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Arinkin V, Granzin J, Jaeger KE, Willbold D, Krauss U, Batra-Safferling R. Conserved Signal Transduction Mechanisms and Dark Recovery Kinetic Tuning in the Pseudomonadaceae Short Light, Oxygen, Voltage (LOV) Protein Family. J Mol Biol 2024; 436:168458. [PMID: 38280482 DOI: 10.1016/j.jmb.2024.168458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
Light-Oxygen-Voltage (LOV) flavoproteins transduce a light signal into variable signaling outputs via a structural rearrangement in the sensory core domain, which is then relayed to fused effector domains via α-helical linker elements. Short LOV proteins from Pseudomonadaceae consist of a LOV sensory core and N- and C-terminal α-helices of variable length, providing a simple model system to study the molecular mechanism of allosteric activation. Here we report the crystal structures of two LOV proteins from Pseudomonas fluorescens - SBW25-LOV in the fully light-adapted state and Pf5-LOV in the dark-state. In a comparative analysis of the Pseudomonadaceae short LOVs, the structures demonstrate light-induced rotation of the core domains and splaying of the proximal A'α and Jα helices in the N and C-termini, highlighting evidence for a conserved signal transduction mechanism. Another distinguishing feature of the Pseudomonadaceae short LOV protein family is their highly variable dark recovery, ranging from seconds to days. Understanding this variability is crucial for tuning the signaling behavior of LOV-based optogenetic tools. At 37 °C, SBW25-LOV and Pf5-LOV exhibit adduct state lifetimes of 1470 min and 3.6 min, respectively. To investigate this remarkable difference in dark recovery rates, we targeted three residues lining the solvent channel entrance to the chromophore pocket where we introduced mutations by exchanging the non-conserved amino acids from SBW25-LOV into Pf5-LOV and vice versa. Dark recovery kinetics of the resulting mutants, as well as MD simulations and solvent cavity calculations on the crystal structures suggest a correlation between solvent accessibility and adduct lifetime.
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Affiliation(s)
- Vladimir Arinkin
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Joachim Granzin
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institut für Bio- und Geowissenschaften (IBG): Biotechnologie (IBG-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institut für Bio- und Geowissenschaften (IBG): Biotechnologie (IBG-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Renu Batra-Safferling
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany.
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2
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Flores-Ibarra A, Maia RNA, Olasz B, Church JR, Gotthard G, Schapiro I, Heberle J, Nogly P. Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation. J Mol Biol 2024; 436:168356. [PMID: 37944792 DOI: 10.1016/j.jmb.2023.168356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.
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Affiliation(s)
- Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raiza N A Maia
- Department of Chemistry, The University of Texas at Austin, 78712-1224 Austin, TX, USA
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | | | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Przemyslaw Nogly
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
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3
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Dikiy I, Swingle D, Toy K, Edupuganti UR, Rivera-Cancel G, Gardner KH. Diversity of function and higher-order structure within HWE sensor histidine kinases. J Biol Chem 2023; 299:104934. [PMID: 37331599 PMCID: PMC10359499 DOI: 10.1016/j.jbc.2023.104934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023] Open
Abstract
Integral to the protein structure/function paradigm, oligomeric state is typically conserved along with function across evolution. However, notable exceptions such as the hemoglobins show how evolution can alter oligomerization to enable new regulatory mechanisms. Here, we examine this linkage in histidine kinases (HKs), a large class of widely distributed prokaryotic environmental sensors. While the majority of HKs are transmembrane homodimers, members of the HWE/HisKA2 family can deviate from this architecture as exemplified by our finding of a monomeric soluble HWE/HisKA2 HK (EL346, a photosensing light-oxygen-voltage [LOV]-HK). To further explore the diversity of oligomerization states and regulation within this family, we biophysically and biochemically characterized multiple EL346 homologs and found a range of HK oligomeric states and functions. Three LOV-HK homologs are primarily dimeric with differing structural and functional responses to light, while two Per-ARNT-Sim-HKs interconvert between differentially active monomers and dimers, suggesting dimerization might control enzymatic activity for these proteins. Finally, we examined putative interfaces in a dimeric LOV-HK, finding that multiple regions contribute to dimerization. Our findings suggest the potential for novel regulatory modes and oligomeric states beyond those traditionally defined for this important family of environmental sensors.
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Affiliation(s)
- Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Danielle Swingle
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; PhD. Program in Biochemistry, The Graduate Center - City University of New York, New York, New York, USA
| | - Kaitlyn Toy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; Department of Chemistry and Biochemistry, City College of New York, New York, New York, USA
| | - Uthama R Edupuganti
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; PhD. Program in Biochemistry, The Graduate Center - City University of New York, New York, New York, USA
| | - Giomar Rivera-Cancel
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; Department of Chemistry and Biochemistry, City College of New York, New York, New York, USA; PhD. Programs in Biochemistry, Biology, and Chemistry, The Graduate Center - City University of New York, New York, New York, USA.
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4
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Berntsson O, Terry AE, Plivelic TS. A setup for millisecond time-resolved X-ray solution scattering experiments at the CoSAXS beamline at the MAX IV Laboratory. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:555-562. [PMID: 35254321 PMCID: PMC8900842 DOI: 10.1107/s1600577522000996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The function of biomolecules is tightly linked to their structure, and changes therein. Time-resolved X-ray solution scattering has proven a powerful technique for interrogating structural changes and signal transduction in photoreceptor proteins. However, these only represent a small fraction of the biological macromolecules of interest. More recently, laser-induced temperature jumps have been introduced as a more general means of initiating structural changes in biomolecules. Here we present the development of a setup for millisecond time-resolved X-ray solution scattering experiments at the CoSAXS beamline, primarily using infrared laser light to trigger a temperature increase, and structural changes. We present results that highlight the characteristics of this setup along with data showing structural changes in lysozyme caused by a temperature jump. Further developments and applications of the setup are also discussed.
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Affiliation(s)
| | - Ann E. Terry
- MAX IV Laboratory, Lund University, Lund, Sweden
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Heo J, Kim JG, Choi EH, Ki H, Ahn DS, Kim J, Lee S, Ihee H. Determining the charge distribution and the direction of bond cleavage with femtosecond anisotropic x-ray liquidography. Nat Commun 2022; 13:522. [PMID: 35082327 PMCID: PMC8792042 DOI: 10.1038/s41467-022-28168-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Energy, structure, and charge are fundamental quantities characterizing a molecule. Whereas the energy flow and structure change in chemical reactions are experimentally characterized, determining the atomic charges of a molecule in solution has been elusive, even for a triatomic molecule such as triiodide ion, I3-. Moreover, it remains to be answered how the charge distribution is coupled to the molecular geometry; which I-I bond, if two I-I bonds are unequal, dissociates depending on the electronic state. Here, femtosecond anisotropic x-ray solution scattering allows us to provide the following answers in addition to the overall rich structural dynamics. The analysis unravels that the negative charge of I3- is highly localized on the terminal iodine atom forming the longer bond with the central iodine atom, and the shorter I-I bond dissociates in the excited state, whereas the longer one in the ground state. We anticipate that this work may open a new avenue for studying the atomic charge distribution of molecules in solution and taking advantage of orientational information in anisotropic scattering data for solution-phase structural dynamics.
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Affiliation(s)
- Jun Heo
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Eun Hyuk Choi
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Doo-Sik Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seonggon Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
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6
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Imelio JA, Trajtenberg F, Buschiazzo A. Allostery and protein plasticity: the keystones for bacterial signaling and regulation. Biophys Rev 2022; 13:943-953. [PMID: 35059019 DOI: 10.1007/s12551-021-00892-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/31/2021] [Indexed: 11/25/2022] Open
Abstract
Bacteria sense intracellular and environmental signals using an array of proteins as antennas. The information is transmitted from such sensory modules to other protein domains that act as output effectors. Sensor and effector can be part of the same polypeptide or instead be separate diffusible proteins that interact specifically. The output effector modules regulate physiologic responses, allowing the cells to adapt to the varying conditions. These biological machineries are known as signal transduction systems (STSs). Despite the captivating architectural diversity exhibited by STS proteins, a universal feature is their allosteric regulation: signal binding at one site modifies the activity at a physically distant site. Allostery requires protein plasticity, precisely encoded within their 3D structures, and implicating programmed molecular motions. This review summarizes how STS proteins connect stimuli to specific responses by exploiting allostery and protein plasticity. Illustrative examples spanning a wide variety of protein folds will focus on one- and two-component systems (TCSs). The former encompass the entire transmission route within a single polypeptide, whereas TCSs have evolved as separate diffusible proteins that interact specifically, sometimes including additional intermediary proteins in the pathway. Irrespective of their structural diversity, STS proteins are able to modulate their own molecular motions, which can be relatively slow, rigid-body movements, all the way to fast fluctuations in the form of macromolecular flexibility, thus spanning a continuous protein dynamics spectrum. In sum, STSs rely on allostery to steer information transmission, going from simple two-state switching to rich multi-state conformational order/disorder transitions.
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Affiliation(s)
- J A Imelio
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - F Trajtenberg
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - A Buschiazzo
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Microbiology, Institut Pasteur, Paris, France
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7
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Choi EH, Lee Y, Heo J, Ihee H. Reaction dynamics studied via femtosecond X-ray liquidography at X-ray free-electron lasers. Chem Sci 2022; 13:8457-8490. [PMID: 35974755 PMCID: PMC9337737 DOI: 10.1039/d2sc00502f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
X-ray free-electron lasers (XFELs) provide femtosecond X-ray pulses suitable for pump–probe time-resolved studies with a femtosecond time resolution. Since the advent of the first XFEL in 2009, recent years have witnessed a great number of applications with various pump–probe techniques at XFELs. Among these, time-resolved X-ray liquidography (TRXL) is a powerful method for visualizing structural dynamics in the liquid solution phase. Here, we classify various chemical and biological molecular systems studied via femtosecond TRXL (fs-TRXL) at XFELs, depending on the focus of the studied process, into (i) bond cleavage and formation, (ii) charge distribution and electron transfer, (iii) orientational dynamics, (iv) solvation dynamics, (v) coherent nuclear wavepacket dynamics, and (vi) protein structural dynamics, and provide a brief review on each category. We also lay out a plausible roadmap for future fs-TRXL studies for areas that have not been explored yet. Femtosecond X-ray liquidography using X-ray free-electron lasers (XFELs) visualizes various aspects of reaction dynamics.![]()
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Affiliation(s)
- Eun Hyuk Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jun Heo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
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8
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Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. J Phys Chem B 2021; 125:12401-12412. [PMID: 34748336 PMCID: PMC9096987 DOI: 10.1021/acs.jpcb.1c05820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins have been found to inhabit a diverse set of three-dimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scales─picoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure-function relationships require atomistic knowledge of the populated states in the ensemble. In this Perspective, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.
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Affiliation(s)
- Adam K Nijhawan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Arnold M Chan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Darren J Hsu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lin X Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Kevin L Kohlstedt
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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Cho HS, Schotte F, Stadnytskyi V, Anfinrud P. Time-resolved X-ray scattering studies of proteins. Curr Opin Struct Biol 2021; 70:99-107. [PMID: 34175665 PMCID: PMC8530917 DOI: 10.1016/j.sbi.2021.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 11/24/2022]
Abstract
Time-resolved small- and wide-angle X-ray scattering studies of proteins in solution based on the pump-probe approach unveil structural information from intermediates over a broad range of length and time scales. In spite of the promise of this methodology, only a fraction of the wealth of information encoded in scattering data has been extracted in studies performed thus far. Here, we discuss the methodology, summarize results from recent time-resolved X-ray scattering studies, and examine the potential to extract additional information from these scattering curves.
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Affiliation(s)
- Hyun Sun Cho
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Friedrich Schotte
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Valentyn Stadnytskyi
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Philip Anfinrud
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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10
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Cellini A, Yuan Wahlgren W, Henry L, Pandey S, Ghosh S, Castillon L, Claesson E, Takala H, Kübel J, Nimmrich A, Kuznetsova V, Nango E, Iwata S, Owada S, Stojković EA, Schmidt M, Ihalainen JA, Westenhoff S. The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. Acta Crystallogr D Struct Biol 2021; 77:1001-1009. [PMID: 34342273 PMCID: PMC8329860 DOI: 10.1107/s2059798321005830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
(6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 Å resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 Å resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Léocadie Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Leticia Castillon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Valentyna Kuznetsova
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Eriko Nango
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Emina A. Stojković
- Department of Biology, Northeastern Illinois University, 5500 North St Louis Avenue, Chicago, IL 60625, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Janne A. Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
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11
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Photoreaction of photoactivated adenylate cyclase from cyanobacterium Microcoleus chthonoplastes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 221:112252. [PMID: 34265548 DOI: 10.1016/j.jphotobiol.2021.112252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 05/19/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022]
Abstract
The photochemical reaction of photoactivated adenylate cyclase from cyanobacterium Microcoleus chthonoplastes PCC 7420 (mPAC), which consists of a Per-Arnt-Sim (PAS), a light‑oxygene-voltage (LOV), and an adenylate cyclase (AC) domain, was investigated mainly using the time-resolved transient grating method. An absorption spectral change associated with an adduct formation between its chromophore (flavin mononucleotide) and a cysteine residue was observed with a time constant of 0.66 μs. After this reaction, a significant diffusion coefficient (D)-change was observed with a time constant of 38 ms. The determined D-value was concentration-dependent indicating a rapid equilibrium between the dimer and tetramer. Combining the results of size exclusion chromatography and CD spectroscopy, we concluded that the photoinduced D-change was mainly attributed to the equilibrium shift from the dimer rich to the tetramer rich states upon light exposure. Since the reaction rate does not depend on concentration, the rate determining step of the tetramer formation is not the collision of proteins by diffusion, but a conformation change. The roles of the PAS and AC domains as well as the N- and C-terminal flanking helices of the LOV domain (A'α- and Jα-helices) were investigated using various truncated mutants. The PAS domain was found to be a strong dimerization site and is related to efficient signal transduction. It was found that simultaneous existence of the A'α- and Jα-helices in mPAC is important for the light-induced conformation change to lead the conformation change which induces the tetramer formation. The results suggest that the angle changes of the coiled-coil structures in the A'α and Jα-helices are essential for this conformation change. The reaction scheme of mPAC is proposed.
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12
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Abstract
Bacteria employ two-component systems (TCSs) to sense and respond to changes in their surroundings. At the core of the TCS signaling pathway is the multidomain sensor histidine kinase, where the enzymatic activity of its output domain is allosterically controlled by the input signal perceived by the sensor domain. The ability to sense and respond to environmental cues is essential for adaptation and survival in living organisms. In bacteria, this process is accomplished by multidomain sensor histidine kinases that undergo autophosphorylation in response to specific stimuli, thereby triggering downstream signaling cascades. However, the molecular mechanism of allosteric activation is not fully understood in these important sensor proteins. Here, we report the full-length crystal structure of a blue light photoreceptor LOV histidine kinase (LOV-HK) involved in light-dependent virulence modulation in the pathogenic bacterium Brucella abortus. Joint analyses of dark and light structures determined in different signaling states have shown that LOV-HK transitions from a symmetric dark structure to a highly asymmetric light state. The initial local and subtle structural signal originated in the chromophore-binding LOV domain alters the dimer asymmetry via a coiled-coil rotary switch and helical bending in the helical spine. These amplified structural changes result in enhanced conformational flexibility and large-scale rearrangements that facilitate the phosphoryl transfer reaction in the HK domain.
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13
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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: 10] [Impact Index Per Article: 3.3] [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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14
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Henry L, Panman MR, Isaksson L, Claesson E, Kosheleva I, Henning R, Westenhoff S, Berntsson O. Real-time tracking of protein unfolding with time-resolved x-ray solution scattering. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:054702. [PMID: 32984436 PMCID: PMC7511240 DOI: 10.1063/4.0000013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/17/2020] [Indexed: 05/14/2023]
Abstract
The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.
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Affiliation(s)
- L. Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - M. R. Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - L. Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - E. Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - I. Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - R. Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - S. Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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15
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Henry L, Berntsson O, Panman MR, Cellini A, Hughes AJ, Kosheleva I, Henning R, Westenhoff S. New Light on the Mechanism of Phototransduction in Phototropin. Biochemistry 2020; 59:3206-3215. [PMID: 32786255 DOI: 10.1021/acs.biochem.0c00324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phototropins are photoreceptor proteins that regulate blue light-dependent biological processes for efficient photosynthesis in plants and algae. The proteins consist of a photosensory domain that responds to the ambient light and an output module that triggers cellular responses. The photosensory domain of phototropin from Chlamydomonas reinhardtii contains two conserved LOV (light-oxygen-voltage) domains with flavin chromophores. Blue light triggers the formation of a covalent cysteine-flavin adduct and upregulates the phototropin kinase activity. Little is known about the structural mechanism that leads to kinase activation and how the two LOV domains contribute to this. Here, we investigate the role of the LOV1 domain from C. reinhardtii phototropin by characterizing the structural changes occurring after blue light illumination with nano- to millisecond time-resolved X-ray solution scattering. By structurally fitting the data with atomic models generated by molecular dynamics simulations, we find that adduct formation induces a rearrangement of the hydrogen bond network from the buried chromophore to the protein surface. In particular, the change in conformation and the associated hydrogen bonding of the conserved glutamine 120 induce a global movement of the β-sheet, ultimately driving a change in the electrostatic potential on the protein surface. On the basis of the change in the electrostatics, we propose a structural model of how LOV1 and LOV2 domains interact and regulate the full-length phototropin from C. reinhardtii. This provides a rationale for how LOV photosensor proteins function and contributes to the optimal design of optogenetic tools based on LOV domains.
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Affiliation(s)
- L Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - O Berntsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,MAX IV Laboratory, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| | - M R Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - A Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - A J Hughes
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - I Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - R Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - S Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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16
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Kim J, Kim JG, Ki H, Ahn CW, Ihee H. Estimating signal and noise of time-resolved X-ray solution scattering data at synchrotrons and XFELs. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:633-645. [PMID: 32381763 PMCID: PMC7206544 DOI: 10.1107/s1600577520002738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
Elucidating the structural dynamics of small molecules and proteins in the liquid solution phase is essential to ensure a fundamental understanding of their reaction mechanisms. In this regard, time-resolved X-ray solution scattering (TRXSS), also known as time-resolved X-ray liquidography (TRXL), has been established as a powerful technique for obtaining the structural information of reaction intermediates and products in the liquid solution phase and is expected to be applied to a wider range of molecules in the future. A TRXL experiment is generally performed at the beamline of a synchrotron or an X-ray free-electron laser (XFEL) to provide intense and short X-ray pulses. Considering the limited opportunities to use these facilities, it is necessary to verify the plausibility of a target experiment prior to the actual experiment. For this purpose, a program has been developed, referred to as S-cube, which is short for a Solution Scattering Simulator. This code allows the routine estimation of the shape and signal-to-noise ratio (SNR) of TRXL data from known experimental parameters. Specifically, S-cube calculates the difference scattering curve and the associated quantum noise on the basis of the molecular structure of the target reactant and product, the target solvent, the energy of the pump laser pulse and the specifications of the beamline to be used. Employing a simplified form for the pair-distribution function required to calculate the solute-solvent cross term greatly increases the calculation speed as compared with a typical TRXL data analysis. Demonstrative applications of S-cube are presented, including the estimation of the expected TRXL data and SNR level for the future LCLS-II HE beamlines.
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Affiliation(s)
- Jungmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Chi Woo Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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17
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Banerjee S, Mitra D. Structural Basis of Design and Engineering for Advanced Plant Optogenetics. TRENDS IN PLANT SCIENCE 2020; 25:35-65. [PMID: 31699521 DOI: 10.1016/j.tplants.2019.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.
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Affiliation(s)
- Sudakshina Banerjee
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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18
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Kuroi K, Kamijo M, Ueki M, Niwa Y, Hiramatsu H, Nakabayashi T. Time-resolved FTIR study on the structural switching of human galectin-1 by light-induced disulfide bond formation. Phys Chem Chem Phys 2020; 22:1137-1144. [DOI: 10.1039/c9cp04881b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The light-induced disulfide bond technique, which we have previously developed, has enabled the time-resolved measurement of the disulfide-induced conformational switching of the lectin protein human galectin-1.
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Affiliation(s)
- Kunisato Kuroi
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
- Faculty of Pharmaceutical Sciences
| | - Mana Kamijo
- Faculty of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Mutsuki Ueki
- Faculty of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Yusuke Niwa
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Hirotsugu Hiramatsu
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao Tung University
- Hsinchu 30010
- Taiwan
- Center for Emergent Functional Matter Science
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
- Faculty of Pharmaceutical Sciences
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19
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Möglich A. Signal transduction in photoreceptor histidine kinases. Protein Sci 2019; 28:1923-1946. [PMID: 31397927 PMCID: PMC6798134 DOI: 10.1002/pro.3705] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022]
Abstract
Two-component systems (TCS) constitute the predominant means by which prokaryotes read out and adapt to their environment. Canonical TCSs comprise a sensor histidine kinase (SHK), usually a transmembrane receptor, and a response regulator (RR). In signal-dependent manner, the SHK autophosphorylates and in turn transfers the phosphoryl group to the RR which then elicits downstream responses, often in form of altered gene expression. SHKs also catalyze the hydrolysis of the phospho-RR, hence, tightly adjusting the overall degree of RR phosphorylation. Photoreceptor histidine kinases are a subset of mostly soluble, cytosolic SHKs that sense light in the near-ultraviolet to near-infrared spectral range. Owing to their experimental tractability, photoreceptor histidine kinases serve as paradigms and provide unusually detailed molecular insight into signal detection, decoding, and regulation of SHK activity. The synthesis of recent results on receptors with light-oxygen-voltage, bacteriophytochrome and microbial rhodopsin sensor units identifies recurring, joint signaling strategies. Light signals are initially absorbed by the sensor module and converted into subtle rearrangements of α helices, mostly through pivoting and rotation. These conformational transitions propagate through parallel coiled-coil linkers to the effector unit as changes in left-handed superhelical winding. Within the effector, subtle conformations are triggered that modulate the solvent accessibility of residues engaged in the kinase and phosphatase activities. Taken together, a consistent view of the entire trajectory from signal detection to regulation of output emerges. The underlying allosteric mechanisms could widely apply to TCS signaling in general.
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Affiliation(s)
- Andreas Möglich
- Department of BiochemistryUniversität BayreuthBayreuthGermany
- Bayreuth Center for Biochemistry & Molecular BiologyUniversität BayreuthBayreuthGermany
- North‐Bavarian NMR CenterUniversität BayreuthBayreuthGermany
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20
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Jacob-Dubuisson F, Mechaly A, Betton JM, Antoine R. Structural insights into the signalling mechanisms of two-component systems. Nat Rev Microbiol 2019; 16:585-593. [PMID: 30008469 DOI: 10.1038/s41579-018-0055-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Two-component systems reprogramme diverse aspects of microbial physiology in response to environmental cues. Canonical systems are composed of a transmembrane sensor histidine kinase and its cognate response regulator. They catalyse three reactions: autophosphorylation of the histidine kinase, transfer of the phosphoryl group to the regulator and dephosphorylation of the phosphoregulator. Elucidating signal transduction between sensor and output domains is highly challenging given the size, flexibility and dynamics of histidine kinases. However, recent structural work has provided snapshots of the catalytic mechanisms of the three enzymatic reactions and described the conformation and dynamics of the enzymatic moiety in the kinase-competent and phosphatase-competent states. Insight into signalling mechanisms across the membrane is also starting to emerge from new crystal structures encompassing both sensor and transducer domains of sensor histidine kinases. In this Progress article, we highlight such important advances towards understanding at the molecular level the signal transduction mechanisms mediated by these fascinating molecular machines.
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Affiliation(s)
- Françoise Jacob-Dubuisson
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204 - Center for Infection and Immunity of Lille, Lille, France.
| | - Ariel Mechaly
- Institut Pasteur, Plateforme de Cristallographie, CNRS-UMR3528, Paris, France
| | - Jean-Michel Betton
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Paris, France
| | - Rudy Antoine
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204 - Center for Infection and Immunity of Lille, Lille, France
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21
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Berntsson O, Rodriguez R, Henry L, Panman MR, Hughes AJ, Einholz C, Weber S, Ihalainen JA, Henning R, Kosheleva I, Schleicher E, Westenhoff S. Photoactivation of Drosophila melanogaster cryptochrome through sequential conformational transitions. SCIENCE ADVANCES 2019; 5:eaaw1531. [PMID: 31328161 PMCID: PMC6636987 DOI: 10.1126/sciadv.aaw1531] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/13/2019] [Indexed: 05/27/2023]
Abstract
Cryptochromes are blue-light photoreceptor proteins, which provide input to circadian clocks. The cryptochrome from Drosophila melanogaster (DmCry) modulates the degradation of Timeless and itself. It is unclear how light absorption by the chromophore and the subsequent redox reactions trigger these events. Here, we use nano- to millisecond time-resolved x-ray solution scattering to reveal the light-activated conformational changes in DmCry and the related (6-4) photolyase. DmCry undergoes a series of structural changes, culminating in the release of the carboxyl-terminal tail (CTT). The photolyase has a simpler structural response. We find that the CTT release in DmCry depends on pH. Mutation of a conserved histidine, important for the biochemical activity of DmCry, does not affect transduction of the structural signal to the CTT. Instead, molecular dynamics simulations suggest that it stabilizes the CTT in the resting-state conformation. Our structural photocycle unravels the first molecular events of signal transduction in an animal cryptochrome.
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Affiliation(s)
- Oskar Berntsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
- MAX IV Laboratory, Lund University, 224 84 Lund, Sweden
| | - Ryan Rodriguez
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Léocadie Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Matthijs R. Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Ashley J. Hughes
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Christopher Einholz
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Janne A. Ihalainen
- Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Erik Schleicher
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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22
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Buschiazzo A, Trajtenberg F. Two-Component Sensing and Regulation: How Do Histidine Kinases Talk with Response Regulators at the Molecular Level? Annu Rev Microbiol 2019; 73:507-528. [PMID: 31226026 DOI: 10.1146/annurev-micro-091018-054627] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Perceiving environmental and internal information and reacting in adaptive ways are essential attributes of living organisms. Two-component systems are relevant protein machineries from prokaryotes and lower eukaryotes that enable cells to sense and process signals. Implicating sensory histidine kinases and response regulator proteins, both components take advantage of protein phosphorylation and flexibility to switch conformations in a signal-dependent way. Dozens of two-component systems act simultaneously in any given cell, challenging our understanding about the means that ensure proper connectivity. This review dives into the molecular level, attempting to summarize an emerging picture of how histidine kinases and cognate response regulators achieve required efficiency, specificity, and directionality of signaling pathways, properties that rely on protein:protein interactions. α helices that carry information through long distances, the fine combination of loose and specific kinase/regulator interactions, and malleable reaction centers built when the two components meet emerge as relevant universal principles.
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Affiliation(s)
- Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; , .,Integrative Microbiology of Zoonotic Agents, Department of Microbiology, Institut Pasteur, Paris 75015, France
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; ,
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23
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Kalvaitis ME, Johnson LA, Mart RJ, Rizkallah P, Allemann RK. A Noncanonical Chromophore Reveals Structural Rearrangements of the Light-Oxygen-Voltage Domain upon Photoactivation. Biochemistry 2019; 58:2608-2616. [PMID: 31082213 PMCID: PMC7007005 DOI: 10.1021/acs.biochem.9b00255] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Light-oxygen-voltage
(LOV) domains are increasingly used to engineer
photoresponsive biological systems. While the photochemical cycle
is well documented, the allosteric mechanism by which formation of
a cysteinyl-flavin adduct leads to activation is unclear. Via replacement
of flavin mononucleotide (FMN) with 5-deazaflavin mononucleotide (5dFMN)
in the Aureochrome1a (Au1a) transcription factor from Ochromonas
danica, a thermally stable cysteinyl-5dFMN adduct was generated.
High-resolution crystal structures (<2 Å) under different
illumination conditions with either FMN or 5dFMN chromophores reveal
three conformations of the highly conserved glutamine 293. An allosteric
hydrogen bond network linking the chromophore via Gln293 to the auxiliary
A′α helix is observed. With FMN, a “flip”
of the Gln293 side chain occurs between dark and lit states. 5dFMN
cannot hydrogen bond through the C5 position and proved to be unable
to support Au1a domain dimerization. Under blue light, the Gln293
side chain instead “swings” away in a conformation distal
to the chromophore and not previously observed in existing LOV domain
structures. Together, the multiple side chain conformations of Gln293
and functional analysis of 5dFMN provide new insight into the structural
requirements for LOV domain activation.
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Affiliation(s)
- Mindaugas E Kalvaitis
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , United Kingdom
| | - Luke A Johnson
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , United Kingdom
| | - Robert J Mart
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , United Kingdom
| | - Pierre Rizkallah
- School of Medicine , University Hospital Wales , Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - Rudolf K Allemann
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , United Kingdom
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24
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Ota K, Yamato T. Energy Exchange Network Model Demonstrates Protein Allosteric Transition: An Application to an Oxygen Sensor Protein. J Phys Chem B 2019; 123:768-775. [DOI: 10.1021/acs.jpcb.8b10489] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kunitaka Ota
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 1 rue Laurent Fries Parc d’Innovation, 67404 Illkirch, Cedex, France
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25
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Abraham B, Kosheleva I, Henning R, Chen LX. Insulin hexamer dissociation dynamics revealed by photoinduced T-jumps and time-resolved X-ray solution scattering. Photochem Photobiol Sci 2018; 17:874-882. [PMID: 29855030 DOI: 10.1039/c8pp00034d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural dynamics of insulin hexamer dissociation were studied by the photoinduced temperature jump technique and monitored by time-resolved X-ray scattering. The process of hexamer dissociation was found to involve several transient intermediates, including an expanded hexamer and an unstable tetramer. Our findings provide insights into the mechanisms of protien-protein association.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.
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26
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Small-angle X-ray scattering study of the kinetics of light-dark transition in a LOV protein. PLoS One 2018; 13:e0200746. [PMID: 30011332 PMCID: PMC6047819 DOI: 10.1371/journal.pone.0200746] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 07/01/2018] [Indexed: 11/19/2022] Open
Abstract
Light, oxygen, voltage (LOV) photoreceptors consist of conserved photo-responsive domains in bacteria, archaea, plants and fungi, and detect blue-light via a flavin cofactor. We investigated the blue-light induced conformational transition of the dimeric photoreceptor PpSB1-LOV-R66I from Pseudomonas putida in solution by using small-angle X-ray scattering (SAXS). SAXS experiments of the fully populated light- and dark-states under steady-state conditions revealed significant structural differences between the two states that are in agreement with the known structures determined by crystallography. We followed the transition from the light- to the dark-state by using SAXS measurements in real-time. A two-state model based on the light- and dark-state conformations could describe the measured time-course SAXS data with a relaxation time τREC of ~ 34 to 35 min being larger than the recovery time found with UV/vis spectroscopy. Unlike the flavin chromophore-based UV/vis method that is sensitive to the local chromophore environment in flavoproteins, SAXS-based assay depends on protein conformational changes and provides with an alternative to measure the recovery kinetics.
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27
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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28
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Kosheleva I, Chen LX. Direct Observation of Insulin Association Dynamics with Time-Resolved X-ray Scattering. J Phys Chem Lett 2017; 8:4413-4418. [PMID: 28853898 PMCID: PMC5804350 DOI: 10.1021/acs.jpclett.7b01720] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Biological functions frequently require protein-protein interactions that involve secondary and tertiary structural perturbation. Here we study protein-protein dissociation and reassociation dynamics in insulin, a model system for protein oligomerization. Insulin dimer dissociation into monomers was induced by a nanosecond temperature-jump (T-jump) of ∼8 °C in aqueous solution, and the resulting protein and solvent dynamics were tracked by time-resolved X-ray solution scattering (TRXSS) on time scales of 10 ns to 100 ms. The protein scattering signals revealed the formation of five distinguishable transient species during the association process that deviate from simple two-state kinetics. Our results show that the combination of T-jump pump coupled to TRXSS probe allows for direct tracking of structural dynamics in nonphotoactive proteins.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Denis Leshchev
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Darren J. Hsu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jiyun Hong
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lin X. Chen
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
- Corresponding Author, ,
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29
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Sequential conformational transitions and α-helical supercoiling regulate a sensor histidine kinase. Nat Commun 2017; 8:284. [PMID: 28819239 PMCID: PMC5561222 DOI: 10.1038/s41467-017-00300-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/20/2017] [Indexed: 12/13/2022] Open
Abstract
Sensor histidine kinases are central to sensing in bacteria and in plants. They usually contain sensor, linker, and kinase modules and the structure of many of these components is known. However, it is unclear how the kinase module is structurally regulated. Here, we use nano- to millisecond time-resolved X-ray scattering to visualize the solution structural changes that occur when the light-sensitive model histidine kinase YF1 is activated by blue light. We find that the coiled coil linker and the attached histidine kinase domains undergo a left handed rotation within microseconds. In a much slower second step, the kinase domains rearrange internally. This structural mechanism presents a template for signal transduction in sensor histidine kinases. Sensor histidine kinases (SHK) consist of sensor, linker and kinase modules and different models for SHK signal transduction have been proposed. Here the authors present nano- to millisecond time-resolved X-ray scattering measurements, which reveal a structural mechanism for kinase domain activation in SHK.
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30
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Engelhard C, Diensthuber RP, Möglich A, Bittl R. Blue-light reception through quaternary transitions. Sci Rep 2017; 7:1385. [PMID: 28469162 PMCID: PMC5431215 DOI: 10.1038/s41598-017-01497-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/28/2017] [Indexed: 11/10/2022] Open
Abstract
Sensory photoreceptors absorb light via their photosensor modules and trigger downstream physiological adaptations via their effector modules. Light reception accordingly depends on precisely orchestrated interactions between these modules, the molecular details of which often remain elusive. Using electron-electron double resonance (ELDOR) spectroscopy and site-directed spin labelling, we chart the structural transitions facilitating blue-light reception in the engineered light-oxygen-voltage (LOV) histidine kinase YF1 which represents a paradigm for numerous natural signal receptors. Structural modelling based on pair-wise distance constraints derived from ELDOR pinpoint light-induced rotation and splaying apart of the two LOV photosensors in the dimeric photoreceptor. Resultant molecular strain likely relaxes as left-handed supercoiling of the coiled-coil linker connecting sensor and effector units. ELDOR data on a photoreceptor variant with an inverted signal response indicate a drastically altered dimer interface but light-induced structural transitions in the linker that are similar to those in YF1. Taken together, we provide mechanistic insight into the signal trajectories of LOV photoreceptors and histidine kinases that inform molecular simulations and the engineering of novel receptors.
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Affiliation(s)
- Christopher Engelhard
- Fachbereich Physik, Institut für Experimentalphysik, Freie Universität Berlin, 14195, Berlin, Germany
| | - Ralph P Diensthuber
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany. .,Lehrstuhl für Biochemie and Research Center for Bio-Macromolecules, Universität Bayreuth, 95440, Bayreuth, Germany.
| | - Robert Bittl
- Fachbereich Physik, Institut für Experimentalphysik, Freie Universität Berlin, 14195, Berlin, Germany.
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