1
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Zielinski KA, Dolamore C, Dalton KM, Smith N, Termini J, Henning R, Srajer V, Hekstra DR, Pollack L, Wilson MA. Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604369. [PMID: 39071394 PMCID: PMC11275809 DOI: 10.1101/2024.07.19.604369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
DJ-1 (PARK7) is an intensively studied protein whose cytoprotective activities are dysregulated in multiple diseases. DJ-1 has been reported as having two distinct enzymatic activities in defense against reactive carbonyl species that are difficult to distinguish in conventional biochemical experiments. Here, we establish the mechanism of DJ-1 using a synchrotron-compatible version of mix-and-inject-serial crystallography (MISC), which was previously performed only at XFELs, to directly observe DJ-1 catalysis. We designed and used new diffusive mixers to collect time-resolved Laue diffraction data of DJ-1 catalysis at a pink beam synchrotron beamline. Analysis of structurally similar methylglyoxal-derived intermediates formed through the DJ-1 catalytic cycle shows that the enzyme catalyzes nearly two turnovers in the crystal and defines key aspects of its glyoxalase mechanism. In addition, DJ-1 shows allosteric communication between a distal site at the dimer interface and the active site that changes during catalysis. Our results rule out the widely cited deglycase mechanism for DJ-1 action and provide an explanation for how DJ-1 produces L-lactate with high chiral purity.
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2
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Vallejos A, Katona G, Neutze R. Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:044302. [PMID: 39056073 PMCID: PMC11272219 DOI: 10.1063/4.0000258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
With the development of serial crystallography at both x-ray free electron laser and synchrotron radiation sources, time-resolved x-ray crystallography is increasingly being applied to study conformational changes in macromolecules. A successful time-resolved serial crystallography study requires the growth of microcrystals, a mechanism for synchronized and homogeneous excitation of the reaction of interest within microcrystals, and tools for structural interpretation. Here, we utilize time-resolved serial femtosecond crystallography data collected from microcrystals of bacteriorhodopsin to compare results from partial occupancy structural refinement and refinement against extrapolated data. We illustrate the domain wherein the amplitude of refined conformational changes is inversely proportional to the activated state occupancy. We illustrate how resampling strategies allow coordinate uncertainty to be estimated and demonstrate that these two approaches to structural refinement agree within coordinate errors. We illustrate how singular value decomposition of a set of difference Fourier electron density maps calculated from resampled data can minimize phase bias in these maps, and we quantify residual densities for transient water molecules by analyzing difference Fourier and Polder omit maps from resampled data. We suggest that these tools may assist others in judging the confidence with which observed electron density differences may be interpreted as functionally important conformational changes.
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Affiliation(s)
- Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Gergely Katona
- 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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3
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Ogata D, Koide S, Kishi H, Yuasa J. Direct observation of electron transfer in solids through X-ray crystallography. Nat Commun 2024; 15:4412. [PMID: 38782903 PMCID: PMC11116525 DOI: 10.1038/s41467-024-48599-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Nanoscale electron transfer (ET) in solids is fundamental to the design of multifunctional nanomaterials, yet its process is not fully understood. Herein, through X-ray crystallography, we directly observe solid-state ET via a crystal-to-crystal process. We first demonstrate the creation of a robust and flexible electron acceptor/acceptor (A/A) double-wall nanotube crystal ([(Zn2+)4(LA)4(LA=O)4]n) with a large window (0.90 nm × 0.92 nm) through the one-dimensional porous crystallization of heteroleptic Zn4 metallocycles ((Zn2+)4(LA)4(LA=O)4) with two different acceptor ligands (2,7-bis((1-ethyl-1H-imidazol-2-yl)ethynyl)acridine (LA) and 2,7-bis((1-ethyl-1H-imidazol-2-yl)ethynyl)acridin-9(10H)-one (LA=O)) in a slow-oxidation-associated crystallization procedure. We then achieve the bottom-up construction of the electron donor incorporated-A/A nanotube crystal ([(D)2⊂(Zn2+)4(LA)4(LA=O)4]n) through the subsequent absorption of electron donor guests (D = tetrathiafulvalene (TTF) and ferrocene (Fc)). Finally, we remove electrons from the electron donor guests inside the nanotube crystal through facile ET in the solid state to accumulate holes inside the nanotube crystal ([(D•+)2⊂(Zn2+)4(LA)4(LA=O)4]n), where the solid-state ET process (D - e- → D•+) is thus observed directly by X-ray crystallography.
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Affiliation(s)
- Daiji Ogata
- Department of Applied Chemistry, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Shota Koide
- Department of Applied Chemistry, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Hiroyuki Kishi
- Department of Applied Chemistry, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Junpei Yuasa
- Department of Applied Chemistry, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan.
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4
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Khusainov G, Standfuss J, Weinert T. The time revolution in macromolecular crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:020901. [PMID: 38616866 PMCID: PMC11015943 DOI: 10.1063/4.0000247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, the advent of cryo-electron microscopy for structure determination of large and increasingly smaller and flexible proteins signaled a paradigm shift in structural biology. The extensive structural and sequence data from crystallography and advanced sequencing techniques have been pivotal for training computational models for accurate structure prediction, unveiling the general fold of most proteins. Here, we present a perspective on the rise of time-resolved crystallography as the new frontier of macromolecular structure determination. We trace the evolution from the pioneering time-resolved crystallography methods to modern serial crystallography, highlighting the synergy between rapid detection technologies and state-of-the-art x-ray sources. These innovations are redefining our exploration of protein dynamics, with high-resolution crystallography uniquely positioned to elucidate rapid dynamic processes at ambient temperatures, thus deepening our understanding of protein functionality. We propose that the integration of dynamic structural data with machine learning advancements will unlock predictive capabilities for protein kinetics, revolutionizing dynamics like macromolecular crystallography revolutionized structural biology.
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Affiliation(s)
- Georgii Khusainov
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
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5
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Fufina TY, Vasilieva LG. Role of hydrogen-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. Biophys Rev 2023; 15:921-937. [PMID: 37974998 PMCID: PMC10643783 DOI: 10.1007/s12551-023-01109-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/01/2023] [Indexed: 11/19/2023] Open
Abstract
For the last decades, significant progress has been made in studying the biological functions of H-bond networks in membrane proteins, proton transporters, receptors, and photosynthetic reaction centers. Increasing availability of the X-ray crystal and cryo-electron microscopy structures of photosynthetic complexes resolved with high atomic resolution provides a platform for their comparative analysis. It allows identifying structural factors that are ensuring the high quantum yield of the photochemical reactions and are responsible for the stability of the membrane complexes. The H-bond networks are known to be responsible for proton transport associated with electron transfer from the primary to the secondary quinone as well as in the processes of water oxidation in photosystem II. Participation of such networks in reactions proceeding on the periplasmic side of bacterial photosynthetic reaction centers is less studied. This review summarizes the current understanding of the role of H-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. It is discussed that the networks may be involved in providing close association with mobile electron carriers, in light-induced proton transport, in regulation of the redox properties of bacteriochlorophyll cofactors, and in stabilization of the membrane protein structure at the interface of membrane and soluble phases.
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Affiliation(s)
- T. Yu. Fufina
- Federal Research Center Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Str, 2, 142290 Pushchino, Russia
| | - L. G. Vasilieva
- Federal Research Center Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Str, 2, 142290 Pushchino, Russia
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6
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Abstract
Proteins guide the flows of information, energy, and matter that make life possible by accelerating transport and chemical reactions, by allosterically modulating these reactions, and by forming dynamic supramolecular assemblies. In these roles, conformational change underlies functional transitions. Time-resolved X-ray diffraction methods characterize these transitions either by directly triggering sequences of functionally important motions or, more broadly, by capturing the motions of which proteins are capable. To date, most successful have been experiments in which conformational change is triggered in light-dependent proteins. In this review, I emphasize emerging techniques that probe the dynamic basis of function in proteins lacking natively light-dependent transitions and speculate about extensions and further possibilities. In addition, I review how the weaker and more distributed signals in these data push the limits of the capabilities of analytical methods. Taken together, these new methods are beginning to establish a powerful paradigm for the study of the physics of protein function.
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Affiliation(s)
- Doeke R Hekstra
- Department of Molecular and Cellular Biology and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA;
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7
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Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. Structural evidence for intermediates during O 2 formation in photosystem II. Nature 2023; 617:629-636. [PMID: 37138085 PMCID: PMC10191843 DOI: 10.1038/s41586-023-06038-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/31/2023] [Indexed: 05/05/2023]
Abstract
In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.
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Affiliation(s)
- Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rana Hussein
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mohamed Ibrahim
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corey J Kaminsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Julia Gätcke
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Stephanie Haupt
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabela I Nangca
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen M Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Leland B Gee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Daniel W Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Holger Dobbek
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Athina Zouni
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden.
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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8
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The role of the γ subunit in the photosystem of the lowest-energy phototrophs. Biochem J 2022; 479:2449-2463. [PMID: 36534468 PMCID: PMC9788563 DOI: 10.1042/bcj20220508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022]
Abstract
Purple phototrophic bacteria use a 'photosystem' consisting of light harvesting complex 1 (LH1) surrounding the reaction centre (RC) that absorbs far-red-near-infrared light and converts it to chemical energy. Blastochloris species, which harvest light >1000 nm, use bacteriochlorophyll b rather than the more common bacteriochlorophyll a as their major photopigment, and assemble LH1 with an additional polypeptide subunit, LH1γ, encoded by multiple genes. To assign a role to γ, we deleted the four encoding genes in the model Blastochloris viridis. Interestingly, growth under halogen bulbs routinely used for cultivation yielded cells displaying an absorption maximum of 825 nm, similar to that of the RC only, but growth under white light yielded cells with an absorption maximum at 972 nm. HPLC analysis of pigment composition and sucrose gradient fractionation demonstrate that the white light-grown mutant assembles RC-LH1, albeit with an absorption maximum blue-shifted by 46 nm. Wavelengths between 900-1000 nm transmit poorly through the atmosphere due to absorption by water, so our results provide an evolutionary rationale for incorporation of γ; this polypeptide red-shifts absorption of RC-LH1 to a spectral range in which photons are of lower energy but are more abundant. Finally, we transformed the mutant with plasmids encoding natural LH1γ variants and demonstrate that the polypeptide found in the wild type complex red-shifts absorption back to 1018 nm, but incorporation of a distantly related variant results in only a moderate shift. This result suggests that tuning the absorption of RC-LH1 is possible and may permit photosynthesis past its current low-energy limit.
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9
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Sipka G, Nagy L, Magyar M, Akhtar P, Shen JR, Holzwarth AR, Lambrev PH, Garab G. Light-induced reversible reorganizations in closed Type II reaction centre complexes: physiological roles and physical mechanisms. Open Biol 2022; 12:220297. [PMID: 36514981 PMCID: PMC9748786 DOI: 10.1098/rsob.220297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The purpose of this review is to outline our understanding of the nature, mechanism and physiological significance of light-induced reversible reorganizations in closed Type II reaction centre (RC) complexes. In the so-called 'closed' state, purple bacterial RC (bRC) and photosystem II (PSII) RC complexes are incapable of generating additional stable charge separation. Yet, upon continued excitation they display well-discernible changes in their photophysical and photochemical parameters. Substantial stabilization of their charge-separated states has been thoroughly documented-uncovering light-induced reorganizations in closed RCs and revealing their physiological importance in gradually optimizing the operation of the photosynthetic machinery during the dark-to-light transition. A range of subtle light-induced conformational changes has indeed been detected experimentally in different laboratories using different bRC and PSII-containing preparations. In general, the presently available data strongly suggest similar structural dynamics of closed bRC and PSII RC complexes, and similar physical mechanisms, in which dielectric relaxation processes and structural memory effects of proteins are proposed to play important roles.
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Affiliation(s)
- G. Sipka
- Institute of Plant Biology, Biological Research Centre, Szeged, Temesvári körút 62, 6726 Szeged, Hungary
| | - L. Nagy
- Institute of Plant Biology, Biological Research Centre, Szeged, Temesvári körút 62, 6726 Szeged, Hungary,Institute of Medical Physics and Informatics, University of Szeged, Rerrich B. tér 1, 6720 Szeged, Hungary
| | - M. Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Temesvári körút 62, 6726 Szeged, Hungary
| | - P. Akhtar
- Institute of Plant Biology, Biological Research Centre, Szeged, Temesvári körút 62, 6726 Szeged, Hungary
| | - J.-R. Shen
- Institute of Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, 700-8530 Okayama, Japan,Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, People's Republic of China
| | - A. R. Holzwarth
- Max-Planck-Institute for Chemical Energy Conversion, 45470 Mülheim a.d. Ruhr, Germany
| | - P. H. Lambrev
- Institute of Plant Biology, Biological Research Centre, Szeged, Temesvári körút 62, 6726 Szeged, Hungary
| | - G. Garab
- Institute of Plant Biology, Biological Research Centre, Szeged, Temesvári körút 62, 6726 Szeged, Hungary,Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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10
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Zamora RA, López-Ortiz M, Sales-Mateo M, Hu C, Croce R, Maniyara RA, Pruneri V, Giannotti MI, Gorostiza P. Light- and Redox-Dependent Force Spectroscopy Reveals that the Interaction between Plastocyanin and Plant Photosystem I Is Favored when One Partner Is Ready for Electron Transfer. ACS NANO 2022; 16:15155-15164. [PMID: 36067071 DOI: 10.1021/acsnano.2c06454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Photosynthesis is a fundamental process that converts photons into chemical energy, driven by large protein complexes at the thylakoid membranes of plants, cyanobacteria, and algae. In plants, water-soluble plastocyanin (Pc) is responsible for shuttling electrons between cytochrome b6f complex and the photosystem I (PSI) complex in the photosynthetic electron transport chain (PETC). For an efficient turnover, a transient complex must form between PSI and Pc in the PETC, which implies a balance between specificity and binding strength. Here, we studied the binding frequency and the unbinding force between suitably oriented plant PSI and Pc under redox control using single molecule force spectroscopy (SMFS). The binding frequency (observation of binding-unbinding events) between PSI and Pc depends on their respective redox states. The interaction between PSI and Pc is independent of the redox state of PSI when Pc is reduced, and it is disfavored in the dark (reduced P700) when Pc is oxidized. The frequency of interaction between PSI and Pc is higher when at least one of the partners is in a redox state ready for electron transfer (ET), and the post-ET situation (PSIRed-PcOx) leads to lower binding. In addition, we show that the binding of ET-ready PcRed to PSI can be regulated externally by Mg2+ ions in solution.
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Affiliation(s)
- Ricardo A Zamora
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
| | - Manuel López-Ortiz
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
| | - Montserrat Sales-Mateo
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Chen Hu
- Biophysics of Photosynthesis. Dep. Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Roberta Croce
- Biophysics of Photosynthesis. Dep. Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Rinu Abraham Maniyara
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels 08860, Spain
| | - Valerio Pruneri
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels 08860, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Marina I Giannotti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
- Department of Materials Science and Physical Chemistry, University of Barcelona, Martí i Franquès 10, Barcelona 08028, Spain
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
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11
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Zharmukhamedov SK, Shabanova MS, Rodionova MV, Huseynova IM, Karacan MS, Karacan N, Aşık KB, Kreslavski VD, Alwasel S, Allakhverdiev SI. Effects of Novel Photosynthetic Inhibitor [CuL2]Br2 Complex on Photosystem II Activity in Spinach. Cells 2022; 11:cells11172680. [PMID: 36078088 PMCID: PMC9455146 DOI: 10.3390/cells11172680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/25/2022] Open
Abstract
The effects of the novel [CuL2]Br2 complex (L = bis{4H-1,3,5-triazino [2,1-b]benzothiazole-2-amine,4-(2-imidazole)}copper(II) bromide complex) on the photosystem II (PSII) activity of PSII membranes isolated from spinach were studied. The absence of photosynthetic oxygen evolution by PSII membranes without artificial electron acceptors, but in the presence of [CuL2]Br2, has shown that it is not able to act as a PSII electron acceptor. In the presence of artificial electron acceptors, [CuL2]Br2 inhibits photosynthetic oxygen evolution. [CuL2]Br2 also suppresses the photoinduced changes of the PSII chlorophyll fluorescence yield (FV) related to the photoreduction of the primary quinone electron acceptor, QA. The inhibition of both characteristic PSII reactions depends on [CuL2]Br2 concentration. At all studied concentrations of [CuL2]Br2, the decrease in the FM level occurs exclusively due to a decrease in Fv. [CuL2]Br2 causes neither changes in the F0 level nor the retardation of the photoinduced rise in FM, which characterizes the efficiency of the electron supply from the donor-side components to QA through the PSII reaction center (RC). Artificial electron donors (sodium ascorbate, DPC, Mn2+) do not cancel the inhibitory effect of [CuL2]Br2. The dependences of the inhibitory efficiency of the studied reactions of PSII on [CuL2]Br2 complex concentration practically coincide. The inhibition constant Ki is about 16 µM, and logKi is 4.8. As [CuL2]Br2 does not change the aromatic amino acids’ intrinsic fluorescence of the PSII protein components, it can be proposed that [CuL2]Br2 has no significant effect on the native state of PSII proteins. The results obtained in the present study are compared to the literature data concerning the inhibitory effects of PSII Cu(II) aqua ions and Cu(II)-organic complexes.
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Affiliation(s)
- Sergey K. Zharmukhamedov
- Institute of Basic Biological Problems, FRC PSCBR RAS, 142290 Pushchino, Russia
- Correspondence: (S.K.Z.); (S.I.A.)
| | - Mehriban S. Shabanova
- Bionanotechnology Laboratory, Institute of Molecular Biology and Biotechnology, Azerbaijan National Academy of Sciences, AZ1073 Baku, Azerbaijan
| | - Margarita V. Rodionova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
| | - Irada M. Huseynova
- Bionanotechnology Laboratory, Institute of Molecular Biology and Biotechnology, Azerbaijan National Academy of Sciences, AZ1073 Baku, Azerbaijan
| | - Mehmet Sayım Karacan
- Department of Chemistry, Science Faculty, Gazi University, Teknikokullar, Ankara 06500, Turkey
| | - Nurcan Karacan
- Department of Chemistry, Science Faculty, Gazi University, Teknikokullar, Ankara 06500, Turkey
| | - Kübra Begüm Aşık
- Department of Chemistry, Science Faculty, Gazi University, Teknikokullar, Ankara 06500, Turkey
| | | | - Saleh Alwasel
- College of Science, King Saud University, Riyadh 12372, Saudi Arabia
| | - Suleyman I. Allakhverdiev
- Institute of Basic Biological Problems, FRC PSCBR RAS, 142290 Pushchino, Russia
- Bionanotechnology Laboratory, Institute of Molecular Biology and Biotechnology, Azerbaijan National Academy of Sciences, AZ1073 Baku, Azerbaijan
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
- Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119991 Moscow, Russia
- Correspondence: (S.K.Z.); (S.I.A.)
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12
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Båth P, Banacore A, Börjesson P, Bosman R, Wickstrand C, Safari C, Dods R, Ghosh S, Dahl P, Ortolani G, Björg Ulfarsdottir T, Hammarin G, García Bonete MJ, Vallejos A, Ostojić L, Edlund P, Linse JB, Andersson R, Nango E, Owada S, Tanaka R, Tono K, Joti Y, Nureki O, Luo F, James D, Nass K, Johnson PJM, Knopp G, Ozerov D, Cirelli C, Milne C, Iwata S, Brändén G, Neutze R. Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre. Acta Crystallogr D Struct Biol 2022; 78:698-708. [PMID: 35647917 PMCID: PMC9159286 DOI: 10.1107/s2059798322004144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/19/2022] [Indexed: 03/28/2024] Open
Abstract
Serial crystallography is a rapidly growing method that can yield structural insights from microcrystals that were previously considered to be too small to be useful in conventional X-ray crystallography. Here, conditions for growing microcrystals of the photosynthetic reaction centre of Blastochloris viridis within a lipidic cubic phase (LCP) crystallization matrix that employ a seeding protocol utilizing detergent-grown crystals with a different crystal packing are described. LCP microcrystals diffracted to 2.25 Å resolution when exposed to XFEL radiation, which is an improvement of 0.15 Å over previous microcrystal forms. Ubiquinone was incorporated into the LCP crystallization media and the resulting electron density within the mobile QB pocket is comparable to that of other cofactors within the structure. As such, LCP microcrystallization conditions will facilitate time-resolved diffraction studies of electron-transfer reactions to the mobile quinone, potentially allowing the observation of structural changes associated with the two electron-transfer reactions leading to complete reduction of the ubiquinone ligand.
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Affiliation(s)
- Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Analia Banacore
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Per Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Tinna Björg Ulfarsdottir
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - María-José García Bonete
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Lucija Ostojić
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Petra Edlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Johanna-Barbara Linse
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Fangjia Luo
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Daniel James
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Karol Nass
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Philip J. M. Johnson
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Claudio Cirelli
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Christopher Milne
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - 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, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
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13
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Puthenveetil R, Christenson ET, Vinogradova O. New Horizons in Structural Biology of Membrane Proteins: Experimental Evaluation of the Role of Conformational Dynamics and Intrinsic Flexibility. MEMBRANES 2022; 12:227. [PMID: 35207148 PMCID: PMC8877495 DOI: 10.3390/membranes12020227] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels.
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Affiliation(s)
- Robbins Puthenveetil
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Dr., Bethesda, MD 20892, USA
| | | | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
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14
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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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15
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Brändén G, Neutze R. Advances and challenges in time-resolved macromolecular crystallography. Science 2021; 373:373/6558/eaba0954. [PMID: 34446579 DOI: 10.1126/science.aba0954] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conformational changes within biological macromolecules control a vast array of chemical reactions in living cells. Time-resolved crystallography can reveal time-dependent structural changes that occur within protein crystals, yielding chemical insights in unparalleled detail. Serial crystallography approaches developed at x-ray free-electron lasers are now routinely used for time-resolved diffraction studies of macromolecules. These techniques are increasingly being applied at synchrotron radiation sources and to a growing diversity of macromolecules. Here, we review recent progress in the field, including visualizing ultrafast structural changes that guide the initial trajectories of light-driven reactions as well as capturing biologically important conformational changes on slower time scales, for which bacteriorhodopsin and photosystem II are presented as illustrative case studies.
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Affiliation(s)
- 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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16
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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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17
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Poddar H, Heyes DJ, Schirò G, Weik M, Leys D, Scrutton NS. A guide to time-resolved structural analysis of light-activated proteins. FEBS J 2021; 289:576-595. [PMID: 33864718 DOI: 10.1111/febs.15880] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023]
Abstract
Dynamical changes in protein structures are essential for protein function and occur over femtoseconds to seconds timescales. X-ray free electron lasers have facilitated investigations of structural dynamics in proteins with unprecedented temporal and spatial resolution. Light-activated proteins are attractive targets for time-resolved structural studies, as the reaction chemistry and associated protein structural changes can be triggered by short laser pulses. Proteins with different light-absorbing centres have evolved to detect light and harness photon energy to bring about downstream chemical and biological output responses. Following light absorption, rapid chemical/small-scale structural changes are typically localised around the chromophore. These localised changes are followed by larger structural changes propagated throughout the photoreceptor/photocatalyst that enables the desired chemical and/or biological output response. Time-resolved serial femtosecond crystallography (SFX) and solution scattering techniques enable direct visualisation of early chemical change in light-activated proteins on timescales previously inaccessible, whereas scattering gives access to slower timescales associated with more global structural change. Here, we review how advances in time-resolved SFX and solution scattering techniques have uncovered mechanisms of photochemistry and its coupling to output responses. We also provide a prospective on how these time-resolved structural approaches might impact on other photoreceptors/photoenzymes that have not yet been studied by these methods.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Giorgio Schirò
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
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18
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Mamedov MD, Milanovsky GE, Malferrari M, Vitukhnovskaya LA, Francia F, Semenov AY, Venturoli G. Trehalose matrix effects on electron transfer in Mn-depleted protein-pigment complexes of Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148413. [PMID: 33716033 DOI: 10.1016/j.bbabio.2021.148413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/15/2021] [Accepted: 03/07/2021] [Indexed: 11/18/2022]
Abstract
The kinetics of flash-induced re-reduction of the Photosystem II (PS II) primary electron donor P680 was studied in solution and in trehalose glassy matrices at different relative humidity. In solution, and in the re-dissolved glass, kinetics were dominated by two fast components with lifetimes in the range of 2-7 μs, which accounted for >85% of the decay. These components were ascribed to the direct electron transfer from the redox-active tyrosine YZ to P680+. The minor slower components were due to charge recombination between the primary plastoquinone acceptor QA- and P680+. Incorporation of the PS II complex into the trehalose glassy matrix and its successive dehydration caused a progressive increase in the lifetime of all kinetic phases, accompanied by an increase of the amplitudes of the slower phases at the expense of the faster phases. At 63% relative humidity the fast components contribution dropped to ~50%. A further dehydration of the trehalose glass did not change the lifetimes and contribution of the kinetic components. This effect was ascribed to the decrease of conformational mobility of the protein domain between YZ and P680, which resulted in the inhibition of YZ → P680+ electron transfer in about half of the PS II population, wherein the recombination between QA- and P680+ occurred. The data indicate that PS II binds a larger number of water molecules as compared to PS I complexes. We conclude that our data disprove the "water replacement" hypothesis of trehalose matrix biopreservation.
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Affiliation(s)
- Mahir D Mamedov
- A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Leninskye gory, 1, b.40, Russia
| | - Georgy E Milanovsky
- A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Leninskye gory, 1, b.40, Russia
| | - Marco Malferrari
- Laboratory of Biochemistry and Molecular Biophysics, Department of Pharmacy and Biotechnology, FaBiT, University of Bologna, Bologna, Via Irnerio, 42, Italy
| | - Liya A Vitukhnovskaya
- A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Leninskye gory, 1, b.40, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Kosygina Street, 4, b.1, Russia
| | - Francesco Francia
- Laboratory of Biochemistry and Molecular Biophysics, Department of Pharmacy and Biotechnology, FaBiT, University of Bologna, Bologna, Via Irnerio, 42, Italy
| | - Alexey Yu Semenov
- A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Leninskye gory, 1, b.40, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Kosygina Street, 4, b.1, Russia.
| | - Giovanni Venturoli
- Laboratory of Biochemistry and Molecular Biophysics, Department of Pharmacy and Biotechnology, FaBiT, University of Bologna, Bologna, Via Irnerio, 42, Italy; Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, CNISM, c/o Department of Physics and Astronomy "Augusto Righi", DIFA, University of Bologna, Bologna, Via Irnerio, 46, Italy.
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19
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Ultrafast structural changes within a photosynthetic reaction centre. Nature 2021; 589:310-314. [PMID: 33268896 DOI: 10.1038/s41586-020-3000-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/28/2020] [Indexed: 01/29/2023]
Abstract
Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.
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20
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Jensen M, Ahlberg Gagnér V, Cabello Sánchez J, Bengtsson ÅUJ, Ekström JC, Björg Úlfarsdóttir T, Garcia-Bonete MJ, Jurgilaitis A, Kroon D, Pham VT, Checcia S, Coudert-Alteirac H, Schewa S, Rössle M, Rodilla H, Stake J, Zhaunerchyk V, Larsson J, Katona G. High-resolution macromolecular crystallography at the FemtoMAX beamline with time-over-threshold photon detection. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:64-70. [PMID: 33399553 PMCID: PMC7842217 DOI: 10.1107/s1600577520014599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
Protein dynamics contribute to protein function on different time scales. Ultrafast X-ray diffraction snapshots can visualize the location and amplitude of atom displacements after perturbation. Since amplitudes of ultrafast motions are small, high-quality X-ray diffraction data is necessary for detection. Diffraction from bovine trypsin crystals using single femtosecond X-ray pulses was recorded at FemtoMAX, which is a versatile beamline of the MAX IV synchrotron. The time-over-threshold detection made it possible that single photons are distinguishable even under short-pulse low-repetition-rate conditions. The diffraction data quality from FemtoMAX beamline enables atomic resolution investigation of protein structures. This evaluation is based on the shape of the Wilson plot, cumulative intensity distribution compared with theoretical distribution, I/σ, Rmerge/Rmeas and CC1/2 statistics versus resolution. The FemtoMAX beamline provides an interesting alternative to X-ray free-electron lasers when studying reversible processes in protein crystals.
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Affiliation(s)
- Maja Jensen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Viktor Ahlberg Gagnér
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Juan Cabello Sánchez
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | | | - J. Carl Ekström
- Department of Physics, Lund University, PO Box 118, Lund 22100, Sweden
| | | | | | | | - David Kroon
- MAX IV Laboratory, Lund University, PO Box 118, Lund 22100, Sweden
| | - Van-Thai Pham
- MAX IV Laboratory, Lund University, PO Box 118, Lund 22100, Sweden
- Center for Quantum Electronics, Institute of Physics, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Stefano Checcia
- MAX IV Laboratory, Lund University, PO Box 118, Lund 22100, Sweden
| | | | | | | | - Helena Rodilla
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | - Jan Stake
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Jörgen Larsson
- Department of Physics, Lund University, PO Box 118, Lund 22100, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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21
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Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A. Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron. IUCRJ 2020; 7:728-736. [PMID: 32695419 PMCID: PMC7340269 DOI: 10.1107/s2052252520007411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/03/2020] [Indexed: 05/23/2023]
Abstract
The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
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22
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Kondo T, Mutoh R, Tabe H, Kurisu G, Oh-Oka H, Fujiyoshi S, Matsushita M. Cryogenic Single-Molecule Spectroscopy of the Primary Electron Acceptor in the Photosynthetic Reaction Center. J Phys Chem Lett 2020; 11:3980-3986. [PMID: 32352789 DOI: 10.1021/acs.jpclett.0c00891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The photosynthetic reaction center (RC) converts light energy into electrochemical energy. The RC of heliobacteria (hRC) is a primitive homodimeric RC containing 58 bacteriochlorophylls and 2 chlorophyll as. The chlorophyll serves as the primary electron acceptor (Chl a-A0) responsible for light harvesting and charge separation. The single-molecule spectroscopy of Chl a-A0 can be used to investigate heterogeneities of the RC photochemical function, though the low fluorescence quantum yield (0.1%) makes it difficult. Here, we show the fluorescence excitation spectroscopy of individual Chl a-A0s in single hRCs at 6 K. The fluorescence quantum yield and absorption cross section of Chl a-A0 increase 2- and 4-fold, respectively, compared to those at room temperature. The two Chl a-A0s in single hRCs are identified as two distinct peaks in the fluorescence excitation spectrum, exhibiting different excitation polarization dependences. The spectral changes caused by photobleaching indicate the energy transfer across subunits in the hRC.
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Affiliation(s)
- Toru Kondo
- Department of Physics, Graduate School of Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Risa Mutoh
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Tabe
- Department of Physics, Graduate School of Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirozo Oh-Oka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Satoru Fujiyoshi
- Department of Physics, Graduate School of Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Michio Matsushita
- Department of Physics, Graduate School of Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
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23
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Miller LC, Zhao L, Canniffe DP, Martin D, Liu LN. Unfolding pathway and intermolecular interactions of the cytochrome subunit in the bacterial photosynthetic reaction center. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148204. [PMID: 32305414 PMCID: PMC7322399 DOI: 10.1016/j.bbabio.2020.148204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/15/2020] [Accepted: 04/14/2020] [Indexed: 11/25/2022]
Abstract
Precise folding of photosynthetic proteins and organization of multicomponent assemblies to form functional entities are fundamental to efficient photosynthetic electron transfer. The bacteriochlorophyll b-producing purple bacterium Blastochloris viridis possesses a simplified photosynthetic apparatus. The light-harvesting (LH) antenna complex surrounds the photosynthetic reaction center (RC) to form the RC-LH1 complex. A non-membranous tetraheme cytochrome (4Hcyt) subunit is anchored at the periplasmic surface of the RC, functioning as the electron donor to transfer electrons from mobile electron carriers to the RC. Here, we use atomic force microscopy (AFM) and single-molecule force spectroscopy (SMFS) to probe the long-range organization of the photosynthetic apparatus from Blc. viridis and the unfolding pathway of the 4Hcyt subunit in its native supramolecular assembly with its functional partners. AFM images reveal that the RC-LH1 complexes are densely organized in the photosynthetic membranes, with restricted lateral protein diffusion. Unfolding of the 4Hcyt subunit represents a multi-step process and the unfolding forces of the 4Hcyt α-helices are approximately 121 picoNewtons. Pulling of 4Hcyt could also result in the unfolding of the RC L subunit that binds with the N-terminus of 4Hcyt, suggesting strong interactions between RC subunits. This study provides new insights into the protein folding and interactions of photosynthetic multicomponent complexes, which are essential for their structural and functional integrity to conduct photosynthetic electron flow. AFM and single-molecule force spectroscopy reveal the membrane organization and unfolding process of Blastochloris viridis RC RC-light-harvesting 1 complexes are densely organized in photosynthetic membranes, with restricted lateral diffusion Unfolding of the non-membranous cytochrome (4Hcyt) subunit represents a multi-step process; The average unfolding forces of the 4Hcyt α-helices are ~121 pN; Pulling of 4Hcyt from the RC suggests strong interactions (> 150 pN) between 4Hcyt and L subunits in the RC structure.
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Affiliation(s)
- Leanne C Miller
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom
| | - Longsheng Zhao
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom; State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Daniel P Canniffe
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - David Martin
- Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China.
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24
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Wickstrand C, Katona G, Nakane T, Nogly P, Standfuss J, Nango E, Neutze R. A tool for visualizing protein motions in time-resolved crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:024701. [PMID: 32266303 PMCID: PMC7113034 DOI: 10.1063/1.5126921] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/06/2020] [Indexed: 05/12/2023]
Abstract
Time-resolved serial femtosecond crystallography (TR-SFX) at an x-ray free electron laser enables protein structural changes to be imaged on time-scales from femtoseconds to seconds. It can, however, be difficult to grasp the nature and timescale of global protein motions when structural changes are not isolated near a single active site. New tools are, therefore, needed to represent the global nature of electron density changes and their correlation with modeled protein structural changes. Here, we use TR-SFX data from bacteriorhodopsin to develop and validate a method for quantifying time-dependent electron density changes and correlating them throughout the protein. We define a spherical volume of difference electron density about selected atoms, average separately the positive and negative electron difference densities within each volume, and walk this spherical volume through all atoms within the protein. By correlating the resulting difference electron density amplitudes with time, our approach facilitates an initial assessment of the number and timescale of structural intermediates and highlights quake-like motions on the sub-picosecond timescale. This tool also allows structural models to be compared with experimental data using theoretical difference electron density changes calculated from refined resting and photo-activated structures.
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Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | | | - Przemyslaw Nogly
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zürich, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
- Author to whom correspondence should be addressed:
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25
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Standfuss J. Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr Opin Struct Biol 2019; 57:63-71. [DOI: 10.1016/j.sbi.2019.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/05/2023]
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26
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Ward LM, Cardona T, Holland-Moritz H. Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2). Front Microbiol 2019; 10:1658. [PMID: 31396180 PMCID: PMC6664022 DOI: 10.3389/fmicb.2019.01658] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/04/2019] [Indexed: 12/15/2022] Open
Abstract
Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2. We demonstrate that phototrophic WPS-2 show significant genetic and metabolic divergence from other phototrophic and non-phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of phototrophic members of this clade.
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Affiliation(s)
- Lewis M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hannah Holland-Moritz
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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27
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Wickstrand C, Nogly P, Nango E, Iwata S, Standfuss J, Neutze R. Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation. Annu Rev Biochem 2019; 88:59-83. [DOI: 10.1146/annurev-biochem-013118-111327] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Directional transport of protons across an energy transducing membrane—proton pumping—is ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all- trans retinal chromophore being photoisomerized to a 13- cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive.
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Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Przemyslaw Nogly
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Eriko Nango
- RIKEN SPring-8 Center, 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, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
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28
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Martin-Garcia JM, Zhu L, Mendez D, Lee MY, Chun E, Li C, Hu H, Subramanian G, Kissick D, Ogata C, Henning R, Ishchenko A, Dobson Z, Zhang S, Weierstall U, Spence JCH, Fromme P, Zatsepin NA, Fischetti RF, Cherezov V, Liu W. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source. IUCRJ 2019; 6:412-425. [PMID: 31098022 PMCID: PMC6503920 DOI: 10.1107/s205225251900263x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/20/2019] [Indexed: 05/29/2023]
Abstract
Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron laser sources. Synchrotron radiation flux may be increased ∼100 times by a moderate increase in the bandwidth ('pink beam' conditions) at some cost to data analysis complexity. Here, we report the first high-viscosity injector-based pink-beam SX experiments. The structures of proteinase K (PK) and A2A adenosine receptor (A2AAR) were determined to resolutions of 1.8 and 4.2 Å using 4 and 24 consecutive 100 ps X-ray pulse exposures, respectively. Strong PK data were processed using existing Laue approaches, while weaker A2AAR data required an alternative data-processing strategy. This demonstration of the feasibility presents new opportunities for time-resolved experiments with microcrystals to study structural changes in real time at pink-beam synchrotron beamlines worldwide.
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Affiliation(s)
- Jose M. Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Derek Mendez
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Eugene Chun
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Chufeng Li
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Hao Hu
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Zachary Dobson
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Shangji Zhang
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
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29
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Meents A, Wiedorn MO, Srajer V, Henning R, Sarrou I, Bergtholdt J, Barthelmess M, Reinke PYA, Dierksmeyer D, Tolstikova A, Schaible S, Messerschmidt M, Ogata CM, Kissick DJ, Taft MH, Manstein DJ, Lieske J, Oberthuer D, Fischetti RF, Chapman HN. Pink-beam serial crystallography. Nat Commun 2017; 8:1281. [PMID: 29097720 PMCID: PMC5668288 DOI: 10.1038/s41467-017-01417-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/14/2017] [Indexed: 02/02/2023] Open
Abstract
Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, "pink", beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized for very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.
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Affiliation(s)
- A Meents
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany. .,Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany.
| | - M O Wiedorn
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - V Srajer
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - R Henning
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - I Sarrou
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - J Bergtholdt
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - M Barthelmess
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - P Y A Reinke
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - D Dierksmeyer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - A Tolstikova
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - S Schaible
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - M Messerschmidt
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - C M Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - D J Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - M H Taft
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - D J Manstein
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - J Lieske
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - D Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - R F Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - H N Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
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30
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Šrajer V, Schmidt M. Watching Proteins Function with Time-resolved X-ray Crystallography. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:373001. [PMID: 29353938 PMCID: PMC5771432 DOI: 10.1088/1361-6463/aa7d32] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.
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Affiliation(s)
- Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, IL, USA
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31
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Luk HL, Feist J, Toppari JJ, Groenhof G. Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry. J Chem Theory Comput 2017; 13:4324-4335. [DOI: 10.1021/acs.jctc.7b00388] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Johannes Feist
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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32
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Aponte-Santamaría C, Fischer G, Båth P, Neutze R, de Groot BL. Temperature dependence of protein-water interactions in a gated yeast aquaporin. Sci Rep 2017; 7:4016. [PMID: 28638135 PMCID: PMC5479825 DOI: 10.1038/s41598-017-04180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/10/2017] [Indexed: 11/18/2022] Open
Abstract
Regulation of aquaporins is a key process of living organisms to counteract sudden osmotic changes. Aqy1, which is a water transporting aquaporin of the yeast Pichia pastoris, is suggested to be gated by chemo-mechanical stimuli as a protective regulatory-response against rapid freezing. Here, we tested the influence of temperature by determining the X-ray structure of Aqy1 at room temperature (RT) at 1.3 Å resolution, and by exploring the structural dynamics of Aqy1 during freezing through molecular dynamics simulations. At ambient temperature and in a lipid bilayer, Aqy1 adopts a closed conformation that is globally better described by the RT than by the low-temperature (LT) crystal structure. Locally, for the blocking-residue Tyr31 and the water molecules inside the pore, both LT and RT data sets are consistent with the positions observed in the simulations at room-temperature. Moreover, as the temperature was lowered, Tyr31 adopted a conformation that more effectively blocked the channel, and its motion was accompanied by a temperature-driven rearrangement of the water molecules inside the channel. We therefore speculate that temperature drives Aqy1 from a loosely- to a tightly-blocked state. This analysis provides high-resolution structural evidence of the influence of temperature on membrane-transport channels.
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Affiliation(s)
- Camilo Aponte-Santamaría
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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33
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Ren Z, Yang X. Angular-split/temporal-delay approach to ultrafast protein dynamics at XFELs. Acta Crystallogr D Struct Biol 2016; 72:871-82. [PMID: 27377384 PMCID: PMC6688658 DOI: 10.1107/s2059798316008573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 05/27/2016] [Indexed: 11/10/2022] Open
Abstract
X-ray crystallography promises direct insights into electron-density changes that lead to and arise from structural changes such as electron and proton transfer and the formation, rupture and isomerization of chemical bonds. The ultrashort pulses of hard X-rays produced by free-electron lasers present an exciting opportunity for capturing ultrafast structural events in biological macromolecules within femtoseconds after photoexcitation. However, shot-to-shot fluctuations, which are inherent to the very process of self-amplified spontaneous emission (SASE) that generates the ultrashort X-ray pulses, are a major source of noise that may conceal signals from structural changes. Here, a new approach is proposed to angularly split a single SASE pulse and to produce a temporal delay of picoseconds between the split pulses. These split pulses will allow the probing of two distinct states before and after photoexcitation triggered by a laser pulse between the split X-ray pulses. The split pulses originate from a single SASE pulse and share many common properties; thus, noise arising from shot-to-shot fluctuations is self-canceling. The unambiguous interpretation of ultrafast structural changes would require diffraction data at atomic resolution, as these changes may or may not involve any atomic displacement. This approach, in combination with the strategy of serial crystallography, offers a solution to study ultrafast dynamics of light-initiated biochemical reactions or biological processes at atomic resolution.
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Affiliation(s)
- Zhong Ren
- Renz Research Inc., Westmont, IL 60559, USA
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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34
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Correy GJ, Carr PD, Meirelles T, Mabbitt PD, Fraser NJ, Weik M, Jackson CJ. Mapping the Accessible Conformational Landscape of an Insect Carboxylesterase Using Conformational Ensemble Analysis and Kinetic Crystallography. Structure 2016; 24:977-87. [PMID: 27210287 DOI: 10.1016/j.str.2016.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 11/26/2022]
Abstract
The proper function of enzymes often depends upon their efficient interconversion between particular conformational sub-states on a free-energy landscape. Experimentally characterizing these sub-states is challenging, which has limited our understanding of the role of protein dynamics in many enzymes. Here, we have used a combination of kinetic crystallography and detailed analysis of crystallographic protein ensembles to map the accessible conformational landscape of an insect carboxylesterase (LcαE7) as it traverses all steps in its catalytic cycle. LcαE7 is of special interest because of its evolving role in organophosphate insecticide resistance. Our results reveal that a dynamically coupled network of residues extends from the substrate-binding site to a surface loop. Interestingly, the coupling of this network that is apparent in the apoenzyme appears to be reduced in the phosphorylated enzyme intermediate. Altogether, the results of this work highlight the importance of protein dynamics to enzyme function and the evolution of new activity.
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Affiliation(s)
- Galen J Correy
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Paul D Carr
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Tamara Meirelles
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Peter D Mabbitt
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nicholas J Fraser
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Martin Weik
- Institut de Biologie Structurale Jean Pierre Ebel, Commisariat a l'Energie Atomique, Centre de National de la Recherche Scientifique, University Josef Fourier, 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
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35
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Kageyama Y, Ikegami T, Kurokome Y, Takeda S. Mechanism of Macroscopic Motion of Oleate Helical Assemblies: Cooperative Deprotonation of Carboxyl Groups Triggered by Photoisomerization of Azobenzene Derivatives. Chemistry 2016; 22:8669-75. [PMID: 27165777 DOI: 10.1002/chem.201600426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Yoshiyuki Kageyama
- Department of Chemistry; Faculty of Science; Hokkaido University; North-10, West-8 Sapporo 060-0810 Japan), Fax: (+81) 11 706 4841
- JST PRESTO, Kawaguchi, 332-0012 (Japan)
| | - Tomonori Ikegami
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; North-10, West-8 Sapporo 060-0810 Japan
| | - Yuta Kurokome
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; North-10, West-8 Sapporo 060-0810 Japan
| | - Sadamu Takeda
- Department of Chemistry; Faculty of Science; Hokkaido University; North-10, West-8 Sapporo 060-0810 Japan), Fax: (+81) 11 706 4841
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36
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Combined use of optical spectroscopy and computational methods to study the binding and the photoinduced conformational modification of proteins when NMR and X-ray structural determinations are not an option. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016. [PMID: 24018324 DOI: 10.1016/b978-0-12-416596-0.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The functions of proteins depend on their interactions with various ligands and these interactions are controlled by the structure of the polypeptides. If one can manipulate the structure of proteins, their functions can in principle be modulated. The issue of protein structure-function relationship is not only a central problem in biophysics, but is becoming clear that the ability to "artificially" modify the structure of proteins could be relevant in fields beyond the biomedical area to provide, for instance, light responses in proteins which would not possess such properties in their native state. This chapter presents an overview of the combination of optical electronic and vibrational spectroscopy with various computational methods to investigate the binding between photoactive ligands and proteins.
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37
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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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38
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Malferrari M, Turina P, Francia F, Mezzetti A, Leibl W, Venturoli G. Dehydration affects the electronic structure of the primary electron donor in bacterial photosynthetic reaction centers: evidence from visible-NIR and light-induced difference FTIR spectroscopy. Photochem Photobiol Sci 2015; 14:238-51. [PMID: 25188921 DOI: 10.1039/c4pp00245h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The photosynthetic reaction center (RC) is a membrane pigment-protein complex that catalyzes the initial charge separation reactions of photosynthesis. Following photoexcitation, the RC undergoes conformational relaxations which stabilize the charge-separated state. Dehydration of the complex inhibits its conformational dynamics, providing a useful tool to gain insights into the relaxational processes. We analyzed the effects of dehydration on the electronic structure of the primary electron donor P, as probed by visible-NIR and light-induced FTIR difference spectroscopy, in RC films equilibrated at different relative humidities r. Previous FTIR and ENDOR spectroscopic studies revealed that P, an excitonically coupled dimer of bacteriochlorophylls, can be switched between two conformations, P866 and P850, which differ in the extent of delocalization of the unpaired electron between the two bacteriochlorophyll moieties (PL and PM) of the photo-oxidized radical P(+). We found that dehydration (at r = 11%) shifts the optical Qy band of P from 866 to 850-845 nm, a large part of the effect occurring already at r = 76%. Such a dehydration weakens light-induced difference FTIR marker bands, which probe the delocalization of charge distribution within the P(+) dimer (the electronic band of P(+) at 2700 cm(-1), and the associated phase-phonon vibrational modes at around 1300, 1480, and 1550 cm(-1)). From the analysis of the P(+) keto C[double bond, length as m-dash]O bands at 1703 and 1713-15 cm(-1), we inferred that dehydration induces a stronger localization of the unpaired electron on PL(+). The observed charge redistribution is discussed in relation to the dielectric relaxation of the photoexcited RC on a long (10(2) s) time scale.
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Affiliation(s)
- Marco Malferrari
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, Bologna, Italy.
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39
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De March M, Brancatelli G, Demitri N, De Zorzi R, Hickey N, Geremia S. A general exit strategy of monoheme cytochromes c and c2 in electron transfer complexes? IUBMB Life 2015; 67:694-700. [PMID: 26311433 DOI: 10.1002/iub.1410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/28/2015] [Indexed: 11/06/2022]
Abstract
Using our previously reported maps of the electrostatic surface of horse heart ferri- and ferro-cyt c, comparisons were made between the complementary electrostatic surfaces of three cyt c peroxidase-cyt c complexes and the photosynthetic reaction center-cyt c complex, considering both iron oxidation states. The results obtained were consistent with a sliding mechanism for the electron shuttle on the surface of the protein complexes, promoted by the change in iron oxidation state. This mechanism was found to be in agreement with theoretical and NMR studies reported in the literature. Importantly, the analysis also provided a rationale for recognition of nonproductive associations. As we have previously reported the same conclusion on examination of redox partners of cyt c in the mitochondrial respiratory pathway, our hypothesis is that the proposed mechanism could represent a general exit strategy of monoheme cyts c and c2 in electron transfer complexes.
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Affiliation(s)
- Matteo De March
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Giovanna Brancatelli
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Nicola Demitri
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Neal Hickey
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
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40
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Malferrari M, Francia F, Venturoli G. Retardation of Protein Dynamics by Trehalose in Dehydrated Systems of Photosynthetic Reaction Centers. Insights from Electron Transfer and Thermal Denaturation Kinetics. J Phys Chem B 2015; 119:13600-18. [DOI: 10.1021/acs.jpcb.5b02986] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Malferrari
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Francesco Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
- Consorzio Nazionale
Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o
Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
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41
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Zeng X, Ren Z, Wu Q, Fan J, Peng PP, Tang K, Zhang R, Zhao KH, Yang X. Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8. NATURE PLANTS 2015; 1:14006. [PMID: 26097745 PMCID: PMC4469132 DOI: 10.1038/nplants.2014.6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/23/2014] [Indexed: 05/19/2023]
Abstract
Arabidopsis thaliana UVR8 (AtUVR8) is a long-sought-after photoreceptor that undergoes dimer dissociation in response to UV-B light. Crystallographic and mutational studies have identified two crucial tryptophan residues for UV-B responses in AtUVR8. However, the mechanism of UV-B perception and structural events leading up to dimer dissociation remain elusive at the molecular level. We applied dynamic crystallography to capture light-induced structural events in photoactive AtUVR8 crystals. Here we report two intermediate structures at 1.67Å resolution. At the epicenter of UV-B signaling, concerted motions associated with Trp285/Trp233 lead to ejection of a water molecule, which weakens an intricate network of hydrogen bonds and salt bridges at the dimer interface. Partial opening of the β-propeller structure due to thermal relaxation of conformational strains originating in the epicenter further disrupts the dimer interface and leads to dimer dissociation. These dynamic crystallographic observations provide structural insights into the photo-perception and signaling mechanism of UVR8.
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Affiliation(s)
- Xiaoli Zeng
- Key State Laboratory of Agricultural Microbiology, Huazhong
Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Zhong Ren
- Renz Research Inc., Westmont, IL 60559, USA
| | - Qi Wu
- Department of Physics and Materials Science, City University of Hong
Kong, Kowloon, Hong Kong
| | - Jun Fan
- Department of Physics and Materials Science, City University of Hong
Kong, Kowloon, Hong Kong
| | - Pan-Pan Peng
- Key State Laboratory of Agricultural Microbiology, Huazhong
Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Kun Tang
- Key State Laboratory of Agricultural Microbiology, Huazhong
Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Ruiqin Zhang
- Department of Physics and Materials Science, City University of Hong
Kong, Kowloon, Hong Kong
| | - Kai-Hong Zhao
- Key State Laboratory of Agricultural Microbiology, Huazhong
Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Xiaojing Yang
- Department of Biochemistry and Molecular Biology, The University of
Chicago, Chicago, IL 60637, USA
- Department of Chemistry, The University of Illinois at Chicago,
Chicago, IL 60607, USA
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42
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Neutze R. Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130318. [PMID: 24914150 PMCID: PMC4052859 DOI: 10.1098/rstb.2013.0318] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X-ray free-electron lasers (XFELs) are revolutionary X-ray sources. Their time structure, providing X-ray pulses of a few tens of femtoseconds in duration; and their extreme peak brilliance, delivering approximately 1012 X-ray photons per pulse and facilitating sub-micrometre focusing, distinguish XFEL sources from synchrotron radiation. In this opinion piece, I argue that these properties of XFEL radiation will facilitate new discoveries in life science. I reason that time-resolved serial femtosecond crystallography and time-resolved wide angle X-ray scattering are promising areas of scientific investigation that will be advanced by XFEL capabilities, allowing new scientific questions to be addressed that are not accessible using established methods at storage ring facilities. These questions include visualizing ultrafast protein structural dynamics on the femtosecond to picosecond time-scale, as well as time-resolved diffraction studies of non-cyclic reactions. I argue that these emerging opportunities will stimulate a renaissance of interest in time-resolved structural biochemistry.
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Affiliation(s)
- Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, 40530 Gothenburg, Sweden
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43
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van Thor JJ, Warren MM, Lincoln CN, Chollet M, Lemke HT, Fritz DM, Schmidt M, Tenboer J, Ren Z, Srajer V, Moffat K, Graber T. Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein. Faraday Discuss 2014; 171:439-55. [PMID: 25415305 DOI: 10.1039/c4fd00011k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Femtosecond time resolved pump-probe protein X-ray crystallography requires highly accurate measurements of the photoinduced structure factor amplitude differences. In the case of femtosecond photolysis of single P63 crystals of the Photoactive Yellow Protein, it is shown that photochemical dynamics place a considerable restraint on the achievable time resolution due to the requirement to stretch and add second order dispersion in order to generate threshold concentration levels in the interaction region. Here, we report on using a 'quasi-cw' approach to use the rotation method with monochromatic radiation and 2 eV bandwidth at 9.465 keV at the Linac Coherent Light Source operated in SASE mode. A source of significant Bragg reflection intensity noise is identified from the combination of mode structure and jitter with very small mosaic spread of the crystals and very low convergence of the XFEL source. The accuracy with which the three dimensional reflection is approximated by the 'quasi-cw' rotation method with the pulsed source is modelled from the experimentally collected X-ray pulse intensities together with the measured rocking curves. This model is extended to predict merging statistics for recently demonstrated self seeded mode generated pulse train with improved stability, in addition to extrapolating to single crystal experiments with increased mosaic spread. The results show that the noise level can be adequately modelled in this manner, indicating that the large intensity fluctuations dominate the merged signal-to-noise (I/σI) value. Furthermore, these results predict that using the self seeded mode together with more mosaic crystals, sufficient accuracy may be obtained in order to resolve typical photoinduced structure factor amplitude differences, as taken from representative synchrotron results.
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Affiliation(s)
- Jasper J van Thor
- Imperial College London, Division of Molecular Biosciences, South Kensington Campus, London SW7 2AZ, UK.
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44
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Johansson LC, Arnlund D, Katona G, White TA, Barty A, DePonte DP, Shoeman RL, Wickstrand C, Sharma A, Williams GJ, Aquila A, Bogan MJ, Caleman C, Davidsson J, Doak RB, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Kassemeyer S, Kirian RA, Kupitz C, Liang M, Lomb L, Malmerberg E, Martin AV, Messerschmidt M, Nass K, Redecke L, Seibert MM, Sjöhamn J, Steinbrener J, Stellato F, Wang D, Wahlgren WY, Weierstall U, Westenhoff S, Zatsepin NA, Boutet S, Spence JCH, Schlichting I, Chapman HN, Fromme P, Neutze R. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat Commun 2014; 4:2911. [PMID: 24352554 PMCID: PMC3905732 DOI: 10.1038/ncomms3911] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/08/2013] [Indexed: 11/22/2022] Open
Abstract
Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure. Serial femtosecond crystallography is an X-ray free-electron-laser-based method that uses X-ray bursts to determine protein structures. Here the authors present the structure of a photosynthetic reaction centre, an integral membrane protein, achieved with no sign of X-ray-induced radiation damage.
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Affiliation(s)
- Linda C Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Thomas A White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel P DePonte
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert L Shoeman
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Amit Sharma
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Garth J Williams
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael J Bogan
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Davidsson
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - R Bruce Doak
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, 94550 California, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Lorenzo Galli
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ingo Grotjohann
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Mark S Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Stephan Kassemeyer
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Richard A Kirian
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lukas Lomb
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Erik Malmerberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Andrew V Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marc Messerschmidt
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - Karol Nass
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Lübeck at DESY, 22607 Hamburg, Germany
| | - M Marvin Seibert
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - Jennie Sjöhamn
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jan Steinbrener
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Weixaio Y Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Ilme Schlichting
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
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Lórenz-Fonfría VA, Heberle J. Proton transfer and protein conformation dynamics in photosensitive proteins by time-resolved step-scan Fourier-transform infrared spectroscopy. J Vis Exp 2014:e51622. [PMID: 24998200 PMCID: PMC4208678 DOI: 10.3791/51622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Monitoring the dynamics of protonation and protein backbone conformation changes during the function of a protein is an essential step towards understanding its mechanism. Protonation and conformational changes affect the vibration pattern of amino acid side chains and of the peptide bond, respectively, both of which can be probed by infrared (IR) difference spectroscopy. For proteins whose function can be repetitively and reproducibly triggered by light, it is possible to obtain infrared difference spectra with (sub)microsecond resolution over a broad spectral range using the step-scan Fourier transform infrared technique. With -10(2)-10(3) repetitions of the photoreaction, the minimum number to complete a scan at reasonable spectral resolution and bandwidth, the noise level in the absorption difference spectra can be as low as -10(-) (4), sufficient to follow the kinetics of protonation changes from a single amino acid. Lower noise levels can be accomplished by more data averaging and/or mathematical processing. The amount of protein required for optimal results is between 5-100 µg, depending on the sampling technique used. Regarding additional requirements, the protein needs to be first concentrated in a low ionic strength buffer and then dried to form a film. The protein film is hydrated prior to the experiment, either with little droplets of water or under controlled atmospheric humidity. The attained hydration level (g of water / g of protein) is gauged from an IR absorption spectrum. To showcase the technique, we studied the photocycle of the light-driven proton-pump bacteriorhodopsin in its native purple membrane environment, and of the light-gated ion channel channelrhodopsin-2 solubilized in detergent.
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Affiliation(s)
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin;
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46
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Feld GK, Frank M. Enabling membrane protein structure and dynamics with X-ray free electron lasers. Curr Opin Struct Biol 2014; 27:69-78. [PMID: 24930119 DOI: 10.1016/j.sbi.2014.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Determining the three-dimensional structures and dynamics of membrane proteins remains one of the great challenges of modern biology. The recent availability of X-ray free electron laser (XFEL) light sources has opened the door to a new and revolutionary approach to performing X-ray analysis of these important biomolecules. Recent advances in sample delivery, data reduction, and phasing have enabled the high-resolution structural probing of membrane proteins at room temperature. While considerable challenges remain, the recent developments described in this review may ultimately provide structural biologists with powerful tools for obtaining unprecedented atomic-scale and dynamic visualization of membrane proteins at near-physiological conditions.
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Affiliation(s)
- Geoffrey K Feld
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Matthias Frank
- Physics Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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47
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Krasilnikov PM. Problems of the theory of electron transfer in biological systems. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914010059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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48
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Zhu J, van Stokkum IHM, Paparelli L, Jones MR, Groot ML. Early bacteriopheophytin reduction in charge separation in reaction centers of Rhodobacter sphaeroides. Biophys J 2014; 104:2493-502. [PMID: 23746522 DOI: 10.1016/j.bpj.2013.04.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 11/16/2022] Open
Abstract
A question at the forefront of biophysical sciences is, to what extent do quantum effects and protein conformational changes play a role in processes such as biological sensing and energy conversion? At the heart of photosynthetic energy transduction lie processes involving ultrafast energy and electron transfers among a small number of tetrapyrrole pigments embedded in the interior of a protein. In the purple bacterial reaction center (RC), a highly efficient ultrafast charge separation takes place between a pair of bacteriochlorophylls: an accessory bacteriochlorophyll (B) and bacteriopheophytin (H). In this work, we applied ultrafast spectroscopy in the visible and near-infrared spectral region to Rhodobacter sphaeroides RCs to accurately track the timing of the electron on BA and HA via the appearance of the BA and HA anion bands. We observed an unexpectedly early rise of the HA⁻ band that challenges the accepted simple picture of stepwise electron transfer with 3 ps and 1 ps time constants. The implications for the mechanism of initial charge separation in bacterial RCs are discussed in terms of a possible adiabatic electron transfer step between BA and HA, and the effect of protein conformation on the electron transfer rate.
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Affiliation(s)
- Jingyi Zhu
- Department of Physics, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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Borfecchia E, Garino C, Salassa L, Ruiu T, Gianolio D, Zhang X, Attenkofer K, Chen LX, Gobetto R, Sadler PJ, Lamberti C. X-ray transient absorption structural characterization of the 3MLCT triplet excited state of cis-[Ru(bpy)2(py)2]2+. Dalton Trans 2013; 42:6564-71. [PMID: 23474490 DOI: 10.1039/c3dt32865a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The excited state dynamics and structure of the photochemically active complex cis-[Ru(bpy)2(py)2](2+) have been investigated using optical transient absorption (OTA) and X-ray transient absorption (XTA) spectroscopy, and density functional theory (DFT). Upon light-excitation in aqueous solution cis-[Ru(bpy)2(py)2](2+) undergoes ultrafast dissociation of one pyridine ligand to form cis-[Ru(bpy)2(py)(H2O)](2+). OTA measurements highlighted the presence of two major time components of 1700 ps and 130 ps through which the system decays to the ground-state and evolves towards the photoproduct. XTA data were acquired after 150 ps, 500 ps, and 3000 ps from laser excitation (λexc = 351 nm) and provided the transient structure of the (3)MLCT state corresponding to the longer time component in the OTA experiment. In excellent agreement with DFT, XTA shows that the (3)MLCT geometry is characterized by an elongation of the dissociating Ru-N(py) bond and a shortening of the trans Ru-N(bpy) bond with respect to the ground state. Conversely, calculations show that the (3)MC state has a highly distorted structure with Ru-N(py) bonds between 2.77-3.05 Å.
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Affiliation(s)
- Elisa Borfecchia
- Department of Chemistry, NIS Centre of Excellence, and INSTM Reference Centre, University of Turin, Turin, Italy
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50
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Müh F, Zouni A. The nonheme iron in photosystem II. PHOTOSYNTHESIS RESEARCH 2013; 116:295-314. [PMID: 24077892 DOI: 10.1007/s11120-013-9926-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/17/2013] [Indexed: 06/02/2023]
Abstract
Photosystem II (PSII), the light-driven water:plastoquinone (PQ) oxidoreductase of oxygenic photosynthesis, contains a nonheme iron (NHI) at its electron acceptor side. The NHI is situated between the two PQs QA and QB that serve as one-electron transmitter and substrate of the reductase part of PSII, respectively. Among the ligands of the NHI is a (bi)carbonate originating from CO2, the substrate of the dark reactions of oxygenic photosynthesis. Based on recent advances in the crystallography of PSII, we review the structure of the NHI in PSII and discuss ideas concerning its function and the role of bicarbonate along with a comparison to the reaction center of purple bacteria and other enzymes containing a mononuclear NHI site.
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