51
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Oda K, Vierock J, Oishi S, Rodriguez-Rozada S, Taniguchi R, Yamashita K, Wiegert JS, Nishizawa T, Hegemann P, Nureki O. Crystal structure of the red light-activated channelrhodopsin Chrimson. Nat Commun 2018; 9:3949. [PMID: 30258177 PMCID: PMC6158191 DOI: 10.1038/s41467-018-06421-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 08/31/2018] [Indexed: 12/12/2022] Open
Abstract
Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Red-light-activated channelrhodopsins are of particular interest, because red light penetrates deeper into biological tissues and also enables dual-color experiments in combination with blue-light-activated optogenetic tools. Here we report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama, Chrimson, at 2.6 Å resolution. Chrimson resembles prokaryotic proton pumps in the retinal binding pocket, while sharing similarity with other channelrhodopsins in the ion-conducting pore. Concomitant mutation analysis identified the structural features that are responsible for Chrimson’s red light sensitivity; namely, the protonation of the counterion for the retinal Schiff base, and the polar residue distribution and rigidity of the retinal binding pocket. Based on these mechanistic insights, we engineered ChrimsonSA, a mutant with a maximum activation wavelength red-shifted beyond 605 nm and accelerated closing kinetics. Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Here, the authors report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama at 2.6 Å resolution.
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Affiliation(s)
- Kazumasa Oda
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo, 113-0034, Japan
| | - Johannes Vierock
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Satomi Oishi
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo, 113-0034, Japan
| | - Silvia Rodriguez-Rozada
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg (ZMNH), 20251, Hamburg, Germany
| | - Reiya Taniguchi
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo, 113-0034, Japan
| | | | - J Simon Wiegert
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg (ZMNH), 20251, Hamburg, Germany
| | - Tomohiro Nishizawa
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo, 113-0034, Japan. .,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan.
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Osamu Nureki
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo, 113-0034, Japan.
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52
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Affiliation(s)
- Keith Moffat
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60615, USA
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53
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Nogly P, Weinert T, James D, Carbajo S, Ozerov D, Furrer A, Gashi D, Borin V, Skopintsev P, Jaeger K, Nass K, Båth P, Bosman R, Koglin J, Seaberg M, Lane T, Kekilli D, Brünle S, Tanaka T, Wu W, Milne C, White T, Barty A, Weierstall U, Panneels V, Nango E, Iwata S, Hunter M, Schapiro I, Schertler G, Neutze R, Standfuss J. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science 2018; 361:science.aat0094. [PMID: 29903883 DOI: 10.1126/science.aat0094] [Citation(s) in RCA: 230] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/29/2018] [Indexed: 12/23/2022]
Abstract
Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.
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Affiliation(s)
- Przemyslaw Nogly
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.,Photon Science Division-Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sergio Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Dardan Gashi
- SwissFEL, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Veniamin Borin
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Petr Skopintsev
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Kathrin Jaeger
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Karol Nass
- SwissFEL, Paul Scherrer Institut, 5232 Villigen, Switzerland.,Photon Science Division-Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE- 40530 Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE- 40530 Gothenburg, Sweden
| | - Jason Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matthew Seaberg
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas Lane
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Demet Kekilli
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - 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
| | - Wenting Wu
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | | | - Thomas White
- Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Valerie Panneels
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - 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
| | - Mark Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gebhard Schertler
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.,Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE- 40530 Gothenburg, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.
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54
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Kandori H, Inoue K, Tsunoda SP. Light-Driven Sodium-Pumping Rhodopsin: A New Concept of Active Transport. Chem Rev 2018. [DOI: 10.1021/acs.chemrev.7b00548] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Satoshi P. Tsunoda
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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55
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Huang H, Yang B, Ge B, Lao J, Zhou S, Huang F. Using self-cleavable ternary fusion pattern for efficient preparation of Bacteriorhodopsin. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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56
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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57
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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.
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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
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58
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Mehler M, Eckert CE, Leeder AJ, Kaur J, Fischer T, Kubatova N, Brown LJ, Brown RCD, Becker-Baldus J, Wachtveitl J, Glaubitz C. Chromophore Distortions in Photointermediates of Proteorhodopsin Visualized by Dynamic Nuclear Polarization-Enhanced Solid-State NMR. J Am Chem Soc 2017; 139:16143-16153. [PMID: 29027800 DOI: 10.1021/jacs.7b05061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteorhodopsin (PR) is the most abundant retinal protein on earth and functions as a light-driven proton pump. Despite extensive efforts, structural data for PR photointermediate states have not been obtained. On the basis of dynamic nuclear polarization (DNP)-enhanced solid-state NMR, we were able to analyze the retinal polyene chain between positions C10 and C15 as well as the Schiff base nitrogen in the ground state in comparison to light-induced, cryotrapped K- and M-states. A high M-state population could be achieved by preventing reprotonation of the Schiff base through a mutation of the primary proton donor (E108Q). Our data reveal unexpected large and alternating 13C chemical shift changes in the K-state propagating away from the Schiff base along the polyene chain. Furthermore, two different M-states have been observed reflecting the Schiff base reorientation after the deprotonation step. Our study provides novel insight into the photocycle of PR and also demonstrates the power of DNP-enhanced solid-state NMR to bridge the gap between functional and structural data and models.
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Affiliation(s)
- Michaela Mehler
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Carl Elias Eckert
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Alexander J Leeder
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Tobias Fischer
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Nina Kubatova
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Lynda J Brown
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Richard C D Brown
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
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59
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Abela R, Beaud P, van Bokhoven JA, Chergui M, Feurer T, Haase J, Ingold G, Johnson SL, Knopp G, Lemke H, Milne CJ, Pedrini B, Radi P, Schertler G, Standfuss J, Staub U, Patthey L. Perspective: Opportunities for ultrafast science at SwissFEL. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061602. [PMID: 29376109 PMCID: PMC5758366 DOI: 10.1063/1.4997222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 10/17/2017] [Indexed: 05/03/2023]
Abstract
We present the main specifications of the newly constructed Swiss Free Electron Laser, SwissFEL, and explore its potential impact on ultrafast science. In light of recent achievements at current X-ray free electron lasers, we discuss the potential territory for new scientific breakthroughs offered by SwissFEL in Chemistry, Biology, and Materials Science, as well as nonlinear X-ray science.
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Affiliation(s)
- Rafael Abela
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Paul Beaud
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jeroen A van Bokhoven
- Laboratory for Catalysis and Sustainable Chemistry, Paul-Scherrer Institute, 5232 Villigen PSI, and Department of Chemistry, ETH-Zürich, 8093 Zürich, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast Science (LACUS), Ecole Polytechnique Fédérale de Lausanne (EPFL), ISIC-FSB, Station 6, 1015 Lausanne, Switzerland
| | - Thomas Feurer
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Johannes Haase
- Laboratory for Catalysis and Sustainable Chemistry, Paul-Scherrer Institute, 5232 Villigen PSI, and Department of Chemistry, ETH-Zürich, 8093 Zürich, Switzerland
| | - Gerhard Ingold
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Steven L Johnson
- Institute for Quantum Electronics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zurich, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Henrik Lemke
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Chris J Milne
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Bill Pedrini
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Peter Radi
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Urs Staub
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Luc Patthey
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
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60
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Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1512-1521. [PMID: 28844743 DOI: 10.1016/j.bbapap.2017.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/06/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022]
Abstract
Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.
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61
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Dods R, Båth P, Arnlund D, Beyerlein KR, Nelson G, Liang M, Harimoorthy R, Berntsen P, Malmerberg E, Johansson L, Andersson R, Bosman R, Carbajo S, Claesson E, Conrad CE, Dahl P, Hammarin G, Hunter MS, Li C, Lisova S, Milathianaki D, Robinson J, Safari C, Sharma A, Williams G, Wickstrand C, Yefanov O, Davidsson J, DePonte DP, Barty A, Brändén G, Neutze R. From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography. Structure 2017; 25:1461-1468.e2. [PMID: 28781082 DOI: 10.1016/j.str.2017.07.002] [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: 04/05/2017] [Revised: 06/19/2017] [Accepted: 07/06/2017] [Indexed: 01/13/2023]
Abstract
Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RCvir). We first crushed these crystals prior to multiple rounds of microseeding. Each cycle of microseeding facilitated improvements in the RCvir serial femtosecond crystallography (SFX) structure from 3.3-Å to 2.4-Å resolution. This approach may allow known crystallization conditions for other proteins to be adapted to exploit novel scientific opportunities created by serial crystallography.
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Affiliation(s)
- Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Mengling Liang
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Erik Malmerberg
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Linda Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; The Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Sergio Carbajo
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mark S Hunter
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Despina Milathianaki
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Joseph Robinson
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Amit Sharma
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Garth Williams
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Jan Davidsson
- Department of Photochemistry and Molecular Science, Uppsala University, Uppsala, Sweden
| | - Daniel P DePonte
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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62
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Bondar AN, Smith JC. Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins. Photochem Photobiol 2017; 93:1336-1344. [DOI: 10.1111/php.12790] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/20/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics Group; Department of Physics; Freie Universität Berlin; Berlin Germany
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics; Oak Ridge TN
- Department of Biochemistry and Cellular and Molecular Biology; University of Tennessee; Knoxville TN
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63
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Abstract
The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na+ pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521:48-53]. To elucidate its molecular mechanism for Na+ pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na+ binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.
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64
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Kamiya M, Hayashi S. Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation. J Phys Chem B 2017; 121:3842-3852. [PMID: 28240904 DOI: 10.1021/acs.jpcb.6b13050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopsin is a G-protein coupled receptor functioning as a photoreceptor for vision through photoactivation of a covalently bound ligand of a retinal protonated Schiff base chromophore. Despite the availability of structural information on the inactivated and activated forms of the receptor, the transition processes initiated by the photoabsorption have not been well understood. Here we theoretically examined the photoactivation processes by means of molecular dynamics (MD) simulations and ab initio quantum mechanical/molecular mechanical (QM/MM) free energy geometry optimizations which enabled accurate geometry determination of the ligand molecule in ample statistical conformational samples of the protein. Structures of the intermediate states of the activation process, blue-shifted intermediate and Lumi, as well as the dark state first generated by MD simulations and then refined by the QM/MM free energy geometry optimizations were characterized by large displacement of the β-ionone ring of retinal along with change in the hydrogen bond of the protonated Schiff base. The ab initio calculations of vibrational and electronic spectroscopic properties of those states well reproduced the experimental observations and successfully identified the molecular origins underlying the spectroscopic features. The structural evolution in the formation of the intermediates provides a molecular insight into the efficient activation processes of the receptor.
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Affiliation(s)
- Motoshi Kamiya
- 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
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65
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Light-Patterned Current Generation in a Droplet Bilayer Array. Sci Rep 2017; 7:46585. [PMID: 28417964 PMCID: PMC5394532 DOI: 10.1038/srep46585] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/17/2017] [Indexed: 11/08/2022] Open
Abstract
We have created a 4 × 4 droplet bilayer array comprising light-activatable aqueous droplet bio-pixels. Aqueous droplets containing bacteriorhodopsin (bR), a light-driven proton pump, were arranged on a common hydrogel surface in lipid-containing oil. A separate lipid bilayer formed at the interface between each droplet and the hydrogel; each bilayer then incorporated bR. Electrodes in each droplet simultaneously measured the light-driven proton-pumping activities of each bio-pixel. The 4 × 4 array derived by this bottom-up synthetic biology approach can detect grey-scale images and patterns of light moving across the device, which are transduced as electrical current generated in each bio-pixel. We propose that synthetic biological light-activatable arrays, produced with soft materials, might be interfaced with living tissues to stimulate neuronal pathways.
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66
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Gunner MR, Koder R. The design features cells use to build their transmembrane proton gradient. Phys Biol 2017; 14:013001. [DOI: 10.1088/1478-3975/14/1/013001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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67
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Nango E, Royant A, Kubo M, Nakane T, Wickstrand C, Kimura T, Tanaka T, Tono K, Song C, Tanaka R, Arima T, Yamashita A, Kobayashi J, Hosaka T, Mizohata E, Nogly P, Sugahara M, Nam D, Nomura T, Shimamura T, Im D, Fujiwara T, Yamanaka Y, Jeon B, Nishizawa T, Oda K, Fukuda M, Andersson R, Båth P, Dods R, Davidsson J, Matsuoka S, Kawatake S, Murata M, Nureki O, Owada S, Kameshima T, Hatsui T, Joti Y, Schertler G, Yabashi M, Bondar AN, Standfuss J, Neutze R, Iwata S. A three-dimensional movie of structural changes in bacteriorhodopsin. Science 2016; 354:1552-1557. [DOI: 10.1126/science.aah3497] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/21/2016] [Indexed: 01/24/2023]
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68
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Hurley BP, Eaton AD, Zimmermann C, Delaney B. Polarized monolayer cultures of human intestinal epithelial cell lines exposed to intractable proteins - In vitro hazard identification studies. Food Chem Toxicol 2016; 98:262-268. [DOI: 10.1016/j.fct.2016.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 12/01/2022]
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69
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Kato HE, Inoue K, Kandori H, Nureki O. The light-driven sodium ion pump: A new player in rhodopsin research. Bioessays 2016; 38:1274-1282. [PMID: 27859420 DOI: 10.1002/bies.201600065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Rhodopsins are one of the most studied photoreceptor protein families, and ion-translocating rhodopsins, both pumps and channels, have recently attracted broad attention because of the development of optogenetics. Recently, a new functional class of ion-pumping rhodopsins, an outward Na+ pump, was discovered, and following structural and functional studies enable us to compare three functionally different ion-pumping rhodopsins: outward proton pump, inward Cl- pump, and outward Na+ pump. Here, we review the current knowledge on structure-function relationships in these three light-driven pumps, mainly focusing on Na+ pumps. A structural and functional comparison reveals both unique and conserved features of these ion pumps, and enhances our understanding about how the structurally similar microbial rhodopsins acquired such diverse functions. We also discuss some unresolved questions and future perspectives in research of ion-pumping rhodopsins, including optogenetics application and engineering of novel rhodopsins.
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Affiliation(s)
- Hideaki E Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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70
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Bronder AM, Bieker A, Elter S, Etzkorn M, Häussinger D, Oesterhelt F. Oriented Membrane Protein Reconstitution into Tethered Lipid Membranes for AFM Force Spectroscopy. Biophys J 2016; 111:1925-1934. [PMID: 27806274 PMCID: PMC5103026 DOI: 10.1016/j.bpj.2016.08.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022] Open
Abstract
Membrane proteins act as a central interface between the extracellular environment and the intracellular response and as such represent one of the most important classes of drug targets. The characterization of the molecular properties of integral membrane proteins, such as topology and interdomain interaction, is key to a fundamental understanding of their function. Atomic force microscopy (AFM) and force spectroscopy have the intrinsic capabilities of investigating these properties in a near-native setting. However, atomic force spectroscopy of membrane proteins is traditionally carried out in a crystalline setup. Alternatively, model membrane systems, such as tethered bilayer membranes, have been developed for surface-dependent techniques. While these setups can provide a more native environment, data analysis may be complicated by the normally found statistical orientation of the reconstituted protein in the model membrane. We have developed a model membrane system that enables the study of membrane proteins in a defined orientation by single-molecule force spectroscopy. Our approach is demonstrated using cell-free expressed bacteriorhodopsin coupled to a quartz glass surface in a defined orientation through a protein anchor and reconstituted inside an artificial membrane system. This approach offers an effective way to study membrane proteins in a planar lipid bilayer. It can be easily transferred to all membrane proteins that possess a suitable tag and can be reconstituted into a lipid bilayer. In this respect, we anticipate that this technique may contribute important information on structure, topology, and intra- and intermolecular interactions of other seven-transmembrane helical receptors.
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Affiliation(s)
- Anna M Bronder
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany.
| | - Adeline Bieker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Shantha Elter
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology and Infectiology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Filipp Oesterhelt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany; Department for Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
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71
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Nogly P, Panneels V, Nelson G, Gati C, Kimura T, Milne C, Milathianaki D, Kubo M, Wu W, Conrad C, Coe J, Bean R, Zhao Y, Båth P, Dods R, Harimoorthy R, Beyerlein KR, Rheinberger J, James D, DePonte D, Li C, Sala L, Williams GJ, Hunter MS, Koglin JE, Berntsen P, Nango E, Iwata S, Chapman HN, Fromme P, Frank M, Abela R, Boutet S, Barty A, White TA, Weierstall U, Spence J, Neutze R, Schertler G, Standfuss J. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Nat Commun 2016; 7:12314. [PMID: 27545823 PMCID: PMC4996941 DOI: 10.1038/ncomms12314] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/22/2016] [Indexed: 01/12/2023] Open
Abstract
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
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Affiliation(s)
- Przemyslaw Nogly
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Valerie Panneels
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Tetsunari Kimura
- Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | | | - Despina Milathianaki
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Minoru Kubo
- Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan.,PRESTO, JST, Saitama 332-0012, Japan
| | - Wenting Wu
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Chelsie Conrad
- Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Jesse Coe
- Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Jan Rheinberger
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Daniel James
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Daniel DePonte
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Leonardo Sala
- SwissFEL, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Garth J Williams
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Eriko Nango
- SACLA Science Research Group, RIKEN/SPring-8 Center, Hyogo 679-5148, Japan
| | - So Iwata
- SACLA Science Research Group, RIKEN/SPring-8 Center, Hyogo 679-5148, Japan.,Department of Cell Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Department of Physics, University of Hamburg, 22761 Hamburg, Germany.,Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore 94550, USA
| | - Rafael Abela
- SwissFEL, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - John Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gebhard Schertler
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland.,Department of Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Jörg Standfuss
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
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72
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Svechtarova MI, Buzzacchera I, Toebes BJ, Lauko J, Anton N, Wilson CJ. Sensor Devices Inspired by the Five Senses: A Review. ELECTROANAL 2016. [DOI: 10.1002/elan.201600047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | | | - B. Jelle Toebes
- NovioSense BV; Transistorweg 5 6534 AT Nijmegen The Netherlands
| | - Jan Lauko
- NovioSense BV; Transistorweg 5 6534 AT Nijmegen The Netherlands
| | - Nicoleta Anton
- Universitatea de Medicina si Farmacie Grigore T.; Popa, Str. Universitatii nr. 16 700115 Iasi Romania
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73
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Ge X, Gunner MR. Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin. Proteins 2016; 84:639-54. [DOI: 10.1002/prot.25013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/24/2016] [Accepted: 02/04/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Xiaoxia Ge
- Physics Department; City College of New York; New York NY 10031
| | - M. R. Gunner
- Physics Department; City College of New York; New York NY 10031
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74
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Kouyama T, Kawaguchi H, Nakanishi T, Kubo H, Murakami M. Crystal structures of the L1, L2, N, and O states of pharaonis halorhodopsin. Biophys J 2016; 108:2680-90. [PMID: 26039169 PMCID: PMC4457492 DOI: 10.1016/j.bpj.2015.04.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 01/15/2023] Open
Abstract
Halorhodopsin from Natronomonas pharaonis (pHR) functions as a light-driven halide ion pump. In the presence of halide ions, the photochemical reaction of pHR is described by the scheme: K→ L1 → L2 → N → O → pHR′ → pHR. Here, we report light-induced structural changes of the pHR-bromide complex observed in the C2 crystal. In the L1-to-L2 transition, the bromide ion that initially exists in the extracellular vicinity of retinal moves across the retinal Schiff base. Upon the formation of the N state with a bromide ion bound to the cytoplasmic vicinity of the retinal Schiff base, the cytoplasmic half of helix F moves outward to create a water channel in the cytoplasmic interhelical space, whereas the extracellular half of helix C moves inward. During the transition from N to an N-like reaction state with retinal assuming the 13-cis/15-syn configuration, the translocated bromide ion is released into the cytoplasmic medium. Subsequently, helix F relaxes into its original conformation, generating the O state. Anion uptake from the extracellular side occurs when helix C relaxes into its original conformation. These structural data provide insight into the structural basis of unidirectional anion transport.
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Affiliation(s)
- Tsutomu Kouyama
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan; RIKEN Harima Branch, 1-1-1, Kouto, Sayo, Hyogo, Japan.
| | - Haruki Kawaguchi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Taichi Nakanishi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Hiroki Kubo
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Midori Murakami
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
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75
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76
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Lindner R, Heintz U, Winkler A. Applications of hydrogen deuterium exchange (HDX) for the characterization of conformational dynamics in light-activated photoreceptors. Front Mol Biosci 2015; 2:33. [PMID: 26157802 PMCID: PMC4477167 DOI: 10.3389/fmolb.2015.00033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 11/13/2022] Open
Abstract
Rational design of optogenetic tools is inherently linked to the understanding of photoreceptor function. Structural analysis of elements involved in signal integration in individual sensor domains provides an initial idea of their mode of operation, but understanding how local structural rearrangements eventually affect signal transmission to output domains requires inclusion of the effector regions in the characterization. However, the dynamic nature of these assemblies renders their structural analysis challenging and therefore a combination of high- and low-resolution techniques is required to appreciate functional aspects of photoreceptors. This review focuses on the potential of hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) for complementing the structural characterization of photoreceptors. In this respect, the ability of HDX-MS to provide information on conformational dynamics and the possibility to address multiple functionally relevant states in solution render this methodology ideally suitable. We highlight recent examples demonstrating the potential of HDX-MS and discuss how these results can help to improve existing optogenetic systems or guide the design of novel optogenetic tools.
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Affiliation(s)
- Robert Lindner
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Udo Heintz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology Graz, Austria
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77
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Petrovskaya LE, Balashov SP, Lukashev EP, Imasheva ES, Gushchin IY, Dioumaev AK, Rubin AB, Dolgikh DA, Gordeliy VI, Lanyi JK, Kirpichnikov MP. ESR — A retinal protein with unusual properties from Exiguobacterium sibiricum. BIOCHEMISTRY (MOSCOW) 2015; 80:688-700. [DOI: 10.1134/s000629791506005x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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78
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da Silva GFZ, Goblirsch BR, Tsai AL, Spudich JL. Cation-Specific Conformations in a Dual-Function Ion-Pumping Microbial Rhodopsin. Biochemistry 2015; 54:3950-9. [PMID: 26037033 DOI: 10.1021/bi501386d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A recently discovered rhodopsin ion pump (DeNaR, also known as KR2) in the marine bacterium Dokdonia eikasta uses light to pump protons or sodium ions from the cell depending on the ionic composition of the medium. In cells suspended in a KCl solution, DeNaR functions as a light-driven proton pump, whereas in a NaCl solution, DeNaR conducts light-driven sodium ion pumping, a novel activity within the rhodopsin family. These two distinct functions raise the questions of whether the conformations of the protein differ in the presence of K(+) or Na(+) and whether the helical movements that result in the canonical E → C conformational change in other microbial rhodopsins are conserved in DeNaR. Visible absorption maxima of DeNaR in its unphotolyzed (dark) state show an 8 nm difference between Na(+) and K(+) in decyl maltopyranoside micelles, indicating an influence of the cations on the retinylidene photoactive site. In addition, electronic paramagnetic resonance (EPR) spectra of the dark states reveal repositioning of helices F and G when K(+) is replaced with Na(+). Furthermore, the conformational changes assessed by EPR spin-spin dipolar coupling show that the light-induced transmembrane helix movements are very similar to those found in bacteriorhodopsin but are altered by the presence of Na(+), resulting in a new feature, the clockwise rotation of helix F. The results establish the first observation of a cation switch controlling the conformations of a microbial rhodopsin and indicate specific interactions of Na(+) with the half-channels of DeNaR to open an appropriate path for ion translocation.
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Affiliation(s)
- Giordano F Z da Silva
- †Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, United States
| | - Brandon R Goblirsch
- †Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, United States
| | - Ah-Lim Tsai
- ‡Department of Internal Medicine, Division of Hematology, University of Texas Medical School, Houston, Texas 77030, United States
| | - John L Spudich
- †Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, United States
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79
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Light-driven Na(+) pumps as next-generation inhibitory optogenetic tools. Nat Struct Mol Biol 2015; 22:351-3. [PMID: 25945883 DOI: 10.1038/nsmb.3017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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80
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Struts AV, Barmasov AV, Brown MF. SPECTRAL METHODS FOR STUDY OF THE G-PROTEIN-COUPLED RECEPTOR RHODOPSIN. I. VIBRATIONAL AND ELECTRONIC SPECTROSCOPY. OPTICS AND SPECTROSCOPY 2015; 118:711-717. [PMID: 28260815 PMCID: PMC5334778 DOI: 10.1134/s0030400x15050240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here we review the application of modern spectral methods for the study of G-protein-coupled receptors (GPCRs) using rhodopsin as a prototype. Because X-ray analysis gives us immobile snapshots of protein conformations, it is imperative to apply spectroscopic methods for elucidating their function: vibrational (Raman, FTIR), electronic (UV-visible absorption, fluorescence) spectroscopies, and magnetic resonance (electron paramagnetic resonance, EPR), and nuclear magnetic resonance, NMR). In the first of the two companion articles, we discuss the application of optical spectroscopy for studying rhodopsin in a membrane environment. Information is obtained regarding the time-ordered sequence of events in rhodopsin activation. Isomerization of the chromophore and deprotonation of the retinal Schiff base leads to a structural change of the protein involving the motion of helices H5 and H6 in a pH-dependent process. Information is obtained that is unavailable from X-ray crystallography, which can be combined with spectroscopic studies to achieve a more complete understanding of GPCR function.
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Affiliation(s)
- A V Struts
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia; University of Arizona, Tucson, AZ 85721 USA
| | - A V Barmasov
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia
| | - M F Brown
- University of Arizona, Tucson, AZ 85721 USA
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Alfinito E, Reggiani L. Mechanisms responsible for the photocurrent in bacteriorhodopsin. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:032702. [PMID: 25871139 DOI: 10.1103/physreve.91.032702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 06/04/2023]
Abstract
Recently, there has been growing interest in the electrical properties of bacteriorhodopsin (bR), a protein belonging to the transmembrane protein family. Several experiments pointed out the role of green light in enhancing the current flow in nanolayers of bR, thus confirming potential applications of this protein in the field of optoelectronics. By contrast, the mechanisms underlying the charge transfer and the associated photocurrent are still far from being understood at a microscopic level. To take into account the structure-dependent nature of the current, in a previous set of papers we suggested a mechanism of sequential tunneling among neighboring amino acids. As a matter of fact, when irradiated with green light, bR undergoes a conformational change at a molecular level. Thus, the role played by the protein tertiary-structure in modeling the charge transfer cannot be neglected. The aim of this paper is to go beyond previous models, in the framework of a new branch of electronics we call proteotronics, which exploits the ability of using proteins as reliable, well-understood materials for the development of novel bioelectronic devices. In particular, the present approach assumes that the conformational change is not the unique transformation the protein undergoes when irradiated by light. Instead, the light can also promote an increase of the protein state free energy that, in turn, should modify its internal degree of connectivity. This phenomenon is here described by the change of the value of an interaction radius associated with the physical interactions among amino acids. The implemented model enables us to achieve a better agreement between theory and experiments in the region of a low applied bias by preserving the level of agreement at high values of applied bias. Furthermore, results provide new insights on the mechanisms responsible for bR photoresponse.
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Affiliation(s)
- Eleonora Alfinito
- Dipartimento di Ingegneria dell'Innovazione, Università del Salento, via Monteroni, I-73100 Lecce, Italy and CNISM, Via della Vasca Navale, 84-00146 Rome, Italy
| | - Lino Reggiani
- Dipartimento di Matematica e Fisica, "Ennio de Giorgi," Università del Salento, via Monteroni, I-73100 Lecce, Italy and CNISM, Via della Vasca Navale, 84-00146 Rome, Italy
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82
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Shevchenko V, Gushchin I, Polovinkin V, Round E, Borshchevskiy V, Utrobin P, Popov A, Balandin T, Büldt G, Gordeliy V. Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form. PLoS One 2014; 9:e112873. [PMID: 25479443 PMCID: PMC4257550 DOI: 10.1371/journal.pone.0112873] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/17/2014] [Indexed: 12/02/2022] Open
Abstract
Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.
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Affiliation(s)
- Vitaly Shevchenko
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Ivan Gushchin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Vitaly Polovinkin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Ekaterina Round
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Petr Utrobin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | | | - Taras Balandin
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Georg Büldt
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- European Synchrotron Radiation Facility, Grenoble, France
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