1
|
Li H, Nakajima Y, Nango E, Owada S, Yamada D, Hashimoto K, Luo F, Tanaka R, Akita F, Kato K, Kang J, Saitoh Y, Kishi S, Yu H, Matsubara N, Fujii H, Sugahara M, Suzuki M, Masuda T, Kimura T, Thao TN, Yonekura S, Yu LJ, Tosha T, Tono K, Joti Y, Hatsui T, Yabashi M, Kubo M, Iwata S, Isobe H, Yamaguchi K, Suga M, Shen JR. Oxygen-evolving photosystem II structures during S 1-S 2-S 3 transitions. Nature 2024; 626:670-677. [PMID: 38297122 PMCID: PMC10866707 DOI: 10.1038/s41586-023-06987-5] [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: 06/29/2023] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0-4) at the Mn4CaO5 cluster1-3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4-7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.
Collapse
Affiliation(s)
- Hongjie Li
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Sayo, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Daichi Yamada
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, Kobe, Japan
| | - Kana Hashimoto
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Fangjia Luo
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Sayo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Koji Kato
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | | | - Yasunori Saitoh
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Shunpei Kishi
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Huaxin Yu
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Naoki Matsubara
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hajime Fujii
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | | | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tetsuya Masuda
- Division of Food and Nutrition, Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Tran Nguyen Thao
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Shinichiro Yonekura
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Long-Jiang Yu
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Takaki Hatsui
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Minoru Kubo
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, Kobe, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Sayo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Kizashi Yamaguchi
- Center for Quantum Information and Quantum Biology, Osaka University, Osaka, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.
| |
Collapse
|
2
|
Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O'Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nat Chem 2023; 15:1549-1558. [PMID: 37723259 PMCID: PMC10624634 DOI: 10.1038/s41557-023-01329-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 08/17/2023] [Indexed: 09/20/2023]
Abstract
Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.
Collapse
Affiliation(s)
- Alexander M Wolff
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Eriko Nango
- RIKEN SPring-8 Center, Sayo-gun, Japan.
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Japan.
| | - Iris D Young
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Minoru Kubo
- RIKEN SPring-8 Center, Sayo-gun, Japan
- Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Takashi Nomura
- RIKEN SPring-8 Center, Sayo-gun, Japan
- Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo, Japan
| | | | | | - Benjamin A Barad
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Kazutaka Ito
- Laboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, Izunokuni-shi, Japan
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sergio Carbajo
- SLAC National Accelerator Laboratory, Linac Coherent Light Source, Menlo Park, CA, USA
- Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tomoya Hino
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
- Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dohyun Im
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Japan
| | - Lee J O'Riordan
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, Sayo-gun, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Sayo-gun, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Japan
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, Linac Coherent Light Source, Menlo Park, CA, USA
| | - Fumiaki Yumoto
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Japan
- Ginward Japan K.K., Tokyo, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, Sayo-gun, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Sayo-gun, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Japan
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers. Proc Natl Acad Sci U S A 2022; 119:2117433119. [PMID: 35197289 PMCID: PMC8892520 DOI: 10.1073/pnas.2117433119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 01/06/2023] Open
Abstract
Light-driven chloride pumps have been identified in various species, including archaea and marine flavobacteria. The function of ion transportation controllable by light is utilized for optogenetics tools in neuroscience. Chloride pumps differ among species, in terms of amino acid homology and structural similarity. Our time-resolved crystallographic studies using X-ray free electron lasers reveal the molecular mechanism of halide ion transfer in a light-driven chloride pump from a marine flavobacterium. Our data indicate a common mechanism in chloride pumping rhodopsins, as compared to previous low-temperature trapping studies of chloride pumps. These findings are significant not only for further improvements of optogenetic tools but also for a general understanding of the ion pumping mechanisms of microbial rhodopsins. Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10-µs and 1-ms time points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied by a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3.
Collapse
|
5
|
Li H, Nakajima Y, Nomura T, Sugahara M, Yonekura S, Chan SK, Nakane T, Yamane T, Umena Y, Suzuki M, Masuda T, Motomura T, Naitow H, Matsuura Y, Kimura T, Tono K, Owada S, Joti Y, Tanaka R, Nango E, Akita F, Kubo M, Iwata S, Shen JR, Suga M. Capturing structural changes of the S 1 to S 2 transition of photosystem II using time-resolved serial femtosecond crystallography. IUCRJ 2021; 8:431-443. [PMID: 33953929 PMCID: PMC8086164 DOI: 10.1107/s2052252521002177] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/24/2021] [Indexed: 05/21/2023]
Abstract
Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.
Collapse
Affiliation(s)
- Hongjie Li
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 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
| | - Shinichiro Yonekura
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Siu Kit Chan
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takahiro Yamane
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Yasufumi Umena
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Taiki Motomura
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, -1 Rokkodai, Nada-ku, Kobe 657-8501, 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 679-5198, 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 679-5198, 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 679-5198, 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
| | - 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
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- 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
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan
| |
Collapse
|
6
|
Carrillo M, Pandey S, Sanchez J, Noda M, Poudyal I, Aldama L, Malla TN, Claesson E, Wahlgren WY, Feliz D, Šrajer V, Maj M, Castillon L, Iwata S, Nango E, Tanaka R, Tanaka T, Fangjia L, Tono K, Owada S, Westenhoff S, Stojković EA, Schmidt M. High-resolution crystal structures of transient intermediates in the phytochrome photocycle. Structure 2021; 29:743-754.e4. [PMID: 33756101 DOI: 10.1016/j.str.2021.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/31/2021] [Accepted: 03/02/2021] [Indexed: 12/17/2022]
Abstract
Phytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting Pr state and the light-activated Pfr state. Light signals are transduced as structural change through the entire protein to modulate its activity. It is unknown how the Pr-to-Pfr interconversion occurs, as the structure of intermediates remains notoriously elusive. Here, we present short-lived crystal structures of the photosensory core modules of the bacteriophytochrome from myxobacterium Stigmatella aurantiaca captured by an X-ray free electron laser 5 ns and 33 ms after light illumination of the Pr state. We observe large structural displacements of the covalently bound bilin chromophore, which trigger a bifurcated signaling pathway that extends through the entire protein. The snapshots show with atomic precision how the signal progresses from the chromophore, explaining how plants, bacteria, and fungi sense red light.
Collapse
Affiliation(s)
- Melissa Carrillo
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL 60625, USA
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Juan Sanchez
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL 60625, USA
| | - Moraima Noda
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL 60625, USA
| | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Luis Aldama
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL 60625, USA
| | - Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Denisse Feliz
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL 60625, USA
| | - Vukica Šrajer
- The University of Chicago, Center for Advanced Radiation Sources, 9700 South Cass Avenue, Bldg 434B, Argonne, IL 60439, USA
| | - Michał Maj
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Leticia Castillon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - 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
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tomoyuki Tanaka
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Luo Fangjia
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, 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 679-5198, 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 679-5198, Japan
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL 60625, USA.
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA.
| |
Collapse
|
7
|
First Experiments in Structural Biology at the European X-ray Free-Electron Laser. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10103642] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ultrabright pulses produced in X-ray free-electron lasers (XFELs) offer new possibilities for industry and research, particularly for biochemistry and pharmaceuticals. The unprecedented brilliance of these next-generation sources enables structure determination from sub-micron crystals as well as radiation-sensitive proteins. The European X-Ray Free-Electron Laser (EuXFEL), with its first light in 2017, ushered in a new era for ultrabright X-ray sources by providing an unparalleled megahertz-pulse repetition rate, with orders of magnitude more pulses per second than previous XFEL sources. This rapid pulse frequency has significant implications for structure determination; not only will data collection be faster (resulting in more structures per unit time), but experiments requiring large quantities of data, such as time-resolved structures, become feasible in a reasonable amount of experimental time. Early experiments at the SPB/SFX instrument of the EuXFEL demonstrate how such closely-spaced pulses can be successfully implemented in otherwise challenging experiments, such as time-resolved studies.
Collapse
|
8
|
Illumination guidelines for ultrafast pump-probe experiments by serial femtosecond crystallography. Nat Methods 2020; 17:681-684. [PMID: 32451477 DOI: 10.1038/s41592-020-0847-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 04/17/2020] [Indexed: 12/20/2022]
Abstract
Time-resolved crystallography with X-ray free-electron lasers enables structural characterization of light-induced reactions on ultrafast timescales. To be biologically and chemically relevant, such studies must be carried out in an appropriate photoexcitation regime to avoid multiphoton artifacts, a common issue in recent studies. We describe numerical and experimental approaches to determine how many photons are needed for single-photon excitation in microcrystals, taking into account losses by scattering.
Collapse
|
9
|
Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson AJ, Tanaka T, Tanaka R, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCRJ 2020; 7:306-323. [PMID: 32148858 PMCID: PMC7055375 DOI: 10.1107/s205225252000072x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.
Collapse
Affiliation(s)
- Alexander M. Wolff
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Iris D. Young
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Eriko Nango
- 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
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazutaka Ito
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Laboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni-shi, Shizuoka 410-2321, Japan
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Justin T. Biel
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Aina E. Cohen
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Saul Cortez
- Department of Biology, San Francisco State University, San Francisco, California, USA
| | - Ana Gonzalez
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Tomoya Hino
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho, Minami, Tottori 680-8552, Japan
- Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Dohyun Im
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jake D. Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Minoru Kubo
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | | | - Takashi Nomura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, 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, Hyogo 679-5198, Japan
| | - Avi J. Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA
| | - 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
| | - 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
| | - Erin M. Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA
| | - Henry van den Bedem
- Bioscience Department, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Rahel A. Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA
| | - Fumiaki Yumoto
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan
| | - Wei Zhao
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - 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, Hyogo 679-5198, Japan
| | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - 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
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA
- Department of Physiology, University of California, Los Angeles, Los Angeles, California, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael C. Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| |
Collapse
|
10
|
Wickstrand C, Katona G, Nakane T, Nogly P, Standfuss J, Nango E, Neutze R. A tool for visualizing protein motions in time-resolved crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:024701. [PMID: 32266303 PMCID: PMC7113034 DOI: 10.1063/1.5126921] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/06/2020] [Indexed: 05/12/2023]
Abstract
Time-resolved serial femtosecond crystallography (TR-SFX) at an x-ray free electron laser enables protein structural changes to be imaged on time-scales from femtoseconds to seconds. It can, however, be difficult to grasp the nature and timescale of global protein motions when structural changes are not isolated near a single active site. New tools are, therefore, needed to represent the global nature of electron density changes and their correlation with modeled protein structural changes. Here, we use TR-SFX data from bacteriorhodopsin to develop and validate a method for quantifying time-dependent electron density changes and correlating them throughout the protein. We define a spherical volume of difference electron density about selected atoms, average separately the positive and negative electron difference densities within each volume, and walk this spherical volume through all atoms within the protein. By correlating the resulting difference electron density amplitudes with time, our approach facilitates an initial assessment of the number and timescale of structural intermediates and highlights quake-like motions on the sub-picosecond timescale. This tool also allows structural models to be compared with experimental data using theoretical difference electron density changes calculated from refined resting and photo-activated structures.
Collapse
Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | | | - Przemyslaw Nogly
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zürich, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
- Author to whom correspondence should be addressed:
| |
Collapse
|
11
|
Pump-Probe Time-Resolved Serial Femtosecond Crystallography at SACLA: Current Status and Data Collection Strategies. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9245505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Structural information on protein dynamics is a critical factor in fully understanding the protein functions. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) is a recently established technique for visualizing the structural changes or reactions in proteins that are at work with high spatial and temporal resolution. In the pump-probe method, protein microcrystals are continuously delivered from an injector and exposed to an X-ray free-electron laser (XFEL) pulse after a trigger to initiate a reaction, such as light, chemicals, temperature, and electric field, which affords the structural snapshots of intermediates that occur in the protein. We are in the process of developing the device and techniques for pump-probe TR-SFX while using XFEL produced at SPring-8 Angstrom Compact Free-Electron Laser (SACLA). In this paper, we described our current development details and data collection strategies for the optical pump X-ray probe TR-SFX experiment at SACLA and then reported the techniques of in crystallo TR spectroscopy, which is useful in clarifying the nature of reaction that takes place in crystals in advance.
Collapse
|
12
|
Standfuss J. Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr Opin Struct Biol 2019; 57:63-71. [DOI: 10.1016/j.sbi.2019.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/05/2023]
|
13
|
Kim D, Echelmeier A, Cruz Villarreal J, Gandhi S, Quintana S, Egatz-Gomez A, Ros A. Electric Triggering for Enhanced Control of Droplet Generation. Anal Chem 2019; 91:9792-9799. [PMID: 31260621 DOI: 10.1021/acs.analchem.9b01449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that uses X-ray free-electron lasers (XFEL) to determine structures of biomolecular complexes. Specifically, it benefits the study of atomic resolution structures of large membrane protein complexes and time-resolved reactions with crystallography. One major drawback of SFX studies with XFELs is the consumption of large amounts of a protein crystal sample to collect a complete X-ray diffraction data set for high-resolution crystal structures. This increases the time and resources required for sample preparation and experimentation. The intrinsic pulsed nature of all current X-ray sources is a major reason why such large amounts of sample are required. Any crystal sample that is delivered in the path of the X-ray beam during its "off-time" is wasted. To address this large sample consumption issue, we developed a 3D printed microfluidic system with integrated metal electrodes for water-in-oil droplet generation to dynamically create and manipulate aqueous droplets. We demonstrate on-demand droplet generation using DC potentials and the ability to tune the frequency of droplet generation through the application of AC potentials. More importantly, to assist with the synchronization of droplets and XFEL pulses, we show that the device can induce a phase shift in the base droplet generation frequency. This novel approach to droplet generation has the potential to reduce sample waste by more than 95% for SFX experiments with XFELs performed with liquid jets and can operate under low- and high-pressure liquid injection systems.
Collapse
Affiliation(s)
- Daihyun Kim
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Austin Echelmeier
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Sahir Gandhi
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Sebastian Quintana
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Ana Egatz-Gomez
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Alexandra Ros
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| |
Collapse
|
14
|
Echelmeier A, Sonker M, Ros A. Microfluidic sample delivery for serial crystallography using XFELs. Anal Bioanal Chem 2019; 411:6535-6547. [PMID: 31250066 DOI: 10.1007/s00216-019-01977-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) is an emerging field for structural biology. One of its major impacts lies in the ability to reveal the structure of complex proteins previously inaccessible with synchrotron-based crystallography techniques and allowing time-resolved studies from femtoseconds to seconds. The nature of this serial technique requires new approaches for crystallization, data analysis, and sample delivery. With continued advancements in microfabrication techniques, various developments have been reported in the past decade for innovative and efficient microfluidic sample delivery for crystallography experiments using XFELs. This article summarizes the recent developments in microfluidic sample delivery with liquid injection and fixed-target approaches, which allow exciting new research with XFELs. Graphical abstract.
Collapse
Affiliation(s)
- Austin Echelmeier
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA. .,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA.
| |
Collapse
|
15
|
Hutchison CDM, van Thor JJ. Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20170474. [PMID: 30929625 PMCID: PMC6452057 DOI: 10.1098/rsta.2017.0474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
Collapse
|
16
|
Schulz EC, Mehrabi P, Müller-Werkmeister HM, Tellkamp F, Jha A, Stuart W, Persch E, De Gasparo R, Diederich F, Pai EF, Miller RJD. The hit-and-return system enables efficient time-resolved serial synchrotron crystallography. Nat Methods 2018; 15:901-904. [DOI: 10.1038/s41592-018-0180-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/10/2018] [Indexed: 11/10/2022]
|
17
|
Nango E. Three-dimensional Movie of Chemical Reactions in Proteins Captured by X-ray Free Electron Lasers. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
18
|
Mizohata E, Nakane T, Fukuda Y, Nango E, Iwata S. Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology. Biophys Rev 2017; 10:209-218. [PMID: 29196935 DOI: 10.1007/s12551-017-0344-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022] Open
Abstract
X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca. 200-50 μm). In recent years, one of the most important technological innovations in structural biology has been the development of X-ray free electron lasers (XFELs). The SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan generates the XFEL beam by accelerating electrons to relativistic speeds and directing them through in-vacuum, short-period undulators. Since user operation started in 2012, we have been involved in the development of serial femtosecond crystallography (SFX) measurement systems using XFEL at the SACLA. The SACLA generates X-rays a billion times brighter than SPring-8. The extremely bright XFEL pulses enable data collection with microcrystals (ca. 50-1 μm). Although many molecular analysis techniques exist, SFX is the only technique that can visualize radiation-damage-free structures of biological macromolecules at room temperature in atomic resolution and fast time resolution. Here, we review the achievements of the SACLA-SFX Project in the past 5 years. In particular, we focus on: (1) the measurement system for SFX; (2) experimental phasing by SFX; (3) enzyme chemistry based on damage-free room-temperature structures; and (4) molecular movie taken by time-resolved SFX.
Collapse
Affiliation(s)
- Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 OQH, UK
| | - Yohta Fukuda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eriko Nango
- 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
| | - 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
| |
Collapse
|