composition and three-dimensional architecture of the granal TMs in plants and the supramolecular organisation of Photosystem II and light-harvesting complex II therein. We next acquaint the non-specialist reader with the fundamentals of CD spectroscopy, recent advances such as anisotropic CD, and applications for studying the structure and macroorganisation of photosynthetic complexes and membranes. Special attention is given to the structural and functional flexibility of light-harvesting complex II in vitro as revealed by CD and fluorescence spectroscopy. We give an account of the dynamic changes in membrane macroorganisation associated with the light-adaptation of the photosynthetic apparatus and the regulation of the excitation energy flow by state transitions and non-photochemical quenching.
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17
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The role of circular dichroism spectroscopy in the era of integrative structural biology. Curr Opin Struct Biol 2019; 58:191-196. [DOI: 10.1016/j.sbi.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022]
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18
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Fujiwara Y, Tamiaki H. Stereoselective self-aggregation of synthetic zinc 3 1-epimeric bacteriochlorophyll-d analogs possessing a methylene group at the 13 2-position as models of green photosynthetic bacterial chlorosomes. Photochem Photobiol Sci 2019; 18:1218-1227. [PMID: 30839974 DOI: 10.1039/c8pp00535d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Zinc bacteriochlorophyll-d analogs possessing a methylene group at the 132-position were prepared by chemical modification of naturally occurring chlorophyll-a. The synthetic 31-epimers were successfully separated by reverse phase HPLC to give diastereomerically pure samples. The stereochemistry of the chiral C31-center in the separated bacteriochlorophyll-d analogs was determined by HPLC analysis of the authentic stereoisomers prepared stereospecifically. Both the epimers were monomeric in tetrahydrofuran to give sharp absorption bands, while they self-aggregated to form chlorosomal oligomers with red-shifted bands in an aqueous Triton X-100 micelle solution. The resulting large oligomers deaggregated by addition of Triton X-100 to give monomeric species. Their aggregation and deaggregation were dependent on the 31-stereochemistry, indicating that each epimer produced self-aggregates that were supramolecularly different. The substitution with the 132-methylene group enhanced their self-aggregation abilities and the stability of their resulting self-aggregates.
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Affiliation(s)
- Yoshiki Fujiwara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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19
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Sun Z, Diebolder CA, Renault L, de Groot H. A Semisynthetic Peptide−Metalloporphyrin Responsive Matrix for Artificial Photosynthesis. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhongwu Sun
- Leiden University Leiden Institute of Chemistry 2333 AL Leiden The Netherlands
| | - Christoph A. Diebolder
- Leiden University The Netherlands Centre for Electron Nanoscopy (NeCEN) 2333 AL Leiden The Netherlands
| | - Ludovic Renault
- Leiden University The Netherlands Centre for Electron Nanoscopy (NeCEN) 2333 AL Leiden The Netherlands
| | - Huub de Groot
- Leiden University Leiden Institute of Chemistry 2333 AL Leiden The Netherlands
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20
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Ranjbar Choubeh R, Koehorst RBM, Bína D, Struik PC, Pšenčík J, van Amerongen H. Efficiency of excitation energy trapping in the green photosynthetic bacterium Chlorobaculum tepidum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:147-154. [PMID: 30537470 DOI: 10.1016/j.bbabio.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 01/05/2023]
Abstract
During the millions of years of evolution, photosynthetic organisms have adapted to almost all terrestrial and aquatic habitats, although some environments are obviously more suitable for photosynthesis than others. Photosynthetic organisms living in low-light conditions require on the one hand a large light-harvesting apparatus to absorb as many photons as possible. On the other hand, the excitation trapping time scales with the size of the light-harvesting system, and the longer the distance over which the formed excitations have to be transferred, the larger the probability to lose excitations. Therefore a compromise between photon capture efficiency and excitation trapping efficiency needs to be found. Here we report results on the whole cells of the green sulfur bacterium Chlorobaculum tepidum. Its efficiency of excitation energy transfer and charge separation enables the organism to live in environments with very low illumination. Using fluorescence measurements with picosecond resolution, we estimate that despite a rather large size and complex composition of its light-harvesting apparatus, the quantum efficiency of its photochemistry is around ~87% at 20 °C, ~83% at 45 °C, and about ~81% at 77 K when part of the excitation energy is trapped by low-energy bacteriochlorophyll a molecules. The data are evaluated using target analysis, which provides further insight into the functional organization of the low-light adapted photosynthetic apparatus.
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Affiliation(s)
| | - Rob B M Koehorst
- Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands; MicroSpectroscopy Research Facility, Wageningen University, Wageningen, the Netherlands
| | - David Bína
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Paul C Struik
- Centre for Crop Systems Analysis, Wageningen University, Wageningen, the Netherlands
| | - Jakub Pšenčík
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands; MicroSpectroscopy Research Facility, Wageningen University, Wageningen, the Netherlands.
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21
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Abstract
Spatial organization is a hallmark of all living systems. Even bacteria, the smallest forms of cellular life, display defined shapes and complex internal organization, showcasing a highly structured genome, cytoskeletal filaments, localized scaffolding structures, dynamic spatial patterns, active transport, and occasionally, intracellular organelles. Spatial order is required for faithful and efficient cellular replication and offers a powerful means for the development of unique biological properties. Here, we discuss organizational features of bacterial cells and highlight how bacteria have evolved diverse spatial mechanisms to overcome challenges cells face as self-replicating entities.
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22
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Akhtar P, Lindorfer D, Lingvay M, Pawlak K, Zsiros O, Siligardi G, Jávorfi T, Dorogi M, Ughy B, Garab G, Renger T, Lambrev PH. Anisotropic Circular Dichroism of Light-Harvesting Complex II in Oriented Lipid Bilayers: Theory Meets Experiment. J Phys Chem B 2019; 123:1090-1098. [PMID: 30604975 DOI: 10.1021/acs.jpcb.8b12474] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anisotropic circular dichroism (ACD) spectroscopy of macroscopically aligned molecules reveals additional information about their excited states that is lost in the CD of randomly oriented solutions. ACD spectra of light-harvesting complex II (LHCII)-the main peripheral antenna of photosystem II in plants-in oriented lipid bilayers were recorded from the far-UV to the visible wavelength region. ACD spectra show a drastically enhanced magnitude and level of detail compared to the isotropic CD spectra, resolving a greater number of bands and weak optical transitions. Exciton calculations show that the spectral features in the chlorophyll Q y region are well-reproduced by an existing Hamiltonian for LHCII, providing further evidence for the identity of energy sinks at chlorophylls a603 and a610 in the stromal layer and chlorophylls a604 and a613 in the luminal layer. We propose ACD spectroscopy to be a valuable tool linking the three-dimensional structure and the photophysical properties of pigment-protein complexes.
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Affiliation(s)
- Parveen Akhtar
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári krt. 62 , 6726 Szeged , Hungary.,ELI-ALPS, ELI-HU Nonprofit Ltd. , Budapesti út 5 , 6728 Szeged , Hungary
| | - Dominik Lindorfer
- Institute for Theoretical Physics , Johannes Kepler University Linz , Altenberger Str. 69 , 4040 Linz , Austria
| | - Mónika Lingvay
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári krt. 62 , 6726 Szeged , Hungary.,Faculty of Science and Informatics, Doctoral School of Physics , University of Szeged , Dóm tér 9 , 6720 Szeged , Hungary
| | - Krzysztof Pawlak
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári krt. 62 , 6726 Szeged , Hungary
| | - Ottó Zsiros
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári krt. 62 , 6726 Szeged , Hungary
| | - Giuliano Siligardi
- Diamond Light Source Ltd. , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , U.K
| | - Tamás Jávorfi
- Diamond Light Source Ltd. , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , U.K
| | - Márta Dorogi
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári krt. 62 , 6726 Szeged , Hungary
| | - Bettina Ughy
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári krt. 62 , 6726 Szeged , Hungary
| | - Győző Garab
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári krt. 62 , 6726 Szeged , Hungary.,Faculty of Science, Department of Physics , University of Ostrava , Chittussiho 10 , 710 00 Ostrava , Czech Republic
| | - Thomas Renger
- Institute for Theoretical Physics , Johannes Kepler University Linz , Altenberger Str. 69 , 4040 Linz , Austria
| | - Petar H Lambrev
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári krt. 62 , 6726 Szeged , Hungary
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23
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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24
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Magdaong NCM, Niedzwiedzki DM, Saer RG, Goodson C, Blankenship RE. Excitation energy transfer kinetics and efficiency in phototrophic green sulfur bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1180-1190. [DOI: 10.1016/j.bbabio.2018.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 01/16/2023]
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25
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Lindorfer D, Renger T. Theory of Anisotropic Circular Dichroism of Excitonically Coupled Systems: Application to the Baseplate of Green Sulfur Bacteria. J Phys Chem B 2018; 122:2747-2756. [PMID: 29420888 DOI: 10.1021/acs.jpcb.7b12832] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A simple exciton theory for the description of anisotropic circular dichroism (ACD) spectra of multichromophoric systems is presented that is expected to be of general use for the analysis of structure-function relationships of molecular aggregates such as photosynthetic light-harvesting antennae. The theory is applied to the baseplate of green sulfur bacteria. It is demonstrated that only the combined analysis of ACD and circular dichroism (CD) spectra for the present baseplate bacteriochlorophyll (BChl) a dimer allows for an unambiguous determination of the parameters of the exciton Hamiltonian from experimental data. The analysis of experimental absorption and linear dichroism spectra suggests that either the NMR structure has to be refined or in addition to the dimers seen in the NMR structure and in the CD and ACD spectra, BChl a monomers are present in the baseplate carotenosome sample. A refined dimer structure is presented, explaining all four optical spectra.
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Affiliation(s)
- Dominik Lindorfer
- Institut für Theoretische Physik , Johannes Kepler Universität Linz , Altenberger Str. 69 , 4040 Linz , Austria
| | - Thomas Renger
- Institut für Theoretische Physik , Johannes Kepler Universität Linz , Altenberger Str. 69 , 4040 Linz , Austria
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26
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Nielsen JT, Mulder FAA. POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2018; 70:141-165. [PMID: 29399725 DOI: 10.1007/s10858-018-0166-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/25/2018] [Indexed: 05/04/2023]
Abstract
Chemical shifts contain important site-specific information on the structure and dynamics of proteins. Deviations from statistical average values, known as random coil chemical shifts (RCCSs), are extensively used to infer these relationships. Unfortunately, the use of imprecise reference RCCSs leads to biased inference and obstructs the detection of subtle structural features. Here we present a new method, POTENCI, for the prediction of RCCSs that outperforms the currently most authoritative methods. POTENCI is parametrized using a large curated database of chemical shifts for protein segments with validated disorder; It takes pH and temperature explicitly into account, and includes sequence-dependent nearest and next-nearest neighbor corrections as well as second-order corrections. RCCS predictions with POTENCI show root-mean-square values that are lower by 25-78%, with the largest improvements observed for 1Hα and 13C'. It is demonstrated how POTENCI can be applied to analyze subtle deviations from RCCSs to detect small populations of residual structure in intrinsically disorder proteins that were not discernible before. POTENCI source code is available for download, or can be deployed from the URL http://www.protein-nmr.org .
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Affiliation(s)
- Jakob Toudahl Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
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27
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Saga Y, Takahashi N, Miyatake T, Tamiaki H. Amphiphilic zinc bacteriochlorophyll a derivatives that function as artificial energy acceptors in photosynthetic antenna complexes chlorosomes of the green sulfur photosynthetic bacterium Chlorobaculum limnaeum. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Orf GS, Collins AM, Niedzwiedzki DM, Tank M, Thiel V, Kell A, Bryant DA, Montaño GA, Blankenship RE. Polymer-Chlorosome Nanocomposites Consisting of Non-Native Combinations of Self-Assembling Bacteriochlorophylls. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6427-6438. [PMID: 28585832 DOI: 10.1021/acs.langmuir.7b01761] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chlorosomes are one of the characteristic light-harvesting antennas from green sulfur bacteria. These complexes represent a unique paradigm: self-assembly of bacteriochlorophyll pigments within a lipid monolayer without the influence of protein. Because of their large size and reduced complexity, they have been targeted as models for the development of bioinspired light-harvesting arrays. We report the production of biohybrid light-harvesting nanocomposites mimicking chlorosomes, composed of amphiphilic diblock copolymer membrane bodies that incorporate thousands of natural self-assembling bacteriochlorophyll molecules derived from green sulfur bacteria. The driving force behind the assembly of these polymer-chlorosome nanocomposites is the transfer of the mixed raw materials from the organic to the aqueous phase. We incorporated up to five different self-assembling pigment types into single nanocomposites that mimic chlorosome morphology. We establish that the copolymer-BChl self-assembly process works smoothly even when non-native combinations of BChl homologues are included. Spectroscopic characterization revealed that the different types of self-assembling pigments participate in ultrafast energy transfer, expanding beyond single chromophore constraints of the natural chlorosome system. This study further demonstrates the utility of flexible short-chain, diblock copolymers for building scalable, tunable light-harvesting arrays for technological use and allows for an in vitro analysis of the flexibility of natural self-assembling chromophores in unique and controlled combinations.
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Affiliation(s)
| | - Aaron M Collins
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
| | | | - Marcus Tank
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
- Department of Biological Sciences, Tokyo Metropolitan University , Tokyo, Japan 192-0397
| | - Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
- Department of Biological Sciences, Tokyo Metropolitan University , Tokyo, Japan 192-0397
| | - Adam Kell
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506, United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Gabriel A Montaño
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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Light harvesting in phototrophic bacteria: structure and function. Biochem J 2017; 474:2107-2131. [DOI: 10.1042/bcj20160753] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 12/23/2022]
Abstract
This review serves as an introduction to the variety of light-harvesting (LH) structures present in phototrophic prokaryotes. It provides an overview of the LH complexes of purple bacteria, green sulfur bacteria (GSB), acidobacteria, filamentous anoxygenic phototrophs (FAP), and cyanobacteria. Bacteria have adapted their LH systems for efficient operation under a multitude of different habitats and light qualities, performing both oxygenic (oxygen-evolving) and anoxygenic (non-oxygen-evolving) photosynthesis. For each LH system, emphasis is placed on the overall architecture of the pigment–protein complex, as well as any relevant information on energy transfer rates and pathways. This review addresses also some of the more recent findings in the field, such as the structure of the CsmA chlorosome baseplate and the whole-cell kinetics of energy transfer in GSB, while also pointing out some areas in need of further investigation.
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Shankar R, Ernst M, Madhu PK, Vosegaard T, Nielsen NC, Nielsen AB. A general theoretical description of the influence of isotropic chemical shift in dipolar recoupling experiments for solid-state NMR. J Chem Phys 2017; 146:134105. [DOI: 10.1063/1.4979123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Two-dimensional electronic spectra of the photosynthetic apparatus of green sulfur bacteria. Sci Rep 2017; 7:45245. [PMID: 28345621 PMCID: PMC5366913 DOI: 10.1038/srep45245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/21/2017] [Indexed: 12/25/2022] Open
Abstract
Advances in time resolved spectroscopy have provided new insight into the energy transmission in natural photosynthetic complexes. Novel theoretical tools and models are being developed in order to explain the experimental results. We provide a model calculation for the two-dimensional electronic spectra of Cholorobaculum tepidum which correctly describes the main features and transfer time scales found in recent experiments. From our calculation one can infer the coupling of the antenna chlorosome with the environment and the coupling between the chlorosome and the Fenna-Matthews-Olson complex. We show that environment assisted transport between the subunits is the required mechanism to reproduce the experimental two-dimensional electronic spectra.
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Thomas B, Rombouts J, Oostergetel GT, Gupta KBSS, Buda F, Lammertsma K, Orru R, de Groot HJM. A Hybrid Solid-State NMR and Electron Microscopy Structure-Determination Protocol for Engineering Advanced para-Crystalline Optical Materials. Chemistry 2017; 23:3280-3284. [PMID: 28117921 PMCID: PMC5347911 DOI: 10.1002/chem.201700324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Indexed: 01/04/2023]
Abstract
Hybrid magic‐angle spinning (MAS) NMR spectroscopy and TEM were demonstrated for de novo structure determination of para‐crystalline materials with a bioinspired fused naphthalene diimide (NDI)–salphen–phenazine prototype light‐harvesting compound. Starting from chiral building blocks with C2 molecular symmetry, the asymmetric unit was determined by MAS NMR spectroscopy, index low‐resolution TEM diffraction data, and resolve reflection conditions, and for the first time the ability to determine the space group from reciprocal space data using this hybrid approach was shown. Transfer of molecular C2 symmetry into P2/c packing symmetry provided a connection across length scales to overcome both lack of long‐range order and missing diffraction‐phase information. Refinement with heteronuclear distance constraints confirmed the racemic P2/c packing that was scaffolded by molecular recognition of salphen zinc in a pseudo‐octahedral environment with bromide and with alkyl chains folding along the phenazine. The NDI light‐harvesting stacks ran orthogonal to the intermolecular electric dipole moment present in the solid. Finally, the orientation of flexible lamellae on an electrode surface was determined.
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Affiliation(s)
- Brijith Thomas
- Leiden Institute of Chemistry, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Jeroen Rombouts
- Vrije University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Gert T Oostergetel
- Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | | | - Francesco Buda
- Leiden Institute of Chemistry, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Koop Lammertsma
- Vrije University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Department of Chemistry, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
| | - Romano Orru
- Vrije University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Einsteinweg 55, 2333CC, Leiden, The Netherlands
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