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Perrett S, Chatrchyan V, Buckup T, van Thor JJ. Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography. J Chem Phys 2024; 160:100901. [PMID: 38456527 DOI: 10.1063/5.0188888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities of XFELs advance, we anticipate that a new range of coherent control and structural Raman measurements will become achievable. Shorter optical and x-ray pulse durations and increasingly more exotic pulse regimes are becoming available at free electron lasers. Moreover, with high repetition enabled by the superconducting technology of European XFEL (EuXFEL) and Linac Coherent Light Source (LCLS-II) , it will be possible to improve the signal-to-noise ratio of the light-induced differences, allowing for the observation of vibronic motion on the sub-Angstrom level. To predict and assign this coherent motion, which is measurable with a structural technique, new theoretical approaches must be developed. In this paper, we present a theoretical density matrix approach to model the various population and coherent dynamics of a system, which considers molecular system parameters and excitation conditions. We emphasize the use of the Wigner transform of the time-dependent density matrix, which provides a phase space representation that can be directly compared to the experimental positional displacements measured in a TR-SFX experiment. Here, we extend the results from simple models to include more realistic schemes that include large relaxation terms. We explore a variety of pulse schemes using multiple model systems using realistic parameters. An open-source software package is provided to perform the density matrix simulation and Wigner transformations. The open-source software allows us to define any arbitrary level schemes as well as any arbitrary electric field in the interaction Hamiltonian.
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Affiliation(s)
- Samuel Perrett
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Viktoria Chatrchyan
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität, D-69120 Heidelberg, Germany
| | - Tiago Buckup
- Physikalisch Chemisches Institut, Ruprecht-Karls Universität, D-69120 Heidelberg, Germany
| | - Jasper J van Thor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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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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Hekstra DR. Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. Annu Rev Biophys 2023; 52:255-274. [PMID: 37159292 PMCID: PMC10687665 DOI: 10.1146/annurev-biophys-111622-091155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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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4
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Macromolecular movies, storybooks written by nature. Biophys Rev 2022; 13:1191-1197. [PMID: 35059037 DOI: 10.1007/s12551-021-00846-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/08/2021] [Indexed: 10/19/2022] Open
Abstract
Twelve years ago, the first free electron laser for hard X-rays (XFEL), the Linac Coherent Light Source (LCLS), came online. Due to the extreme brilliance and the ultrashort pulse duration of their X-ray radiation, XFELs are exceptionally well positioned to conduct time-resolved studies on biological macromolecules. Here, some of the pioneering experiments and recent results are summarized.
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van Thor JJ. Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:050901. [PMID: 31559317 PMCID: PMC6759419 DOI: 10.1063/1.5110685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/29/2019] [Indexed: 05/02/2023]
Abstract
Both nuclear and electronic dynamics contribute to protein function and need multiple and complementary techniques to reveal their ultrafast structural dynamics response. Real-space information obtained from the measurement of electron density dynamics by X-ray crystallography provides aspects of both, while the molecular physics of coherence parameters and frequency-frequency correlation needs spectroscopy methods. Ultrafast pump-probe applications of protein dynamics in crystals provide real-space information through direct X-ray crystallographic structure analysis or through structural optical crystallographic analysis. A discussion of methods of analysis using ultrafast macromolecular X-ray crystallography and ultrafast nonlinear structural optical crystallography is presented. The current and future high repetition rate capabilities provided by X-ray free electron lasers for ultrafast diffraction studies provide opportunities for optical control and optical selection of nuclear coherence which may develop to access higher frequency dynamics through improvements of sensitivity and time resolution to reveal coherence directly. Specific selection of electronic coherence requires optical probes, which can provide real-space structural information through photoselection of oriented samples and specifically in birefringent crystals. Ultrafast structural optical crystallography of photosynthetic energy transfer has been demonstrated, and the theory of two-dimensional structural optical crystallography has shown a method for accessing the structural selection of electronic coherence.
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Affiliation(s)
- Jasper J. van Thor
- Molecular Biophysics, Imperial College London, London SW7 2AZ, United Kingdom
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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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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: 32] [Impact Index Per Article: 6.4] [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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Šrajer V, Schmidt M. Watching Proteins Function with Time-resolved X-ray Crystallography. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:373001. [PMID: 29353938 PMCID: PMC5771432 DOI: 10.1088/1361-6463/aa7d32] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.
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Affiliation(s)
- Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, IL, USA
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Hutchison CDM, Cordon-Preciado V, Morgan RML, Nakane T, Ferreira J, Dorlhiac G, Sanchez-Gonzalez A, Johnson AS, Fitzpatrick A, Fare C, Marangos JP, Yoon CH, Hunter MS, DePonte DP, Boutet S, Owada S, Tanaka R, Tono K, Iwata S, van Thor JJ. X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature. Int J Mol Sci 2017; 18:E1918. [PMID: 28880248 PMCID: PMC5618567 DOI: 10.3390/ijms18091918] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 01/03/2023] Open
Abstract
The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.
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Affiliation(s)
- Christopher D. M. Hutchison
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Violeta Cordon-Preciado
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Rhodri M. L. Morgan
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan;
| | - Josie Ferreira
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Gabriel Dorlhiac
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Alvaro Sanchez-Gonzalez
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Allan S. Johnson
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Ann Fitzpatrick
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK;
| | - Clyde Fare
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Jon P. Marangos
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Chun Hong Yoon
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Mark S. Hunter
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Daniel P. DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jasper J. van Thor
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
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Ren Z, Yang X. Angular-split/temporal-delay approach to ultrafast protein dynamics at XFELs. Acta Crystallogr D Struct Biol 2016; 72:871-82. [PMID: 27377384 PMCID: PMC6688658 DOI: 10.1107/s2059798316008573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 05/27/2016] [Indexed: 11/10/2022] Open
Abstract
X-ray crystallography promises direct insights into electron-density changes that lead to and arise from structural changes such as electron and proton transfer and the formation, rupture and isomerization of chemical bonds. The ultrashort pulses of hard X-rays produced by free-electron lasers present an exciting opportunity for capturing ultrafast structural events in biological macromolecules within femtoseconds after photoexcitation. However, shot-to-shot fluctuations, which are inherent to the very process of self-amplified spontaneous emission (SASE) that generates the ultrashort X-ray pulses, are a major source of noise that may conceal signals from structural changes. Here, a new approach is proposed to angularly split a single SASE pulse and to produce a temporal delay of picoseconds between the split pulses. These split pulses will allow the probing of two distinct states before and after photoexcitation triggered by a laser pulse between the split X-ray pulses. The split pulses originate from a single SASE pulse and share many common properties; thus, noise arising from shot-to-shot fluctuations is self-canceling. The unambiguous interpretation of ultrafast structural changes would require diffraction data at atomic resolution, as these changes may or may not involve any atomic displacement. This approach, in combination with the strategy of serial crystallography, offers a solution to study ultrafast dynamics of light-initiated biochemical reactions or biological processes at atomic resolution.
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Affiliation(s)
- Zhong Ren
- Renz Research Inc., Westmont, IL 60559, USA
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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Hutchison CD, Kaucikas M, Tenboer J, Kupitz C, Moffat K, Schmidt M, van Thor JJ. Photocycle populations with femtosecond excitation of crystalline photoactive yellow protein. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.087] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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van Thor JJ, Madsen A. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:014102. [PMID: 26798786 PMCID: PMC4711627 DOI: 10.1063/1.4906354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 01/09/2015] [Indexed: 05/14/2023]
Abstract
In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or "probe-pump-probe") which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.
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Affiliation(s)
- Jasper J van Thor
- Division of Molecular Biosciences, Imperial College London , South Kensington Campus. SW7 2AZ London, United Kingdom
| | - Anders Madsen
- European X-Ray Free-Electron Laser Facility , Albert-Einstein-Ring 19, 22761 Hamburg, Germany
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13
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Tenboer J, Basu S, Zatsepin N, Pande K, Milathianaki D, Frank M, Hunter M, Boutet S, Williams GJ, Koglin JE, Oberthuer D, Heymann M, Kupitz C, Conrad C, Coe J, Roy-Chowdhury S, Weierstall U, James D, Wang D, Grant T, Barty A, Yefanov O, Scales J, Gati C, Seuring C, Srajer V, Henning R, Schwander P, Fromme R, Ourmazd A, Moffat K, Van Thor JJ, Spence JCH, Fromme P, Chapman HN, Schmidt M. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science 2014; 346:1242-6. [PMID: 25477465 DOI: 10.1126/science.1259357] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.
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Affiliation(s)
- Jason Tenboer
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Shibom Basu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Kanupriya Pande
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Despina Milathianaki
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Mark Hunter
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dominik Oberthuer
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Michael Heymann
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie Conrad
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse Coe
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas Grant
- Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jennifer Scales
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Cornelius Gati
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany.,Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Vukica Srajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Keith Moffat
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Jasper J Van Thor
- Faculty of Natural Sciences, Life Sciences, Imperial College, London SW7 2AZ, UK
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Henry N Chapman
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany.,Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marius Schmidt
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA.,Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA.
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14
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB, Station 6, CH-1015 Lausanne, Switzerland.
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15
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Chapman HN. Disruptive photon technologies for chemical dynamics. Faraday Discuss 2014; 171:525-43. [DOI: 10.1039/c4fd00156g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A perspective of new and emerging technologies for chemical dynamics is given, with an emphasis on the use of X-ray sources that generate sub-picosecond pulses. The two classes of experimental techniques used for time-resolved measurements of chemical processes and their effects are spectroscopy and imaging, where the latter includes microscopy, diffractive imaging, and crystallography. X-Ray free-electron lasers have brought new impetus to the field, allowing not only temporal and spatial resolution at atomic time and length scales, but also bringing a new way to overcome limitations due to perturbation of the sample by the X-ray probe by out-running radiation damage. Associated instrumentation and methods are being developed to take advantage of the new opportunities of these sources. Once these methods of observational science have been mastered it should be possible to use the new tools to directly control those chemical processes.
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Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science
- DESY
- 22607 Hamburg, Germany
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