1
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Łaski P, Bosman L, Drapała J, Kamiński R, Szarejko D, Borowski P, Roodt A, Henning R, Brink A, Jarzembska KN. Nanosecond-Lived Excimer Observation in a Crystal of a Rhodium(I) Complex via Time-Resolved X-ray Laue Diffraction. J Phys Chem Lett 2024; 15:10301-10306. [PMID: 39382182 DOI: 10.1021/acs.jpclett.4c02476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
Abstract
The rare observation of transient Rh···Rh excimer formation in a single crystal is reported. The estimated excited-state lifetime at 100 K is 2 ns, which makes it the shortest-lived small-molecule species caught experimentally using the laser-pump/X-ray-probe time-resolved Laue method. Upon excitation with 390 nm laser light, the intermolecular Rh···Rh distance decreases from 3.379(4) to 3.19(1) Å, and the metal-metal contact gains more bonding character. On the basis of the experimental results and theoretical modeling, the structural changes determined with 100 ps time resolution reflect principally the S0 → S1 electronic transition.
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Affiliation(s)
- Piotr Łaski
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Lerato Bosman
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein 9301, South Africa
| | - Jakub Drapała
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Radosław Kamiński
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dariusz Szarejko
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Patryk Borowski
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Andreas Roodt
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein 9301, South Africa
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago, 5734 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein 9301, South Africa
| | - Katarzyna N Jarzembska
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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2
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Hekstra DR, Wang HK, Klureza MA, Greisman JB, Dalton KM. Sensitive Detection of Structural Differences using a Statistical Framework for Comparative Crystallography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604476. [PMID: 39091831 PMCID: PMC11291090 DOI: 10.1101/2024.07.22.604476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Chemical and conformational changes underlie the functional cycles of proteins. Comparative crystallography can reveal these changes over time, over ligands, and over chemical and physical perturbations in atomic detail. A key difficulty, however, is that the resulting observations must be placed on the same scale by correcting for experimental factors. We recently introduced a Bayesian framework for correcting (scaling) X-ray diffraction data by combining deep learning with statistical priors informed by crystallographic theory. To scale comparative crystallography data, we here combine this framework with a multivariate statistical theory of comparative crystallography. By doing so, we find strong improvements in the detection of protein dynamics, element-specific anomalous signal, and the binding of drug fragments.
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Affiliation(s)
- Doeke R. Hekstra
- Department of Molecular and Cellular Biology
- School of Engineering and Applied Sciences
| | - Harrison K. Wang
- Department of Molecular and Cellular Biology
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
| | - Margaret A. Klureza
- Department of Molecular and Cellular Biology
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jack B. Greisman
- Department of Molecular and Cellular Biology
- Current address: D. E. Shaw Research New York, NY 10036, USA
| | - Kevin M. Dalton
- Department of Molecular and Cellular Biology
- New York University, New York, NY 10003, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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3
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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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4
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Biener G, Malla TN, Schwander P, Schmidt M. KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography. IUCRJ 2024; 11:405-422. [PMID: 38662478 PMCID: PMC11067743 DOI: 10.1107/s2052252524002392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/12/2024] [Indexed: 05/04/2024]
Abstract
Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. The method is named KINNTREX (kinetics-informed NN for time-resolved X-ray crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels of complexity. For the simulations, time-resolved X-ray data were generated that mimic data collected from the photocycle of the photoactive yellow protein. KINNTREX only requires the number of intermediates and approximate relaxation times (both obtained from a singular valued decomposition) and does not require an assumption of a candidate mechanism. It successfully predicts a consistent chemical kinetic mechanism, together with difference electron-density maps of the intermediates that appear during the reaction. These features make KINNTREX attractive for tackling a wide range of biomolecular questions. In addition, the versatility of KINNTREX can inspire more NN-based applications to time-resolved data from biological macromolecules obtained by other methods.
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Affiliation(s)
- Gabriel Biener
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, WI 53211, USA
| | - Tek Narsingh Malla
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, WI 53211, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, WI 53211, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, WI 53211, USA
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5
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Schotte F, Cho HS, Dyda F, Anfinrud P. Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:021303. [PMID: 38595979 PMCID: PMC11003764 DOI: 10.1063/4.0000241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 03/21/2024] [Indexed: 04/11/2024]
Abstract
Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.
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Affiliation(s)
- Friedrich Schotte
- National Institutes of Health, NIDDK, LCP, Bethesda, Maryland 20892, USA
| | - Hyun Sun Cho
- National Institutes of Health, NIDDK, LCP, Bethesda, Maryland 20892, USA
| | - Fred Dyda
- National Institutes of Health, NIDDK, LMB, Bethesda, Maryland 20892, USA
| | - Philip Anfinrud
- National Institutes of Health, NIDDK, LCP, Bethesda, Maryland 20892, USA
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6
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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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7
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Schmidt M, Stojković EA. Blue and red in the protein world: Photoactive yellow protein and phytochromes as revealed by time-resolved crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014701. [PMID: 38304445 PMCID: PMC10834066 DOI: 10.1063/4.0000233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales. Originally a synchrotron-based method, TRX is enabled by the development of TR Laue crystallography (TRLX). TR serial crystallography (TR-SX) is an extension of TRLX. As the foundations of TRLX were evolving from the late 1980s to the turn of the millennium, TR-SX has been inspired by the development of Free Electron Lasers for hard X-rays. Extremely intense, ultrashort x-ray pulses could probe micro and nanocrystals, but at the same time, they inflicted radiation damage that necessitated the replacement by a new crystal. Consequently, a large number of microcrystals are exposed to X-rays one by one in a serial fashion. With TR-SX methods, one of the largest obstacles of previous approaches, namely, the unsurmountable challenges associated with the investigation of non-cyclic (irreversible) reactions, can be overcome. This article describes successes and transformative contributions to the TRX field by Keith Moffat and his collaborators, highlighting two major projects on protein photoreceptors initiated in the Moffat lab at the turn of the millennium.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, Wisconsin 53211, USA
| | - Emina A. Stojković
- Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, Illinois 60625, USA
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8
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Henning RW, Kosheleva I, Šrajer V, Kim IS, Zoellner E, Ranganathan R. BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014301. [PMID: 38304444 PMCID: PMC10834067 DOI: 10.1063/4.0000238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods-UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
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Affiliation(s)
- Robert W. Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Vukica Šrajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - In-Sik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Eric Zoellner
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rama Ranganathan
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
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9
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Hutchison CDM, Baxter JM, Fitzpatrick A, Dorlhiac G, Fadini A, Perrett S, Maghlaoui K, Lefèvre SB, Cordon-Preciado V, Ferreira JL, Chukhutsina VU, Garratt D, Barnard J, Galinis G, Glencross F, Morgan RM, Stockton S, Taylor B, Yuan L, Romei MG, Lin CY, Marangos JP, Schmidt M, Chatrchyan V, Buckup T, Morozov D, Park J, Park S, Eom I, Kim M, Jang D, Choi H, Hyun H, Park G, Nango E, Tanaka R, Owada S, Tono K, DePonte DP, Carbajo S, Seaberg M, Aquila A, Boutet S, Barty A, Iwata S, Boxer SG, Groenhof G, van Thor JJ. Optical control of ultrafast structural dynamics in a fluorescent protein. Nat Chem 2023; 15:1607-1615. [PMID: 37563326 PMCID: PMC10624617 DOI: 10.1038/s41557-023-01275-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/12/2023] [Indexed: 08/12/2023]
Abstract
The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.
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Affiliation(s)
| | - James M Baxter
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Ann Fitzpatrick
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Gabriel Dorlhiac
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Samuel Perrett
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Karim Maghlaoui
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Salomé Bodet Lefèvre
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Violeta Cordon-Preciado
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Josie L Ferreira
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Volha U Chukhutsina
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Douglas Garratt
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Jonathan Barnard
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Gediminas Galinis
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Flo Glencross
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Rhodri M Morgan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Sian Stockton
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Ben Taylor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Letong Yuan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jon P Marangos
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Viktoria Chatrchyan
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Heidelberg, Germany
| | - Tiago Buckup
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Heidelberg, Germany
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
- Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea
| | - Sehan Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Dogeun Jang
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Hyeongi Choi
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - HyoJung Hyun
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Gisu Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea
| | - Eriko Nango
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
| | - Daniel P DePonte
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sergio Carbajo
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Matt Seaberg
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew Aquila
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sebastien Boutet
- Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - So Iwata
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Jasper J van Thor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.
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10
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Yang C, Kim Y, Kim SO, Lee SJ, Choi J, Ihee H. Length and Charge of the N-terminus Regulate the Lifetime of the Signaling State of Photoactive Yellow Protein. J Phys Chem B 2023; 127:9001-9013. [PMID: 37819381 DOI: 10.1021/acs.jpcb.3c03841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Photoactive yellow protein (PYP) is one of the most extensively studied photoreceptors. Nevertheless, the role of the N-terminus in the photocycle and structural transitions is still elusive. Here, we attached additional amino acids to the N-terminus of PYP and investigated the effect of the length and charge of additional N-terminal residues using circular dichroism, two-dimensional nuclear magnetic resonance (2D-NMR), transient absorption (TA), and transient grating (TG) spectroscopic techniques. TA experiments showed that, except for negatively charged residues (5D-PYP), additional N-terminal residues of PYP generally enable faster dark recovery from the putative signaling state (pB2) to the ground state (pG). TG data showed that although the degree of structural changes can be controlled by adjusting specific amino acid residues in the extended N-terminus of N-terminal extended PYPs (NE-PYPs), the dark recovery times of wt-PYP and NE-PYPs, except for 5D-PYP, are independent of the structural differences between pG and pB2 states. These results demonstrate that the recovery time and the degree of structural change can be regulated by controlling the length and sequence of N-terminal residues of PYP. The findings in this study emphasize the need for careful attention to the remaining amino acid residues when designing recombinant proteins for genetic engineering purposes.
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Affiliation(s)
- Cheolhee Yang
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Youngmin Kim
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seong Ok Kim
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Jin Lee
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Jungkweon Choi
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
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11
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Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia JM, Mariani V, Pandey S, Poudyal I, Sierra RG, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman HN, Stojkovic EA, Batyuk A, Boutet S, Phillips GN, Pollack L, Schmidt M. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam. Nat Commun 2023; 14:5507. [PMID: 37679343 PMCID: PMC10485065 DOI: 10.1038/s41467-023-41246-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.
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Affiliation(s)
- Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kara Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Luis Aldama
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Sasa Bajt
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Denisse Feliz
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Brendon Hayes
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark Hunter
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher Kupitz
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Stella Lisova
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Valerio Mariani
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Raymond G Sierra
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Chung Hong Yoon
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, 20 Arizona State University, Tempe, AZ, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Emina A Stojkovic
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Alexander Batyuk
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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12
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Schmidt M. Practical considerations for the analysis of time-resolved x-ray data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:044303. [PMID: 37600452 PMCID: PMC10435274 DOI: 10.1063/4.0000196] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
The field of time-resolved macromolecular crystallography has been expanding rapidly after free electron lasers for hard x rays (XFELs) became available. Techniques to collect and process data from XFELs spread to synchrotron light sources. Although time-scales and data collection modalities can differ substantially between these types of light sources, the analysis of the resulting x-ray data proceeds essentially along the same pathway. At the base of a successful time-resolved experiment is a difference electron density (DED) map that contains chemically meaningful signal. If such a difference map cannot be obtained, the experiment has failed. Here, a practical approach is presented to calculate DED maps and use them to determine structural models.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53211, USA
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13
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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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14
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Kosheleva I, Henning R, Kim I, Kim SO, Kusel M, Srajer V. Sample-minimizing co-flow cell for time-resolved pump-probe X-ray solution scattering. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:490-499. [PMID: 36891863 PMCID: PMC10000795 DOI: 10.1107/s1600577522012127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/22/2022] [Indexed: 06/10/2023]
Abstract
A fundamental problem in biological sciences is understanding how macromolecular machines work and how the structural changes of a molecule are connected to its function. Time-resolved techniques are vital in this regard and essential for understanding the structural dynamics of biomolecules. Time-resolved small- and wide-angle X-ray solution scattering has the capability to provide a multitude of information about the kinetics and global structural changes of molecules under their physiological conditions. However, standard protocols for such time-resolved measurements often require significant amounts of sample, which frequently render time-resolved measurements impossible. A cytometry-type sheath co-flow cell, developed at the BioCARS 14-ID beamline at the Advanced Photon Source, USA, allows time-resolved pump-probe X-ray solution scattering measurements to be conducted with sample consumption reduced by more than ten times compared with standard sample cells and protocols. The comparative capabilities of the standard and co-flow experimental setups were demonstrated by studying time-resolved signals in photoactive yellow protein.
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Affiliation(s)
- Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Robert Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Insik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Seong Ok Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, E6-6 #513, 291 Daehak-ro, Daejeon, Yuseong-gu 34141, Republic of Korea
| | - Michael Kusel
- Kusel Design, 12 Coghlan Street, Niddrie, Wurundjeri Country 3042, Australia
| | - Vukica Srajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
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15
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Schmidt M, Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia J, Mariani V, Pandey S, Poudyal I, Sierra R, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman H, Stojković E, Batyuk A, Boutet S, Phillips G, Pollack L. Heterogeneity in the M. tuberculosis β-Lactamase Inhibition by Sulbactam. RESEARCH SQUARE 2023:rs.3.rs-2334665. [PMID: 36712138 PMCID: PMC9882615 DOI: 10.21203/rs.3.rs-2334665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
For decades, researchers have been determined to elucidate essential enzymatic functions on the atomic lengths scale by tracing atomic positions in real time. Our work builds on new possibilities unleashed by mix-and-inject serial crystallography (MISC) 1-5 at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals 6 . Here, we report in atomic detail and with millisecond time-resolution how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating 7-9 , cooperativity, induced fit 10,11 and conformational selection 11-13 all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme non-covalently before reacting to a trans- enamine. This was made possible in part by the application of the singular value decomposition 14 to the MISC data using a newly developed program that remains functional even if unit cell parameters change during the reaction.
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16
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Schmidt M. Biological function investigated by time-resolved structure determination. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:010901. [PMID: 36846099 PMCID: PMC9946696 DOI: 10.1063/4.0000177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life. This is illustrated by examples where chemical and physical stimuli spawn biological responses on various length and time-scales, from fractions of Ångströms to micro-meters and from femtoseconds to hours.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, USA
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17
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Malla TN, Schmidt M. Transient state measurements on proteins by time-resolved crystallography. Curr Opin Struct Biol 2022; 74:102376. [DOI: 10.1016/j.sbi.2022.102376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022]
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18
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van Wilderen LJGW, Blankenburg L, Bredenbeck J. Femtosecond-to-millisecond mid-IR spectroscopy of Photoactive Yellow Protein uncovers structural micro-transitions of the chromophore's protonation mechanism. J Chem Phys 2022; 156:205103. [DOI: 10.1063/5.0091918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Protein structural dynamics can span many orders of magnitude in time. Photoactive Yellow Protein's (PYP) reversible photocycle encompasses picosecond isomerization of the light-absorbing chromophore as well as large scale protein backbone motions occurring on a millisecond timescale. Femtosecond-to-millisecond time-resolved mid-Infrared (IR) spectroscopy is employed here to uncover structural details of photocycle intermediates up to chromophore protonation and the first structural changes leading to formation of the partially-unfolded signalling state pB. The data show that a commonly thought stable transient photocycle intermediate is actually formed after a sequence of several smaller structural changes. We provide residue-specific spectroscopic evidence that protonation of the chromophore on a hundreds of microseconds timescale is delayed with respect to deprotonation of the nearby E46 residue. That implies that the direct proton donor is not E46 but most likely a water molecule. Such details may assist ongoing photocycle and protein folding simulation efforts on the complex and wide time-spanning photocycle of the model system PYP.
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19
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Absorption wavelength along chromophore low-barrier hydrogen bonds. iScience 2022; 25:104247. [PMID: 35521532 PMCID: PMC9062252 DOI: 10.1016/j.isci.2022.104247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/18/2022] [Accepted: 04/07/2022] [Indexed: 11/22/2022] Open
Abstract
In low-barrier hydrogen bonds (H-bonds), the pKa values for the H-bond donor and acceptor moieties are nearly equal, whereas the redox potential values depend on the H+ position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form between Glu46 and p-coumaric acid (pCA) in the intermediate pRCW state of photoactive yellow protein and between Asp116 and the retinal Schiff base in the intermediate M-state of the sodium-pumping rhodopsin KR2. The H+ displacement of only ∼0.4 Å, which does not easily occur without low-barrier H-bonds, is responsible for the ∼50 nm-shift in the absorption wavelength. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons. The low-barrier H-bond formation is a prerequisite for proton transfer How the absorption wavelength changes as H+ moves is an open question The H+ displacement of ∼0.4 Å leads to the absorption wavelength shift of ∼50 nm The localization of the molecular orbitals plays a key role in the wavelength shift
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20
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Wilson MA. Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light. Annu Rev Biophys 2021; 51:79-98. [PMID: 34932909 PMCID: PMC9132212 DOI: 10.1146/annurev-biophys-100421-110959] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Directly observing enzyme catalysis in real time at the molecular level has been a long-standing goal of structural enzymology. Time-resolved serial crystallography methods at synchrotron and X-ray free electron laser (XFEL) sources have enabled researchers to follow enzyme catalysis and other nonequilibrium events at ambient conditions with unprecedented time resolution. X-ray crystallography provides detailed information about conformational heterogeneity and protein dynamics, which is enhanced when time-resolved approaches are used. This review outlines the ways in which information about the underlying energy landscape of a protein can be extracted from X-ray crystallographic data, with an emphasis on new developments in XFEL and synchrotron time-resolved crystallography. The emerging view of enzyme catalysis afforded by these techniques can be interpreted as enzymes moving on a time-dependent energy landscape. Some consequences of this view are discussed, including the proposal that irreversible enzymes or enzymes that use covalent catalytic mechanisms may commonly exhibit catalysis-activated motions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, USA;
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21
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Mix LT, Hara M, Fuzell J, Kumauchi M, Kaledhonkar S, Xie A, Hoff WD, Larsen DS. Not All Photoactive Yellow Proteins Are Built Alike: Surprises and Insights into Chromophore Photoisomerization, Protonation, and Thermal Reisomerization of the Photoactive Yellow Protein Isolated from Salinibacter ruber. J Am Chem Soc 2021; 143:19614-19628. [PMID: 34780163 DOI: 10.1021/jacs.1c08910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We demonstrate that the Halorhodospira halophila (Hhal) photoactive yellow protein (PYP) is not representative of the greater PYP family. The photodynamics of the PYP isolated from Salinibacter ruber (Srub) is characterized with a comprehensive range of spectroscopic techniques including ultrafast transient absorption, photostationary light titrations, Fourier transform infrared, and cryokinetics spectroscopies. We demonstrate that the dark-adapted pG state consists of two subpopulations differing in the protonation state of the chromophore and that both are photoactive, with the protonated species undergoing excited-state proton transfer. However, the primary I0 photoproduct observed in the Hhal PYP photocycle is absent in the Srub PYP photodynamics, which indicates that this intermediate, while important in Hhal photodynamics, is not a critical intermediate in initiating all PYP photocycles. The excited-state lifetime of Srub PYP is the longest of any PYP resolved to date (∼30 ps), which we ascribe to the more constrained chromophore binding pocket of Srub PYP and the absence of the critical Arg52 residue found in Hhal PYP. The final stage of the Srub PYP photocycle involves the slowest known thermal dark reversion of a PYP (∼40 min vs 350 ms in Hhal PYP). This property allowed the characterization of a pH-dependent equilibrium between the light-adapted pB state with a protonated cis chromophore and a newly resolved pG' intermediate with a deprotonated cis chromophore and pG-like protein conformation. This result demonstates that protein conformational changes and chromophore deprotonation precede chromophore reisomerization during the thermal recovery of the PYP photocycle.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Miwa Hara
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jack Fuzell
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Sandip Kaledhonkar
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, United States.,Center for Advanced Infrared Biology College of Arts and Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States.,Center for Advanced Infrared Biology College of Arts and Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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22
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Lee SJ, Kim Y, Kim TW, Yang C, Thamilselvan K, Jeong H, Hyun J, Ihee H. Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100512. [PMID: 35509376 PMCID: PMC9062587 DOI: 10.1016/j.xcrp.2021.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Youngmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
| | - Jaekyung Hyun
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology (OIST), Okinawa 904-0495, Japan
| | - 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 Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Lead contact
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23
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Kuramochi H, Takeuchi S, Kamikubo H, Kataoka M, Tahara T. Skeletal Structure of the Chromophore of Photoactive Yellow Protein in the Excited State Investigated by Ultraviolet Femtosecond Stimulated Raman Spectroscopy. J Phys Chem B 2021; 125:6154-6161. [PMID: 34102843 DOI: 10.1021/acs.jpcb.1c02828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied ultrafast structural dynamics of photoactive yellow protein (PYP) using ultraviolet femtosecond stimulated Raman spectroscopy. By employing the Raman pump and probe pulses in the ultraviolet region, resonantly enhanced, rich vibrational features of the excited-state chromophore were observed in the fingerprint region. In contrast to the marked spectral change reported for the excited-state chromophore in solution, in the protein, all of the observed Raman bands in the fingerprint region did not show any noticeable spectral shifts nor band shape changes during the excited-state lifetime of PYP. This indicates that the significant skeletal change does not occur on the chromophore in the excited state of PYP and that the trans conformation is retained in its lifetime. Based on the femtosecond Raman data of PYP obtained so far, we discuss a comprehensive picture of the excited-state structural dynamics of PYP.
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Affiliation(s)
- Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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24
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Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future. CRYSTALS 2021. [DOI: 10.3390/cryst11050521] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources.
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25
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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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26
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Kim S, Nakasone Y, Takakado A, Yamazaki Y, Kamikubo H, Terazima M. Wavelength-Dependent Photoreaction of PYP from Rhodobacter capsulatus. Biochemistry 2020; 59:4810-4821. [DOI: 10.1021/acs.biochem.0c00821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suhyang Kim
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Akira Takakado
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichi Yamazaki
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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27
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Konold PE, Arik E, Weißenborn J, Arents JC, Hellingwerf KJ, van Stokkum IHM, Kennis JTM, Groot ML. Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein. Nat Commun 2020; 11:4248. [PMID: 32843623 PMCID: PMC7447820 DOI: 10.1038/s41467-020-18065-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 07/31/2020] [Indexed: 11/27/2022] Open
Abstract
Femtosecond time-resolved crystallography (TRC) on proteins enables resolving the spatial structure of short-lived photocycle intermediates. An open question is whether confinement and lower hydration of the proteins in the crystalline state affect the light-induced structural transformations. Here, we measured the full photocycle dynamics of a signal transduction protein often used as model system in TRC, Photoactive Yellow Protein (PYP), in the crystalline state and compared those to the dynamics in solution, utilizing electronic and vibrational transient absorption measurements from 100 fs over 12 decades in time. We find that the photocycle kinetics and structural dynamics of PYP in the crystalline form deviate from those in solution from the very first steps following photon absorption. This illustrates that ultrafast TRC results cannot be uncritically extrapolated to in vivo function, and that comparative spectroscopic experiments on proteins in crystalline and solution states can help identify structural intermediates under native conditions. Protein structural dynamics can be studied by time-resolved crystallography (TRC) and ultrafast transient spectroscopic methods. Here, the authors perform electronic and vibrational transient absorption measurements to characterise the full photocycle of Photoactive Yellow Protein (PYP) both in the crystalline and solution state and find that the photocycle kinetics and structural intermediates of PYP deviate in the crystalline state, which must be taken into consideration when planning TRC experiments.
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Affiliation(s)
- Patrick E Konold
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Enis Arik
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Jörn Weißenborn
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Jos C Arents
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, 1098, XH, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, 1098, XH, Amsterdam, The Netherlands
| | - Ivo H M van Stokkum
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Marie Louise Groot
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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28
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Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers. CRYSTALS 2020. [DOI: 10.3390/cryst10070628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs.
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29
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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30
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Zhang TS, Fang YG, Song XF, Fang WH, Cui G. Hydrogen-Bonding Interaction Regulates Photoisomerization of a Single-Bond-Rotation Locked Photoactive Yellow Protein Chromophore in Protein. J Phys Chem Lett 2020; 11:2470-2476. [PMID: 32150415 DOI: 10.1021/acs.jpclett.0c00294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We have employed the QM(CASPT2//CASSCF)/MM method to explore the excited-state isomerization and decay mechanism of a single-bond-rotation locked photoactive yellow protein (PYP) chromophore in wild-type and mutant proteins. The S1 state is a spectroscopically bright state in the Franck-Condon region. In this state, there exist two excited-state isomerization pathways separately related to the clockwise and anticlockwise rotations of the C=C bond. The clockwise path is favorable because of a small barrier of 2 kcal/mol and uses a novel bicycle-pedal unidirectional photoisomerization mechanism in which the involved two dihedral angles rotate asynchronously because of the reinforced hydrogen-bonding interaction between the chromophore and Cys69. Near the twisted S1 minimum, the chromophore hops to the S0 state via the S1/S0 conical intersection. Finally, the R52A mutation has small effects on the excited-state properties and photoisomerization of the locked PYP chromophore. The present work provides new insights for understanding the photochemistry of PYP chromophores in protein surroundings.
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Affiliation(s)
- Teng-Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Ye-Guang Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Xiu-Fang Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
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31
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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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32
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Schmidt-Engler JM, Blankenburg L, Zangl R, Hoffmann J, Morgner N, Bredenbeck J. Local dynamics of the photo-switchable protein PYP in ground and signalling state probed by 2D-IR spectroscopy of –SCN labels. Phys Chem Chem Phys 2020; 22:22963-22972. [DOI: 10.1039/d0cp04307a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ 2D-IR spectroscopy of the protein label –SCN to describe the local dynamics in the photo-switchable protein PYP in its dark state (pG) and after photoactivation, concomitant with vast structural rearrangements, in its signalling state (pB).
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Affiliation(s)
| | - Larissa Blankenburg
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Rene Zangl
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jan Hoffmann
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Nina Morgner
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
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33
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Pandey S, Bean R, Sato T, Poudyal I, Bielecki J, Cruz Villarreal J, Yefanov O, Mariani V, White TA, Kupitz C, Hunter M, Abdellatif MH, Bajt S, Bondar V, Echelmeier A, Doppler D, Emons M, Frank M, Fromme R, Gevorkov Y, Giovanetti G, Jiang M, Kim D, Kim Y, Kirkwood H, Klimovskaia A, Knoska J, Koua FHM, Letrun R, Lisova S, Maia L, Mazalova V, Meza D, Michelat T, Ourmazd A, Palmer G, Ramilli M, Schubert R, Schwander P, Silenzi A, Sztuk-Dambietz J, Tolstikova A, Chapman HN, Ros A, Barty A, Fromme P, Mancuso AP, Schmidt M. Time-resolved serial femtosecond crystallography at the European XFEL. Nat Methods 2020; 17:73-78. [PMID: 31740816 PMCID: PMC9113060 DOI: 10.1038/s41592-019-0628-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/03/2019] [Indexed: 11/08/2022]
Abstract
The European XFEL (EuXFEL) is a 3.4-km long X-ray source, which produces femtosecond, ultrabrilliant and spatially coherent X-ray pulses at megahertz (MHz) repetition rates. This X-ray source has been designed to enable the observation of ultrafast processes with near-atomic spatial resolution. Time-resolved crystallographic investigations on biological macromolecules belong to an important class of experiments that explore fundamental and functional structural displacements in these molecules. Due to the unusual MHz X-ray pulse structure at the EuXFEL, these experiments are challenging. Here, we demonstrate how a biological reaction can be followed on ultrafast timescales at the EuXFEL. We investigate the picosecond time range in the photocycle of photoactive yellow protein (PYP) with MHz X-ray pulse rates. We show that difference electron density maps of excellent quality can be obtained. The results connect the previously explored femtosecond PYP dynamics to timescales accessible at synchrotrons. This opens the door to a wide range of time-resolved studies at the EuXFEL.
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Affiliation(s)
- Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | | | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | - Jorvani Cruz Villarreal
- School of Molecular Sciences, and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Christopher Kupitz
- Linac Coherent Light Source, Stanford Linear Accelerator Center, National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark Hunter
- Linac Coherent Light Source, Stanford Linear Accelerator Center, National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mohamed H Abdellatif
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Saša Bajt
- Deutsches Elektronen Synchrotron, Hamburg, Germany
| | | | - Austin Echelmeier
- School of Molecular Sciences, and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Diandra Doppler
- School of Molecular Sciences, and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | | | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Raimund Fromme
- School of Molecular Sciences, and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
- Institute of Vision Systems, Hamburg University of Technology, Hamburg, Germany
| | | | - Man Jiang
- European XFEL GmbH, Schenefeld, Germany
| | - Daihyun Kim
- School of Molecular Sciences, and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | | | | | | | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | | | - Stella Lisova
- Physics Department, Arizona State University, Tempe, AZ, USA
| | - Luis Maia
- European XFEL GmbH, Schenefeld, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Domingo Meza
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL, Schenefeld, Germany
| | | | - Abbas Ourmazd
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | | | - Robin Schubert
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL, Schenefeld, Germany
| | - Peter Schwander
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | | | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
- Centre for Ultrafast Imaging, Hamburg, Germany
| | - Alexandra Ros
- School of Molecular Sciences, and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Petra Fromme
- School of Molecular Sciences, and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Adrian P Mancuso
- European XFEL GmbH, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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34
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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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35
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Hutchison CDM, van Thor JJ. Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20170474. [PMID: 30929625 PMCID: PMC6452057 DOI: 10.1098/rsta.2017.0474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
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36
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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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37
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Blankenburg L, Schroeder L, Habenstein F, Błasiak B, Kottke T, Bredenbeck J. Following local light-induced structure changes and dynamics of the photoreceptor PYP with the thiocyanate IR label. Phys Chem Chem Phys 2019; 21:6622-6634. [PMID: 30855039 DOI: 10.1039/c8cp05399e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoactive Yellow Protein (PYP) is a bacterial blue light receptor that enters a photocycle after excitation. The intermediate states are formed on time scales ranging from femtoseconds up to hundreds of milliseconds, after which the signaling state with a lifetime of about 1 s is reached. To investigate structural changes and dynamics, we incorporated the SCN IR label at distinct positions of the photoreceptor via cysteine mutation and cyanylation. FT-IR measurements of the SCN label at different sites of the well-established dark state structure of PYP characterized the spectral response of the label to differences in the environment. Under constant blue light irradiation, we observed the formation of the signaling state with significant changes of wavenumber and lineshape of the SCN bands. Thereby we deduced light-induced structural changes in the local environment of the labels. These results were supported by molecular dynamics simulations on PYP providing the solvent accessible surface area (SASA) at the different positions. To follow protein dynamics via the SCN label during the photocycle, we performed step-scan FT-IR measurements with a time resolution of 10 μs. Global analysis yielded similar time constants of τ1 = 70 μs, τ2 = 640 μs, and τ3 > 20 ms for the wild type and τ1 = 36 μs, τ2 = 530 μs, and τ3 > 20 ms for the SCN-labeled mutant PYP-A44C*, a mutant which provided a sufficiently large SCN difference signal to measure step-scan FT-IR spectra. In comparison to the protein (amide, E46) and chromophore bands the dynamics of the SCN label show a different behavior. This result indicates that the local kinetics sensed by the label are different from the global protein kinetics.
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Affiliation(s)
- Larissa Blankenburg
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
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Krekic S, Nagy D, Taneva SG, Fábián L, Zimányi L, Dér A. Spectrokinetic characterization of photoactive yellow protein films for integrated optical applications. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:465-473. [PMID: 30905045 PMCID: PMC6647221 DOI: 10.1007/s00249-019-01353-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/19/2019] [Accepted: 03/04/2019] [Indexed: 11/02/2022]
Abstract
In this paper, the photocycle of the dried photoactive yellow protein film has been investigated in different humidity environments, in order to characterize its nonlinear optical properties for possible integrated optical applications. The light-induced spectral changes of the protein films were monitored by an optical multichannel analyser set-up, while the accompanying refractive index changes were measured with the optical waveguide lightmode spectroscopy method. To determine the number and kinetics of spectral intermediates in the photocycle, the absorption kinetic data were analysed by singular value decomposition and multiexponential fitting methods, whose results were used in a subsequent step of fitting a photocycle model to the data. The absorption signals of the films were found to be in strong correlation with the measured light-induced refractive index changes, whose size and kinetics imply that photoactive yellow protein may be a good alternative for utilization as an active nonlinear optical material in future integrated optical applications.
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Affiliation(s)
- Szilvia Krekic
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary.
| | - Dávid Nagy
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - Stefka G Taneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, Sofia, 1113, Bulgaria
| | - László Fábián
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - András Dér
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
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39
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Schmidt M. Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources. Int J Mol Sci 2019; 20:ijms20061401. [PMID: 30897736 PMCID: PMC6470897 DOI: 10.3390/ijms20061401] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 11/30/2022] Open
Abstract
The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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40
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Martiel I, Müller-Werkmeister HM, Cohen AE. Strategies for sample delivery for femtosecond crystallography. Acta Crystallogr D Struct Biol 2019; 75:160-177. [PMID: 30821705 PMCID: PMC6400256 DOI: 10.1107/s2059798318017953] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/19/2018] [Indexed: 11/11/2022] Open
Abstract
Highly efficient data-collection methods are required for successful macromolecular crystallography (MX) experiments at X-ray free-electron lasers (XFELs). XFEL beamtime is scarce, and the high peak brightness of each XFEL pulse destroys the exposed crystal volume. It is therefore necessary to combine diffraction images from a large number of crystals (hundreds to hundreds of thousands) to obtain a final data set, bringing about sample-refreshment challenges that have previously been unknown to the MX synchrotron community. In view of this experimental complexity, a number of sample delivery methods have emerged, each with specific requirements, drawbacks and advantages. To provide useful selection criteria for future experiments, this review summarizes the currently available sample delivery methods, emphasising the basic principles and the specific sample requirements. Two main approaches to sample delivery are first covered: (i) injector methods with liquid or viscous media and (ii) fixed-target methods using large crystals or using microcrystals inside multi-crystal holders or chips. Additionally, hybrid methods such as acoustic droplet ejection and crystal extraction are covered, which combine the advantages of both fixed-target and injector approaches.
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Affiliation(s)
- Isabelle Martiel
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Henrike M. Müller-Werkmeister
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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41
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Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker. Int J Mol Sci 2018; 19:ijms19123714. [PMID: 30469528 PMCID: PMC6321067 DOI: 10.3390/ijms19123714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
Proteins have the potential to serve as nanomachines with well-controlled structural movements, and artificial control of their conformational changes is highly desirable for successful applications exploiting their dynamic structural characteristics. Here, we demonstrate an experimental approach for regulating the degree of conformational change in proteins by incorporating a small-molecule linker into a well-known photosensitive protein, photoactive yellow protein (PYP), which is sensitized by blue light and undergoes a photo-induced N-terminal protrusion coupled with chromophore-isomerization-triggered conformational changes. Specifically, we introduced thiol groups into specific sites of PYP through site-directed mutagenesis and then covalently conjugated a small-molecule linker into these sites, with the expectation that the linker is likely to constrain the structural changes associated with the attached positions. To investigate the structural dynamics of PYP incorporated with the small-molecule linker (SML-PYP), we employed the combination of small-angle X-ray scattering (SAXS), transient absorption (TA) spectroscopy and experiment-restrained rigid-body molecular dynamics (MD) simulation. Our results show that SML-PYP exhibits much reduced structural changes during photo-induced signaling as compared to wild-type PYP. This demonstrates that incorporating an external molecular linker can limit photo-induced structural dynamics of the protein and may be used as a strategy for fine control of protein structural dynamics in nanomachines.
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42
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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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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44
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Abstract
The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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45
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Kirpich JS, Chang CW, Madsen D, Gottlieb SM, Martin SS, Rockwell NC, Lagarias JC, Larsen DS. Noncanonical Photodynamics of the Orange/Green Cyanobacteriochrome Power Sensor NpF2164g7 from the PtxD Phototaxis Regulator of Nostoc punctiforme. Biochemistry 2018; 57:2636-2648. [PMID: 29633829 DOI: 10.1021/acs.biochem.7b01252] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Forward and reverse primary (<10 ns) and secondary (>10 ns) photodynamics of cyanobacteriochrome (CBCR) NpF2164g7 were characterized by global analysis of ultrafast broadband transient absorption measurements. NpF2164g7 is the most C-terminal bilin-binding GAF domain in the Nostoc punctiforme phototaxis sensor PtxD (locus Npun_F2164). Although a member of the canonical red/green CBCR subfamily phylogenetically, NpF2164g7 exhibits an orange-absorbing 15ZPo dark-adapted state instead of the typical red-absorbing 15ZPr dark-adapted state characteristic of this subfamily. The green-absorbing 15EPg photoproduct of NpF2164g7 is unstable, allowing this CBCR domain to function as a power sensor. Photoexcitation of the 15ZPo state triggers inhomogeneous excited-state dynamics with three spectrally and temporally distinguishable pathways to generate the light-adapted 15EPg state in high yield (estimated at 25-30%). Although observed in other CBCR domains, the inhomogeneity in NpF2164g7 extends far into secondary relaxation dynamics (10 ns -1 ms) through to formation of 15EPg. In the reverse direction, the primary dynamics after photoexcitation of 15EPg are qualitatively similar to those of other red/green CBCRs, but secondary dynamics involve a "pre-equilibrium" step before regenerating 15ZPo. The anomalous photodynamics of NpF2164g7 may reflect an evolutionary adaptation of CBCR sensors that function as broadband light intensity sensors.
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46
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Domratcheva T, Schlichting I. Spiers Memorial Lecture. Introductory lecture: the impact of structure on photoinduced processes in nucleic acids and proteins. Faraday Discuss 2018; 207:9-26. [PMID: 29583144 DOI: 10.1039/c8fd00058a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light is an important environmental variable and most organisms have evolved means to sense, exploit or avoid it and to repair detrimental effects on their genome. In general, light absorption is the task of specific chromophores, however other biomolecules such as oligonucleotides also do so which can result in undesired outcomes such as mutations and cancer. Given the biological importance of light-induced processes and applications for imaging, optogenetics, photodynamic therapy or photovoltaics, there is a great interest in understanding the detailed molecular mechanisms of photoinduced processes in proteins and nucleic acids. The processes are typically characterized by time-resolved spectroscopic approaches or computation, inferring structural information on transient species from stable ground state structures. Recently, however, structure determination of excited states or other short-lived species has become possible with the advent of X-ray free-electron lasers. This review gives an overview of the impact of structure on the understanding of photoinduced processes in macromolecules, focusing on systems presented at this Faraday Discussion meeting.
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Affiliation(s)
- Tatiana Domratcheva
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany.
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany.
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47
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Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS. Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila. Biochemistry 2018; 57:1733-1747. [PMID: 29465990 DOI: 10.1021/acs.biochem.7b01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elizabeth C Carroll
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Dmitry Morozov
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Jie Pan
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | | | | | - Jack Fuzell
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Ivo van Stokkum
- Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1081 , 1081 HV Amsterdam , The Netherlands
| | - Gerrit Groenhof
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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48
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Lee K, Kim Y, Jung J, Ihee H, Park Y. Measurements of complex refractive index change of photoactive yellow protein over a wide wavelength range using hyperspectral quantitative phase imaging. Sci Rep 2018; 8:3064. [PMID: 29449627 PMCID: PMC5814402 DOI: 10.1038/s41598-018-21403-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/31/2018] [Indexed: 12/25/2022] Open
Abstract
A novel optical holographic technique is presented to simultaneously measure both the real and imaginary components of the complex refractive index (CRI) of a protein solution over a wide visible wavelength range. Quantitative phase imaging was employed to precisely measure the optical field transmitted from a protein solution, from which the CRIs of the protein solution were retrieved using the Fourier light scattering technique. Using this method, we characterized the CRIs of the two dominant structural states of a photoactive yellow protein solution over a broad wavelength range (461-582 nm). The significant CRI deviation between the two structural states was quantified and analysed. The results of both states show the similar overall shape of the expected rRI obtained from the Kramers-Kronig relations.
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Affiliation(s)
- KyeoReh Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Youngmin Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - JaeHwang Jung
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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49
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Selikhanov GK, Fando MS, Dontsova MV, Gabdulkhakov AG. Investigations of Photosensitive Proteins by Serial Crystallography. BIOCHEMISTRY (MOSCOW) 2018; 83:S163-S175. [DOI: 10.1134/s0006297918140134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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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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