1
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Chu J, Ejaz A, Lin KM, Joseph MR, Coraor AE, Drummond DA, Squires AH. Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01672-8. [PMID: 38750166 DOI: 10.1038/s41565-024-01672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
Multiplexed, real-time fluorescence detection at the single-molecule level can reveal the stoichiometry, dynamics and interactions of multiple molecular species in mixtures and other complex samples. However, fluorescence-based sensing is typically limited to the detection of just 3-4 colours at a time due to low signal-to-noise ratio, high spectral overlap and the need to maintain the chemical compatibility of dyes. Here we engineered a palette of several dozen composite fluorescent labels, called FRETfluors, for multiplexed spectroscopic measurements at the single-molecule level. FRETfluors are compact nanostructures constructed from three chemical components (DNA, Cy3 and Cy5) with tunable spectroscopic properties due to variations in geometry, fluorophore attachment chemistry and DNA sequence. We demonstrate FRETfluor labelling and detection for low-concentration (<100 fM) mixtures of mRNA, dsDNA and proteins using an anti-Brownian electrokinetic trap. In addition to identifying the unique spectroscopic signature of each FRETfluor, this trap differentiates FRETfluors attached to a target from unbound FRETfluors, enabling wash-free sensing. Although usually considered an undesirable complication of fluorescence, here the inherent sensitivity of fluorophores to the local physicochemical environment provides a new design axis complementary to changing the FRET efficiency. As a result, the number of distinguishable FRETfluor labels can be combinatorically increased while chemical compatibility is maintained, expanding prospects for spectroscopic multiplexing at the single-molecule level using a minimal set of chemical building blocks.
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Affiliation(s)
- Jiachong Chu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Ayesha Ejaz
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
- Interdisicplinary Scientist Training Program, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Madeline R Joseph
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Aria E Coraor
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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2
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García-Oneto TM, Moyano-Bellido C, Domínguez-Martín MA. Structure and function of the light-protective orange carotenoid protein families. Curr Res Struct Biol 2024; 7:100141. [PMID: 38736459 PMCID: PMC11087925 DOI: 10.1016/j.crstbi.2024.100141] [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: 01/14/2024] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 05/14/2024] Open
Abstract
Orange carotenoid proteins (OCPs) are unique photoreceptors that are critical for cyanobacterial photoprotection. Upon exposure to blue-green light, OCPs are activated from a stable orange form, OCPO, to an active red form, OCPR, which binds to phycobilisomes (PBSs) and performs photoprotective non-photochemical quenching (NPQ). OCPs can be divided into three main families: the most abundant and best studied OCP1, and two others, OCP2 and OCP3, which have different activation and quenching properties and are yet underexplored. Crystal structures have been acquired for the three OCP clades, providing a glimpse into the conformational underpinnings of their light-absorption and energy dissipation attributes. Recently, the structure of the PBS-OCPR complex has been obtained allowing for an unprecedented insight into the photoprotective action of OCPs. Here, we review the latest findings in the field that have substantially improved our understanding of how cyanobacteria protect themselves from the toxic consequences of excess light absorption. Furthermore, current research is applying the structure of OCPs to bio-inspired optogenetic tools, to function as carotenoid delivery devices, as well as engineering the NPQ mechanism of cyanobacteria to enhance their photosynthetic biomass production.
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Affiliation(s)
| | | | - M. Agustina Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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3
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Sauer PV, Cupellini L, Sutter M, Bondanza M, Domínguez Martin MA, Kirst H, Bína D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polívka7 T, Mennucci B, Kerfeld CA. Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. SCIENCE ADVANCES 2024; 10:eadk7535. [PMID: 38578996 PMCID: PMC10997198 DOI: 10.1126/sciadv.adk7535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.
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Affiliation(s)
- Paul V. Sauer
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - María Agustina Domínguez Martin
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henning Kirst
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Bína
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | | | - Basil J. Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Tomáš Polívka7
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Thermo Fisher Scientific, Eindhoven, Netherlands
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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4
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Assefa GT, Botha JL, van Heerden B, Kyeyune F, Krüger TPJ, Gwizdala M. ApcE plays an important role in light-induced excitation energy dissipation in the Synechocystis PCC6803 phycobilisomes. PHOTOSYNTHESIS RESEARCH 2024; 160:17-29. [PMID: 38407779 PMCID: PMC11006782 DOI: 10.1007/s11120-024-01078-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Phycobilisomes (PBs) play an important role in cyanobacterial photosynthesis. They capture light and transfer excitation energy to the photosynthetic reaction centres. PBs are also central to some photoprotective and photoregulatory mechanisms that help sustain photosynthesis under non-optimal conditions. Amongst the mechanisms involved in excitation energy dissipation that are activated in response to excessive illumination is a recently discovered light-induced mechanism that is intrinsic to PBs and has been the least studied. Here, we used single-molecule spectroscopy and developed robust data analysis methods to explore the role of a terminal emitter subunit, ApcE, in this intrinsic, light-induced mechanism. We isolated the PBs from WT Synechocystis PCC 6803 as well as from the ApcE-C190S mutant of this strain and compared the dynamics of their fluorescence emission. PBs isolated from the mutant (i.e., ApcE-C190S-PBs), despite not binding some of the red-shifted pigments in the complex, showed similar global emission dynamics to WT-PBs. However, a detailed analysis of dynamics in the core revealed that the ApcE-C190S-PBs are less likely than WT-PBs to enter quenched states under illumination but still fully capable of doing so. This result points to an important but not exclusive role of the ApcE pigments in the light-induced intrinsic excitation energy dissipation mechanism in PBs.
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Affiliation(s)
- Gonfa Tesfaye Assefa
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Joshua L Botha
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Bertus van Heerden
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
| | - Farooq Kyeyune
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Department of Physics, Faculty of Science, Kyambogo University, P.O. Box 1, Kyambogo, Kampala, Uganda
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
| | - Michal Gwizdala
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain.
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5
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Stadnichuk IN, Krasilnikov PM. Relationship between non-photochemical quenching efficiency and the energy transfer rate from phycobilisomes to photosystem II. PHOTOSYNTHESIS RESEARCH 2024; 159:177-189. [PMID: 37328680 DOI: 10.1007/s11120-023-01031-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023]
Abstract
The chromophorylated PBLcm domain of the ApcE linker protein in the cyanobacterial phycobilisome (PBS) serves as a bottleneck for Förster resonance energy transfer (FRET) from the PBS to the antennal chlorophyll of photosystem II (PS II) and as a redirection point for energy distribution to the orange protein ketocarotenoid (OCP), which is excitonically coupled to the PBLcm chromophore in the process of non-photochemical quenching (NPQ) under high light conditions. The involvement of PBLcm in the quenching process was first directly demonstrated by measuring steady-state fluorescence spectra of cyanobacterial cells at different stages of NPQ development. The time required to transfer energy from the PBLcm to the OCP is several times shorter than the time it takes to transfer energy from the PBLcm to the PS II, ensuring quenching efficiency. The data obtained provide an explanation for the different rates of PBS quenching in vivo and in vitro according to the half ratio of OCP/PBS in the cyanobacterial cell, which is tens of times lower than that realized for an effective NPQ process in solution.
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Affiliation(s)
- Igor N Stadnichuk
- K.A. Timiryazev Institute of Plant Physiology, RAS, Botanicheskaya 35, 127726, Moscow, Russia.
| | - Pavel M Krasilnikov
- Biological Faculty of M.V., Lomonosov State University, Lenin Hills 12, 119991, Moscow, Russia
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6
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Tarasashvili MV, Elbakidze K, Doborjginidze ND, Gharibashvili ND. Carbonate precipitation and nitrogen fixation in AMG (Artificial Martian Ground) by cyanobacteria. LIFE SCIENCES IN SPACE RESEARCH 2023; 37:65-77. [PMID: 37087180 DOI: 10.1016/j.lssr.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 05/03/2023]
Abstract
This article describes experiments performed to study the survival, growth, specific adaptations and bioremediation potential of certain extreme cyanobacteria strains within a simulation of the atmospheric composition, temperature and pressure expected in a future Martian greenhouse. Initial species have been obtained from Mars-analogue sites in Georgia. The results clearly demonstrate that specific biochemical adaptations allow these autotrophs to metabolize within AMG (Artificial Martian Ground) and accumulate biogenic carbon and nitrogen. These findings may thus contribute to the development of future Martian agriculture, as well as other aspects of the life-support systems at habitable Mars stations. The study shows that carbonate precipitation and nitrogen fixation, performed by cyanobacterial communities thriving within the simulated Martian greenhouse conditions, are cross-linked biological processes. At the same time, the presence of the perchlorates (at low concentrations) in the Martian ground may serve as the initial source of oxygen and, indirectly, hydrogen via photo-Fenton reactions. Various carbonates, ammonium and nitrate salts were obtained as the result of these experiments. These affect the pH, salinity and solubility of the AMG and its components, and so the AMG's scanty biogenic properties improved, which is essential for the sustainable growth of the agricultural crops. Therefore, the use of microorganisms for the biological remediation and continuous in situ fertilization of Artificial Martian Ground is possible.
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Affiliation(s)
- M V Tarasashvili
- BTU - Business and Technology University, 82 Ilia Chavchavadze Avenue, 0179, Tbilisi, Georgia.
| | - Kh Elbakidze
- BTU - Business and Technology University, 82 Ilia Chavchavadze Avenue, 0179, Tbilisi, Georgia
| | - N D Doborjginidze
- GSRA - Georgian Space Research Agency, 4 Vasil Petriashvili Street, 0179, Tbilisi, Georgia
| | - N D Gharibashvili
- GSRA - Georgian Space Research Agency, 4 Vasil Petriashvili Street, 0179, Tbilisi, Georgia; SpaceFarms Ltd, 14 Kostava Street, 0108, Tbilisi, Georgia
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7
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Brenner B, Sun C, Raymo FM, Zhang HF. Spectroscopic single-molecule localization microscopy: applications and prospective. NANO CONVERGENCE 2023; 10:14. [PMID: 36943541 PMCID: PMC10030755 DOI: 10.1186/s40580-023-00363-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/05/2023] [Indexed: 05/25/2023]
Abstract
Single-molecule localization microscopy (SMLM) breaks the optical diffraction limit by numerically localizing sparse fluorescence emitters to achieve super-resolution imaging. Spectroscopic SMLM or sSMLM further allows simultaneous spectroscopy and super-resolution imaging of fluorescence molecules. Hence, sSMLM can extract spectral features with single-molecule sensitivity, higher precision, and higher multiplexity than traditional multicolor microscopy modalities. These new capabilities enabled advanced multiplexed and functional cellular imaging applications. While sSMLM suffers from reduced spatial precision compared to conventional SMLM due to splitting photons to form spatial and spectral images, several methods have been reported to mitigate these weaknesses through innovative optical design and image processing techniques. This review summarizes the recent progress in sSMLM, its applications, and our perspective on future work.
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Affiliation(s)
- Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Françisco M Raymo
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
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8
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Golub M, Moldenhauer M, Matsarskaia O, Martel A, Grudinin S, Soloviov D, Kuklin A, Maksimov EG, Friedrich T, Pieper J. Stages of OCP-FRP Interactions in the Regulation of Photoprotection in Cyanobacteria, Part 2: Small-Angle Neutron Scattering with Partial Deuteration. J Phys Chem B 2023; 127:1901-1913. [PMID: 36815674 DOI: 10.1021/acs.jpcb.2c07182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We used small-angle neutron scattering partially coupled with size-exclusion chromatography to unravel the solution structures of two variants of the Orange Carotenoid Protein (OCP) lacking the N-terminal extension (OCP-ΔNTE) and its complex formation with the Fluorescence Recovery Protein (FRP). The dark-adapted, orange form OCP-ΔNTEO is fully photoswitchable and preferentially binds the pigment echinenone. Its complex with FRP consists of a monomeric OCP component, which closely resembles the compact structure expected for the OCP ground state, OCPO. In contrast, the pink form OCP-ΔNTEP, preferentially binding the pigment canthaxanthin, is mostly nonswitchable. The pink OCP form appears to occur as a dimer and is characterized by a separation of the N- and C-terminal domains, with the canthaxanthin embedded only into the N-terminal domain. Therefore, OCP-ΔNTEP can be viewed as a prototypical model system for the active, spectrally red-shifted state of OCP, OCPR. The dimeric structure of OCP-ΔNTEP is retained in its complex with FRP. Small-angle neutron scattering using partially deuterated OCP-FRP complexes reveals that FRP undergoes significant structural changes upon complex formation with OCP. The observed structures are assigned to individual intermediates of the OCP photocycle in the presence of FRP.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Marcus Moldenhauer
- Institute of Chemistry PC 14, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Olga Matsarskaia
- Institut Laue-Langevin, Avenue des Martyrs 71, 38042 Cedex 9 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, Avenue des Martyrs 71, 38042 Cedex 9 Grenoble, France
| | - Sergei Grudinin
- Université Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000 Grenoble, France
| | - Dmytro Soloviov
- Faculty of Physics, Adam Mickiewicz University, ul. Wieniawskiego 1, 61-712 Poznan, Poland.,Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kirova 36a, 07270 Chornobyl, Ukraine
| | - Alexander Kuklin
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia.,Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - Eugene G Maksimov
- Department of Biophysics, M. V. Lomonosov Moscow State University, Vorob'jovy Gory 1-12, 119899 Moscow, Russia
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
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9
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Structures of a phycobilisome in light-harvesting and photoprotected states. Nature 2022; 609:835-845. [PMID: 36045294 DOI: 10.1038/s41586-022-05156-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 07/27/2022] [Indexed: 11/08/2022]
Abstract
Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae1,2. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching3-6. Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34 kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60 Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties7, we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.
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10
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Carpenter W, Lavania AA, Borden JS, Oltrogge LM, Perez D, Dahlberg PD, Savage DF, Moerner WE. Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution. J Phys Chem Lett 2022; 13:4455-4462. [PMID: 35549289 PMCID: PMC9150107 DOI: 10.1021/acs.jpclett.2c00782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diffusion of biological nanoparticles in solution impedes our ability to continuously monitor individual particles and measure their physical and chemical properties. To overcome this, we previously developed the interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which uses scattering to localize a particle and applies electrokinetic forces that counteract Brownian motion, thus enabling extended observation. Here we present an improved ISABEL trap that incorporates a near-infrared scatter illumination beam and rapidly interleaves 405 and 488 nm fluorescence excitation reporter beams. With the ISABEL trap, we monitored the internal redox environment of individual carboxysomes labeled with the ratiometric redox reporter roGFP2. Carboxysomes widely vary in scattering contrast (reporting on size) and redox-dependent ratiometric fluorescence. Furthermore, we used redox sensing to explore the chemical kinetics within intact carboxysomes, where bulk measurements may contain unwanted contributions from aggregates or interfering fluorescent proteins. Overall, we demonstrate the ISABEL trap's ability to sensitively monitor nanoscale biological objects, enabling new experiments on these systems.
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Affiliation(s)
- William
B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Abhijit A. Lavania
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Julia S. Borden
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National
Accelerator Laboratory, Menlo Park, California 94025, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
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11
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Kondo T, Mutoh R, Arai S, kurisu G, Oh-oka H, Fujiyoshi S, Matsushita M. Energy transfer fluctuation observed by single-molecule spectroscopy of red-shifted bacteriochlorophyll in the homodimeric photosynthetic reaction center. J Chem Phys 2022; 156:105102. [DOI: 10.1063/5.0077290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Toru Kondo
- Department of Life Science and Technology, Tokyo Institute of Technology, Japan
| | | | - Shun Arai
- Tokyo Institute of Technology, Japan
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12
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Sielaff H, Dienerowitz F, Dienerowitz M. Single-molecule FRET combined with electrokinetic trapping reveals real-time enzyme kinetics of individual F-ATP synthases. NANOSCALE 2022; 14:2327-2336. [PMID: 35084006 DOI: 10.1039/d1nr05754e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a key technique to observe conformational changes in molecular motors and to access the details of single-molecule static and dynamic disorder during catalytic processes. However, studying freely diffusing molecules in solution is limited to a few tens of milliseconds, while surface attachment often bears the risk to restrict their natural motion. In this paper we combine smFRET and electrokinetic trapping (ABEL trap) to non-invasively hold single FOF1-ATP synthases for up to 3 s within the detection volume, thereby extending the observation time by a factor of 10 as compared to Brownian diffusion without surface attachment. In addition, we are able to monitor complete reaction cycles and to selectively trap active molecules based on their smFRET signal, thus speeding up the data acquisition process. We demonstrate the capability of our method to study the dynamics of single molecules by recording the ATP-hydrolysis driven rotation of individual FOF1-ATP synthase molecules over numerous reaction cycles and extract their kinetic rates. We argue that our method is not limited to motor proteins. Instead, it can be applied to monitor conformational changes with millisecond time resolution for a wide range of enzymes, thereby making it a versatile tool for studying protein dynamics.
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Affiliation(s)
- Hendrik Sielaff
- Department of Chemistry, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore
| | - Frank Dienerowitz
- Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Maria Dienerowitz
- Single-Molecule Microscopy Group, Universitätsklinikum Jena, Nonnenplan 2-4, 07743 Jena, Germany.
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13
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Squires A, Wang Q, Dahlberg P, Moerner WE. A bottom-up perspective on photodynamics and photoprotection in light-harvesting complexes using anti-Brownian trapping. J Chem Phys 2022; 156:070901. [DOI: 10.1063/5.0079042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Quan Wang
- Genomics, Princeton University, United States of America
| | | | - W. E. Moerner
- Department of Chemistry, Stanford University, United States of America
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14
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Navotnaya P, Sohoni S, Lloyd LT, Abdulhadi SM, Ting PC, Higgins JS, Engel GS. Annihilation of Excess Excitations along Phycocyanin Rods Precedes Downhill Flow to Allophycocyanin Cores in the Phycobilisome of Synechococcus elongatus PCC 7942. J Phys Chem B 2022; 126:23-29. [PMID: 34982932 PMCID: PMC8762654 DOI: 10.1021/acs.jpcb.1c06509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Cyanobacterial phycobilisome
complexes absorb visible sunlight
and funnel photogenerated excitons to the photosystems where charge
separation occurs. In the phycobilisome complex of Synechococcus
elongatus PCC 7942, phycocyanin protein rods that absorb
bluer wavelengths are assembled on allophycocyanin cores that absorb
redder wavelengths. This arrangement creates a natural energy gradient
toward the reaction centers of the photosystems. Here, we employ broadband
pump–probe spectroscopy to observe the fate of excess excitations
in the phycobilisome complex of this organism. We show that excess
excitons are quenched through exciton–exciton annihilation
along the phycocyanin rods prior to transfer to the allophycocyanin
cores. Our observations are especially relevant in comparison to other
antenna proteins, where exciton annihilation primarily occurs in the
lowest-energy chlorophylls. The observed effect could play a limited
photoprotective role in physiological light fluences. The exciton
decay dynamics is faster in the intact phycobilisome than in isolated
C-phycocyanin trimers studied in earlier work, confirming that this
effect is an emergent property of the complex assembly. Using the
obtained annihilation data, we calculate exciton hopping times of
2.2–6.4 ps in the phycocyanin rods. This value agrees with
earlier FRET calculations of exciton hopping times along phycocyanin
hexamers by Sauer and Scheer.
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Affiliation(s)
- Polina Navotnaya
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Siddhartha Sohoni
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lawson T Lloyd
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sami M Abdulhadi
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Po-Chieh Ting
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jacob S Higgins
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory S Engel
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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15
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Wilson A, Muzzopappa F, Kirilovsky D. Elucidation of the essential amino acids involved in the binding of the cyanobacterial Orange Carotenoid Protein to the phycobilisome. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2022; 1863:148504. [PMID: 34619092 DOI: 10.1016/j.bbabio.2021.148504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 02/06/2023]
Abstract
The Orange Carotenoid Protein (OCP) is a soluble photoactive protein involved in cyanobacterial photoprotection. It is formed by the N-terminal domain (NTD) and C-terminal (CTD) domain, which establish interactions in the orange inactive form and share a ketocarotenoid molecule. Upon exposure to intense blue light, the carotenoid molecule migrates into the NTD and the domains undergo separation. The free NTD can then interact with the phycobilisome (PBS), the extramembrane cyanobacterial antenna, and induces thermal dissipation of excess absorbed excitation energy. The OCP and PBS amino acids involved in their interactions remain undetermined. To identify the OCP amino acids essential for this interaction, we constructed several OCP mutants (23) with modified amino acids located on different NTD surfaces. We demonstrated that only the NTD surface that establishes interactions with the CTD in orange OCP is involved in the binding of OCP to PBS. All amino acids surrounding the carotenoid β1 ring in the OCPR-NTD (L51, P56, G57, N104, I151, R155, N156) are important for binding OCP to PBS. Additionally, modification of the amino acids influences OCP photoactivation and/or recovery rates, indicating that they are also involved in the translocation of the carotenoid.
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Affiliation(s)
- Adjélé Wilson
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif sur Yvette, France.
| | - Fernando Muzzopappa
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif sur Yvette, France
| | - Diana Kirilovsky
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif sur Yvette, France.
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16
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Wilson H, Wang Q. Joint Detection of Change Points in Multichannel Single-Molecule Measurements. J Phys Chem B 2021; 125:13425-13435. [PMID: 34870418 DOI: 10.1021/acs.jpcb.1c08869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recent developments in single-molecule measurement technology have expanded the capability to measure multiple parameters. These emergent modalities provide more holistic observations of complex biomolecular processes and call for new analysis methods to detect state changes in multichannel data. Here we develop an algorithm called MULLR (MUlti-channel Log-Likelihood Ratio test) to jointly identify change points in multichannel single-molecule measurements. MULLR is an extension of the popular single-channel implementation for change point detection based on a binary segmentation and log-likelihood ratio test framework. We validate the algorithm on simulated data and characterize the power of detection and false positive rate. We show that MULLR can identify change points in experimental multichannel data and naturally works with different noise statistics and time resolutions across channels. Further, we quantify the benefit of MULLR compared to single-channel analysis. We envision that the MULLR algorithm will be useful to a range of multiparameter single-molecule measurements.
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Affiliation(s)
- Hugh Wilson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, United States
| | - Quan Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, United States
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17
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State of the phycobilisome determines effective absorption cross-section of Photosystem II in Synechocystis sp. PCC 6803. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148494. [PMID: 34534546 DOI: 10.1016/j.bbabio.2021.148494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/23/2021] [Accepted: 09/07/2021] [Indexed: 11/23/2022]
Abstract
Quenching of excess excitation energy is necessary for the photoprotection of light-harvesting complexes. In cyanobacteria, quenching of phycobilisome (PBS) excitation energy is induced by the Orange Carotenoid Protein (OCP), which becomes photoactivated under high light conditions. A decrease in energy transfer efficiency from the PBSs to the reaction centers decreases photosystem II (PS II) activity. However, quantitative analysis of OCP-induced photoprotection in vivo is complicated by similar effects of both photochemical and non-photochemical quenching on the quantum yield of the PBS fluorescence overlapping with the emission of chlorophyll. In the present study, we have analyzed chlorophyll a fluorescence induction to estimate the effective cross-section of PS II and compared the effects of reversible OCP-dependent quenching of PBS fluorescence with reduction of PBS content upon nitrogen starvation or mutations of key PBS components. This approach allowed us to estimate the dependency of the rate constant of PS II primary electron acceptor reduction on the amount of PBSs in the cell. We found that OCP-dependent quenching triggered by blue light affects approximately half of PBSs coupled to PS II, indicating that under normal conditions, the concentration of OCP is not sufficient for quenching of all PBSs coupled to PS II.
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18
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Höller C, Schnoering G, Eghlidi H, Suomalainen M, Greber UF, Poulikakos D. On-chip transporting arresting and characterizing individual nano-objects in biological ionic liquids. SCIENCE ADVANCES 2021; 7:eabd8758. [PMID: 34215575 PMCID: PMC11057703 DOI: 10.1126/sciadv.abd8758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
Understanding and controlling the individual behavior of nanoscopic matter in liquids, the environment in which many such entities are functioning, is both inherently challenging and important to many natural and man-made applications. Here, we transport individual nano-objects, from an assembly in a biological ionic solution, through a nanochannel network and confine them in electrokinetic nanovalves, created by the collaborative effect of an applied ac electric field and a rationally engineered nanotopography, locally amplifying this field. The motion of so-confined fluorescent nano-objects is tracked, and its kinetics provides important information, enabling the determination of their particle diffusion coefficient, hydrodynamic radius, and electrical conductivity, which are elucidated for artificial polystyrene nanospheres and subsequently for sub-100-nm conjugated polymer nanoparticles and adenoviruses. The on-chip, individual nano-object resolution method presented here is a powerful approach to aid research and development in broad application areas such as medicine, chemistry, and biology.
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Affiliation(s)
- Christian Höller
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Sonneggstrasse 3, Zurich, Switzerland
| | - Gabriel Schnoering
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Sonneggstrasse 3, Zurich, Switzerland
| | - Hadi Eghlidi
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Sonneggstrasse 3, Zurich, Switzerland
| | - Maarit Suomalainen
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Dimos Poulikakos
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Sonneggstrasse 3, Zurich, Switzerland.
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19
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Yaroshevich IA, Maksimov EG, Sluchanko NN, Zlenko DV, Stepanov AV, Slutskaya EA, Slonimskiy YB, Botnarevskii VS, Remeeva A, Gushchin I, Kovalev K, Gordeliy VI, Shelaev IV, Gostev FE, Khakhulin D, Poddubnyy VV, Gostev TS, Cherepanov DA, Polívka T, Kloz M, Friedrich T, Paschenko VZ, Nadtochenko VA, Rubin AB, Kirpichnikov MP. Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein. Commun Biol 2021; 4:539. [PMID: 33972665 PMCID: PMC8110590 DOI: 10.1038/s42003-021-02022-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion. Yaroshevich et al. present a chemical reaction mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP). They find that photoactivation critically involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. This study suggests the role of charge-transfer states during OCP photoconversion.
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Affiliation(s)
- Igor A Yaroshevich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Eugene G Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia. .,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Zlenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey V Stepanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Slutskaya
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yury B Slonimskiy
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Viacheslav S Botnarevskii
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.,Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan V Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Fedor E Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Timofey S Gostev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Moscow, Russia
| | - Tomáš Polívka
- Institute of Physics, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Kloz
- ELI-Beamlines, Institute of Physics, Praha, Czech Republic
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC14, Berlin, Germany
| | | | - Victor A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Andrew B Rubin
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P Kirpichnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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20
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Dienerowitz M, Howard JAL, Quinn SD, Dienerowitz F, Leake MC. Single-molecule FRET dynamics of molecular motors in an ABEL trap. Methods 2021; 193:96-106. [PMID: 33571667 DOI: 10.1016/j.ymeth.2021.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Single-molecule Förster resonance energy transfer (smFRET) of molecular motors provides transformative insights into their dynamics and conformational changes both at high temporal and spatial resolution simultaneously. However, a key challenge of such FRET investigations is to observe a molecule in action for long enough without restricting its natural function. The Anti-Brownian ELectrokinetic Trap (ABEL trap) sets out to combine smFRET with molecular confinement to enable observation times of up to several seconds while removing any requirement of tethered surface attachment of the molecule in question. In addition, the ABEL trap's inherent ability to selectively capture FRET active molecules accelerates the data acquisition process. In this work we exemplify the capabilities of the ABEL trap in performing extended timescale smFRET measurements on the molecular motor Rep, which is crucial for removing protein blocks ahead of the advancing DNA replication machinery and for restarting stalled DNA replication. We are able to monitor single Rep molecules up to 6 seconds with sub-millisecond time resolution capturing multiple conformational switching events during the observation time. Here we provide a step-by-step guide for the rational design, construction and implementation of the ABEL trap for smFRET detection of Rep in vitro. We include details of how to model the electric potential at the trap site and use Hidden Markov analysis of the smFRET trajectories.
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Affiliation(s)
- Maria Dienerowitz
- Single-Molecule Microscopy Group, Universitätsklinikum Jena, Nonnenplan 2 - 4, 07743 Jena, Germany.
| | - Jamieson A L Howard
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven D Quinn
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Frank Dienerowitz
- Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Mark C Leake
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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21
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A new ultrafast energy funneling material harvests three times more diffusive solar energy for GaInP photovoltaics. Proc Natl Acad Sci U S A 2020; 117:32929-32938. [PMID: 33318220 PMCID: PMC7776598 DOI: 10.1073/pnas.2019198117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using molecular systems that harvest diffusive sunlight on large areas and funnel it onto much smaller areas of precious high-performance solar cells could pave the way to affordable high-efficiency photovoltaics. Here, we discovered important structural principles of molecules suitable to align diffusive light, the underlying ultrafast depolarization/repolarization dynamics, and a material with significantly higher light harvesting in the peak of the solar spectrum. There is no theoretical limit in using molecular networks to harvest diffusive sun photons on large areas and funnel them onto much smaller areas of highly efficient but also precious energy-converting materials. The most effective concept reported so far is based on a pool of randomly oriented, light-harvesting donor molecules that funnel all excitation quanta by ultrafast energy transfer to individual light-redirecting acceptor molecules oriented parallel to the energy converters. However, the best practical light-harvesting system could only be discovered by empirical screening of molecules that either align or not within stretched polymers and the maximum absorption wavelength of the empirical system was far away from the solar maximum. No molecular property was known explaining why certain molecules would align very effectively whereas similar molecules did not. Here, we first explore what molecular properties are responsible for a molecule to be aligned. We found a parameter derived directly from the molecular structure with a high predictive power for the alignability. In addition, we found a set of ultrafast funneling molecules that harvest three times more energy in the solar’s spectrum peak for GaInP photovoltaics. A detailed study on the ultrafast dipole moment reorientation dynamics demonstrates that refocusing of the diffusive light is based on ∼15-ps initial dipole moment depolarization followed by ∼50-ps repolarization into desired directions. This provides a detailed understanding of the molecular depolarization/repolarization processes responsible for refocusing diffusively scattered photons without violating the second law of thermodynamics.
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22
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Squires AH. Engineering improved measurement and actuation for nanoscale biophysics. Biophys Rev 2020; 12:1107-1109. [PMID: 32909236 DOI: 10.1007/s12551-020-00751-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022] Open
Abstract
This commentary profiles the research interests of my recently established research group at The University of Chicago, as well as my own research trajectory and contributions to the field of nanoscale biophysics. I describe here certain open challenges of interest that drive my group's current research efforts, along with my past efforts that have impacted these areas.
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Affiliation(s)
- Allison H Squires
- Pritzker School for Molecular Engineering, The University of Chicago, 5640 South Ellis Ave, Chicago, IL, 60637, USA.
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23
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24
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Structural dynamics in the C terminal domain homolog of orange carotenoid Protein reveals residues critical for carotenoid uptake. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148214. [DOI: 10.1016/j.bbabio.2020.148214] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/19/2020] [Accepted: 04/27/2020] [Indexed: 01/01/2023]
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25
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Maksimov EG, Protasova EA, Tsoraev GV, Yaroshevich IA, Maydykovskiy AI, Shirshin EA, Gostev TS, Jelzow A, Moldenhauer M, Slonimskiy YB, Sluchanko NN, Friedrich T. Probing of carotenoid-tryptophan hydrogen bonding dynamics in the single-tryptophan photoactive Orange Carotenoid Protein. Sci Rep 2020; 10:11729. [PMID: 32678150 PMCID: PMC7366913 DOI: 10.1038/s41598-020-68463-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/25/2020] [Indexed: 01/07/2023] Open
Abstract
The photoactive Orange Carotenoid Protein (OCP) plays a key role in cyanobacterial photoprotection. In OCP, a single non-covalently bound keto-carotenoid molecule acts as a light intensity sensor, while the protein is responsible for forming molecular contacts with the light-harvesting antenna, the fluorescence of which is quenched by OCP. Activation of this physiological interaction requires signal transduction from the photoexcited carotenoid to the protein matrix. Recent works revealed an asynchrony between conformational transitions of the carotenoid and the protein. Intrinsic tryptophan (Trp) fluorescence has provided valuable information about the protein part of OCP during its photocycle. However, wild-type OCP contains five Trp residues, which makes extraction of site-specific information impossible. In this work, we overcame this problem by characterizing the photocycle of a fully photoactive OCP variant (OCP-3FH) with only the most critical tryptophan residue (Trp-288) in place. Trp-288 is of special interest because it forms a hydrogen bond to the carotenoid's keto-oxygen to keep OCP in its dark-adapted state. Using femtosecond pump-probe fluorescence spectroscopy we analyzed the photocycle of OCP-3FH and determined the formation rate of the very first intermediate suggesting that generation of the recently discovered S* state of the carotenoid in OCP precedes the breakage of the hydrogen bonds. Therefore, following Trp fluorescence of the unique photoactive OCP-3FH variant, we identified the rate of the H-bond breakage and provided novel insights into early events accompanying photoactivation of wild-type OCP.
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Affiliation(s)
- Eugene G. Maksimov
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia ,0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Elena A. Protasova
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Georgy V. Tsoraev
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Igor A. Yaroshevich
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anton I. Maydykovskiy
- 0000 0001 2342 9668grid.14476.30Department of Quantum Electronics, Faculty of Physics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Evgeny A. Shirshin
- 0000 0001 2342 9668grid.14476.30Department of Quantum Electronics, Faculty of Physics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Timofey S. Gostev
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | - Marcus Moldenhauer
- 0000 0001 2292 8254grid.6734.6Technical University of Berlin, Institute of Chemistry PC 14, Straße des des 17. Juni 135, 10623 Berlin, Germany
| | - Yury B. Slonimskiy
- 0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Nikolai N. Sluchanko
- 0000 0001 2342 9668grid.14476.30Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia ,0000 0004 0468 2555grid.425156.1A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Thomas Friedrich
- 0000 0001 2292 8254grid.6734.6Technical University of Berlin, Institute of Chemistry PC 14, Straße des des 17. Juni 135, 10623 Berlin, Germany
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26
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Wahadoszamen M, Krüger TPJ, Ara AM, van Grondelle R, Gwizdala M. Charge transfer states in phycobilisomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148187. [PMID: 32173383 DOI: 10.1016/j.bbabio.2020.148187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/17/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
Phycobilisomes (PBs) absorb light and supply downstream photosynthetic processes with excitation energy in many cyanobacteria and algae. In response to a sudden increase in light intensity, excess excitation energy is photoprotectively dissipated in PBs by means of the orange carotenoid protein (OCP)-related mechanism or via a light-activated intrinsic decay channel. Recently, we have identified that both mechanisms are associated with far-red emission states. Here, we investigate the far-red states involved with the light-induced intrinsic mechanism by exploring the energy landscape and electro-optical properties of the pigments in PBs. While Stark spectroscopy showed that the far-red states in PBs exhibit a strong charge-transfer (CT) character at cryogenic temperatures, single molecule spectroscopy revealed that CT states should also be present at room temperature. Owing to the strong environmental sensitivity of CT states, the knowledge gained from this study may contribute to the design of a new generation of fluorescence markers.
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Affiliation(s)
- Md Wahadoszamen
- Department of Physics, University of Dhaka, Dhaka 1000, Bangladesh
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Pretoria 0023, South Africa
| | - Anjue Mane Ara
- Department of Physics, Jagannath University, Dhaka 1100, Bangladesh
| | - Rienk van Grondelle
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, the Netherlands
| | - Michal Gwizdala
- Department of Physics, University of Pretoria, Pretoria 0023, South Africa; Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, the Netherlands.
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27
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Lou W, Niedzwiedzki DM, Jiang RJ, Blankenship RE, Liu H. Binding of red form of Orange Carotenoid Protein (OCP) to phycobilisome is not sufficient for quenching. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148155. [PMID: 31935359 DOI: 10.1016/j.bbabio.2020.148155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/06/2019] [Accepted: 01/08/2020] [Indexed: 10/25/2022]
Abstract
The Orange Carotenoid Protein (OCP) is responsible for photoprotection in many cyanobacteria. Absorption of blue light drives the conversion of the orange, inactive form (OCPO) to the red, active form (OCPR). Concomitantly, the N-terminal domain (NTD) and the C-terminal domain (CTD) of OCP separate, which ultimately leads to the formation of a quenched OCPR-PBS complex. The details of the photoactivation of OCP have been intensely researched. Binding site(s) of OCPR on the PBS core have also been proposed. However, the post-binding events of the OCPR-PBS complex remain unclear. Here, we demonstrate that PBS-bound OCPR is not sufficient as a PBS excitation energy quencher. Using site-directed mutagenesis, we generated a suite of single point mutations at OCP Leucine 51 (L51) of Synechocystis 6803. Steady-state and time-resolved fluorescence analyses demonstrated that all mutant proteins are unable to quench the PBS fluorescence, owing to either failed OCP binding to PBS, or, if bound, an OCP-PBS quenching state failed to form. The SDS-PAGE and Western blot analysis support that the L51A (Alanine) mutant binds to the PBS and therefore belongs to the second category. We hypothesize that upon binding to PBS, OCPR likely reorganizes and adopts a new conformational state (OCP3rd) different than either OCPO or OCPR to allow energy quenching, depending on the cross-talk between OCPR and its PBS core-binding counterpart.
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Affiliation(s)
- Wenjing Lou
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Dariusz M Niedzwiedzki
- Center for Solar Energy and Energy Storage, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ruidong J Jiang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert E Blankenship
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Haijun Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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28
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Muzzopappa F, Kirilovsky D. Changing Color for Photoprotection: The Orange Carotenoid Protein. TRENDS IN PLANT SCIENCE 2020; 25:92-104. [PMID: 31679992 DOI: 10.1016/j.tplants.2019.09.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 05/09/2023]
Abstract
Under high irradiance, light becomes dangerous for photosynthetic organisms and they must protect themselves. Cyanobacteria have developed a simple mechanism, involving a photoactive soluble carotenoid protein, the orange carotenoid protein (OCP), which increases thermal dissipation of excess energy by interacting with the cyanobacterial antenna, the phycobilisome. Here, we summarize our knowledge of the OCP-related photoprotective mechanism, including the remarkable progress that has been achieved in recent years on OCP photoactivation and interaction with phycobilisomes, as well as with the fluorescence recovery protein, which is necessary to end photoprotection. A recently discovered unique mechanism of carotenoid transfer between soluble proteins related to OCP is also described.
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Affiliation(s)
- Fernando Muzzopappa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France.
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29
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Krasilnikov PM, Zlenko DV, Stadnichuk IN. Rates and pathways of energy migration from the phycobilisome to the photosystem II and to the orange carotenoid protein in cyanobacteria. FEBS Lett 2019; 594:1145-1154. [PMID: 31799708 DOI: 10.1002/1873-3468.13709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 02/01/2023]
Abstract
The phycobilisome (PBS) is the cyanobacterial antenna complex which transfers absorbed light energy to the photosystem II (PSII), while the excess energy is nonphotochemically quenched by interaction of the PBS with the orange carotenoid protein (OCP). Here, the molecular model of the PBS-PSII-OCP supercomplex was utilized to assess the resonance energy transfer from PBS to PSII and, using the excitonic theory, the transfer from PBS to OCP. Our estimates show that the effective energy migration from PBS to PSII is realized due to the existence of several transfer pathways from phycobilin chromophores of the PBS to the neighboring antennal chlorophyll molecules of the PSII. At the same time, the single binding site of photoactivated OCP and the PBS is sufficient to realize the quenching.
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Affiliation(s)
| | - Dmitry V Zlenko
- Faculty of Biology, M.V. Lomonosov State University, Moscow, Russia
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30
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Pishchalnikov RY, Yaroshevich IA, Slastnikova TA, Ashikhmin AA, Stepanov AV, Slutskaya EA, Friedrich T, Sluchanko NN, Maksimov EG. Structural peculiarities of keto-carotenoids in water-soluble proteins revealed by simulation of linear absorption. Phys Chem Chem Phys 2019; 21:25707-25719. [PMID: 31720635 DOI: 10.1039/c9cp04508b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To prevent irreversible damage caused by an excess of incident light, the photosynthetic machinery of many cyanobacteria uniquely utilizes the water-soluble orange carotenoid protein (OCP) containing a single keto-carotenoid molecule. This molecule is non-covalently embedded into the two OCP domains which are interconnected by a flexible linker. The phenomenon of OCP photoactivation, causing significant changes in carotenoid absorption in the orange and red form of OCP, is currently being thoroughly studied. Numerous additional spectral forms of natural and synthetic OCP-like proteins have been unearthed. The optical properties of carotenoids are strongly determined by the interaction of their electronic states with vibrational modes, the surrounding protein matrix, and the solvent. In this work, the effects of the pigment-protein interaction and vibrational relaxation in OCP were studied by computational simulation of linear absorption. Taking into account Raman spectroscopy data and applying the multimode Brownian oscillator model as well as the cumulant expansion technique, we have calculated a set of characteristic microparameters sufficient to demarcate different carotenoid states in OCP forms, using the model carotenoids spheroidene and spheroidenone in methanol/acetone solution as benchmarks. The most crucial microparameters, which determine the effect of solvent and protein environment, are the Huang-Rhys factors and the frequencies of C[double bond, length as m-dash]C and C-C stretching modes, the low-frequency mode and the FWHM due to inhomogeneous line broadening. Considering the difference of linear absorption between spheroidene and spheroidenone, which remarkably resembles the photoinduced changes of OCP absorption, and applying quantum chemical calculations, we discuss structural and functional determinants of carotenoid binding proteins.
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Affiliation(s)
- Roman Y Pishchalnikov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str., 38, 119991, Moscow, Russia.
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31
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Sansalone L, Zhang Y, Mazza MMA, Davis JL, Song KH, Captain B, Zhang HF, Raymo FM. High-Throughput Single-Molecule Spectroscopy Resolves the Conformational Isomers of BODIPY Chromophores. J Phys Chem Lett 2019; 10:6807-6812. [PMID: 31622551 PMCID: PMC7427264 DOI: 10.1021/acs.jpclett.9b02250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A borondipyrromethene (BODIPY) chromophore is connected to a benzoxazole, benzothiazole, or nitrobenzothiazole heterocycle through an olefinic bridge with trans configuration. Rotation about the two [C-C] bonds flanking the olefinic bridge occurs with fast kinetics in solution, leading to the equilibration of four conformational isomers for each compound. Ensemble spectroscopic measurements in solutions fail to distinguish the coexisting isomers. They reveal instead averaged absorption and emission bands with dependence of the latter on the excitation wavelength. Using high-throughput single-molecule spectroscopy, two main populations of single molecules with distinct spectral centroids are observed for each compound on glass substrates. Computational analyses suggest the two populations of molecules to be conformational isomers with antiperiplanar and periplanar arrangements of the BODIPY chromophores about its [C-C] bond to the olefinic bridge. Thus, statistical analysis of multiple single-molecule emission spectra can discriminate stereoisomers that would otherwise be impossible to distinguish by ensemble measurements alone.
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Affiliation(s)
- Lorenzo Sansalone
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
| | - Yang Zhang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
- Corresponding Authors ,
| | - Mercedes M. A. Mazza
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
| | - Janel L. Davis
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Ki-Hee Song
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Burjor Captain
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
| | - Hao F. Zhang
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Françisco M. Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
- Corresponding Authors ,
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32
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Golub M, Moldenhauer M, Schmitt FJ, Feoktystov A, Mändar H, Maksimov E, Friedrich T, Pieper J. Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein: Part I. Small-Angle Scattering. J Phys Chem B 2019; 123:9525-9535. [DOI: 10.1021/acs.jpcb.9b05071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Marcus Moldenhauer
- Technische Universität Berlin, Institute of Chemistry, Physical Chemistry, 10623 Berlin, Germany
| | - Franz-Josef Schmitt
- Technische Universität Berlin, Institute of Chemistry, Physical Chemistry, 10623 Berlin, Germany
| | - Artem Feoktystov
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstraße 1, 85748 Garching, Germany
| | - Hugo Mändar
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Eugene Maksimov
- M. V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry, Physical Chemistry, 10623 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
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33
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Maksimov EG, Li WJ, Protasova EA, Friedrich T, Ge B, Qin S, Sluchanko NN. Hybrid coupling of R-phycoerythrin and the orange carotenoid protein supports the FRET-based mechanism of cyanobacterial photoprotection. Biochem Biophys Res Commun 2019; 516:699-704. [DOI: 10.1016/j.bbrc.2019.06.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/18/2019] [Indexed: 12/31/2022]
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34
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Adir N, Bar-Zvi S, Harris D. The amazing phycobilisome. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148047. [PMID: 31306623 DOI: 10.1016/j.bbabio.2019.07.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/19/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Cyanobacteria and red-algae share a common light-harvesting complex which is different than all other complexes that serve as photosynthetic antennas - the Phycobilisome (PBS). The PBS is found attached to the stromal side of thylakoid membranes, filling up most of the gap between individual thylakoids. The PBS self assembles from similar homologous protein units that are soluble and contain conserved cysteine residues that covalently bind the light absorbing chromophores, linear tetra-pyrroles. Using similar construction principles, the PBS can be as large as 16.8 MDa (68×45×39nm), as small as 1.2 MDa (24 × 11.5 × 11.5 nm), and in some unique cases smaller still. The PBS can absorb light between 450 nm to 650 nm and in some cases beyond 700 nm, depending on the species, its composition and assembly. In this review, we will present new observations and structures that expand our understanding of the distinctive properties that make the PBS an amazing light harvesting system. At the end we will suggest why the PBS, for all of its excellent properties, was discarded by photosynthetic organisms that arose later in evolution such as green algae and higher plants.
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Affiliation(s)
- Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel.
| | - Shira Bar-Zvi
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Dvir Harris
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
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35
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Lou W, Wolf BM, Blankenship RE, Liu H. Cu+ Contributes to the Orange Carotenoid Protein-Related Phycobilisome Fluorescence Quenching and Photoprotection in Cyanobacteria. Biochemistry 2019; 58:3109-3115. [DOI: 10.1021/acs.biochem.9b00409] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenjing Lou
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Benjamin M. Wolf
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Robert E. Blankenship
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Haijun Liu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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36
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Squires A, Lavania AA, Dahlberg PD, Moerner WE. Interferometric Scattering Enables Fluorescence-Free Electrokinetic Trapping of Single Nanoparticles in Free Solution. NANO LETTERS 2019; 19:4112-4117. [PMID: 31117762 PMCID: PMC6604838 DOI: 10.1021/acs.nanolett.9b01514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/13/2019] [Indexed: 05/05/2023]
Abstract
Anti-Brownian traps confine single particles in free solution by closed-loop feedback forces that directly counteract Brownian motion. Extended-duration measurements on trapped objects allow detailed characterization of photophysical and transport properties as well as observation of infrequent or rare dynamics. However, this approach has been generally limited to particles that can be tracked by fluorescence emission. Here we present the Interferometric Scattering Anti-Brownian ELectrokinetic (ISABEL) trap, which uses interferometric scattering rather than fluorescence to monitor particle position. By decoupling the ability to track (and therefore trap) a particle from collection of its spectroscopic data, the ISABEL trap enables confinement and extended study of single particles that do not fluoresce, only weakly fluoresce, or exhibit intermittent fluorescence or photobleaching. This new technique significantly expands the range of nanoscale objects that may be investigated at the single-particle level in free solution.
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Affiliation(s)
- Allison
H. Squires
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Abhijit A. Lavania
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
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