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Su Z, Dasgupta M, Poitevin F, Mathews II, van den Bedem H, Wall ME, Yoon CH, Wilson MA. Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:044701. [PMID: 34258328 PMCID: PMC8270650 DOI: 10.1063/4.0000087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks-diffuse scattering-is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.
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Affiliation(s)
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Irimpan I. Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Michael E. Wall
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, USA
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52
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Gu DH, Eo C, Hwangbo SA, Ha SC, Kim JH, Kim H, Lee CS, Seo ID, Yun YD, Lee W, Choi H, Kim J, Lim J, Rah S, Kim JS, Lee JO, Kim YG, Park SY. BL-11C Micro-MX: a high-flux microfocus macromolecular-crystallography beamline for micrometre-sized protein crystals at Pohang Light Source II. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1210-1215. [PMID: 34212886 PMCID: PMC8284399 DOI: 10.1107/s1600577521004355] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/22/2021] [Indexed: 05/06/2023]
Abstract
BL-11C, a new protein crystallography beamline, is an in-vacuum undulator-based microfocus beamline used for macromolecular crystallography at the Pohang Accelerator Laboratory and it was made available to users in June 2017. The beamline is energy tunable in the range 5.0-20 keV to support conventional single- and multi-wavelength anomalous-dispersion experiments against a wide range of heavy metals. At the standard working energy of 12.659 keV, the monochromated beam is focused to 4.1 µm (V) × 8.5 µm (H) full width at half-maximum at the sample position and the measured photon flux is 1.3 × 1012 photons s-1. The experimental station is equipped with a Pilatus3 6M detector, a micro-diffractometer (MD2S) incorporating a multi-axis goniometer, and a robotic sample exchanger (CATS) with a dewar capacity of 90 samples. This beamline is suitable for structural determination of weakly diffracting crystalline substances, such as biomaterials, including protein, nucleic acids and their complexes. In addition, serial crystallography experiments for determining crystal structures at room temperature are possible. Herein, the current beamline characteristics, technical information for users and some recent scientific highlights are described.
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Affiliation(s)
- Do-Heon Gu
- Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea
| | - Cheolsoo Eo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Seung-A Hwangbo
- Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sung-Chul Ha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Jin Hong Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Hyoyun Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Chae-Soon Lee
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - In Deuk Seo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Young Duck Yun
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Woulwoo Lee
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Hyeongju Choi
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Jangwoo Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Jun Lim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Seungyu Rah
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea
| | - Jie-Oh Lee
- Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
- Correspondence e-mail: ,
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-Beongil, Pohang, Nam-gu, Gyeongbuk 37673, Republic of Korea
- Correspondence e-mail: ,
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53
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Na H, Hinsen K, Song G. The amounts of thermal vibrations and static disorder in protein X-ray crystallographic B-factors. Proteins 2021; 89:1442-1457. [PMID: 34174110 DOI: 10.1002/prot.26165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 12/20/2022]
Abstract
Crystallographic B-factors provide direct dynamical information on the internal mobility of proteins that is closely linked to function, and are also widely used as a benchmark in assessing elastic network models. A significant question in the field is: what is the exact amount of thermal vibrations in protein crystallographic B-factors? This work sets out to answer this question. First, we carry out a thorough, statistically sound analysis of crystallographic B-factors of over 10 000 structures. Second, by employing a highly accurate all-atom model based on the well-known CHARMM force field, we obtain computationally the magnitudes of thermal vibrations of nearly 1000 structures. Our key findings are: (i) the magnitude of thermal vibrations, surprisingly, is nearly protein-independent, as a corollary to the universality for the vibrational spectra of globular proteins established earlier; (ii) the magnitude of thermal vibrations is small, less than 0.1 Å2 at 100 K; (iii) the percentage of thermal vibrations in B-factors is the lowest at low resolution and low temperature (<10%) but increases to as high as 60% for structures determined at high resolution and at room temperature. The significance of this work is that it provides for the first time, using an extremely large dataset, a thorough analysis of B-factors and their thermal and static disorder components. The results clearly demonstrate that structures determined at high resolution and at room temperature have the richest dynamics information. Since such structures are relatively rare in the PDB database, the work naturally calls for more such structures to be determined experimentally.
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Affiliation(s)
- Hyuntae Na
- Department of Computer Science, Penn State Harrisburg, Middletown, Pennsylvania, USA
| | - Konrad Hinsen
- Centre de Biophysique Moleculaire, CNRS, Orleans, France.,Synchrotron SOLEIL, Division Expériences, Gif sur Yvette, France
| | - Guang Song
- Department of Computer Science, Program of Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, USA
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Tetreau G, Andreeva EA, Banneville AS, De Zitter E, Colletier JP. Can (We Make) Bacillus thuringiensis Crystallize More Than Its Toxins? Toxins (Basel) 2021; 13:toxins13070441. [PMID: 34206749 PMCID: PMC8309801 DOI: 10.3390/toxins13070441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
The development of finely tuned and reliable crystallization processes to obtain crystalline formulations of proteins has received growing interest from different scientific fields, including toxinology and structural biology, as well as from industry, notably for biotechnological and medical applications. As a natural crystal-making bacterium, Bacillus thuringiensis (Bt) has evolved through millions of years to produce hundreds of highly structurally diverse pesticidal proteins as micrometer-sized crystals. The long-term stability of Bt protein crystals in aqueous environments and their specific and controlled dissolution are characteristics that are particularly sought after. In this article, we explore whether the crystallization machinery of Bt can be hijacked as a means to produce (micro)crystalline formulations of proteins for three different applications: (i) to develop new bioinsecticidal formulations based on rationally improved crystalline toxins, (ii) to functionalize crystals with specific characteristics for biotechnological and medical applications, and (iii) to produce microcrystals of custom proteins for structural biology. By developing the needs of these different fields to figure out if and how Bt could meet each specific requirement, we discuss the already published and/or patented attempts and provide guidelines for future investigations in some underexplored yet promising domains.
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55
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Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography. Sci Rep 2021; 11:13115. [PMID: 34162965 PMCID: PMC8222285 DOI: 10.1038/s41598-021-92687-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/11/2021] [Indexed: 01/07/2023] Open
Abstract
The serial crystallography (SX) technique enables the determination of the room-temperature structure of a macromolecule while causing minimal radiation damage, as well as the visualization of the molecular dynamics by time-resolved studies. The fixed-target (FT) scanning approach is one method for SX sample delivery that minimizes sample consumption and minimizes physical damage to crystals during data collection. Settling of the crystals on the sample holder in random orientation is important for complete three dimensional data collection. To increase the random orientation of crystals on the sample holder, we developed a polyimide mesh-based sample holder with irregular crystal mounting holes for FT-SX. The polyimide mesh was fabricated using a picosecond laser. Each hole in the polyimide mesh has irregularly shaped holes because of laser thermal damage, which may cause more crystals to settle at random orientations compared to regular shaped sample holders. A crystal sample was spread onto a polyimide-mesh, and a polyimide film was added to both sides to prevent dehydration. Using this sample holder, FT-SX was performed at synchrotron and determined the room-temperature lysozyme structure at 1.65 Å. The polyimide mesh with irregularly shaped holes will allow for expanded applications in sample delivery for FT-SX experiments.
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56
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Kwon H, Basran J, Pathak C, Hussain M, Freeman SL, Fielding AJ, Bailey AJ, Stefanou N, Sparkes HA, Tosha T, Yamashita K, Hirata K, Murakami H, Ueno G, Ago H, Tono K, Yamamoto M, Sawai H, Shiro Y, Sugimoto H, Raven EL, Moody PCE. XFEL Crystal Structures of Peroxidase Compound II. Angew Chem Int Ed Engl 2021; 60:14578-14585. [PMID: 33826799 PMCID: PMC8251747 DOI: 10.1002/anie.202103010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 01/07/2023]
Abstract
Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an FeIV =O or FeIV -OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated FeIV =O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme.
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Affiliation(s)
- Hanna Kwon
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Chinar Pathak
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Mahdi Hussain
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Samuel L. Freeman
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Alistair J. Fielding
- Centre for Natural Products Discovery, Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityJames Parsons Building, Byrom StreetLiverpoolL3 3AFUK
| | - Anna J. Bailey
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Natalia Stefanou
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Hazel A. Sparkes
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | - Keitaro Yamashita
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Present address: MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB1 0QHUK
| | - Kunio Hirata
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hironori Murakami
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | - Go Ueno
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hideo Ago
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Hitomi Sawai
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | - Yoshitsugu Shiro
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | | | - Emma L. Raven
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Peter C. E. Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
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57
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Kwon H, Basran J, Pathak C, Hussain M, Freeman SL, Fielding AJ, Bailey AJ, Stefanou N, Sparkes HA, Tosha T, Yamashita K, Hirata K, Murakami H, Ueno G, Ago H, Tono K, Yamamoto M, Sawai H, Shiro Y, Sugimoto H, Raven EL, Moody PCE. XFEL Crystal Structures of Peroxidase Compound II. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:14699-14706. [PMID: 38505375 PMCID: PMC10947387 DOI: 10.1002/ange.202103010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 03/21/2024]
Abstract
Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an FeIV=O or FeIV-OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated FeIV=O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme.
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Affiliation(s)
- Hanna Kwon
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Chinar Pathak
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Mahdi Hussain
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Samuel L. Freeman
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Alistair J. Fielding
- Centre for Natural Products Discovery, Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityJames Parsons Building, Byrom StreetLiverpoolL3 3AFUK
| | - Anna J. Bailey
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Natalia Stefanou
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Hazel A. Sparkes
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | - Keitaro Yamashita
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Present address: MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB1 0QHUK
| | - Kunio Hirata
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hironori Murakami
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | - Go Ueno
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hideo Ago
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Hitomi Sawai
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | - Yoshitsugu Shiro
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | | | - Emma L. Raven
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Peter C. E. Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
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58
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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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59
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Mehrabi P, Bücker R, Bourenkov G, Ginn HM, von Stetten D, Müller-Werkmeister HM, Kuo A, Morizumi T, Eger BT, Ou WL, Oghbaey S, Sarracini A, Besaw JE, Pare-Labrosse O, Meier S, Schikora H, Tellkamp F, Marx A, Sherrell DA, Axford D, Owen RL, Ernst OP, Pai EF, Schulz EC, Miller RJD. Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison. SCIENCE ADVANCES 2021; 7:7/12/eabf1380. [PMID: 33731353 PMCID: PMC7968842 DOI: 10.1126/sciadv.abf1380] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/28/2021] [Indexed: 05/09/2023]
Abstract
For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.
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Affiliation(s)
- P Mehrabi
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R Bücker
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - G Bourenkov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany
| | - H M Ginn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - D von Stetten
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany
| | - H M Müller-Werkmeister
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - A Kuo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - T Morizumi
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - B T Eger
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - W-L Ou
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - S Oghbaey
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - A Sarracini
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - J E Besaw
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - O Pare-Labrosse
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - S Meier
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - H Schikora
- Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - F Tellkamp
- Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Marx
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - D A Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - D Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - R L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - O P Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - E F Pai
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - E C Schulz
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R J D Miller
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
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60
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Analysis of Multi-Hit Crystals in Serial Synchrotron Crystallography Experiments Using High-Viscosity Injectors. CRYSTALS 2021. [DOI: 10.3390/cryst11010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Serial Synchrotron Crystallography (SSX) is rapidly emerging as a promising technique for collecting data for time-resolved structural studies or for performing room temperature micro-crystallography measurements using micro-focused beamlines. SSX is often performed using high frame rate detectors in combination with continuous sample scanning or high-viscosity or liquid jet injectors. When performed using ultra-bright X-ray Free Electron Laser (XFEL) sources serial crystallography typically involves a process known as ’diffract-and-destroy’ where each crystal is measured just once before it is destroyed by the intense XFEL pulse. In SSX, however, particularly when using high-viscosity injectors (HVIs) such as Lipidico, the crystal can be intercepted multiple times by the X-ray beam prior to exiting the interaction region. This has a number of important consequences for SSX including whether these multiple-hits can be incorporated into the data analysis or whether they need to be excluded due to the potential impact of radiation damage. Here, we investigate the occurrence and characteristics of multiple hits on single crystals using SSX with lipidico. SSX data are collected from crystals as they tumble within a high viscous stream of silicone grease flowing through a micro-focused X-ray beam. We confirmed that, using the Eiger 16M, we are able to collect up to 42 frames of data from the same single crystal prior to it leaving the X-ray interaction region. The frequency and occurrence of multiple hits may be controlled by varying the sample flow rate and X-ray beam size. Calculations of the absorbed dose confirm that these crystals are likely to undergo radiation damage but that nonetheless incorporating multiple hits into damage-free data should lead to a significant reduction in the number of crystals required for structural analysis when compared to just looking at a single diffraction pattern from each crystal.
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61
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Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
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62
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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63
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Li J, Triana CA, Wan W, Adiyeri Saseendran DP, Zhao Y, Balaghi SE, Heidari S, Patzke GR. Molecular and heterogeneous water oxidation catalysts: recent progress and joint perspectives. Chem Soc Rev 2021; 50:2444-2485. [DOI: 10.1039/d0cs00978d] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The recent synthetic and mechanistic progress in molecular and heterogeneous water oxidation catalysts highlights the new, overarching strategies for knowledge transfer and unifying design concepts.
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Affiliation(s)
- J. Li
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
| | - C. A. Triana
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
| | - W. Wan
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
| | | | - Y. Zhao
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
| | - S. E. Balaghi
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
| | - S. Heidari
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
| | - G. R. Patzke
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
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64
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Doukov T, Herschlag D, Yabukarski F. Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures. J Appl Crystallogr 2020; 53:1493-1501. [PMID: 33312102 PMCID: PMC7710493 DOI: 10.1107/s1600576720013503] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/08/2020] [Indexed: 11/10/2022] Open
Abstract
Traditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Furthermore, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that can be directly related to biological function. Given this capability, the next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperature. This challenge is addressed herein. The approach described provides complete diffraction data sets with total collection times as short as ∼5 s from single protein crystals, dramatically increasing the quantity of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293-363 K for proteinase K, thaumatin and lysozyme crystals at BL14-1 at the Stanford Synchrotron Radiation Lightsource. The analyses presented here indicate that the diffraction data are of high quality and do not suffer from excessive dehydration or radiation damage.
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Affiliation(s)
- Tzanko Doukov
- SMB, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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65
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation. Angew Chem Int Ed Engl 2020; 59:21656-21662. [PMID: 32780931 PMCID: PMC7756461 DOI: 10.1002/anie.202008622] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 01/06/2023]
Abstract
Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (FeIV =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the FeIII and FeIV =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | | | - Michael T. Wilson
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Amanda K. Chaplin
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Bradley Davy
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Ali Ebrahim
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Danny Axford
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | | | | | - Shigeki Owada
- RIKEN Spring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Ivo Tews
- Biological SciencesInstitute for Life SciencesUniversity of SouthamptonUniversity RoadSouthamptonSO17 1BJUK
| | - Robin L. Owen
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Michael A. Hough
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
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66
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water‐Free Distal Heme Site in a Dye‐Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe
IV
=O Formation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marina Lučić
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | | | - Michael T. Wilson
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Amanda K. Chaplin
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Bradley Davy
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Ali Ebrahim
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Danny Axford
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Takehiko Tosha
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Shigeki Owada
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
- Japan Synchrotron Radiation Research Institute 1-1-1 Kouto Sayo Hyogo 679-5198 Japan
| | | | - Ivo Tews
- Biological Sciences Institute for Life Sciences University of Southampton University Road Southampton SO17 1BJ UK
| | - Robin L. Owen
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Michael A. Hough
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
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67
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Stachowski TR, Snell ME, Snell EH. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique. PLoS One 2020; 15:e0239702. [PMID: 33201877 PMCID: PMC7671560 DOI: 10.1371/journal.pone.0239702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022] Open
Abstract
A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.
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Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Materials Design and Innovation, State University at New York at Buffalo, Buffalo, New York, United States of America
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68
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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69
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Orville AM. Recent results in time resolved serial femtosecond crystallography at XFELs. Curr Opin Struct Biol 2020; 65:193-208. [PMID: 33049498 DOI: 10.1016/j.sbi.2020.08.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022]
Abstract
Time-resolved serial femtosecond crystallography (tr-SFX) methods exploit slurries of crystalline samples that range in size from hundreds of nanometers to a few tens of micrometers, at near-physiological temperature and pressure, to generate atomic resolution models and probe authentic function with the same experiment. 'Dynamic structural biology' is often used to encompass the research philosophy and techniques. Reaction cycles for tr-SFX studies are initiated by photons or ligand addition/mixing strategies, wherein the latter are potentially generalizable across enzymology. Thus, dynamic structural biology often creates stop-motion molecular movies of macromolecular function. In metal-dependent systems, complementary spectroscopic information can also be collected from the same samples and X-ray pulses, which provides even more detailed mechanistic insights. These types of experimental data also complement quantum mechanical and classical dynamics numerical calculations. Correlated structural-functional results will yield more detailed mechanistic insights and will likely translate into better drugs and treatments impacting human health, and better catalysis for clean energy and agriculture.
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Affiliation(s)
- Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom; Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom.
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70
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Shilova A, Lebrette H, Aurelius O, Nan J, Welin M, Kovacic R, Ghosh S, Safari C, Friel RJ, Milas M, Matej Z, Högbom M, Brändén G, Kloos M, Shoeman RL, Doak B, Ursby T, Håkansson M, Logan DT, Mueller U. Current status and future opportunities for serial crystallography at MAX IV Laboratory. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1095-1102. [PMID: 32876583 PMCID: PMC7467353 DOI: 10.1107/s1600577520008735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Over the last decade, serial crystallography, a method to collect complete diffraction datasets from a large number of microcrystals delivered and exposed to an X-ray beam in random orientations at room temperature, has been successfully implemented at X-ray free-electron lasers and synchrotron radiation facility beamlines. This development relies on a growing variety of sample presentation methods, including different fixed target supports, injection methods using gas-dynamic virtual-nozzle injectors and high-viscosity extrusion injectors, and acoustic levitation of droplets, each with unique requirements. In comparison with X-ray free-electron lasers, increased beam time availability makes synchrotron facilities very attractive to perform serial synchrotron X-ray crystallography (SSX) experiments. Within this work, the possibilities to perform SSX at BioMAX, the first macromolecular crystallography beamline at MAX IV Laboratory in Lund, Sweden, are described, together with case studies from the SSX user program: an implementation of a high-viscosity extrusion injector to perform room temperature serial crystallography at BioMAX using two solid supports - silicon nitride membranes (Silson, UK) and XtalTool (Jena Bioscience, Germany). Future perspectives for the dedicated serial crystallography beamline MicroMAX at MAX IV Laboratory, which will provide parallel and intense micrometre-sized X-ray beams, are discussed.
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Affiliation(s)
- Anastasya Shilova
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm 10691, Sweden
| | - Oskar Aurelius
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Martin Welin
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Rebeka Kovacic
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Ross J. Friel
- School of Information Technology, Halmstad University, Halmstad 30118, Sweden
| | - Mirko Milas
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Zdenek Matej
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm 10691, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas Ursby
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Derek T. Logan
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Uwe Mueller
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
- Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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71
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Srinivas V, Banerjee R, Lebrette H, Jones JC, Aurelius O, Kim IS, Pham CC, Gul S, Sutherlin KD, Bhowmick A, John J, Bozkurt E, Fransson T, Aller P, Butryn A, Bogacz I, Simon P, Keable S, Britz A, Tono K, Kim KS, Park SY, Lee SJ, Park J, Alonso-Mori R, Fuller FD, Batyuk A, Brewster AS, Bergmann U, Sauter NK, Orville AM, Yachandra VK, Yano J, Lipscomb JD, Kern J, Högbom M. High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States. J Am Chem Soc 2020; 142:14249-14266. [PMID: 32683863 PMCID: PMC7457426 DOI: 10.1021/jacs.0c05613] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.
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Affiliation(s)
- Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Jason C. Jones
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Cindy C. Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Kyle D. Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Esra Bozkurt
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Philipp Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Stephen Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Alexander Britz
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025 U.S.A
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-gun 679 5198, Japan
| | - Kyung Sook Kim
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Sang-Youn Park
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Sang Jae Lee
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Jaehyun Park
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025 U.S.A
| | - Franklin D. Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025 U.S.A
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025 U.S.A
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, 94025 U.S.A
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0FA, UK
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
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EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm. CRYSTALS 2020. [DOI: 10.3390/cryst10070588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises when the symmetry of Bravais lattice is higher than the space group symmetry, making some diffraction signals wrongly merged to the total intensity in twinned orientations. In this research, we developed a program within the CrystFEL framework, the EM-detwin, to resolve this indexing ambiguity problem based on the expectation-maximization algorithm. Testing results on the performance of the EM-detwin have demonstrated its usefulness in correctly indexing diffraction data as a valuable tool for SX data analysis.
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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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