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Mazal H, Wieser FF, Sandoghdar V. Insights into protein structure using cryogenic light microscopy. Biochem Soc Trans 2023; 51:2041-2059. [PMID: 38015555 PMCID: PMC10754291 DOI: 10.1042/bst20221246] [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: 08/26/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.
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Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
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Brütting M, Foerster JM, Kümmel S. Understanding Primary Charge Separation in the Heliobacterial Reaction Center. J Phys Chem Lett 2023; 14:3092-3102. [PMID: 36951395 DOI: 10.1021/acs.jpclett.3c00377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The homodimeric reaction center of heliobacteria retains features of the ancestral reaction center and can thus provide insights into the evolution of photosynthesis. Primary charge separation is expected to proceed in a two-step mechanism along either of the two reaction center branches. We reveal the first charge-separation step from first-principles calculations based on time-dependent density functional theory with an optimally tuned range-separated hybrid and ab initio Born-Oppenheimer molecular dynamics: the electron is most likely localized on the electron transfer cofactor 3 (EC3, OH-chlorophyll a), and the hole on the adjacent EC2. Including substantial parts of the surrounding protein environment into the calculations shows that a distinct structural mechanism is decisive for the relative energetic positioning of the electronic excitations: specific charged amino acids in the vicinity of EC3 lower the energy of charge-transfer excitations and thus facilitate efficient charge separation. These results are discussed considering recent experimental insights.
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Kimura A, Kitoh-Nishioka H, Aota T, Hamaguchi T, Yonekura K, Kawakami K, Shinzawa-Itoh K, Inoue-Kashino N, Ifuku K, Yamashita E, Kashino Y, Itoh S. Theoretical Model of the Far-Red-Light-Adapted Photosystem I Reaction Center of Cyanobacterium Acaryochloris marina Using Chlorophyll d and the Effect of Chlorophyll Exchange. J Phys Chem B 2022; 126:4009-4021. [PMID: 35617171 DOI: 10.1021/acs.jpcb.2c00869] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A theoretical model of the far-red-light-adapted photosystem I (PSI) reaction center (RC) complex of a cyanobacterium, Acaryochloris marina (AmPSI), was constructed based on the exciton theory and the recently identified molecular structure of AmPSI by Hamaguchi et al. (Nat. Commun., 2021, 12, 2333). A. marina performs photosynthesis under the visible to far-red light (400-750 nm), which is absorbed by chlorophyll d (Chl-d). It is in contrast to the situation of all the other oxygenic photosynthetic processes of cyanobacteria and plants, which contains chlorophyll a (Chl-a) that absorbs only 400-700 nm visible light. AmPSI contains 70 Chl-d, 1 Chl-d', 2 pheophytin a (Pheo-a), and 12 carotenoids in the currently available structure. A special pair of Chl-d/Chl-d' acts as the electron donor (P740) and two Pheo-a act as the primary electron acceptor A0 as the counterparts of P700 and Chl-a, respectively, of Chl-a-type PSIs. The exciton Hamiltonian of AmPSI was constructed considering the excitonic coupling strength and site energy shift of individual pigments using the Poisson-TrESP (P-TrESP) and charge density coupling (CDC) methods. The model was constructed to fit the experimentally measured spectra of absorption and circular dichroism (CD) spectra during downhill/uphill excitation energy transfer processes. The constructed theoretical model of AmPSI was further compared with the Chl-a-type PSI of Thermosynechococcus elongatus (TePSI), which contains only Chl-a and Chl-a'. The functional properties of AmPSI and TePSI were further examined by the in silico exchange of Chl-d by Chl-a in the models.
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Affiliation(s)
- Akihiro Kimura
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | | | - Toshimichi Aota
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 776 Sayo, Hyogo 679-5148, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 776 Sayo, Hyogo 679-5148, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 776 Sayo, Hyogo 679-5148, Japan
| | - Kyoko Shinzawa-Itoh
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | | | - Kentaro Ifuku
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Eiki Yamashita
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuhiro Kashino
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Shigeru Itoh
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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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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Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism. Proc Natl Acad Sci U S A 2021; 118:2116439118. [PMID: 34907018 DOI: 10.1073/pnas.2116439118] [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] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides were engineered to vary the electronic properties of a key tyrosine (M210) close to an essential electron transfer component via its replacement with site-specific, genetically encoded noncanonical amino acid tyrosine analogs. High fidelity of noncanonical amino acid incorporation was verified with mass spectrometry and X-ray crystallography and demonstrated that RC variants exhibit no significant structural alterations relative to wild type (WT). Ultrafast transient absorption spectroscopy indicates the excited primary electron donor, P*, decays via a ∼4-ps and a ∼20-ps population to produce the charge-separated state P+HA - in all variants. Global analysis indicates that in the ∼4-ps population, P+HA - forms through a two-step process, P*→ P+BA -→ P+HA -, while in the ∼20-ps population, it forms via a one-step P* → P+HA - superexchange mechanism. The percentage of the P* population that decays via the superexchange route varies from ∼25 to ∼45% among variants, while in WT, this percentage is ∼15%. Increases in the P* population that decays via superexchange correlate with increases in the free energy of the P+BA - intermediate caused by a given M210 tyrosine analog. This was experimentally estimated through resonance Stark spectroscopy, redox titrations, and near-infrared absorption measurements. As the most energetically perturbative variant, 3-nitrotyrosine at M210 creates an ∼110-meV increase in the free energy of P+BA - along with a dramatic diminution of the 1,030-nm transient absorption band indicative of P+BA - formation. Collectively, this work indicates the tyrosine at M210 tunes the mechanism of primary electron transfer in the RC.
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Kimura A, Kitoh-Nishioka H, Shigeta Y, Itoh S. Comparison between the Light-Harvesting Mechanisms of Type-I Photosynthetic Reaction Centers of Heliobacteria and Photosystem I: Pigment Site Energy Distribution and Exciton State. J Phys Chem B 2021; 125:3727-3738. [DOI: 10.1021/acs.jpcb.0c09400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Akihiro Kimura
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hirotaka Kitoh-Nishioka
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Graduate School of System Informatics, Kobe University, Kobe 657-8501, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Shigeru Itoh
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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