1
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Hammarin G, Norder P, Harimoorthy R, Chen G, Berntsen P, Widlund PO, Stoij C, Rodilla H, Swenson J, Brändén G, Neutze R. No observable non-thermal effect of microwave radiation on the growth of microtubules. Sci Rep 2024; 14:18286. [PMID: 39112501 PMCID: PMC11306338 DOI: 10.1038/s41598-024-68852-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
Despite widespread public interest in the health impact of exposure to microwave radiation, studies of the influence of microwave radiation on biological samples are often inconclusive or contradictory. Here we examine the influence of microwave radiation of frequencies 3.5 GHz, 20 GHz and 29 GHz on the growth of microtubules, which are biological nanotubes that perform diverse functions in eukaryotic cells. Since microtubules are highly polar and can extend several micrometres in length, they are predicted to be sensitive to non-ionizing radiation. Moreover, it has been speculated that tubulin dimers within microtubules might rapidly toggle between different conformations, potentially participating in computational or other cooperative processes. Our data show that exposure to microwave radiation yields a microtubule growth curve that is distorted relative to control studies utilizing a homogeneous temperature jump. However, this apparent effect of non-ionizing radiation is reproduced by control experiments using an infrared laser or hot air to heat the sample and thereby mimic the thermal history of samples exposed to microwaves. As such, no non-thermal effects of microwave radiation on microtubule growth can be assigned. Our results highlight the need for appropriate control experiments in biophysical studies that may impact on the sphere of public interest.
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Affiliation(s)
- Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Per Norder
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Guo Chen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Monash Health Imaging, Monash Health, Clayton, VIC, Australia
| | - Per O Widlund
- Institution of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Helena Rodilla
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - 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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2
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Magkakis K, Orädd F, Ahn B, Da Silva V, Appio R, Plivelic TS, Andersson M. Real-time structural characterization of protein response to a caged compound by fast detector readout and high-brilliance synchrotron radiation. Structure 2024:S0969-2126(24)00192-8. [PMID: 38889721 DOI: 10.1016/j.str.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/19/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024]
Abstract
Protein dynamics are essential to biological function, and methods to determine such structural rearrangements constitute a frontier in structural biology. Synchrotron radiation can track real-time protein dynamics, but accessibility to dedicated high-flux single X-ray pulse time-resolved beamlines is scarce and protein targets amendable to such characterization are limited. These limitations can be alleviated by triggering the reaction by laser-induced activation of a caged compound and probing the structural dynamics by fast-readout detectors. In this work, we established time-resolved X-ray solution scattering (TR-XSS) at the CoSAXS beamline at the MAX IV Laboratory synchrotron. Laser-induced activation of caged ATP initiated phosphoryl transfer in the adenylate kinase (AdK) enzyme, and the reaction was monitored up to 50 ms with a 2-ms temporal resolution achieved by the detector readout. The time-resolved structural signal of the protein showed minimal radiation damage effects and excellent agreement to data collected by a single X-ray pulse approach.
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Affiliation(s)
| | - Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Byungnam Ahn
- MAX IV Laboratory, Lund University, Lund, Sweden
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3
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Struts AV, Barmasov AV, Fried SDE, Hewage KSK, Perera SMDC, Brown MF. Osmotic stress studies of G-protein-coupled receptor rhodopsin activation. Biophys Chem 2024; 304:107112. [PMID: 37952496 DOI: 10.1016/j.bpc.2023.107112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 11/14/2023]
Abstract
We summarize and critically review osmotic stress studies of the G-protein-coupled receptor rhodopsin. Although small amounts of structural water are present in these receptors, the effect of bulk water on their function remains uncertain. Studies of the influences of osmotic stress on the GPCR archetype rhodopsin have given insights into the functional role of water in receptor activation. Experimental work has discovered that osmolytes shift the metarhodopsin equilibrium after photoactivation, either to the active or inactive conformations according to their molar mass. At least 80 water molecules are found to enter rhodopsin in the transition to the photoreceptor active state. We infer that this movement of water is both necessary and sufficient for receptor activation. If the water influx is prevented, e.g., by large polymer osmolytes or by dehydration, then the receptor functional transition is back shifted. These findings imply a new paradigm in which rhodopsin becomes solvent swollen in the activation mechanism. Water thus acts as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.
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Affiliation(s)
- Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Laboratory of Biomolecular NMR, St.-Petersburg State University, 199034 St.-Petersburg, Russia
| | - Alexander V Barmasov
- Department of Biophysics, St.-Petersburg State Pediatric Medical University, 194100 St.-Petersburg, Russia; Department of Physics, St.-Petersburg State University, 199034 St.-Petersburg, Russia
| | - Steven D E Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kushani S K Hewage
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | | | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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4
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Role of Monomer/Tetramer Equilibrium of Rod Visual Arrestin in the Interaction with Phosphorylated Rhodopsin. Int J Mol Sci 2023; 24:ijms24054963. [PMID: 36902393 PMCID: PMC10003454 DOI: 10.3390/ijms24054963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
The phototransduction cascade in vertebrate rod visual cells is initiated by the photoactivation of rhodopsin, which enables the activation of the visual G protein transducin. It is terminated by the phosphorylation of rhodopsin, followed by the binding of arrestin. Here we measured the solution X-ray scattering of nanodiscs containing rhodopsin in the presence of rod arrestin to directly observe the formation of the rhodopsin/arrestin complex. Although arrestin self-associates to form a tetramer at physiological concentrations, it was found that arrestin binds to phosphorylated and photoactivated rhodopsin at 1:1 stoichiometry. In contrast, no complex formation was observed for unphosphorylated rhodopsin upon photoactivation, even at physiological arrestin concentrations, suggesting that the constitutive activity of rod arrestin is sufficiently low. UV-visible spectroscopy demonstrated that the rate of the formation of the rhodopsin/arrestin complex well correlates with the concentration of arrestin monomer rather than the tetramer. These findings indicate that arrestin monomer, whose concentration is almost constant due to the equilibrium with the tetramer, binds to phosphorylated rhodopsin. The arrestin tetramer would act as a reservoir of monomer to compensate for the large changes in arrestin concentration in rod cells caused by intense light or adaptation.
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5
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Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
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Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
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Sarabi D, Ostojić L, Bosman R, Vallejos A, Linse JB, Wulff M, Levantino M, Neutze R. Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054102. [PMID: 36329868 PMCID: PMC9625836 DOI: 10.1063/4.0000157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging. This step often builds from complementary structural information, including secondary structural changes extracted from crystallographic studies or molecular dynamics simulations. When working with integral membrane proteins, another challenge arises because x-ray scattering from the protein and the surrounding detergent micelle interfere and these effects should be considered during structural modeling. Here, we utilize molecular dynamics simulations to explicitly incorporate the x-ray scattering cross term between a membrane protein and its surrounding detergent micelle when modeling TR-XSS data from photoactivated samples of detergent solubilized bacteriorhodopsin. This analysis provides theoretical foundations in support of our earlier approach to structural modeling that did not explicitly incorporate this cross term and improves agreement between experimental data and theoretical predictions at lower x-ray scattering angles.
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Affiliation(s)
- Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Lucija Ostojić
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Johanna-Barbara Linse
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michael Wulff
- European Synchrotron Radiation Facility, 38043 Grenoble Cedex 9, France
| | - Matteo Levantino
- European Synchrotron Radiation Facility, 38043 Grenoble Cedex 9, France
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
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7
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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8
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Jeong H, Ki H, Kim JG, Kim J, Lee Y, Ihee H. Sensitivity of
time‐resolved
diffraction data to changes in internuclear distances and atomic positions. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Haeyun Jeong
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
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9
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Orädd F, Ravishankar H, Goodman J, Rogne P, Backman L, Duelli A, Nors Pedersen M, Levantino M, Wulff M, Wolf-Watz M, Andersson M. Tracking the ATP-binding response in adenylate kinase in real time. SCIENCE ADVANCES 2021; 7:eabi5514. [PMID: 34788091 PMCID: PMC8597995 DOI: 10.1126/sciadv.abi5514] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/27/2021] [Indexed: 05/25/2023]
Abstract
The biological function of proteins is critically dependent on dynamics inherent to the native structure. Such structural dynamics obey a predefined order and temporal timing to execute the specific reaction. Determination of the cooperativity of key structural rearrangements requires monitoring protein reactions in real time. In this work, we used time-resolved x-ray solution scattering (TR-XSS) to visualize structural changes in the Escherichia coli adenylate kinase (AdK) enzyme upon laser-induced activation of a protected ATP substrate. A 4.3-ms transient intermediate showed partial closing of both the ATP- and AMP-binding domains, which indicates a cooperative closing mechanism. The ATP-binding domain also showed local unfolding and breaking of an Arg131-Asp146 salt bridge. Nuclear magnetic resonance spectroscopy data identified similar unfolding in an Arg131Ala AdK mutant, which refolded in a closed, substrate-binding conformation. The observed structural dynamics agree with a “cracking mechanism” proposed to underlie global structural transformation, such as allostery, in proteins.
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Harsha Ravishankar
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Jack Goodman
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Per Rogne
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Lars Backman
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Martin Nors Pedersen
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Matteo Levantino
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Michael Wulff
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Magnus Andersson
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
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10
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Monteiro DCF, Amoah E, Rogers C, Pearson AR. Using photocaging for fast time-resolved structural biology studies. Acta Crystallogr D Struct Biol 2021; 77:1218-1232. [PMID: 34605426 PMCID: PMC8489231 DOI: 10.1107/s2059798321008809] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Careful selection of photocaging approaches is critical to achieve fast and well synchronized reaction initiation and perform successful time-resolved structural biology experiments. This review summarizes the best characterized and most relevant photocaging groups previously described in the literature. It also provides a walkthrough of the essential factors to consider in designing a suitable photocaged molecule to address specific biological questions, focusing on photocaging groups with well characterized spectroscopic properties. The relationships between decay rates (k in s-1), quantum yields (ϕ) and molar extinction coefficients (ϵmax in M-1 cm-1) are highlighted for different groups. The effects of the nature of the photocaged group on these properties is also discussed. Four main photocaging scaffolds are presented in detail, o-nitrobenzyls, p-hydroxyphenyls, coumarinyls and nitrodibenzofuranyls, along with three examples of the use of this technology. Furthermore, a subset of specialty photocages are highlighted: photoacids, molecular photoswitches and metal-containing photocages. These extend the range of photocaging approaches by, for example, controlling pH or generating conformationally locked molecules.
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Affiliation(s)
- Diana C. F. Monteiro
- Hauptman–Woodward Medical Research Institute, 700 Ellicot Street, Buffalo, NY 14203, USA
| | - Emmanuel Amoah
- Hauptman–Woodward Medical Research Institute, 700 Ellicot Street, Buffalo, NY 14203, USA
| | - Cromarte Rogers
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Arwen R. Pearson
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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11
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Abstract
The four vertebrate arrestins play a key role in the desensitization and internalization of G protein-coupled receptors (GPCRs) and also mediate receptor-dependent signaling. Recent work has shown that bias for arrestin vs G protein signaling could offer certain therapeutic advantages (or disadvantages) in different systems, making assays that measure arrestin binding to receptors important for drug discovery efforts. Herein, we briefly review several commonly used techniques for measuring arrestin binding to receptors, as well as provide an in-depth and methodologically focused review of two methods that do not require receptor modification. The first approach measures direct binding between purified arrestin and rhodopsin, and the second measures the recruitment of arrestin to receptors in living cells.
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12
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Orädd F, Andersson M. Tracking Membrane Protein Dynamics in Real Time. J Membr Biol 2021; 254:51-64. [PMID: 33409541 PMCID: PMC7936944 DOI: 10.1007/s00232-020-00165-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022]
Abstract
Abstract Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by the vast ranges of structural dynamics—both in the spatial and time regime—displayed in the protein and surrounding membrane. The membrane lipids have emerged as allosteric modulators of membrane protein function, which further adds to the complexity. In this review, we discuss several examples of membrane dependency. A particular focus is on how molecular dynamics (MD) simulation have aided to map membrane protein dynamics and how enhanced sampling methods can enable observing the otherwise inaccessible biological time scale. Also, time-resolved X-ray scattering in solution is highlighted as a powerful tool to track membrane protein dynamics, in particular when combined with MD simulation to identify transient intermediate states. Finally, we discuss future directions of how to further develop this promising approach to determine structural dynamics of both the protein and the surrounding lipids. Graphic Abstract ![]()
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
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13
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Kim J, Kim JG, Ki H, Ahn CW, Ihee H. Estimating signal and noise of time-resolved X-ray solution scattering data at synchrotrons and XFELs. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:633-645. [PMID: 32381763 PMCID: PMC7206544 DOI: 10.1107/s1600577520002738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
Elucidating the structural dynamics of small molecules and proteins in the liquid solution phase is essential to ensure a fundamental understanding of their reaction mechanisms. In this regard, time-resolved X-ray solution scattering (TRXSS), also known as time-resolved X-ray liquidography (TRXL), has been established as a powerful technique for obtaining the structural information of reaction intermediates and products in the liquid solution phase and is expected to be applied to a wider range of molecules in the future. A TRXL experiment is generally performed at the beamline of a synchrotron or an X-ray free-electron laser (XFEL) to provide intense and short X-ray pulses. Considering the limited opportunities to use these facilities, it is necessary to verify the plausibility of a target experiment prior to the actual experiment. For this purpose, a program has been developed, referred to as S-cube, which is short for a Solution Scattering Simulator. This code allows the routine estimation of the shape and signal-to-noise ratio (SNR) of TRXL data from known experimental parameters. Specifically, S-cube calculates the difference scattering curve and the associated quantum noise on the basis of the molecular structure of the target reactant and product, the target solvent, the energy of the pump laser pulse and the specifications of the beamline to be used. Employing a simplified form for the pair-distribution function required to calculate the solute-solvent cross term greatly increases the calculation speed as compared with a typical TRXL data analysis. Demonstrative applications of S-cube are presented, including the estimation of the expected TRXL data and SNR level for the future LCLS-II HE beamlines.
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Affiliation(s)
- Jungmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Chi Woo Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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14
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Li W. Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding. J Chem Theory Comput 2020; 16:1834-1842. [PMID: 31972074 DOI: 10.1021/acs.jctc.9b01035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Energetic contributions at the single-residue level for retinal-opsin interactions in rhodopsin were studied by combining molecular dynamics simulations, transition path sampling, and a newly developed energy decomposition approach. The virtual work at an infinitesimal time interval was decomposed into the work components on one residue due to its interaction with another residue, which were then averaged over the transition path ensemble along a proposed reaction coordinate. Such residue-residue mutual work analysis on 62 residues within the active center of rhodopsin resulted in a very sparse interaction matrix, which is generally not symmetric but antisymmetric to some extent. Fourteen residues were identified to be major players in retinal relaxation along a plausible pathway from bathorhodopsin to the blue-shifted intermediate, which is in good agreement with an existing NMR study. Based on the matrix of mutual work, a comprehensive network was constructed to provide detailed insights into the chromophore-protein interaction from a viewpoint of energy flow.
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Affiliation(s)
- Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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15
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Ravishankar H, Pedersen MN, Eklund M, Sitsel A, Li C, Duelli A, Levantino M, Wulff M, Barth A, Olesen C, Nissen P, Andersson M. Tracking Ca 2+ ATPase intermediates in real time by x-ray solution scattering. SCIENCE ADVANCES 2020; 6:eaaz0981. [PMID: 32219166 PMCID: PMC7083613 DOI: 10.1126/sciadv.aaz0981] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/23/2019] [Indexed: 05/14/2023]
Abstract
Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca2]E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release of caged ATP, a 1.5-ms intermediate was formed that showed closure of the cytoplasmic domains typical of E1 states with bound Ca2+ and ATP. A subsequent 13-ms transient state showed a previously unresolved actuator (A) domain arrangement that exposed the ADP-binding site after phosphorylation. Hence, the obtained TR-XSS models determine the relative timing of so-far elusive domain rearrangements in a native environment.
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Affiliation(s)
- Harsha Ravishankar
- Department of Chemistry, Umeå University. Linnaeus Väg 10, 901 87 Umeå, Sweden
| | | | | | - Aljona Sitsel
- DANDRITE–Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University. Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Chenge Li
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius Väg 16C, 106 91 Stockholm, Sweden
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen. Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Matteo Levantino
- European Synchrotron Radiation Facility, Grenoble, Cedex 38043, BP 220, France
- Department of Physics and Chemistry, University of Palermo, Viale delle Scienze -Ed 18, 90128 Palermo, Italy
| | - Michael Wulff
- European Synchrotron Radiation Facility, Grenoble, Cedex 38043, BP 220, France
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius Väg 16C, 106 91 Stockholm, Sweden
| | - Claus Olesen
- Department of Biomedicine, Aarhus University, Vest Ole Worms Allé 3, 113 8000 Aarhus C, Denmark
| | - Poul Nissen
- DANDRITE–Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University. Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Magnus Andersson
- Department of Chemistry, Umeå University. Linnaeus Väg 10, 901 87 Umeå, Sweden
- Corresponding author.
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16
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Imamoto Y, Kojima K, Oka T, Maeda R, Shichida Y. Conformational Differences among Metarhodopsin I, Metarhodopsin II, and Opsin Probed by Wide-Angle X-ray Scattering. J Phys Chem B 2019; 123:9134-9142. [PMID: 31580080 DOI: 10.1021/acs.jpcb.9b08311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the photoproducts of vertebrate rhodopsin, only metarhodopsin II (Meta-II) preferentially adopts the active structure in which transmembrane helices are rearranged. Light-induced helical rearrangement of rhodopsin in membrane-embedded form was directly monitored by wide-angle X-ray scattering (WAXS) using nanodiscs. The change in the WAXS curve for the formation of Meta-II was characterized by a peak at 0.2 Å-1 and a valley at 0.6 Å-1, which were not observed in metarhodopsin I and opsin. However, acid-induced active opsin (Opsin*) showed a 0.2 Å-1 peak, but no 0.6 Å-1 valley. Analyses using the model structures based on the crystal structures of dark state and Meta-II suggest that the outward movement of helix VI occurred in Opsin*. However, the displaced helices III and V in Meta-II resulting from the disruption of cytoplasmic ionic lock were restored in Opsin*, which is likely to destabilize the G-protein-activating structure of opsin.
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Affiliation(s)
- Yasushi Imamoto
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | - Keiichi Kojima
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | | | - Ryo Maeda
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | - Yoshinori Shichida
- Research Organization for Science and Technology , Ritsumeikan University , Kusatsu , Shiga 525-8577 , Japan
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17
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Kjær KS, Van Driel TB, Harlang TCB, Kunnus K, Biasin E, Ledbetter K, Hartsock RW, Reinhard ME, Koroidov S, Li L, Laursen MG, Hansen FB, Vester P, Christensen M, Haldrup K, Nielsen MM, Dohn AO, Pápai MI, Møller KB, Chabera P, Liu Y, Tatsuno H, Timm C, Jarenmark M, Uhlig J, Sundstöm V, Wärnmark K, Persson P, Németh Z, Szemes DS, Bajnóczi É, Vankó G, Alonso-Mori R, Glownia JM, Nelson S, Sikorski M, Sokaras D, Canton SE, Lemke HT, Gaffney KJ. Finding intersections between electronic excited state potential energy surfaces with simultaneous ultrafast X-ray scattering and spectroscopy. Chem Sci 2019; 10:5749-5760. [PMID: 31293761 PMCID: PMC6568243 DOI: 10.1039/c8sc04023k] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 04/21/2019] [Indexed: 12/12/2022] Open
Abstract
Combined X-ray free-electron laser techniques pinpoints loci of intersections between potential energy surfaces of a photo-excited 3d transition-metal centered molecule.
Light-driven molecular reactions are dictated by the excited state potential energy landscape, depending critically on the location of conical intersections and intersystem crossing points between potential surfaces where non-adiabatic effects govern transition probabilities between distinct electronic states. While ultrafast studies have provided significant insight into electronic excited state reaction dynamics, experimental approaches for identifying and characterizing intersections and seams between electronic states remain highly system dependent. Here we show that for 3d transition metal systems simultaneously recorded X-ray diffuse scattering and X-ray emission spectroscopy at sub-70 femtosecond time-resolution provide a solid experimental foundation for determining the mechanistic details of excited state reactions. In modeling the mechanistic information retrieved from such experiments, it becomes possible to identify the dominant trajectory followed during the excited state cascade and to determine the relevant loci of intersections between states. We illustrate our approach by explicitly mapping parts of the potential energy landscape dictating the light driven low-to-high spin-state transition (spin crossover) of [Fe(2,2′-bipyridine)3]2+, where the strongly coupled nuclear and electronic dynamics have been a source of interest and controversy. We anticipate that simultaneous X-ray diffuse scattering and X-ray emission spectroscopy will provide a valuable approach for mapping the reactive trajectories of light-triggered molecular systems involving 3d transition metals.
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Affiliation(s)
- Kasper S Kjær
- PULSE Institute , SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , USA . ; .,Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark.,Department of Chemical Physics , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Tim B Van Driel
- LCLS , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - Tobias C B Harlang
- Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark.,Department of Chemical Physics , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Kristjan Kunnus
- PULSE Institute , SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , USA . ;
| | - Elisa Biasin
- Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark
| | - Kathryn Ledbetter
- PULSE Institute , SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , USA . ;
| | - Robert W Hartsock
- PULSE Institute , SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , USA . ;
| | - Marco E Reinhard
- PULSE Institute , SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , USA . ;
| | - Sergey Koroidov
- PULSE Institute , SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , USA . ;
| | - Lin Li
- PULSE Institute , SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , USA . ;
| | - Mads G Laursen
- Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark
| | - Frederik B Hansen
- Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark
| | - Peter Vester
- Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark
| | - Morten Christensen
- Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark
| | - Kristoffer Haldrup
- Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark
| | - Martin M Nielsen
- Department of Physics , Technical University of Denmark , DK-2800 , Lyngby , Denmark
| | - Asmus O Dohn
- Science Institute , University of Iceland , 107 Reykjavík , Iceland
| | - Mátyás I Pápai
- Science Institute , University of Iceland , 107 Reykjavík , Iceland.,Wigner Research Centre for Physics , Hungarian Academy of Sciences , P.O. Box 49 , H-1525 Budapest , Hungary
| | - Klaus B Møller
- Science Institute , University of Iceland , 107 Reykjavík , Iceland
| | - Pavel Chabera
- Department of Chemical Physics , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Yizhu Liu
- Department of Chemical Physics , Lund University , P.O. Box 124 , 22100 Lund , Sweden.,Centre for Analysis and Synthesis , Department of Chemistry , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Hideyuki Tatsuno
- Department of Chemical Physics , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Cornelia Timm
- Department of Chemical Physics , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Martin Jarenmark
- Department of Geology , Department of Chemistry , Lund University , 223 62 Lund , Sweden
| | - Jens Uhlig
- Department of Chemical Physics , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Villy Sundstöm
- Department of Chemical Physics , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Kenneth Wärnmark
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Petter Persson
- Theoretical Chemistry Division , Department of Chemistry , Lund University , P.O. Box 124 , 22100 Lund , Sweden
| | - Zoltán Németh
- Wigner Research Centre for Physics , Hungarian Academy of Sciences , P.O. Box 49 , H-1525 Budapest , Hungary
| | - Dorottya Sárosiné Szemes
- Wigner Research Centre for Physics , Hungarian Academy of Sciences , P.O. Box 49 , H-1525 Budapest , Hungary
| | - Éva Bajnóczi
- Wigner Research Centre for Physics , Hungarian Academy of Sciences , P.O. Box 49 , H-1525 Budapest , Hungary
| | - György Vankó
- Wigner Research Centre for Physics , Hungarian Academy of Sciences , P.O. Box 49 , H-1525 Budapest , Hungary
| | - Roberto Alonso-Mori
- LCLS , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - James M Glownia
- LCLS , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - Silke Nelson
- LCLS , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - Marcin Sikorski
- LCLS , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - Dimosthenis Sokaras
- SSRL , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - Sophie E Canton
- ELI-ALPS , ELI-HU Non-Profit Ltd. , Dugonics ter 13 , Szeged 6720 , Hungary.,FS-ATTO , Deutsches Elektronen-Synchrotron (DESY) , Notkestrasse 85 , D-22607 Hamburg , Germany
| | - Henrik T Lemke
- LCLS , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA.,SwissFEL , Paul Scherrer Institut , Villigen PSI 5232 , Switzerland
| | - Kelly J Gaffney
- PULSE Institute , SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , USA . ; .,SSRL , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
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18
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Sharma A, Berntsen P, Harimoorthy R, Appio R, Sjöhamn J, Järvå M, Björling A, Hammarin G, Westenhoff S, Brändén G, Neutze R. A simple adaptation to a protein crystallography station to facilitate difference X-ray scattering studies. J Appl Crystallogr 2019; 52:378-386. [PMID: 30996717 PMCID: PMC6448683 DOI: 10.1107/s1600576719001900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/01/2019] [Indexed: 11/10/2022] Open
Abstract
The X-ray crystallography station I911-2 at MAXLab II (Lund, Sweden) has been adapted to enable difference small- and wide-angle X-ray scattering (SAXS/WAXS) data to be recorded. Modifications to the beamline included a customized flow cell, a motorized flow cell holder, a helium cone, a beam stop, a sample stage and a sample delivery system. This setup incorporated external devices such as infrared lasers, LEDs and reaction mixers to induce conformational changes in macromolecules. This platform was evaluated through proof-of-principle experiments capturing light-induced conformational changes in phytochromes. A difference WAXS signature of conformational changes in a plant aqua-porin was also demonstrated using caged calcium.
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Affiliation(s)
- Amit Sharma
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
- ARC Centre of Exellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | | | - Jennie Sjöhamn
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michael Järvå
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Alexander Björling
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
- MAX IV Laboratory, Box 118, 221 00 Lund, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
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19
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Perera SMDC, Chawla U, Shrestha UR, Bhowmik D, Struts AV, Qian S, Chu XQ, Brown MF. Small-Angle Neutron Scattering Reveals Energy Landscape for Rhodopsin Photoactivation. J Phys Chem Lett 2018; 9:7064-7071. [PMID: 30489081 DOI: 10.1021/acs.jpclett.8b03048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Knowledge of the activation principles for G-protein-coupled receptors (GPCRs) is critical to development of new pharmaceuticals. Rhodopsin is the archetype for the largest GPCR family, yet the changes in protein dynamics that trigger signaling are not fully understood. Here we show that rhodopsin can be investigated by small-angle neutron scattering (SANS) in fully protiated detergent micelles under contrast matching to resolve light-induced changes in the protein structure. In SANS studies of membrane proteins, the zwitterionic detergent [(cholamidopropyl)dimethylammonio]-propanesulfonate (CHAPS) is advantageous because of the low contrast difference between the hydrophobic core and hydrophilic head groups as compared with alkyl glycoside detergents. Combining SANS results with quasielastic neutron scattering reveals how changes in volumetric protein shape are coupled (slaved) to the aqueous solvent. Upon light exposure, rhodopsin is swollen by the penetration of water into the protein core, allowing interactions with effector proteins in the visual signaling mechanism.
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Affiliation(s)
- Suchithranga M D C Perera
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Udeep Chawla
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Utsab R Shrestha
- Department of Physics and Astronomy , Wayne State University , Detroit , Michigan 48201 , United States
| | - Debsindhu Bhowmik
- Department of Physics and Astronomy , Wayne State University , Detroit , Michigan 48201 , United States
| | - Andrey V Struts
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
- Laboratory of Biomolecular NMR , St. Petersburg State University , St. Petersburg 199034 , Russia
| | - Shuo Qian
- Neutron Scattering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Xiang-Qiang Chu
- Graduate School of China Academy of Engineering Physics , Beijing 100193 , China
| | - Michael F Brown
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
- Department of Physics , University of Arizona , Tucson , Arizona 85721 , United States
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20
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Brinkmann A, Sternberg U, Bovee-Geurts PHM, Fernández Fernández I, Lugtenburg J, Kentgens APM, DeGrip WJ. Insight into the chromophore of rhodopsin and its Meta-II photointermediate by 19F solid-state NMR and chemical shift tensor calculations. Phys Chem Chem Phys 2018; 20:30174-30188. [PMID: 30484791 DOI: 10.1039/c8cp05886e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
19F nuclei are useful labels in solid-state NMR studies, since their chemical shift and tensor elements are very sensitive to the electrostatic and space-filling properties of their local environment. In this study we have exploited a fluorine substituent, strategically placed at the C-12-position of 11-cis retinal, the chromophore of visual rhodopsins. This label was used to explore the local environment of the chromophore in the ground state of bovine rhodopsin and its active photo-intermediate Meta II. In addition, the chemical shift and tensor elements of the chromophore in the free state in a membrane environment and the bound state in the protein were determined. Upon binding of the chromophore into rhodopsin and Meta II, the isotropic chemical shift changes in the opposite direction by +9.7 and -8.4 ppm, respectively. An unusually large isotropic shift difference of 35.9 ppm was observed between rhodopsin and Meta II. This partly originates in the light-triggered 11-cis to all-trans isomerization of the chromophore. The other part reflects the local conformational rearrangements in the chromophore and the binding pocket. These NMR data were correlated with the available X-ray structures of rhodopsin and Meta II using bond polarization theory. For this purpose hydrogen atoms have to be inserted and hereto a family of structures were derived that best correlated with the well-established 13C chemical shifts. Based upon these structures, a 12-F derivative was obtained that best corresponded with the experimentally determined 19F chemical shifts and tensor elements. The combined data indicate strong changes in the local environment of the C-12 position and a substantially different interaction pattern with the protein in Meta II as compared to rhodopsin.
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Affiliation(s)
- Andreas Brinkmann
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada.
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21
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Srinivasan S, Fernández-Sampedro MA, Morillo M, Ramon E, Jiménez-Rosés M, Cordomí A, Garriga P. Human Blue Cone Opsin Regeneration Involves Secondary Retinal Binding with Analog Specificity. Biophys J 2018; 114:1285-1294. [PMID: 29590586 PMCID: PMC5883618 DOI: 10.1016/j.bpj.2018.01.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
Human color vision is mediated by the red, green, and blue cone visual pigments. Cone opsins are G-protein-coupled receptors consisting of an opsin apoprotein covalently linked to the 11-cis-retinal chromophore. All visual pigments share a common evolutionary origin, and red and green cone opsins exhibit a higher homology, whereas blue cone opsin shows more resemblance to the dim light receptor rhodopsin. Here we show that chromophore regeneration in photoactivated blue cone opsin exhibits intermediate transient conformations and a secondary retinoid binding event with slower binding kinetics. We also detected a fine-tuning of the conformational change in the photoactivated blue cone opsin binding site that alters the retinal isomer binding specificity. Furthermore, the molecular models of active and inactive blue cone opsins show specific molecular interactions in the retinal binding site that are not present in other opsins. These findings highlight the differential conformational versatility of human cone opsin pigments in the chromophore regeneration process, particularly compared to rhodopsin, and point to relevant functional, unexpected roles other than spectral tuning for the cone visual pigments.
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Affiliation(s)
| | | | | | - Eva Ramon
- Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Mireia Jiménez-Rosés
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Garriga
- Universitat Politècnica de Catalunya, Terrassa, Spain.
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22
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23
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Oang KY, Yang C, Muniyappan S, Kim J, Ihee H. SVD-aided pseudo principal-component analysis: A new method to speed up and improve determination of the optimum kinetic model from time-resolved data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044013. [PMID: 28405591 PMCID: PMC5382018 DOI: 10.1063/1.4979854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/24/2017] [Indexed: 05/22/2023]
Abstract
Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model. In addition, the results of SAPPA for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of the same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy.
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Affiliation(s)
| | | | | | - Jeongho Kim
- Department of Chemistry, Inha University , Incheon 22212, South Korea
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24
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Kim TW, Yang C, Kim Y, Kim JG, Kim J, Jung YO, Jun S, Lee SJ, Park S, Kosheleva I, Henning R, van Thor JJ, Ihee H. Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein. Phys Chem Chem Phys 2017; 18:8911-8919. [PMID: 26960811 DOI: 10.1039/c6cp00476h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Real-time probing of structural transitions of a photoactive protein is challenging owing to the lack of a universal time-resolved technique that can probe the changes in both global conformation and light-absorbing chromophores of the protein. In this work, we combine time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) spectroscopy to investigate how the global conformational changes involved in the photoinduced signal transduction of photoactive yellow protein (PYP) is temporally and spatially related to the local structural change around the light-absorbing chromophore. In particular, we examine the role of internal proton transfer in developing a signaling state of PYP by employing its E46Q mutant (E46Q-PYP), where the internal proton transfer is inhibited by the replacement of a proton donor. The comparison of TRXSS and TA spectroscopy data directly reveals that the global conformational change of the protein, which is probed by TRXSS, is temporally delayed by tens of microseconds from the local structural change of the chromophore, which is probed by TA spectroscopy. The molecular shape of the signaling state reconstructed from the TRXSS curves directly visualizes the three-dimensional conformations of protein intermediates and reveals that the smaller structural change in E46Q-PYP than in wild-type PYP suggested by previous studies is manifested in terms of much smaller protrusion, confirming that the signaling state of E46Q-PYP is only partially developed compared with that of wild-type PYP. This finding provides direct evidence of how the environmental change in the vicinity of the chromophore alters the conformational change of the entire protein matrix.
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Affiliation(s)
- Tae Wu Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Cheolhee Yang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Youngmin Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Jong Goo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Yang Ouk Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sunhong Jun
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sungjun Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago IL 60637, USA
| | - Jasper J van Thor
- Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
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25
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Abstract
Preparation and storage of functional membrane proteins such as G-protein-coupled receptors (GPCRs) are crucial to the processes of drug delivery and discovery. Here, we describe a method of preparing powdered GPCRs using rhodopsin as the prototype. We purified rhodopsin in CHAPS detergent with low detergent to protein ratio so the bulk of the sample represented protein (ca. 72% w/w). Our new method for generating powders of membrane proteins followed by rehydration paves the way for conducting functional and biophysical experiments. As an illustrative application, powdered rhodopsin was prepared with and without the cofactor 11-cis-retinal to enable partial rehydration of the protein with D2O in a controlled manner. Quasi-elastic neutron scattering studies using both spatial motion and energy landscape models form the basis for crucial insights into structural fluctuations and thermodynamics of GPCR activation.
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Affiliation(s)
| | - Udeep Chawla
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Department of Physics, University of Arizona, Tucson, AZ 85721, USA
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26
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Shrestha UR, Perera SMDC, Bhowmik D, Chawla U, Mamontov E, Brown MF, Chu XQ. Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor. J Phys Chem Lett 2016; 7:4130-4136. [PMID: 27628201 PMCID: PMC5378701 DOI: 10.1021/acs.jpclett.6b01632] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Light activation of the visual G-protein-coupled receptor (GPCR) rhodopsin leads to significant structural fluctuations of the protein embedded within the membrane yielding the activation of cognate G-protein (transducin), which initiates biological signaling. Here, we report a quasi-elastic neutron scattering study of the activation of rhodopsin as a GPCR prototype. Our results reveal a broadly distributed relaxation of hydrogen atom dynamics of rhodopsin on a picosecond-nanosecond time scale, crucial for protein function, as only observed for globular proteins previously. Interestingly, the results suggest significant differences in the intrinsic protein dynamics of the dark-state rhodopsin versus the ligand-free apoprotein, opsin. These differences can be attributed to the influence of the covalently bound retinal ligand. Furthermore, an idea of the generic free-energy landscape is used to explain the GPCR dynamics of ligand-binding and ligand-free protein conformations, which can be further applied to other GPCR systems.
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Affiliation(s)
- Utsab R. Shrestha
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
| | | | - Debsindhu Bhowmik
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
| | - Udeep Chawla
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Eugene Mamontov
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Department of Physics, University of Arizona, Tucson, AZ 85721, USA
| | - Xiang-qiang Chu
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
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27
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Imamoto Y, Kojima K, Oka T, Maeda R, Shichida Y. Helical rearrangement of photoactivated rhodopsin in monomeric and dimeric forms probed by high-angle X-ray scattering. Photochem Photobiol Sci 2016; 14:1965-73. [PMID: 26293780 DOI: 10.1039/c5pp00175g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Light-induced helical rearrangement of vertebrate visual rhodopsin was directly monitored by high-angle X-ray scattering (HAXS), ranging from Q (= 4π sin θ/λ) = 0.03 Å(-1) to Q = 1.5 Å(-1). HAXS of nanodiscs containing a single rhodopsin molecule was performed before and after photoactivation of rhodopsin. The intensity difference curve obtained by HAXS agreed with that calculated from the crystal structure of dark state rhodopsin and metarhodopsin II, indicating that the conformational change of monomeric rhodopsin in the membrane is consistent with that occurring in the crystal. On the other hand, the HAXS intensity difference curve of nanodiscs containing two rhodopsin molecules was significantly reduced, similar to that calculated from the crystal structure of the deprotonated intermediate, without a large conformational change. These results suggest that rhodopsin is dimerized in the membrane and that the interaction between rhodopsin molecules modulates structural changes.
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Affiliation(s)
- Yasushi Imamoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Keiichi Kojima
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Toshihiko Oka
- Department of Physics, Faculty of Science, Shizuoka University, Shizuoka 422-8529, Japan and Nanomaterials Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka 432-8011, Japan
| | - Ryo Maeda
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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28
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Kim J, Kim KH, Oang KY, Lee JH, Hong K, Cho H, Huse N, Schoenlein RW, Kim TK, Ihee H. Tracking reaction dynamics in solution by pump–probe X-ray absorption spectroscopy and X-ray liquidography (solution scattering). Chem Commun (Camb) 2016; 52:3734-49. [DOI: 10.1039/c5cc08949b] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
TRXL and TRXAS are powerful techniques for real-time probing of structural and electronic dynamics of photoinduced reactions in solution phase.
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29
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Blankenship E, Vahedi-Faridi A, Lodowski DT. The High-Resolution Structure of Activated Opsin Reveals a Conserved Solvent Network in the Transmembrane Region Essential for Activation. Structure 2015; 23:2358-2364. [PMID: 26526852 DOI: 10.1016/j.str.2015.09.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/27/2015] [Accepted: 09/06/2015] [Indexed: 11/15/2022]
Abstract
Rhodopsin, a light-activated G protein coupled receptor (GPCR), has been the subject of numerous biochemical and structural investigations, serving as a model receptor for GPCRs and their activation. We present the 2.3-Å resolution structure of native source rhodopsin stabilized in a conformation competent for G protein binding. An extensive water-mediated hydrogen bond network linking the chromophore binding site to the site of G protein binding is observed, providing connections to conserved motifs essential for GPCR activation. Comparison of this extensive solvent-mediated hydrogen-bonding network with the positions of ordered solvent in earlier crystallographic structures of rhodopsin photointermediates reveals both static structural and dynamic functional water-protein interactions present during the activation process. When considered along with observations that solvent occupies similar positions in the structures of other GPCRs, these analyses strongly support an integral role for this dynamic ordered water network in both rhodopsin and GPCR activation.
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Affiliation(s)
- Elise Blankenship
- Department of Nutrition, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Ardeschir Vahedi-Faridi
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T Lodowski
- Department of Nutrition, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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30
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Yang C, Choi J, Ihee H. The time scale of the quaternary structural changes in hemoglobin revealed using the transient grating technique. Phys Chem Chem Phys 2015; 17:22571-5. [PMID: 26272458 DOI: 10.1039/c5cp03059e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quaternary structural transition between the R and T states of human hemoglobin was investigated using the transient grating technique. The results presented herein reveal that the quaternary structural change accompanied by the R-T transition occurs within a few microseconds.
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Affiliation(s)
- Cheolhee Yang
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea.
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31
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Levantino M, Yorke BA, Monteiro DC, Cammarata M, Pearson AR. Using synchrotrons and XFELs for time-resolved X-ray crystallography and solution scattering experiments on biomolecules. Curr Opin Struct Biol 2015; 35:41-8. [PMID: 26342489 DOI: 10.1016/j.sbi.2015.07.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/27/2015] [Accepted: 07/31/2015] [Indexed: 11/17/2022]
Abstract
Time-resolved structural information is key to understand the mechanism of biological processes, such as catalysis and signalling. Recent developments in X-ray sources as well as data collection and analysis methods are making routine time-resolved X-ray crystallography and solution scattering experiments a real possibility for structural biologists. Here we review the information that can be obtained from these techniques and discuss the considerations that must be taken into account when designing a time-resolved experiment.
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Affiliation(s)
- Matteo Levantino
- Department of Physics and Chemistry, University of Palermo, Palermo 90128, Italy
| | - Briony A Yorke
- Hamburg Centre for Ultrafast Imaging & Institute of Nanostructure and Solid State Physics, University of Hamburg, Hamburg 22607, Germany
| | - Diana Cf Monteiro
- Astbury Centre for Structural Molecular Biology & School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Marco Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, Rennes 35042, France
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging & Institute of Nanostructure and Solid State Physics, University of Hamburg, Hamburg 22607, Germany.
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32
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Panneels V, Wu W, Tsai CJ, Nogly P, Rheinberger J, Jaeger K, Cicchetti G, Gati C, Kick LM, Sala L, Capitani G, Milne C, Padeste C, Pedrini B, Li XD, Standfuss J, Abela R, Schertler G. Time-resolved structural studies with serial crystallography: A new light on retinal proteins. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041718. [PMID: 26798817 PMCID: PMC4711639 DOI: 10.1063/1.4922774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/03/2015] [Indexed: 05/19/2023]
Abstract
Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination.
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Affiliation(s)
- Valérie Panneels
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Wenting Wu
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Przemek Nogly
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Jan Rheinberger
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Kathrin Jaeger
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Gregor Cicchetti
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | | | - Leonhard M Kick
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Leonardo Sala
- Scientific Computing, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Chris Milne
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Celestino Padeste
- Lab for Micro- and Nanotechnology, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Bill Pedrini
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Xiao-Dan Li
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Rafael Abela
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
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33
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Neutze R, VanHook AM. Science Signaling
Podcast: 10 March 2015. Sci Signal 2015. [DOI: 10.1126/scisignal.aaa9415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Structural analysis of rhodopsin in native membranes shows real-time conformational changes induced by light.
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Affiliation(s)
- Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Annalisa M. VanHook
- Web Editor, Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, NW, Washington, DC 20005, USA
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