1
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Mous S, Hunter MS, Poitevin F, Boutet S, Gee LB. Macromolecular crystallography and biology at the Linac Coherent Light Source. JOURNAL OF SYNCHROTRON RADIATION 2025; 32:548-566. [PMID: 40266725 PMCID: PMC12067347 DOI: 10.1107/s1600577525002735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Accepted: 03/26/2025] [Indexed: 04/25/2025]
Abstract
The Linac Coherent Light Source (LCLS) has significantly impacted the field of biology by providing advanced capabilities for probing the structure and dynamics of biological molecules with high precision. The ultrashort coherent X-ray pulses from the LCLS have enabled ultrafast, time-resolved, serial femtosecond crystallography that is inaccessible at conventional synchrotron light sources. Since the facility's founding, scientists have captured detailed insights into biological processes at atomic resolution and fundamental timescales. The ability to observe these processes in real time and under conditions closely resembling their natural state is transforming our approach to studying biochemical mechanisms and developing new medical and energy applications. This work recounts some of the history of the LCLS, advances in biological research enabled by the LCLS, key biological areas that have been impacted and how the LCLS has helped to unravel complex biological phenomena in these fields.
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Affiliation(s)
- Sandra Mous
- Linac Coherent Light SourceSLAC National Accelerator LaboratoryMenlo ParkCA94025USA
| | - Mark S. Hunter
- Linac Coherent Light SourceSLAC National Accelerator LaboratoryMenlo ParkCA94025USA
| | - Frédéric Poitevin
- Linac Coherent Light SourceSLAC National Accelerator LaboratoryMenlo ParkCA94025USA
| | - Sébastien Boutet
- Linac Coherent Light SourceSLAC National Accelerator LaboratoryMenlo ParkCA94025USA
| | - Leland B. Gee
- Linac Coherent Light SourceSLAC National Accelerator LaboratoryMenlo ParkCA94025USA
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2
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Bosman R, Ortolani G, Ghosh S, James D, Norder P, Hammarin G, Úlfarsdóttir TB, Ostojić L, Weinert T, Dworkowski F, Tomizaki T, Standfuss J, Brändén G, Neutze R. Structural basis for the prolonged photocycle of sensory rhodopsin II revealed by serial synchrotron crystallography. Nat Commun 2025; 16:3460. [PMID: 40216733 PMCID: PMC11992208 DOI: 10.1038/s41467-025-58263-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/15/2025] [Indexed: 04/14/2025] Open
Abstract
Microbial rhodopsins form a diverse family of light-sensitive seven-transmembrane helix retinal proteins that function as active proton or ion pumps, passive light-gated ion channels, and photosensors. To understand how light-sensing in archaea is initiated by sensory rhodopsins, we perform serial synchrotron X-ray crystallography (SSX) studies of light induced conformational changes in sensory rhodopsin II (NpSRII) from the archaea Natronomonas pharaonis, both collecting time-resolved SSX data and collecting SSX data during continuous illumination. Comparing light-induced electron density changes in NpSRII with those reported for bacteriorhodopsin (bR) reveals several common light-induced structural perturbations. Unlike bR, however, helix G of NpSRII does not unwind near the conserved lysine residue to which retinal is covalently bound and therefore transient water molecule binding sites do not arise immediately to the cytoplasmic side of retinal. These structural differences prolong the duration of the NpSRII photocycle relative to bR, allowing time for the light-initiated sensory signal to be amplified.
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Affiliation(s)
- Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Daniel James
- Laboratory of Biomolecular Research, Center for Life Sciences, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Per Norder
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | | | - Lucija Ostojić
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Center for Life Sciences, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Florian Dworkowski
- Laboratory of Femtochemistry, Center for Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Takashi Tomizaki
- Laboratory of Macromolecules and Bioimaging, Center for Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Center for Life Sciences, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
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3
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Avelar M, Coppola C, d’Ettorre A, Ienco A, Parisi ML, Basosi R, Santucci A, Olivucci M, Sinicropi A. In Silico Study of a Bacteriorhodopsin/TiO 2 Hybrid System at the Molecular Level. J Chem Theory Comput 2025; 21:3231-3245. [PMID: 40037620 PMCID: PMC11948329 DOI: 10.1021/acs.jctc.4c01370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Revised: 01/27/2025] [Accepted: 02/07/2025] [Indexed: 03/06/2025]
Abstract
Bacteriorhodopsin (bR) is a light-harvesting membrane protein that represents a promising sensitizer of TiO2 for photovoltaic and photoelectrochemical devices. However, despite numerous experimental studies, the molecular-level understanding of the bR/TiO2 hybrid system is still unsatisfactory. In this contribution, we report the construction and analysis of an atomistic model of such a system. To do so, both steered molecular dynamics-molecular dynamics and quantum mechanics/molecular mechanics computations are applied to four different bR orientations on the anatase TiO2 surface. The resulting bR/TiO2 models are then used to compute the light absorption maxima changes relative to those of bR. We show that all four models reproduce the experimentally observed blue-shift value induced by bR binding on TiO2 and could be used to study the binding and binding-induced protein modifications. We conclude that the constructed models could provide a basis for future studies aiming to simulate the complex long-range electron transfer mechanism in bR/TiO2-based solar energy conversion devices as well as in engineering bR to achieve enhanced efficiencies.
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Affiliation(s)
- Mayra Avelar
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Carmen Coppola
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi
a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Alessio d’Ettorre
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Andrea Ienco
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
| | - Maria Laura Parisi
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi
a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Riccardo Basosi
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi
a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Annalisa Santucci
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Massimo Olivucci
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Department
of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Adalgisa Sinicropi
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi
a Grande Interfase, 50019 Sesto Fiorentino, Italy
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4
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Wang Z, Chen Y, Jiang J, Zhao X, Liu W. Mapping photoisomerization dynamics on a three-state model potential energy surface in bacteriorhodopsin using femtosecond stimulated Raman spectroscopy. Chem Sci 2025; 16:3713-3719. [PMID: 39886431 PMCID: PMC11775652 DOI: 10.1039/d4sc07540d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 11/19/2024] [Indexed: 02/01/2025] Open
Abstract
The process of proton translocation in Halobacterium salinarum, triggered by light, is powered by the photoisomerization of all-trans-retinal in bacteriorhodopsin (bR). The primary events in bR involving rapid structural changes upon light absorption occur within subpicoseconds to picoseconds. While the three-state model has received extensive support in describing the primary events between the H and K states, precise characterization of each excited state in the three-state model during photoisomerization remains elusive. In this study, we investigate the ultrafast structural dynamics of all-trans-retinal in bR using femtosecond stimulated Raman spectroscopy. We report Raman modes at 1820 cm-1 which arise from C[double bond, length as m-dash]C stretch vibronic coupling and provide direct experimental evidence for the involvement of the I and J states with 2A- g symmetric character in the three-state model. The detection of the C[double bond, length as m-dash]C vibronic coupling mode, C[double bond, length as m-dash]N stretching mode (1700 cm-1), and hydrogen out-of-plane (HOOP) mode (954 cm-1) further supports the three-state model that elucidates the initial charge translocation along the conjugated chain accompanied by trans-to-cis photoisomerization dynamics through H(1B+ u) → I(2A- g) → J(2A- g) → K(13-cis ground state) transitions in all-trans-retinal in bR.
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Affiliation(s)
- Ziyu Wang
- School of Physical Science and Technology, ShanghaiTech University Shanghai 201210 China
| | - Yu Chen
- School of Physical Science and Technology, ShanghaiTech University Shanghai 201210 China
| | - Jiaming Jiang
- School of Physical Science and Technology, ShanghaiTech University Shanghai 201210 China
| | - Xin Zhao
- Department of Physics, East China Normal University Shanghai 200062 P. R. China
| | - Weimin Liu
- School of Physical Science and Technology, ShanghaiTech University Shanghai 201210 China
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5
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Trujillo J, Fung R, Shankar MK, Schwander P, Hosseinizadeh A. Filling data analysis gaps in time-resolved crystallography by machine learning. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2025; 12:014101. [PMID: 39868355 PMCID: PMC11758283 DOI: 10.1063/4.0000280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 12/18/2024] [Indexed: 01/28/2025]
Abstract
There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural changes in proteins. Nevertheless, this technique comes with some limitations. One major challenge is the quality of data from TR-SFX measurements, which often faces issues like data sparsity, partial recording of Bragg reflections, timing errors, and pixel noise. To overcome these difficulties, conventionally, large volumes of data are collected and grouped into a few temporal bins. The data in each bin are then averaged and paired with the mean of their corresponding jittered timestamps. This procedure provides one structure per bin, resulting in a limited number of averaged structures for the entire time interval spanned by the experiment. Therefore, the information on ultrafast structural dynamics at high temporal resolution is lost. This has initiated research for advanced methods of analyzing experimental TR-SFX data beyond the standard binning and averaging method. To address this problem, we use a machine learning algorithm called Nonlinear Laplacian Spectral Analysis (NLSA), which has emerged as a promising technique for studying the dynamics of complex systems. In this work, we demonstrate the power of this algorithm using synthetic x-ray diffraction snapshots from a protein with significant data incompleteness, timing uncertainties, and noise. Our study confirms that NLSA is a suitable approach that effectively mitigates the effects of these artifacts in TR-SFX data and recovers accurate structural dynamics information hidden in such data.
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Affiliation(s)
- Justin Trujillo
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, Wisconsin 53211, USA
| | - Russell Fung
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, Wisconsin 53211, USA
| | - Madan Kumar Shankar
- Department of Chemistry-BMC Biochemistry, Uppsala University, Husargatan 3, Uppsala 75237, Sweden
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, Wisconsin 53211, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, Wisconsin 53211, USA
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6
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Bertrand Q, Nogly P, Nango E, Kekilli D, Khusainov G, Furrer A, James D, Dworkowski F, Skopintsev P, Mous S, Martiel I, Börjesson P, Ortolani G, Huang CY, Kepa M, Ozerov D, Brünle S, Panneels V, Tanaka T, Tanaka R, Tono K, Owada S, Johnson PJM, Nass K, Knopp G, Cirelli C, Milne C, Schertler G, Iwata S, Neutze R, Weinert T, Standfuss J. Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate. Nat Commun 2024; 15:10278. [PMID: 39604356 PMCID: PMC11603225 DOI: 10.1038/s41467-024-54422-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 11/11/2024] [Indexed: 11/29/2024] Open
Abstract
Time-resolved serial crystallography at X-ray Free Electron Lasers offers the opportunity to observe ultrafast photochemical reactions at the atomic level. The technique has yielded exciting molecular insights into various biological processes including light sensing and photochemical energy conversion. However, to achieve sufficient levels of activation within an optically dense crystal, high laser power densities are often used, which has led to an ongoing debate to which extent photodamage may compromise interpretation of the results. Here we compare time-resolved serial crystallographic data of the bacteriorhodopsin K-intermediate collected at laser power densities ranging from 0.04 to 2493 GW/cm2 and follow energy dissipation of the absorbed photons logarithmically from picoseconds to milliseconds. Although the effects of high laser power densities on the overall structure are small, in the upper excitation range we observe significant changes in retinal conformation and increased heating of the functionally critical counterion cluster. We compare light-activation within crystals to that in solution and discuss the impact of the observed changes on bacteriorhodopsin biology.
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Affiliation(s)
- Quentin Bertrand
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Przemyslaw Nogly
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Eriko Nango
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, Japan
| | - Demet Kekilli
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Georgii Khusainov
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | | | - Petr Skopintsev
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Sandra Mous
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Per Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, Sweden
| | - Chia-Ying Huang
- Photon Science Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Michal Kepa
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Dmitry Ozerov
- Photon Science Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Valerie Panneels
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Tomoyuki Tanaka
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Rie Tanaka
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Shigeki Owada
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | | | - Karol Nass
- Photon Science Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Gregor Knopp
- Photon Science Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Christopher Milne
- Photon Science Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, Japan
- Japan Science and Technology Agency (JST)-Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, Sweden
| | - Tobias Weinert
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.
| | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.
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7
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Aoyama M, Katayama K, Kandori H. Unique hydrogen-bonding network in a viral channelrhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149148. [PMID: 38906314 DOI: 10.1016/j.bbabio.2024.149148] [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: 03/15/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
Channelrhodopsins (CRs) are used as key tools in optogenetics, and novel CRs, either found from nature or engineered by mutation, have greatly contributed to the development of optogenetics. Recently CRs were discovered from viruses, and crystal structure of a viral CR, OLPVR1, reported a very similar water-containing hydrogen-bonding network near the retinal Schiff base to that of a light-driven proton-pump bacteriorhodopsin (BR). In both OLPVR1 and BR, nearly planar pentagonal cluster structures are comprised of five oxygen atoms, three oxygens from water molecules and two oxygens from the Schiff base counterions. The planar pentagonal cluster stabilizes a quadrupole, two positive charges at the Schiff base and an arginine, and two negative charges at the counterions, and thus plays important roles in light-gated channel function of OLPVR1 and light-driven proton pump function of BR. Despite similar pentagonal cluster structures, present FTIR analysis revealed different hydrogen-bonding networks between OLPVR1 and BR. The hydrogen bond between the protonated Schiff base and a water is stronger in OLPVR1 than in BR, and internal water molecules donate hydrogen bonds much weaker in OLPVR1 than in BR. In OLPVR1, the bridged water molecule between the Schiff base and counterions forms hydrogen bonds to D76 and D200 equally, while the hydrogen-bonding interaction is much stronger to D85 than to D212 in BR. The present interpretation is supported by the mutation results, where D76 and D200 equally work as the Schiff base counterions in OLPVR1, but D85 is the primary counterion in BR. This work reports highly sensitive hydrogen-bonding network in the Schiff base region, which would be closely related to each function through light-induced alterations of the network.
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Affiliation(s)
- Mako Aoyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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8
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Smitienko O, Feldman T, Shelaev I, Gostev F, Aybush A, Cherepanov D, Nadtochenko V, Ostrovsky M. Reversible Photochromic Reactions of Bacteriorhodopsin from Halobacterium salinarum at Femto- and Picosecond Times. Molecules 2024; 29:4847. [PMID: 39459214 PMCID: PMC11510181 DOI: 10.3390/molecules29204847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 10/11/2024] [Accepted: 10/11/2024] [Indexed: 10/28/2024] Open
Abstract
The operation of bacteriorhodopsin (BR) from the archaeon Halobacterium salinarum is based on the photochromic reaction of isomerization of the chromophore group (the retinal protonated Schiff base, RPSB) from the all-trans to the 13-cis form. The ultrafast dynamics of the reverse 13-cis → all-trans photoreaction was studied using femtosecond transient absorption spectroscopy in comparison with the forward photoreaction. The forward photoreaction was initiated by photoexcitation of BR by pulse I (540 nm). The reverse photoreaction was initiated by photoexcitation of the product K590 at an early stage of its formation (5 ps) by pulse II (660 nm). The conversion of the excited K590 to the ground state proceeds at times of 0.19, 1.1, and 16 ps with the relative contributions of ~20/60/20, respectively. All these decay channels lead to the formation of the initial state of BR as a product with a quantum yield of ~1. This state is preceded by vibrationally excited intermediates, the relaxation of which occurs in the 16 ps time range. Likely, the heterogeneity of the excited state of K590 is determined by the heterogeneity of its chromophore center. The forward photoreaction includes two components-0.52 and 3.5 ps, with the relative contributions of 91/9, respectively. The reverse photoreaction initiated from K590 proceeds more efficiently in the conical intersection (CI) region but on the whole at a lower rate compared to the forward photoreaction, due to significant heterogeneity of the potential energy surface.
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Affiliation(s)
- Olga Smitienko
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygin St., 4, Moscow 119334, Russia; (T.F.); (M.O.)
| | - Tatyana Feldman
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygin St., 4, Moscow 119334, Russia; (T.F.); (M.O.)
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia;
| | - Ivan Shelaev
- Moscow Center for Advanced Studies, Kulakova Str. 20, Moscow 123592, Russia; (I.S.); (F.G.)
- N.N. Semenov Federal Research Center for Chemical Physics of the Russian Academy of Sciences, Kosygin St., 4, Moscow 119991, Russia
| | - Fedor Gostev
- Moscow Center for Advanced Studies, Kulakova Str. 20, Moscow 123592, Russia; (I.S.); (F.G.)
- N.N. Semenov Federal Research Center for Chemical Physics of the Russian Academy of Sciences, Kosygin St., 4, Moscow 119991, Russia
| | - Arseniy Aybush
- Moscow Center for Advanced Studies, Kulakova Str. 20, Moscow 123592, Russia; (I.S.); (F.G.)
- N.N. Semenov Federal Research Center for Chemical Physics of the Russian Academy of Sciences, Kosygin St., 4, Moscow 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia
| | - Dmitry Cherepanov
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia;
- Moscow Center for Advanced Studies, Kulakova Str. 20, Moscow 123592, Russia; (I.S.); (F.G.)
- N.N. Semenov Federal Research Center for Chemical Physics of the Russian Academy of Sciences, Kosygin St., 4, Moscow 119991, Russia
| | - Victor Nadtochenko
- Moscow Center for Advanced Studies, Kulakova Str. 20, Moscow 123592, Russia; (I.S.); (F.G.)
- N.N. Semenov Federal Research Center for Chemical Physics of the Russian Academy of Sciences, Kosygin St., 4, Moscow 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia
| | - Mikhail Ostrovsky
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygin St., 4, Moscow 119334, Russia; (T.F.); (M.O.)
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia;
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9
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Hutchison CM, Perrett S, van Thor JJ. XFEL Beamline Optical Instrumentation for Ultrafast Science. J Phys Chem B 2024; 128:8855-8868. [PMID: 39087627 PMCID: PMC11421085 DOI: 10.1021/acs.jpcb.4c01492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
Free electron lasers operating in the soft and hard X-ray regime provide capabilities for ultrafast science in many areas, including X-ray spectroscopy, diffractive imaging, solution and material scattering, and X-ray crystallography. Ultrafast time-resolved applications in the picosecond, femtosecond, and attosecond regimes are often possible using single-shot experimental configurations. Aside from X-ray pump and X-ray probe measurements, all other types of ultrafast experiments require the synchronized operation of pulsed laser excitation for resonant or nonresonant pumping. This Perspective focuses on the opportunities for the optical control of structural dynamics by applying techniques from nonlinear spectroscopy to ultrafast X-ray experiments. This typically requires the synthesis of two or more optical pulses with full control of pulse and interpulse parameters. To this end, full characterization of the femtosecond optical pulses is also highly desirable. It has recently been shown that two-color and two-pulse femtosecond excitation of fluorescent protein crystals allowed a Tannor-Rice coherent control experiment, performed under characterized conditions. Pulse shaping and the ability to synthesize multicolor and multipulse conditions are highly desirable and would enable XFEL facilities to offer capabilities for structural dynamics. This Perspective will give a summary of examples of the types of experiments that could be achieved, and it will additionally summarize the laser, pulse shaping, and characterization that would be recommended as standard equipment for time-resolved XFEL beamlines, with an emphasis on ultrafast time-resolved serial femtosecond crystallography.
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Affiliation(s)
- Christopher
D. M. Hutchison
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
| | - Samuel Perrett
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
| | - Jasper J. van Thor
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
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10
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Padula D. Discriminating Clockwise and Counterclockwise Photoisomerization Paths in Achiral Photoswitches by Excited-State Electronic Circular Dichroism. J Phys Chem B 2024; 128:8303-8312. [PMID: 39171863 DOI: 10.1021/acs.jpcb.4c02384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Despite the numerous investigations of photoisomerization reactions from both the computational and experimental points of view, even in complex environments, to date there is no direct demonstration of the direction of rotation of the retinal chromophore, initiating the vision process in several organisms, occurring upon light irradiation. In the literature, many proposals have been formulated to shed light on the details of this process, most of which are extracted from semiclassical simulations. Although high hopes are held in the development of time-resolved X-ray spectroscopy, I argue in this work that simpler but less known techniques can be used to unravel the details of this fascinating photochemical process. In fact, chiroptical spectroscopy would unambiguously prove the direction of the rotatory motion of the chromophore during the photoisomerization process by probing excited state chirality, a piece of information that, so far, has been exclusively extracted from atomistic simulations. I demonstrate this statement by computing the expected chiroptical response along photoisomerization pathways for several models of the retinal chromophores that are found in nature bound to rhodopsins, including nuclear ensemble spectra from semiclassical dynamics simulations, that can be compared with time-resolved experiments.
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Affiliation(s)
- Daniele Padula
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, Siena 53100, Italy
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11
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Joshi K, Bhuyan AK. Glycerol-slaved 1H- 1H NMR cross-relaxation in quasi-native lysozyme. Biophys Chem 2024; 312:107286. [PMID: 38964115 DOI: 10.1016/j.bpc.2024.107286] [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: 05/11/2024] [Revised: 06/14/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
1H-1H nuclear cross-relaxation experiments have been carried out with lysozyme in variable glycerol viscosity to study intramolecular motion, self-diffusion, and isotropic rigid-body rotational tumbling at 298 K, pH 3.8. Dynamics of intramolecular 1H-1H cross-relaxation rates, the increase in internuclear spatial distances, and lateral and rotational diffusion coefficients all show fractional viscosity dependence with a power law exponent κ in the 0.17-0.83 range. The diffusion coefficient of glycerol Ds with the bulk viscosity itself is non-Stokesian, having a fractional viscosity dependence on the medium viscosity (Ds ∼ η-κ, κ ≈ 0.71). The concurrence and close similarity of the fractional viscosity dependence of glycerol diffusion on the one hand, and diffusion and intramolecular cross-relaxation rates of the protein on the other lead to infer that relaxation of glycerol slaves protein relaxations. Glycerol-transformed native lysozyme to a quasi-native state does not affect the conclusion that both global and internal fluctuations are slaved to glycerol relaxation.
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Affiliation(s)
- Kirthi Joshi
- School of Chemistry, University of Hyderabad, Hyderabad 50046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 50046, India.
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12
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Gotthard G, Flores-Ibarra A, Carrillo M, Kepa MW, Mason TJ, Stegmann DP, Olasz B, Pachota M, Dworkowski F, Ozerov D, Pedrini BF, Padeste C, Beale JH, Nogly P. Fixed-target pump-probe SFX: eliminating the scourge of light contamination. IUCRJ 2024; 11:749-761. [PMID: 38980142 PMCID: PMC11364036 DOI: 10.1107/s2052252524005591] [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: 12/08/2023] [Accepted: 06/11/2024] [Indexed: 07/10/2024]
Abstract
X-ray free-electron laser (XFEL) light sources have enabled the rapid growth of time-resolved structural experiments, which provide crucial information on the function of macromolecules and their mechanisms. Here, the aim was to commission the SwissMX fixed-target sample-delivery system at the SwissFEL Cristallina experimental station using the PSI-developed micro-structured polymer (MISP) chip for pump-probe time-resolved experiments. To characterize the system, crystals of the light-sensitive protein light-oxygen-voltage domain 1 (LOV1) from Chlamydomonas reinhardtii were used. Using different experimental settings, the accidental illumination, referred to as light contamination, of crystals mounted in wells adjacent to those illuminated by the pump laser was examined. It was crucial to control the light scattering from and through the solid supports otherwise significant contamination occurred. However, the results here show that the opaque MISP chips are suitable for defined pump-probe studies of a light-sensitive protein. The experiment also probed the sub-millisecond structural dynamics of LOV1 and indicated that at Δt = 10 µs a covalent thioether bond is established between reactive Cys57 and its flavin mononucleotide cofactor. This experiment validates the crystals to be suitable for in-depth follow-up studies of this still poorly understood signal-transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared with the more common high-viscosity extrusion-based delivery system. This development creates the prospect of an increase in XFEL project throughput for the field.
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Affiliation(s)
- Guillaume Gotthard
- Institute of Molecular Biology and BiophysicsETH ZurichRämistrasse 1018092ZürichSwitzerland
- Laboratory of Biomolecular ResearchPaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
- Swiss Light SourcePaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityGronostajowa 730-380KrakowPoland
| | - Melissa Carrillo
- Laboratory of Nanoscale BiologyPaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Michal W. Kepa
- Laboratory of Biomolecular ResearchPaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Thomas J. Mason
- Laboratory of Biomolecular ResearchPaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
- Swiss Light SourcePaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Dennis P. Stegmann
- Swiss Light SourcePaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityGronostajowa 730-380KrakowPoland
| | - Magdalena Pachota
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityGronostajowa 730-380KrakowPoland
| | - Florian Dworkowski
- Laboratory for Synchrotron Radiation and FemtochemistryPaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Dmitry Ozerov
- Science IT Infrastructure and ServicesPaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Bill F. Pedrini
- Laboratory for X-ray Nanoscience and TechnologiesPaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Celestino Padeste
- Laboratory of Nanoscale BiologyPaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - John H. Beale
- Swiss Light SourcePaul Scherrer InstitutForschungsstrasse 1115232VilligenSwitzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and BiophysicsETH ZurichRämistrasse 1018092ZürichSwitzerland
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityGronostajowa 730-380KrakowPoland
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13
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Gotthard G, Mous S, Weinert T, Maia RNA, James D, Dworkowski F, Gashi D, Furrer A, Ozerov D, Panepucci E, Wang M, Schertler GFX, Heberle J, Standfuss J, Nogly P. Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography. IUCRJ 2024; 11:792-808. [PMID: 39037420 PMCID: PMC11364019 DOI: 10.1107/s2052252524005608] [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: 10/30/2023] [Accepted: 06/11/2024] [Indexed: 07/23/2024]
Abstract
Light-oxygen-voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.
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Affiliation(s)
- Guillaume Gotthard
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Raiza Nara Antonelli Maia
- Experimental Molecular Biophysics, Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Daniel James
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Florian Dworkowski
- Macromolecular Crystallography, Swiss Light SourcePaul Scherrer Institute5232Villigen PSISwitzerland
| | - Dardan Gashi
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
- Laboratory of Femtochemistry, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Dmitry Ozerov
- Science ITPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Ezequiel Panepucci
- Laboratory for Macromolecules and Bioimaging, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Meitian Wang
- Laboratory for Macromolecules and Bioimaging, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
- Department of BiologyETH Zürich8093ZürichSwitzerland
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian University in Kraków30-387KrakówPoland
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14
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Henkel A, Oberthür D. A snapshot love story: what serial crystallography has done and will do for us. Acta Crystallogr D Struct Biol 2024; 80:563-579. [PMID: 38984902 PMCID: PMC11301758 DOI: 10.1107/s2059798324005588] [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: 02/29/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
Serial crystallography, born from groundbreaking experiments at the Linac Coherent Light Source in 2009, has evolved into a pivotal technique in structural biology. Initially pioneered at X-ray free-electron laser facilities, it has now expanded to synchrotron-radiation facilities globally, with dedicated experimental stations enhancing its accessibility. This review gives an overview of current developments in serial crystallography, emphasizing recent results in time-resolved crystallography, and discussing challenges and shortcomings.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFELDeutsches Elektronen-Synchrotron DESYNotkestr. 8522607HamburgGermany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFELDeutsches Elektronen-Synchrotron DESYNotkestr. 8522607HamburgGermany
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15
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Ren Z, Yang X. Deconvolution of dynamic heterogeneity in protein structure. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:041302. [PMID: 39165899 PMCID: PMC11335360 DOI: 10.1063/4.0000261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/30/2024] [Indexed: 08/22/2024]
Abstract
Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.
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Affiliation(s)
- Zhong Ren
- Authors to whom correspondence should be addressed: and
| | - Xiaojing Yang
- Authors to whom correspondence should be addressed: and
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16
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Wijesiri K, Gascón JA. Structural Models of the First Molecular Events in the Heliorhodopsin Photocycle. J Phys Chem B 2024; 128:5966-5972. [PMID: 38877606 DOI: 10.1021/acs.jpcb.4c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Retinylidene conformations and rearrangements of the hydrogen-bond network in the vicinity of the protonated Schiff base (PSB) play a key role in the proton transfer process in the Heliorhodopsin photocycle. Photoisomerization of the retinylidene chromophore and the formation of photoproducts corresponding to the early intermediates were modeled using a combination of molecular dynamics simulations and quantum mechanical/molecular mechanics calculations. The resulting structures were refined, and the respective excitation energies were calculated. Aided by metadynamics simulations, we constructed a photoisomerized intermediate where the 13-cis retinylidene chromophore is rotated about a parallel pair of double bonds at C13=C14 and C15=NZ double bonds. We demonstrate how the deprotonation of the Schiff base and the concomitant protonation of the Glu107 counterion are only favored because of these rearrangements.
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Affiliation(s)
- Kithmini Wijesiri
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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17
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Baxter J, Hutchison CD, Fadini A, Maghlaoui K, Cordon-Preciado V, Morgan RML, Agthe M, Horrell S, Tellkamp F, Mehrabi P, Pfeifer Y, Müller-Werkmeister HM, von Stetten D, Pearson AR, van Thor JJ. Power Density Titration of Reversible Photoisomerization of a Fluorescent Protein Chromophore in the Presence of Thermally Driven Barrier Crossing Shown by Quantitative Millisecond Serial Synchrotron X-ray Crystallography. J Am Chem Soc 2024; 146:16394-16403. [PMID: 38848551 PMCID: PMC11191680 DOI: 10.1021/jacs.3c12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
We present millisecond quantitative serial X-ray crystallography at 1.7 Å resolution demonstrating precise optical control of reversible population transfer from Trans-Cis and Cis-Trans photoisomerization of a reversibly switchable fluorescent protein, rsKiiro. Quantitative results from the analysis of electron density differences, extrapolated structure factors, and occupancy refinements are shown to correspond to optical measurements of photoinduced population transfer and have sensitivity to a few percent in concentration differences. Millisecond time-resolved concentration differences are precisely and reversibly controlled through intense continuous wave laser illuminations at 405 and 473 nm for the Trans-to-Cis and Cis-to-Trans reactions, respectively, while the X-ray crystallographic measurement and laser illumination of the metastable Trans chromophore conformation causes partial thermally driven reconversion across a 91.5 kJ/mol thermal barrier from which a temperature jump between 112 and 128 K is extracted.
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Affiliation(s)
- James
M. Baxter
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | | | - Alisia Fadini
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Karim Maghlaoui
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | | | - R. Marc L. Morgan
- Center
for Structural Biology, Imperial College
London, London SW7 2AZ, U.K.
| | - Michael Agthe
- European
Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Sam Horrell
- Department
of Physics, Center for Free-Electron Laser Science, Institute for
Nanostructure and Solid State Physics, University
of Hamburg, Hamburg 22607, Germany
| | - Friedjof Tellkamp
- Scientific
Support Unit Machine Physics, Max-Planck-Institute
for Structure and Dynamics of Matter, Hamburg 22761, Germany
| | - Pedram Mehrabi
- Max
Planck Institute for the Structure and Dynamics of Matter, CFEL, Hamburg 22607, Germany
| | - Yannik Pfeifer
- Institute
of Chemistry—Physical Chemistry, University of Potsdam, Potsdam 14469, Germany
| | | | - David von Stetten
- European
Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Arwen R. Pearson
- Institute
for Nanostructure and Solid State Physics & The Hamburg Centre
for Ultrafast Imaging, HARBOR, Universität
Hamburg, Hamburg 22607, Germany
| | - Jasper J. van Thor
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
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18
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Heyne K, Haacke S, Miller RJD. Watching atomically resolved structural dynamics-Blinded by the light. Structure 2024; 32:650-651. [PMID: 38848681 DOI: 10.1016/j.str.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
In a recent issue of Nature, Barends et al.1 studied the photodissociation of carboxymyoglobin with ultrafast laser pump-probe serial femtosecond crystallography experiments. They observed significant differences in heme protein structural dynamics for biologically relevant 1-photon excitation relative to high excitation leading to the absorption of several photons per heme.
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Affiliation(s)
- Karsten Heyne
- Department of Physics, Free University, Berlin, 14195 Berlin, Germany
| | - Stefan Haacke
- Université de Strasbourg-CNRS, IPCMS, 67034 Strasbourg, France
| | - R J Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON M5S 3H6, Canada.
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19
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Lee Y, Oang KY, Kim D, Ihee H. A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:031301. [PMID: 38706888 PMCID: PMC11065455 DOI: 10.1063/4.0000249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.
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Affiliation(s)
| | - Key Young Oang
- Radiation Center for Ultrafast Science, Korea Atomic Energy Research Institute (KAERI), Daejeon 34057, South Korea
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20
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Kaziannis S, Broser M, van Stokkum IHM, Dostal J, Busse W, Munhoven A, Bernardo C, Kloz M, Hegemann P, Kennis JTM. Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction. Proc Natl Acad Sci U S A 2024; 121:e2318996121. [PMID: 38478688 PMCID: PMC10962995 DOI: 10.1073/pnas.2318996121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable P540 state with an unusual 11-cis RSB. The primary photoproduct P682 corresponds to a mixture of highly distorted 11-cis and 13-cis RSB directly formed from the excited state in 1.4 ps. P673 evolves from P682 in 500 ps and contains highly distorted 13-cis RSB, indicating that the 11-cis fraction in P682 converts to 13-cis. Next, P673 establishes an equilibrium with P595 in 1.2 µs, during which RSB converts to 11-cis and then further proceeds to P560 in 48 µs and P540 in 1.0 ms while remaining 11-cis. Hence, extensive isomeric switching occurs on the early ground state potential energy surface (PES) on the hundreds of ps to µs timescale before finally settling on a metastable 11-cis photoproduct. We propose that P682 and P673 are trapped high up on the ground-state PES after passing through either of two closely located conical intersections that result in 11-cis and 13-cis RSB. Co-rotation of C11=C12 and C13=C14 bonds results in a constricted conformational landscape that allows thermal switching between 11-cis and 13-cis species of highly strained RSB chromophores. Protein relaxation may release RSB strain, allowing it to evolve to a stable 11-cis isomeric configuration in microseconds.
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Affiliation(s)
- Spyridon Kaziannis
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
- Department of Physics, University of Ioannina, IoanninaGr-45110, Greece
| | - Matthias Broser
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Ivo H. M. van Stokkum
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Jakub Dostal
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Wayne Busse
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Arno Munhoven
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Cesar Bernardo
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Miroslav Kloz
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Peter Hegemann
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - John T. M. Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
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21
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Do TN, Menendez D, Bizhga D, Stojković EA, Kennis JTM. Two-photon Absorption and Photoionization of a Bacterial Phytochrome. J Mol Biol 2024; 436:168357. [PMID: 37944794 DOI: 10.1016/j.jmb.2023.168357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Phytochromes constitute a family of photosensory proteins that are utilized by various organisms to regulate several physiological processes. Phytochromes bind a bilin pigment that switches its isomeric state upon absorption of red or far-red photons, resulting in protein conformational changes that are sensed by the organism. Previously, the ultrafast dynamics in bacterial phytochrome was resolved to atomic resolution by time-resolved serial femtosecond X-ray diffraction (TR-SFX), showing extensive changes in its molecular conformation at 1 picosecond delay time. However, the large excitation fluence of mJ/mm2 used in TR-SFX questions the validity of the observed dynamics. In this work, we present an excitation-dependent ultrafast transient absorption study to test the response of a related bacterial phytochrome to excitation fluence. We observe excitation power-dependent sub-picosecond dynamics, assigned to the population of high-lying excited state Sn through resonantly enhanced two-photon absorption, followed by rapid internal conversion to the low-lying S1 state. Inspection of the long-lived spectrum under high fluence shows that in addition to the primary intermediate Lumi-R, spectroscopic signatures of solvated electrons and ionized chromophore radicals are observed. Supported by numerical modelling, we propose that under excitation fluences of tens of μJ/mm2 and higher, bacterial phytochrome partly undergoes photoionization from the Sn state in competition with internal conversion to the S1 state in 300 fs. We suggest that the extensive structural changes of related, shorter bacterial phytochrome, lacking the PHY domain, resolved from TR-SFX may have been affected by the ionized species. We propose approaches to minimize the two-photon absorption process by tuning the excitation spectrum away from the S1 absorption or using phytochromes exhibiting minimized or shifted S1 absorption.
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Affiliation(s)
- Thanh Nhut Do
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - David Menendez
- Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, IL 60625, USA
| | - Dorina Bizhga
- Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, IL 60625, USA
| | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, IL 60625, USA
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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22
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Francis WJC, Grewal H, Wainwright AAC, Yang X, Olivucci M, Miller RJD. Resonant multiphoton processes and excitation limits to structural dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:024301. [PMID: 38433875 PMCID: PMC10908556 DOI: 10.1063/4.0000239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
Understanding the chemical reactions that give rise to functional biological systems is at the core of structural biology. As techniques are developed to study the chemical reactions that drive biological processes, it must be ensured that the reaction occurring is indeed a biologically relevant pathway. There is mounting evidence indicating that there has been a propagation of systematic error in the study of photoactive biological processes; the optical methods used to probe the structural dynamics of light activated protein functions have failed to ensure that the photoexcitation prepares a well-defined initial state relevant to the biological process of interest. Photoexcitation in nature occurs in the linear (one-photon per chromophore) regime; however, the extreme excitation conditions used experimentally give rise to biologically irrelevant multiphoton absorption. To evaluate and ensure the biological relevance of past and future experiments, a theoretical framework has been developed to determine the excitation conditions, which lead to resonant multiphoton absorption (RMPA) and thus define the excitation limit in general for the study of structural dynamics within the 1-photon excitation regime. Here, we apply the theoretical model to bacteriorhodopsin (bR) and show that RMPA occurs when excitation conditions exceed the linear saturation threshold, well below typical excitation conditions used in this class of experiments. This work provides the guidelines to ensure excitation in the linear 1-photon regime is relevant to biological and chemical processes.
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Affiliation(s)
- William J C Francis
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 3J1, Canada
| | - Harmanjot Grewal
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 3J1, Canada
| | - Alexander A C Wainwright
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 3J1, Canada
| | | | | | - R J Dwayne Miller
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 3J1, Canada
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23
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Khusainov G, Standfuss J, Weinert T. The time revolution in macromolecular crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:020901. [PMID: 38616866 PMCID: PMC11015943 DOI: 10.1063/4.0000247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, the advent of cryo-electron microscopy for structure determination of large and increasingly smaller and flexible proteins signaled a paradigm shift in structural biology. The extensive structural and sequence data from crystallography and advanced sequencing techniques have been pivotal for training computational models for accurate structure prediction, unveiling the general fold of most proteins. Here, we present a perspective on the rise of time-resolved crystallography as the new frontier of macromolecular structure determination. We trace the evolution from the pioneering time-resolved crystallography methods to modern serial crystallography, highlighting the synergy between rapid detection technologies and state-of-the-art x-ray sources. These innovations are redefining our exploration of protein dynamics, with high-resolution crystallography uniquely positioned to elucidate rapid dynamic processes at ambient temperatures, thus deepening our understanding of protein functionality. We propose that the integration of dynamic structural data with machine learning advancements will unlock predictive capabilities for protein kinetics, revolutionizing dynamics like macromolecular crystallography revolutionized structural biology.
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Affiliation(s)
- Georgii Khusainov
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
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24
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Jacobson DR, Perkins TT. Quantifying a light-induced energetic change in bacteriorhodopsin by force spectroscopy. Proc Natl Acad Sci U S A 2024; 121:e2313818121. [PMID: 38324569 PMCID: PMC10873598 DOI: 10.1073/pnas.2313818121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
Ligand-induced conformational changes are critical to the function of many membrane proteins and arise from numerous intramolecular interactions. In the photocycle of the model membrane protein bacteriorhodopsin (bR), absorption of a photon by retinal triggers a conformational cascade that results in pumping a proton across the cell membrane. While decades of spectroscopy and structural studies have probed this photocycle in intricate detail, changes in intramolecular energetics that underlie protein motions have remained elusive to experimental quantification. Here, we measured these energetics on the millisecond time scale using atomic-force-microscopy-based single-molecule force spectroscopy. Precisely, timed light pulses triggered the bR photocycle while we measured the equilibrium unfolding and refolding of the terminal 8-amino-acid region of bR's G-helix. These dynamics changed when the EF-helix pair moved ~9 Å away from this end of the G helix during the "open" portion of bR's photocycle. In ~60% of the data, we observed abrupt light-induced destabilization of 3.4 ± 0.3 kcal/mol, lasting 38 ± 3 ms. The kinetics and pH-dependence of this destabilization were consistent with prior measurements of bR's open phase. The frequency of light-induced destabilization increased with the duration of illumination and was dramatically reduced in the triple mutant (D96G/F171C/F219L) thought to trap bR in its open phase. In the other ~40% of the data, photoexcitation unexpectedly stabilized a longer-lived putative misfolded state. Through this work, we establish a general single-molecule force spectroscopy approach for measuring ligand-induced energetics and lifetimes in membrane proteins.
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Affiliation(s)
- David R. Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO80309
| | - Thomas T. Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO80309
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO80309
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25
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Barends TRM, Gorel A, Bhattacharyya S, Schirò G, Bacellar C, Cirelli C, Colletier JP, Foucar L, Grünbein ML, Hartmann E, Hilpert M, Holton JM, Johnson PJM, Kloos M, Knopp G, Marekha B, Nass K, Nass Kovacs G, Ozerov D, Stricker M, Weik M, Doak RB, Shoeman RL, Milne CJ, Huix-Rotllant M, Cammarata M, Schlichting I. Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Nature 2024; 626:905-911. [PMID: 38355794 PMCID: PMC10881388 DOI: 10.1038/s41586-024-07032-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
High-intensity femtosecond pulses from an X-ray free-electron laser enable pump-probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1,2. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore3-17. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern18,19 whether this experimental approach20 allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions18,19. Here we describe ultrafast pump-probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics21) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump-probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump-probe experiments20 such that mechanistically relevant insight emerges.
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Affiliation(s)
| | - Alexander Gorel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | | | | | - Lutz Foucar
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | - Mario Hilpert
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | | | - Bogdan Marekha
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France
| | - Karol Nass
- Paul Scherrer Institute, Villigen, Switzerland
| | | | | | | | - Martin Weik
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
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26
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Caramello N, Royant A. From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons. Acta Crystallogr D Struct Biol 2024; 80:60-79. [PMID: 38265875 PMCID: PMC10836399 DOI: 10.1107/s2059798323011002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump-probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.
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Affiliation(s)
- Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 1 Avenue des Martyrs, CS 40220, 38043 Grenoble CEDEX 9, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 1 Avenue des Martyrs, CS 40220, 38043 Grenoble CEDEX 9, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
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27
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Engilberge S, Caramello N, Bukhdruker S, Byrdin M, Giraud T, Jacquet P, Scortani D, Biv R, Gonzalez H, Broquet A, van der Linden P, Rose SL, Flot D, Balandin T, Gordeliy V, Lahey-Rudolph JM, Roessle M, de Sanctis D, Leonard GA, Mueller-Dieckmann C, Royant A. The TR-icOS setup at the ESRF: time-resolved microsecond UV-Vis absorption spectroscopy on protein crystals. Acta Crystallogr D Struct Biol 2024; 80:16-25. [PMID: 38088897 PMCID: PMC10833346 DOI: 10.1107/s2059798323010483] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
The technique of time-resolved macromolecular crystallography (TR-MX) has recently been rejuvenated at synchrotrons, resulting in the design of dedicated beamlines. Using pump-probe schemes, this should make the mechanistic study of photoactive proteins and other suitable systems possible with time resolutions down to microseconds. In order to identify relevant time delays, time-resolved spectroscopic experiments directly performed on protein crystals are often desirable. To this end, an instrument has been built at the icOS Lab (in crystallo Optical Spectroscopy Laboratory) at the European Synchrotron Radiation Facility using reflective focusing objectives with a tuneable nanosecond laser as a pump and a microsecond xenon flash lamp as a probe, called the TR-icOS (time-resolved icOS) setup. Using this instrument, pump-probe spectra can rapidly be recorded from single crystals with time delays ranging from a few microseconds to seconds and beyond. This can be repeated at various laser pulse energies to track the potential presence of artefacts arising from two-photon absorption, which amounts to a power titration of a photoreaction. This approach has been applied to monitor the rise and decay of the M state in the photocycle of crystallized bacteriorhodopsin and showed that the photocycle is increasingly altered with laser pulses of peak fluence greater than 100 mJ cm-2, providing experimental laser and delay parameters for a successful TR-MX experiment.
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Affiliation(s)
- Sylvain Engilberge
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
| | - Nicolas Caramello
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Sergei Bukhdruker
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Byrdin
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Philippe Jacquet
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
| | - Damien Scortani
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Rattana Biv
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Hervé Gonzalez
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Antonin Broquet
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Peter van der Linden
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- PSCM (Partnership for Soft Condensed Matter), ESRF, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Samuel L. Rose
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Valentin Gordeliy
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - J. Mia Lahey-Rudolph
- Technische Hochschule Lübeck – University of Applied Sciences, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - Manfred Roessle
- Technische Hochschule Lübeck – University of Applied Sciences, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - Daniele de Sanctis
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
| | | | - Antoine Royant
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38403 Grenoble CEDEX 9, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
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28
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Safari C, Ghosh S, Andersson R, Johannesson J, Båth P, Uwangue O, Dahl P, Zoric D, Sandelin E, Vallejos A, Nango E, Tanaka R, Bosman R, Börjesson P, Dunevall E, Hammarin G, Ortolani G, Panman M, Tanaka T, Yamashita A, Arima T, Sugahara M, Suzuki M, Masuda T, Takeda H, Yamagiwa R, Oda K, Fukuda M, Tosha T, Naitow H, Owada S, Tono K, Nureki O, Iwata S, Neutze R, Brändén G. Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. SCIENCE ADVANCES 2023; 9:eadh4179. [PMID: 38064560 PMCID: PMC10708180 DOI: 10.1126/sciadv.adh4179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.
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Affiliation(s)
- Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Jonatan Johannesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Owens Uwangue
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Doris Zoric
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Emil Sandelin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Per Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Matthijs Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Toshi Arima
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mamoru Suzuki
- Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Japan
| | - Hanae Takeda
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Raika Yamagiwa
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kazumasa Oda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
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29
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Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Müller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD. Visualizing the DNA repair process by a photolyase at atomic resolution. Science 2023; 382:eadd7795. [PMID: 38033054 DOI: 10.1126/science.add7795] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
Abstract
Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.
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Affiliation(s)
- Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Po-Hsun Wang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Yuhei Hosokawa
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Antonia Furrer
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | | | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Hans-Joachim Emmerich
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Nicolas Caramello
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Sophie Franz-Badur
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Chao Yang
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Sylvain Engilberge
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Tobias Weinert
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wael Gad
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Chiung-Wen Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Chun Yang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Wei-Ting Lin
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Yu-Chen Chang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Dardan Gashi
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Emma Beale
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Karol Nass
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Chris Milne
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fangjia Luo
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Wiktoria Zarzycka
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pavel Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maisa Alkheder Alahmad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Filipp Bezold
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Valerie Fuchs
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Petra Gnau
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Stephan Kiontke
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Lukas Korf
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Viktoria Reithofer
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Elisa Marie Seiler
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Mohamed Watad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Laura Werel
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Roberta Spadaccini
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
- Dipartimento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dongping Zhong
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for Ultrafast Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jörg Standfuss
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Antoine Royant
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
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30
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Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Günther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ. Time-resolved crystallography captures light-driven DNA repair. Science 2023; 382:1015-1020. [PMID: 38033070 DOI: 10.1126/science.adj4270] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
Abstract
Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.
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Affiliation(s)
- Nina-Eleni Christou
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Virginia Apostolopoulou
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diogo V M Melo
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Matthias Ruppert
- Institute for Nanostructure and Solid-State Physics, CFEL Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anastasios Pateras
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr M Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Viviane Kremling
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - T Emilie S Scheer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Esther R Lange
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Elke De Zitter
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Koya Lumbao-Conradson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA
| | - Jonathan Herrmann
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
| | - Simin Rahighi
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
| | - Ajda Kunavar
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, Slovenia
| | - Emma V Beale
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - John H Beale
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | | | | | | | - Dmitry Ozerov
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | | | | | | | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA
| | - Jonas A Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Nils Huse
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute for Nanostructure and Solid-State Physics, CFEL Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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31
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Li Z, Mizuno M, Ejiri T, Hayashi S, Kandori H, Mizutani Y. Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins. J Phys Chem B 2023; 127:9873-9886. [PMID: 37940604 DOI: 10.1021/acs.jpcb.3c02146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.
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Affiliation(s)
- Zixuan Li
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Tomo Ejiri
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
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32
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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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33
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Hutchison CDM, Baxter JM, Fitzpatrick A, Dorlhiac G, Fadini A, Perrett S, Maghlaoui K, Lefèvre SB, Cordon-Preciado V, Ferreira JL, Chukhutsina VU, Garratt D, Barnard J, Galinis G, Glencross F, Morgan RM, Stockton S, Taylor B, Yuan L, Romei MG, Lin CY, Marangos JP, Schmidt M, Chatrchyan V, Buckup T, Morozov D, Park J, Park S, Eom I, Kim M, Jang D, Choi H, Hyun H, Park G, Nango E, Tanaka R, Owada S, Tono K, DePonte DP, Carbajo S, Seaberg M, Aquila A, Boutet S, Barty A, Iwata S, Boxer SG, Groenhof G, van Thor JJ. Optical control of ultrafast structural dynamics in a fluorescent protein. Nat Chem 2023; 15:1607-1615. [PMID: 37563326 PMCID: PMC10624617 DOI: 10.1038/s41557-023-01275-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/12/2023] [Indexed: 08/12/2023]
Abstract
The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.
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Affiliation(s)
| | - James M Baxter
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Ann Fitzpatrick
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Gabriel Dorlhiac
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Samuel Perrett
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Karim Maghlaoui
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Salomé Bodet Lefèvre
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Violeta Cordon-Preciado
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Josie L Ferreira
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Volha U Chukhutsina
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Douglas Garratt
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Jonathan Barnard
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Gediminas Galinis
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Flo Glencross
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Rhodri M Morgan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Sian Stockton
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Ben Taylor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Letong Yuan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jon P Marangos
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Viktoria Chatrchyan
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Heidelberg, Germany
| | - Tiago Buckup
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Heidelberg, Germany
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
- Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea
| | - Sehan Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Dogeun Jang
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Hyeongi Choi
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - HyoJung Hyun
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Gisu Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Eriko Nango
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
| | - Daniel P DePonte
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sergio Carbajo
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Matt Seaberg
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew Aquila
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sebastien Boutet
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - So Iwata
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Jasper J van Thor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.
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34
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Leighton RE, Frontiera RR. Quantifying Bacteriorhodopsin Activity as a Function of its Local Environment with a Raman-Based Assay. J Phys Chem B 2023; 127:8833-8841. [PMID: 37812499 DOI: 10.1021/acs.jpcb.3c04802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Bacteriorhodopsin (bR) is a transmembrane protein that functions as a light-driven proton pump in halophilic archaea. The bR photocycle has been well-characterized; however, these measurements almost exclusively measured purified bR, outside of its native membrane. To investigate what effect the cellular environment has on the bR photocycle, we have developed a Raman-based assay that can monitor the activity of the bR in a variety of conditions, including in its native membrane. The assay uses two continuous-wave lasers, one to initiate photochemistry and one to monitor bR activity. The excitation leads to the steady-state depletion of ground-state bR, which directly relates to the population of photocycle intermediate states. We have used this assay to monitor bR activity both in vitro and in vivo. Our in vitro measurements confirm that our assay is sensitive to bulk environmental changes reported in the literature. Our in vivo measurements show a decrease in bR activity with increasing extracellular pH for bR in its native membrane. The difference in activity with increasing pH indicates that the native membrane environment affects the function of bR. This assay opens the door to future measurements into understanding how the local environment of this transmembrane protein affects function.
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Affiliation(s)
- Ryan E Leighton
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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35
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Birch J, Kwan TOC, Judge PJ, Axford D, Aller P, Butryn A, Reis RI, Bada Juarez JF, Vinals J, Owen RL, Nango E, Tanaka R, Tono K, Joti Y, Tanaka T, Owada S, Sugahara M, Iwata S, Orville AM, Watts A, Moraes I. A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography. J Appl Crystallogr 2023; 56:1361-1370. [PMID: 37791355 PMCID: PMC10543674 DOI: 10.1107/s1600576723006428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/24/2023] [Indexed: 10/05/2023] Open
Abstract
Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Tristan O. C. Kwan
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Peter J. Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Pierre Aller
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Agata Butryn
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Rosana I. Reis
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Juan F. Bada Juarez
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, Lausanne, CH-1015, Switzerland
| | - Javier Vinals
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Allen M. Orville
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Isabel Moraes
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
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36
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Nango E, Iwata S. Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins. Curr Opin Struct Biol 2023; 81:102629. [PMID: 37354789 DOI: 10.1016/j.sbi.2023.102629] [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: 01/28/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 06/26/2023]
Abstract
Microbial rhodopsin is a membrane protein with a domain of seven-transmembrane helices and a retinal chromophore. The main function of this protein is to perform light-induced ion transport, either actively or passively, by acting as pumps, channels, and light sensors. It is widely used for optogenetic application to control the activity of specific cells in living tissues by light. Time-resolved serial femtosecond crystallography (TR-SFX) with the use of X-ray free electron lasers is an effective technique for capturing dynamic ion transport and efflux structures across membranes with high spatial and temporal resolutions. Here, we outline recent TR-SFX studies of microbial rhodopsins, including a pump and a channel. We also discuss differences and similarities observed in the structural dynamics derived from the TR-SFX structures.
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Affiliation(s)
- Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. https://twitter.com/@enango_5
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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37
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Besaw JE, Miller RJD. Addressing high excitation conditions in time-resolved X-ray diffraction experiments and issues of biological relevance. Curr Opin Struct Biol 2023; 81:102624. [PMID: 37331203 DOI: 10.1016/j.sbi.2023.102624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
One of the most important fundamental questions connecting chemistry to biology is how chemistry scales in complexity up to biological systems where there are innumerable possible pathways and competing processes. With the development of ultrabright electron and x-ray sources, it has been possible to literally light up atomic motions to directly observe the reduction in dimensionality in the barrier crossing region to a few key reaction modes. How do these chemical processes further couple to the surrounding protein or macromolecular assembly to drive biological functions? Optical methods to trigger photoactive biological processes are needed to probe this issue on the relevant timescales. However, the excitation conditions have been in the highly nonlinear regime, which questions the biological relevance of the observed structural dynamics.
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Affiliation(s)
- Jessica E Besaw
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - R J Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
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38
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Meng X, Ganapathy S, van Roemburg L, Post M, Brinks D. Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway. ACS PHYSICAL CHEMISTRY AU 2023; 3:320-333. [PMID: 37520318 PMCID: PMC10375888 DOI: 10.1021/acsphyschemau.3c00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 08/01/2023]
Abstract
Voltage imaging using genetically encoded voltage indicators (GEVIs) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered microbial rhodopsins form a GEVI subclass known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of microbial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these proteins and link them to insights from efforts to create faster, brighter and more sensitive microbial rhodopsin-based GEVIs.
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Affiliation(s)
- Xin Meng
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Srividya Ganapathy
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Pediatrics & Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California 92093, United States
| | - Lars van Roemburg
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Marco Post
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Daan Brinks
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Molecular Genetics, Erasmus University
Medical Center, 3015 GD Rotterdam, The Netherlands
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39
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Casadei CM, Hosseinizadeh A, Bliven S, Weinert T, Standfuss J, Fung R, Schertler GFX, Santra R. Low-pass spectral analysis of time-resolved serial femtosecond crystallography data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:034101. [PMID: 37275629 PMCID: PMC10233406 DOI: 10.1063/4.0000178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
Low-pass spectral analysis (LPSA) is a recently developed dynamics retrieval algorithm showing excellent retrieval properties when applied to model data affected by extreme incompleteness and stochastic weighting. In this work, we apply LPSA to an experimental time-resolved serial femtosecond crystallography (TR-SFX) dataset from the membrane protein bacteriorhodopsin (bR) and analyze its parametric sensitivity. While most dynamical modes are contaminated by nonphysical high-frequency features, we identify two dominant modes, which are little affected by spurious frequencies. The dynamics retrieved using these modes shows an isomerization signal compatible with previous findings. We employ synthetic data with increasing timing uncertainty, increasing incompleteness level, pixel-dependent incompleteness, and photon counting errors to investigate the root cause of the high-frequency contamination of our TR-SFX modes. By testing a range of methods, we show that timing errors comparable to the dynamical periods to be retrieved produce a smearing of dynamical features, hampering dynamics retrieval, but with no introduction of spurious components in the solution, when convergence criteria are met. Using model data, we are able to attribute the high-frequency contamination of low-order dynamical modes to the high levels of noise present in the data. Finally, we propose a method to handle missing observations that produces a substantial dynamics retrieval improvement from synthetic data with a significant static component. Reprocessing of the bR TR-SFX data using the improved method yields dynamical movies with strong isomerization signals compatible with previous findings.
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Affiliation(s)
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
| | - Spencer Bliven
- Science IT Infrastructure and Services, Division Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Russell Fung
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
| | | | - Robin Santra
- Authors to whom correspondence should be addressed: and
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40
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Asido M, Wachtveitl J. Photochemistry of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2 and Its Implications on Microbial Rhodopsin Research: Retrospective and Perspective. J Phys Chem B 2023; 127:3766-3773. [PMID: 36919947 DOI: 10.1021/acs.jpcb.2c08933] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The discovery of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) in 2013 has changed the paradigm that cation transport in microbial rhodopsins is restricted to the translocation of protons. Even though this finding is already remarkable by itself, it also reignited more general discussions about the functional mechanism of ion transport. The unique composition of the retinal binding pocket in KR2 with a tight interaction between the retinal Schiff base and its respective counterion D116 also has interesting implications on the photochemical pathway of the chromophore. Here, we discuss the most recent advances in our understanding of the KR2 functionality from the primary event of photon absorption by all-trans retinal up to the actual protein response in the later phases of the photocycle, mainly from the point of view of optical spectroscopy. In this context, we furthermore highlight some of the ongoing debates on the photochemistry of microbial rhodopsins and give some perspectives for promising future directions in this field of research.
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Affiliation(s)
- Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
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41
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Rodrigues MJ, Casadei CM, Weinert T, Panneels V, Schertler GFX. Correction of rhodopsin serial crystallography diffraction intensities for a lattice-translocation defect. Acta Crystallogr D Struct Biol 2023; 79:224-233. [PMID: 36876432 PMCID: PMC9986800 DOI: 10.1107/s2059798323000931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/01/2023] [Indexed: 03/01/2023] Open
Abstract
Rhodopsin is a G-protein-coupled receptor that detects light and initiates the intracellular signalling cascades that underpin vertebrate vision. Light sensitivity is achieved by covalent linkage to 11-cis retinal, which isomerizes upon photo-absorption. Serial femtosecond crystallography data collected from rhodopsin microcrystals grown in the lipidic cubic phase were used to solve the room-temperature structure of the receptor. Although the diffraction data showed high completeness and good consistency to 1.8 Å resolution, prominent electron-density features remained unaccounted for throughout the unit cell after model building and refinement. A deeper analysis of the diffraction intensities uncovered the presence of a lattice-translocation defect (LTD) within the crystals. The procedure followed to correct the diffraction intensities for this pathology enabled the building of an improved resting-state model. The correction was essential to both confidently model the structure of the unilluminated state and interpret the light-activated data collected after photo-excitation of the crystals. It is expected that similar cases of LTD will be observed in other serial crystallography experiments and that correction will be required in a variety of systems.
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Affiliation(s)
- Matthew J. Rodrigues
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Cecilia M. Casadei
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Biology, ETH-Zurich, Zurich, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Valerie Panneels
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Biology, ETH-Zurich, Zurich, Switzerland
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42
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Gruhl T, Weinert T, Rodrigues MJ, Milne CJ, Ortolani G, Nass K, Nango E, Sen S, Johnson PJM, Cirelli C, Furrer A, Mous S, Skopintsev P, James D, Dworkowski F, Båth P, Kekilli D, Ozerov D, Tanaka R, Glover H, Bacellar C, Brünle S, Casadei CM, Diethelm AD, Gashi D, Gotthard G, Guixà-González R, Joti Y, Kabanova V, Knopp G, Lesca E, Ma P, Martiel I, Mühle J, Owada S, Pamula F, Sarabi D, Tejero O, Tsai CJ, Varma N, Wach A, Boutet S, Tono K, Nogly P, Deupi X, Iwata S, Neutze R, Standfuss J, Schertler G, Panneels V. Ultrafast structural changes direct the first molecular events of vision. Nature 2023; 615:939-944. [PMID: 36949205 PMCID: PMC10060157 DOI: 10.1038/s41586-023-05863-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 02/17/2023] [Indexed: 03/24/2023]
Abstract
Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
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Affiliation(s)
- Thomas Gruhl
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Matthew J Rodrigues
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Christopher J Milne
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- European XFEL, Schenefeld, Germany
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Karol Nass
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Saumik Sen
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Philip J M Johnson
- Photon Science Division, Laboratory for Nonlinear Optics, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Biologics Center, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Petr Skopintsev
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Daniel James
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Physics, Utah Valley University, Orem, UT, USA
| | - Florian Dworkowski
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Demet Kekilli
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Division Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hannah Glover
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Camila Bacellar
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Azeglio D Diethelm
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Guillaume Gotthard
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Victoria Kabanova
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- Laboratory for Ultrafast X-ray Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gregor Knopp
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Elena Lesca
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pikyee Ma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jonas Mühle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Filip Pamula
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oliver Tejero
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Niranjan Varma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Anna Wach
- Institute of Nuclear Physics Polish Academy of Sciences, Kraców, Poland
- Operando X-ray Spectroscopy, Energy and Environment Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
- Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
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43
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Taguchi S, Niwa S, Dao HA, Tanaka Y, Takeda R, Fukai S, Hasegawa K, Takeda K. Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin. Commun Biol 2023; 6:190. [PMID: 36808185 PMCID: PMC9938236 DOI: 10.1038/s42003-023-04554-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
The K intermediate of proton pumping bacteriorhodopsin is the first intermediate generated after isomerization of retinal to the 13-cis form. Although various structures have been reported for the K intermediate until now, these differ from each other, especially in terms of the conformation of the retinal chromophore and its interaction with surrounding residues. We report here an accurate X-ray crystallographic analysis of the K structure. The polyene chain of 13-cis retinal is observed to be S-shaped. The side chain of Lys216, which is covalently bound to retinal via the Schiff-base linkage, interacts with residues, Asp85 and Thr89. In addition, the Nζ-H of the protonated Schiff-base linkage interacts with a residue, Asp212 and a water molecule, W402. Based on quantum chemical calculations for this K structure, we examine the stabilizing factors of distorted conformation of retinal and propose a relaxation manner to the next L intermediate.
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Affiliation(s)
- Shoun Taguchi
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Satomi Niwa
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Hoang-Anh Dao
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Yoshihiro Tanaka
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Ryota Takeda
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Shuya Fukai
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Kazuya Hasegawa
- grid.410592.b0000 0001 2170 091XStructural Biology Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198 Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku, 606-8502, Japan.
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44
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Kojima K, Sudo Y. Convergent evolution of animal and microbial rhodopsins. RSC Adv 2023; 13:5367-5381. [PMID: 36793294 PMCID: PMC9923458 DOI: 10.1039/d2ra07073a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
Rhodopsins, a family of photoreceptive membrane proteins, contain retinal as a chromophore and were firstly identified as reddish pigments from frog retina in 1876. Since then, rhodopsin-like proteins have been identified mainly from animal eyes. In 1971, a rhodopsin-like pigment was discovered from the archaeon Halobacterium salinarum and named bacteriorhodopsin. While it was believed that rhodopsin- and bacteriorhodopsin-like proteins were expressed only in animal eyes and archaea, respectively, before the 1990s, a variety of rhodopsin-like proteins (called animal rhodopsins or opsins) and bacteriorhodopsin-like proteins (called microbial rhodopsins) have been progressively identified from various tissues of animals and microorganisms, respectively. Here, we comprehensively introduce the research conducted on animal and microbial rhodopsins. Recent analysis has revealed that the two rhodopsin families have common molecular properties, such as the protein structure (i.e., 7-transmembrane structure), retinal structure (i.e., binding ability to cis- and trans-retinal), color sensitivity (i.e., UV- and visible-light sensitivities), and photoreaction (i.e., triggering structural changes by light and heat), more than what was expected at the early stages of rhodopsin research. Contrastingly, their molecular functions are distinctively different (e.g., G protein-coupled receptors and photoisomerases for animal rhodopsins and ion transporters and phototaxis sensors for microbial rhodopsins). Therefore, based on their similarities and dissimilarities, we propose that animal and microbial rhodopsins have convergently evolved from their distinctive origins as multi-colored retinal-binding membrane proteins whose activities are regulated by light and heat but independently evolved for different molecular and physiological functions in the cognate organism.
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Affiliation(s)
- Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
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45
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Yang Y, Stensitzki T, Lang C, Hughes J, Mroginski MA, Heyne K. Ultrafast protein response in the Pfr state of Cph1 phytochrome. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2023; 22:919-930. [PMID: 36653574 DOI: 10.1007/s43630-023-00362-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023]
Abstract
Photoisomerization is a fundamental process in several classes of photoreceptors. Phytochromes sense red and far-red light in their Pr and Pfr states, respectively. Upon light absorption, these states react via individual photoreactions to the other state. Cph1 phytochrome shows a photoisomerization of its phycocyanobilin (PCB) chromophore in the Pfr state with a time constant of 0.7 ps. The dynamics of the PCB chromophore has been described, but whether or not the apoprotein exhibits an ultrafast response too, is not known. Here, we compare the photoreaction of 13C/15N labeled apoprotein with unlabeled apoprotein to unravel ultrafast apoprotein dynamics in Cph1. In the spectral range from 1750 to 1620 cm-1 we assigned several signals due to ultrafast apoprotein dynamics. A bleaching signal at 1724 cm-1 is tentatively assigned to deprotonation of a carboxylic acid, probably Asp207, and signals around 1670 cm-1 are assigned to amide I vibrations of the capping helix close to the chromophore. These signals remain after photoisomerization. The apoprotein dynamics appear upon photoexcitation or concomitant with chromophore isomerization. Thus, apoprotein dynamics occur prior to and after photoisomerization on an ultrafast time-scale. We discuss the origin of the ultrafast apoprotein response with the 'Coulomb hammer' mechanism, i.e. an impulsive change of electric field and Coulombic force around the chromophore upon excitation.
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Affiliation(s)
- Yang Yang
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Till Stensitzki
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Christina Lang
- Institut für Pflanzenphysiologie, Justus-Liebig Universität Giessen, Senckenbergstr. 3, 35390, Giessen, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig Universität Giessen, Senckenbergstr. 3, 35390, Giessen, Germany
| | - Maria Andrea Mroginski
- Institut Für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Karsten Heyne
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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46
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Bertalan É, Bondar AN. Graphs of protein-water hydrogen bond networks to dissect structural movies of ion-transfer microbial rhodopsins. Front Chem 2023; 10:1075648. [PMID: 36712989 PMCID: PMC9880326 DOI: 10.3389/fchem.2022.1075648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
Microbial rhodopsins are membrane proteins that use the energy absorbed by the covalently bound retinal chromophore to initiate reaction cycles resulting in ion transport or signal transduction. Thousands of distinct microbial rhodopsins are known and, for many rhodopsins, three-dimensional structures have been solved with structural biology, including as entire sets of structures solved with serial femtosecond crystallography. This sets the stage for comprehensive studies of large datasets of static protein structures to dissect structural elements that provide functional specificity to the various microbial rhodopsins. A challenge, however, is how to analyze efficiently intra-molecular interactions based on large datasets of static protein structures. Our perspective discusses the usefulness of graph-based approaches to dissect structural movies of microbial rhodopsins solved with time-resolved crystallography.
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Affiliation(s)
- Éva Bertalan
- Physikzentrum, RWTH Aachen University, Aachen, Germany
| | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany,Faculty of Physics, University of Bucharest, Măgurele, Romania,*Correspondence: Ana-Nicoleta Bondar, ,
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47
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Noji T, Ishikita H. Mechanism of Absorption Wavelength Shift of Bacteriorhodopsin During Photocycle. J Phys Chem B 2022; 126:9945-9955. [PMID: 36413506 DOI: 10.1021/acs.jpcb.2c04359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteriorhodopsin, a light-driven proton pump, alters the absorption wavelengths in the range of 410-617 nm during the photocycle. Here, we report the absorption wavelengths, calculated using 12 bacteriorhodopsin crystal structures (including the BR, BR13-cis, J, K0, KE, KL, L, M, N, and O state structures) and a combined quantum mechanical/molecular mechanical/polarizable continuum model (QM/MM/PCM) approach. The QM/MM/PCM calculations reproduced the experimentally measured absorption wavelengths with a standard deviation of 4 nm. The shifts in the absorption wavelengths can be explained mainly by the following four factors: (i) retinal Schiff base deformation/twist induced by the protein environment, leading to a decrease in the electrostatic interaction between the protein environment and the retinal Schiff base; (ii) changes in the protonation state of the protein environment, directly altering the electrostatic interaction between the protein environment and the retinal Schiff base; (iii) changes in the protonation state; or (iv) isomerization of the retinal Schiff base, where the absorption wavelengths of the isomers originally differ.
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Affiliation(s)
- Tomoyasu Noji
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
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48
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Westenhoff S, Meszaros P, Schmidt M. Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins. Curr Opin Struct Biol 2022; 77:102481. [PMID: 36252455 DOI: 10.1016/j.sbi.2022.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022]
Abstract
Proteins are dynamic objects and undergo conformational changes when functioning. These changes range from interconversion between states in equilibrium to ultrafast and coherent structural motions within one perturbed state. Time-resolved serial femtosecond crystallography at free-electron X-ray lasers can unravel structural changes with atomic resolution and down to femtosecond time scales. In this review, we summarize recent advances on detecting structural changes for phytochrome photosensor proteins and a bacterial photosynthetic reaction center. In the phytochrome structural changes are extensive and involve major rearrangements of many amino acids and water molecules, accompanying the regulation of its biochemical activity, whereas in the photosynthetic reaction center protein the structural changes are smaller, more localized, and are optimized to facilitate electron transfer along the chromophores. The detected structural motions underpin the proteins' function, providing a showcase for the importance of detecting ultrafast protein structural dynamics.
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Affiliation(s)
- Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden.
| | - Petra Meszaros
- Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden
| | - Marius Schmidt
- Physics Department, Physic, University of Wisconsin-Milwaukee, 3134 N. Maryland Ave., Milwaukee, WI 53211, United States
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49
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Weik M, Domratcheva T. Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations. Curr Opin Struct Biol 2022; 77:102496. [PMID: 36462226 DOI: 10.1016/j.sbi.2022.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 12/03/2022]
Abstract
The structural dynamics underlying molecular mechanisms of light-sensitive proteins can be studied by a variety of experimental and computational biophysical techniques. Here we review recent progress in combining time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations to study structural changes in photoenzymes, photosynthetic proteins, photoreceptors, and photoswitchable fluorescent proteins following photoexcitation.
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Affiliation(s)
- Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia; Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
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50
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Chukhutsina VU, Baxter JM, Fadini A, Morgan RM, Pope MA, Maghlaoui K, Orr CM, Wagner A, van Thor JJ. Light activation of Orange Carotenoid Protein reveals bicycle-pedal single-bond isomerization. Nat Commun 2022; 13:6420. [PMID: 36307413 PMCID: PMC9616832 DOI: 10.1038/s41467-022-34137-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Orange Carotenoid protein (OCP) is the only known photoreceptor which uses carotenoid for its activation. It is found exclusively in cyanobacteria, where it functions to control light-harvesting of the photosynthetic machinery. However, the photochemical reactions and structural dynamics of this unique photosensing process are not yet resolved. We present time-resolved crystal structures at second-to-minute delays under bright illumination, capturing the early photoproduct and structures of the subsequent reaction intermediates. The first stable photoproduct shows concerted isomerization of C9'-C8' and C7'-C6' single bonds in the bicycle-pedal (s-BP) manner and structural changes in the N-terminal domain with minute timescale kinetics. These are followed by a thermally-driven recovery of the s-BP isomer to the dark state carotenoid configuration. Structural changes propagate to the C-terminal domain, resulting, at later time, in the H-bond rupture of the carotenoid keto group with protein residues. Solution FTIR and UV/Vis spectroscopy support the single bond isomerization of the carotenoid in the s-BP manner and subsequent thermal structural reactions as the basis of OCP photoreception.
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Affiliation(s)
- Volha U. Chukhutsina
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - James M. Baxter
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Alisia Fadini
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Rhodri M. Morgan
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Matthew A. Pope
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Karim Maghlaoui
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - Christian M. Orr
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE UK
| | - Armin Wagner
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE UK
| | - Jasper J. van Thor
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
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