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Barends TRM, Gorel A, Bhattacharyya S, Schirò G, Bacellar C, Cirelli C, Colletier JP, Foucar L, Grünbein ML, Hartmann E, Hilpert M, Holton JM, Johnson PJM, Kloos M, Knopp G, Marekha B, Nass K, Nass Kovacs G, Ozerov D, Stricker M, Weik M, Doak RB, Shoeman RL, Milne CJ, Huix-Rotllant M, Cammarata M, Schlichting I. Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Nature 2024; 626:905-911. [PMID: 38355794 PMCID: PMC10881388 DOI: 10.1038/s41586-024-07032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
High-intensity femtosecond pulses from an X-ray free-electron laser enable pump-probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1,2. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore3-17. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern18,19 whether this experimental approach20 allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions18,19. Here we describe ultrafast pump-probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics21) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump-probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump-probe experiments20 such that mechanistically relevant insight emerges.
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Affiliation(s)
| | - Alexander Gorel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | | | | | - Lutz Foucar
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | - Mario Hilpert
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | | | - Bogdan Marekha
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France
| | - Karol Nass
- Paul Scherrer Institute, Villigen, Switzerland
| | | | | | | | - Martin Weik
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
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Haymaker A, Nannenga BL. Advances and applications of microcrystal electron diffraction (MicroED). Curr Opin Struct Biol 2024; 84:102741. [PMID: 38086321 PMCID: PMC10882645 DOI: 10.1016/j.sbi.2023.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 02/08/2024]
Abstract
Microcrystal electron diffraction, commonly referred to as MicroED, has become a powerful tool for high-resolution structure determination. The method makes use of cryogenic transmission electron microscopes to collect electron diffraction data from crystals that are several orders of magnitude smaller than those used by other conventional diffraction techniques. MicroED has been used on a variety of samples including soluble proteins, membrane proteins, small organic molecules, and materials. Here we will review the MicroED method and highlight recent advancements to the methodology, as well as describe applications of MicroED within the fields of structural biology and chemical crystallography.
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Affiliation(s)
- Alison Haymaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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3
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Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Müller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD. Visualizing the DNA repair process by a photolyase at atomic resolution. Science 2023; 382:eadd7795. [PMID: 38033054 DOI: 10.1126/science.add7795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
Abstract
Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.
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Affiliation(s)
- Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Po-Hsun Wang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Yuhei Hosokawa
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Antonia Furrer
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | | | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Hans-Joachim Emmerich
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Nicolas Caramello
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Sophie Franz-Badur
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Chao Yang
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Sylvain Engilberge
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Tobias Weinert
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wael Gad
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Chiung-Wen Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Chun Yang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Wei-Ting Lin
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Yu-Chen Chang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Dardan Gashi
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Emma Beale
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Karol Nass
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Chris Milne
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - 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
| | - Yasumasa Joti
- 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
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fangjia Luo
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- 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
| | - Wiktoria Zarzycka
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pavel Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maisa Alkheder Alahmad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Filipp Bezold
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Valerie Fuchs
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Petra Gnau
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Stephan Kiontke
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Lukas Korf
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Viktoria Reithofer
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Elisa Marie Seiler
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Mohamed Watad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Laura Werel
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Roberta Spadaccini
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
- Dipartimento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dongping Zhong
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for Ultrafast Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jörg Standfuss
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Antoine Royant
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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Yonekura K, Maki-Yonekura S, Takaba K. Applications and limitations of electron 3D crystallography. Structure 2023; 31:1328-1334. [PMID: 37797620 DOI: 10.1016/j.str.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/27/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Three-dimensional electron diffraction (3D ED) is a measurement and analysis technique in transmission electron microscopy that is used for determining atomic structures from small crystals. Diverse targets such as proteins, polypeptides, and organic compounds, whose crystals exist in aqueous solutions and organic solvents, or as dried powders, can be studied with 3D ED. We have been involved in the development of this technique, which can now rapidly process a large number of data collected through AI control, enabling efficient structure determination. Here, we introduce this method and describe our recent results. These include the structures and pathogenic mechanisms of wild-type and mutant polypeptides associated with the debilitating disease amyotrophic lateral sclerosis (ALS), the double helical structure of nanographene promoting nanofiber formation, and the structural properties of an organic semiconductor containing disordered regions. We also discuss the limitations and prospects of 3D ED compared to microcrystallography with X-ray free electron lasers.
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Affiliation(s)
- Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
| | - Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Stagno JR. Preparation of RNA Microcrystals for Serial Femtosecond Crystallography Experiments. Methods Mol Biol 2023; 2568:233-242. [PMID: 36227572 DOI: 10.1007/978-1-0716-2687-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Serial femtosecond crystallography (SFX) experiments using an X-ray free electron laser (XFEL) is a burgeoning method for time-resolved structural studies of biomacromolecules. As with any crystallography experiment, the most important component is quality sample preparation. Whereas dozens of SFX experiments, including batch crystallization methods, have been reported for proteins, very few have been reported for RNA. This chapter outlines standard procedures for preparing RNA microcrystalline samples suitable for SFX studies.
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Affiliation(s)
- Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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Stagno JR, Knoska J, Chapman HN, Wang YX. Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates. Methods Mol Biol 2023; 2568:243-249. [PMID: 36227573 DOI: 10.1007/978-1-0716-2687-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Time-resolved structure determination of macromolecular conformations and ligand-bound intermediates is extremely challenging, particularly for RNA. With rapid technological advances in both microfluidic liquid injection and X-ray free electron lasers (XFEL), a new frontier has emerged in time-resolved crystallography whereby crystals can be mixed with ligand and then probed with X-rays (mix-and-inject) in real time and at room temperature. This chapter outlines the basic setup and procedures for mix-and-inject experiments for recording time-resolved crystallographic data of riboswitch RNA reaction states using serial femtosecond crystallography (SFX) and an XFEL.
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Affiliation(s)
- Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
- Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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Abstract
Like an article narrative is deemed by an editor and referees to be worthy of being a version of record on acceptance as a publication, so must the underpinning data also be scrutinized before passing it as a version of record. Indeed without the underpinning data, a study and its conclusions cannot be reproduced at any stage of evaluation, pre- or post-publication. Likewise, an independent study without its own underpinning data also cannot be reproduced let alone be considered a replicate of the first study. The PDB is a modern marvel of achievement providing an organized open access to depositor and user of the data held there opening numerous applications. Methods for modeling protein structures and for determination of structures are still improving their precision, and artifacts of the method exist. So their accuracy is realized if they are reproduced by other methods. It is on such foundations that reproducible data mining is based. Data rates are expanding considerably be they at synchrotrons, the X-ray free electron lasers (XFELs), electron cryomicroscopes (cryoEM), or at the neutron facilities. The work of a person as a referee or user with a narrative and its underpinning data may well be complemented in future by artificial intelligence with machine learning, the former for specific refereeing and the latter for the more general validation, both ideally before publication. Examples are described involving rhenium theranostics, the anti-cancer platins and the SARS-CoV-2 main protease.
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Affiliation(s)
- John R Helliwell
- Department of Chemistry, University of Manchester, Manchester, UK.
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Flores-Moreno JM, De La Torre MH, Frausto-Reyes C, Casillas R. Imaging of bee honey sugar crystals by second-harmonic generation microscopy. Appl Opt 2021; 60:7706-7713. [PMID: 34613240 DOI: 10.1364/ao.431309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
Bee honey is an exceptionally nutritious food with unique chemical and mineral contents. This report introduces the use of the second-harmonic generation (SHG) microscopy for imaging honey sugar crystals' morphology as an alternative for its authentication process. The crystals and their boundaries are clearly observed with SHG compared with bright-field microscopy, where the liquid honey avoids the visualization of a sharp image. Four different honey samples of Mexico's various floral origins and geographical regions are analyzed in our study. These samples are representative of the diversity and valuable quality of bee honey production. The SHG image information is complemented with Raman spectroscopy (RS) analysis, since this optical technique is widely used to validate the bee's honey composition stated by its floral origin. We relate the SHG imaging of honey crystals with the well-defined fructose and glucose peaks measured by RS. Size measurement is introduced using the crystal´s length ratio to differentiate its floral origin. From our observations, we can state that SHG is a promising and suitable technique to provide a sort of optical fingerprint based on the floral origin of bee honey.
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10
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Roman C, Lewicka A, Koirala D, Li NS, Piccirilli JA. The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography. ACS Chem Biol 2021; 16:1469-1481. [PMID: 34328734 PMCID: PMC8353986 DOI: 10.1021/acschembio.1c00324] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022]
Abstract
The programmed -1 ribosomal frameshifting element (PFSE) of SARS-CoV-2 is a well conserved structured RNA found in all coronaviruses' genomes. By adopting a pseudoknot structure in the presence of the ribosome, the PFSE promotes a ribosomal frameshifting event near the stop codon of the first open reading frame Orf1a during translation of the polyprotein pp1a. Frameshifting results in continuation of pp1a via a new open reading frame, Orf1b, that produces the longer pp1ab polyprotein. Polyproteins pp1a and pp1ab produce nonstructural proteins NSPs 1-10 and NSPs 1-16, respectively, which contribute vital functions during the viral life cycle and must be present in the proper stoichiometry. Both drugs and sequence alterations that affect the stability of the -1 programmed ribosomal frameshifting element disrupt the stoichiometry of the NSPs produced, which compromise viral replication. For this reason, the -1 programmed frameshifting element is considered a promising drug target. Using chaperone assisted RNA crystallography, we successfully crystallized and solved the three-dimensional structure of the PFSE. We observe a three-stem H-type pseudoknot structure with the three stems stacked in a vertical orientation stabilized by two triple base pairs at the stem 1/stem 2 and stem 1/stem 3 junctions. This structure provides a new conformation of PFSE distinct from the bent conformations inferred from midresolution cryo-EM models and provides a high-resolution framework for mechanistic investigations and structure-based drug design.
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Affiliation(s)
- Christina Roman
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Anna Lewicka
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Deepak Koirala
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County (UMBC), Baltimore, Maryland 21250, United States
| | - Nan-Sheng Li
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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11
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Abstract
The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of computational predictions of NMR chemical shieldings of candidate structures, which are usually taken to be local minima in the potential energy. To test the limits of this approximation, we systematically study the importance of finite-temperature and quantum nuclear fluctuations for 1H, 13C, and 15N shieldings in polymorphs of three paradigmatic molecular crystals: benzene, glycine, and succinic acid. The effect of quantum fluctuations is comparable to the typical errors of shielding predictions for static nuclei with respect to experiments, and their inclusion improves the agreement with measurements, translating to more reliable assignment of the NMR spectra to the correct candidate structure. The use of integrated machine-learning models, trained on first-principles energies and shieldings, renders rigorous sampling of nuclear fluctuations affordable, setting a new standard for the calculations underlying NMR structure determinations.
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Affiliation(s)
- Edgar A Engel
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Venkat Kapil
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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12
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Cordova M, Balodis M, Hofstetter A, Paruzzo F, Nilsson Lill SO, Eriksson ESE, Berruyer P, Simões de Almeida B, Quayle MJ, Norberg ST, Svensk Ankarberg A, Schantz S, Emsley L. Structure determination of an amorphous drug through large-scale NMR predictions. Nat Commun 2021; 12:2964. [PMID: 34016980 PMCID: PMC8137699 DOI: 10.1038/s41467-021-23208-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/25/2021] [Indexed: 11/17/2022] Open
Abstract
Knowledge of the structure of amorphous solids can direct, for example, the optimization of pharmaceutical formulations, but atomic-level structure determination in amorphous molecular solids has so far not been possible. Solid-state nuclear magnetic resonance (NMR) is among the most popular methods to characterize amorphous materials, and molecular dynamics (MD) simulations can help describe the structure of disordered materials. However, directly relating MD to NMR experiments in molecular solids has been out of reach until now because of the large size of these simulations. Here, using a machine learning model of chemical shifts, we determine the atomic-level structure of the hydrated amorphous drug AZD5718 by combining dynamic nuclear polarization-enhanced solid-state NMR experiments with predicted chemical shifts for MD simulations of large systems. From these amorphous structures we then identify H-bonding motifs and relate them to local intermolecular complex formation energies.
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Affiliation(s)
- Manuel Cordova
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Martins Balodis
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Federico Paruzzo
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sten O Nilsson Lill
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Emma S E Eriksson
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Pierrick Berruyer
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bruno Simões de Almeida
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael J Quayle
- New Modalities and Parenteral Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Stefan T Norberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Anna Svensk Ankarberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Staffan Schantz
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden.
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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13
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun 2021; 12:2578. [PMID: 33972532 PMCID: PMC8110528 DOI: 10.1038/s41467-021-22590-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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Affiliation(s)
- Max T B Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Susannah Holmes
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Timothy W Muusse
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Parimala R Vajjhala
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sara J Thygesen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia
| | - Dominic J B Hunter
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Leonie Flueckiger
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Md Habibur Rahaman
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Nadia A Zatsepin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Brian Abbey
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Connie Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia.
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14
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Kneller D, Phillips G, Weiss KL, Zhang Q, Coates L, Kovalevsky A. Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography. J Med Chem 2021; 64:4991-5000. [PMID: 33755450 PMCID: PMC8009097 DOI: 10.1021/acs.jmedchem.1c00058] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 02/08/2023]
Abstract
The main protease (3CL Mpro) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is an essential enzyme for viral replication with no human counterpart, making it an attractive drug target. To date, no small-molecule clinical drugs are available that specifically inhibit SARS-CoV-2 Mpro. To aid rational drug design, we determined a neutron structure of Mpro in complex with the α-ketoamide inhibitor telaprevir at near-physiological (22 °C) temperature. We directly observed protonation states in the inhibitor complex and compared them with those in the ligand-free Mpro, revealing modulation of the active-site protonation states upon telaprevir binding. We suggest that binding of other α-ketoamide covalent inhibitors can lead to the same protonation state changes in the Mpro active site. Thus, by studying the protonation state changes induced by inhibitors, we provide crucial insights to help guide rational drug design, allowing precise tailoring of inhibitors to manipulate the electrostatic environment of SARS-CoV-2 Mpro.
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Affiliation(s)
- Daniel
W. Kneller
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
| | - Gwyndalyn Phillips
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
| | - Kevin L. Weiss
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
| | - Qiu Zhang
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
| | - Leighton Coates
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
- Second
Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Andrey Kovalevsky
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
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15
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Tian X, Ma K, Ji G, Cui J, Liao Y, Xiang M. Anisotropic shock responses of nanoporous Al by molecular dynamics simulations. PLoS One 2021; 16:e0247172. [PMID: 33730074 PMCID: PMC7968703 DOI: 10.1371/journal.pone.0247172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/02/2021] [Indexed: 11/19/2022] Open
Abstract
Mechanical responses of nanoporous aluminum samples under shock in different crystallographic orientations (<100>, <111>, <110>, <112> and <130>) are investigated by molecular dynamics simulations. The shape evolution of void during collapse is found to have no relationship with the shock orientation. Void collapse rate and dislocation activities at the void surface are found to strongly dependent on the shock orientation. For a relatively weaker shock, void collapses fastest when shocked along the <100> orientation; while for a relatively stronger shock, void collapses fastest in the <110> orientation. The dislocation nucleation position is strongly depended on the impacting crystallographic orientation. A theory based on resolved shear stress is used to explain which slip planes the earliest-appearing dislocations prefer to nucleate on under different shock orientations.
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Affiliation(s)
- Xia Tian
- College of Mechanics and Materials, HoHai University, Nanjing, China
- * E-mail: (XT); (MX)
| | - Kaipeng Ma
- College of Mechanics and Materials, HoHai University, Nanjing, China
| | - Guangyu Ji
- College of Civil and Transportation Engineering, HoHai University, Nanjing, China
| | - Junzhi Cui
- LSEC, ICMSEC, Academy of Mathematics and Systems Science, CAS, Beijing, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yi Liao
- School of Mechanical Engineering, Southwest Petroleum University, Chengdu, China
| | - Meizhen Xiang
- Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Beijing, China
- * E-mail: (XT); (MX)
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16
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Reinknecht C, Riga A, Rivera J, Snyder DA. Patterns in Protein Flexibility: A Comparison of NMR "Ensembles", MD Trajectories, and Crystallographic B-Factors. Molecules 2021; 26:molecules26051484. [PMID: 33803249 PMCID: PMC7967184 DOI: 10.3390/molecules26051484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/18/2021] [Accepted: 02/28/2021] [Indexed: 11/16/2022] Open
Abstract
Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural “ensembles” first noted in the development of FindCore2 (previously called Expanded FindCore: DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, Proteins: Structure, Function, and Bioinformatics 82 (S2), 219–230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR “ensembles” capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations.
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17
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Abstract
Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
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Affiliation(s)
- Max T. B. Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
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18
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Hasegawa K, Baba S, Kawamura T, Yamamoto M, Kumasaka T. Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method. Acta Crystallogr D Struct Biol 2021; 77:300-312. [PMID: 33645534 PMCID: PMC7919407 DOI: 10.1107/s2059798321001686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/11/2021] [Indexed: 11/11/2023] Open
Abstract
Synchrotron serial crystallography (SSX) is an emerging data-collection method for micro-crystallography on synchrotron macromolecular (MX) crystallography beamlines. At SPring-8, the feasibility of the fixed-target approach was examined by collecting data using a 2D raster scan combined with goniometer rotation. Results at cryogenic temperatures demonstrated that rotation is effective for efficient data collection in SSX and the method was named serial synchrotron rotation crystallography (SS-ROX). To use this method for room-temperature (RT) data collection, a humid air and glue-coating (HAG) method was developed in which data were collected from polyvinyl alcohol-coated microcrystals fixed on a loop under humidity-controlled air. The performance and the RT data-collection strategy for micro-crystallography were evaluated using microcrystals of lysozyme. Although a change in unit-cell dimensions of up to 1% was observed during data collection, the impact on data quality was marginal. A comparison of data obtained at various absorbed doses revealed that absorbed doses of up to 210 kGy were tolerable in both global and local damage. Although this limits the number of photons deposited on each crystal, increasing the number of merged images improved the resolution. On the basis of these results, an equation was proposed that relates the achievable resolution to the total photon flux used to obtain a data set.
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Affiliation(s)
- Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kawamura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
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19
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Chen SW, Lu JY, Hung BY, Chiesa M, Tung PH, Lin JH, Yang TCK. Random lasers from photonic crystal wings of butterfly and moth for speckle-free imaging. Opt Express 2021; 29:2065-2076. [PMID: 33726407 DOI: 10.1364/oe.414334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Several biological membranes have been served as scattering materials of random lasers, but few of them include natural photonic crystals. Here, we propose and demonstrate a facile approach to fabricating high-performance biological photonic crystal random lasers, which is cost-effective and reproducible for mass production. As a benchmark, optical and lasing properties of dye-coated Lepidoptera wings, including Papilio ulysses butterfly and Chrysiridia rhipheus moth, are characterized and show a stable laser emission with a superior threshold of 0.016 mJ/cm2, as compared to previous studies. To deploy the proposed devices in practical implementation, we have applied the as-fabricated biological devices to bright speckle-free imaging applications, which is a more sustainable and more accessible imaging strategy.
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20
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Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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21
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Keiffer S, Carneiro MG, Hollander J, Kobayashi M, Pogoryelev D, Ab E, Theisgen S, Müller G, Siegal G. NMR in target driven drug discovery: why not? J Biomol NMR 2020; 74:521-529. [PMID: 32901320 PMCID: PMC7683447 DOI: 10.1007/s10858-020-00343-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/17/2020] [Indexed: 05/09/2023]
Abstract
No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.
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Affiliation(s)
| | | | | | | | | | - Eiso Ab
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands
| | | | - Gerhard Müller
- Gotham GmbH, Am Klopferspitz 19a, 82152, Martinsried, Germany
| | - Gregg Siegal
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands.
- Amsterdam Institute of Molecular and Life Sciences, Free University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
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22
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Zhou Y, Wang W, Salauddin NM, Lin L, You M, You S, Yuchi Z. Crystal structure of the N-terminal domain of ryanodine receptor from the honeybee, Apis mellifera. Insect Biochem Mol Biol 2020; 125:103454. [PMID: 32781205 DOI: 10.1016/j.ibmb.2020.103454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/24/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Ryanodine receptors (RyRs) are the molecular target of diamides, a new chemical class of insecticides. Diamide insecticides are used to control lepidopteran pests and were considered relatively safe for mammals and non-targeted beneficial insects, including honey bees. However, recent studies showed that exposure to diamides could cause long-lasting locomotor deficits of bees. Here we report the crystal structure of RyR N-terminal domain A (NTD-A) from the honeybee, Apis mellifera, at 2.5 Å resolution. It shows a similar overall fold as the RyR NTD-A from mammals and the diamondback moth (DBM), Plutella xylostella, and still several loops located at the inter-domain interfaces show insect-specific or bee-specific structural features. A potential insecticide-binding pocket formed by loop9 and loop13 is conserved in lepidopteran but different in both mammals and bees, making it a good candidate targeting site for the development of pest-selective insecticides. Furthermore, a conserved intra-domain disulfide bond was observed in both DBM and bee RyR NTD-A crystal structures, which explains their higher thermal stability compared to mammalian RyR NTD-A. This work provides a basis for the development of novel insecticides with better selectivity between pests and bees by targeting a distinct site on pest RyRs, which would be a promising strategy to overcome the current toxicity problem.
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Affiliation(s)
- Yuanyuan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Wenlan Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Nahiyan Mohammad Salauddin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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23
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Bücker R, Hogan-Lamarre P, Mehrabi P, Schulz EC, Bultema LA, Gevorkov Y, Brehm W, Yefanov O, Oberthür D, Kassier GH, Dwayne Miller RJ. Serial protein crystallography in an electron microscope. Nat Commun 2020; 11:996. [PMID: 32081905 PMCID: PMC7035385 DOI: 10.1038/s41467-020-14793-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.
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Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lindsey A Bultema
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Vision Systems, Hamburg University of Technology, Harburger Schlossstrasse 20, 21079, Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Günther H Kassier
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany.
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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24
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Latychevskaia T, Abrahams JP. Inelastic scattering and solvent scattering reduce dynamical diffraction in biological crystals. Acta Crystallogr B Struct Sci Cryst Eng Mater 2019; 75:523-531. [PMID: 32830710 PMCID: PMC6690131 DOI: 10.1107/s2052520619009661] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/07/2019] [Indexed: 05/05/2023]
Abstract
Multi-slice simulations of electron diffraction by three-dimensional protein crystals have indicated that structure solution would be severely impeded by dynamical diffraction, especially when crystals are more than a few unit cells thick. In practice, however, dynamical diffraction turned out to be less of a problem than anticipated on the basis of these simulations. Here it is shown that two scattering phenomena, which are usually omitted from multi-slice simulations, reduce the dynamical effect: solvent scattering reduces the phase differences within the exit beam and inelastic scattering followed by elastic scattering results in diffusion of dynamical scattering out of Bragg peaks. Thus, these independent phenomena provide potential reasons for the apparent discrepancy between theory and practice in protein electron crystallography.
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Affiliation(s)
- Tatiana Latychevskaia
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Jan Pieter Abrahams
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
- Biozentrum, Basel University, C-CINA, Mattenstrasse 26, Basel, 4058, Switzerland
- IBL, Leiden University, Sylviusweg 72, Leiden, 2333 BE, The Netherlands
- Correspondence e-mail:
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25
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Zatsepin NA, Li C, Colasurd P, Nannenga BL. The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals. Curr Opin Struct Biol 2019; 58:286-293. [PMID: 31345629 DOI: 10.1016/j.sbi.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022]
Abstract
In recent years, nano and microcrystals have emerged as a valuable source of high-resolution structural information owing to the invention of serial femtosecond crystallography (SFX) with X-ray free electron lasers and microcrystal electron diffraction (MicroED) using electron cryomicroscopes. Once considered useless for structure determination, nano/microcrystals now confer significant advantages for static and time-resolved structure determination from a wide variety of difficult-to-study targets. MicroED has been used to obtain sub-Ångstrom resolution maps in which hydrogen atoms can be clearly resolved from only a few nano/microcrystals, while SFX has been used to probe protein dynamics following reaction initiation on time scales from femtoseconds to minutes. We review these two complementary techniques and their abilities for high-resolution structure determination.
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Affiliation(s)
- Nadia A Zatsepin
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA
| | - Paige Colasurd
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA.
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26
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Checa AG, Yáñez-Ávila ME, González-Segura A, Varela-Feria F, Griesshaber E, Schmahl WW. Bending and branching of calcite laths in the foliated microstructure of pectinoidean bivalves occurs at coherent crystal lattice orientation. J Struct Biol 2019; 205:7-17. [PMID: 30576768 DOI: 10.1016/j.jsb.2018.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 11/19/2022]
Abstract
Foliated calcite is widely employed by some important pteriomorph bivalve groups as a construction material. It is made from calcite laths, which are inclined at a low angle to the internal shell surface, although their arrangement is different among the different groups. They are strictly ordered into folia in the anomiids, fully independent in scallops, and display an intermediate arrangement in oysters. Pectinids have particularly narrow laths characterized by their ability to change their growth direction by bending or winding, as well as to bifurcate and polyfurcate. Electron backscatter analysis indicates that the c-axes of laths are at a high, though variable, angle to the growth direction, and that the laths grow preferentially along the projection of an intermediate axis between two a-axes, although they can grow in any intermediate direction. Their main surfaces are not particular crystallographic faces. Analyses done directly on the lath surfaces demonstrate that, during the bending/branching events, all crystallographic axes remain invariant. The growth flexibility of pectinid laths makes them an excellent space-filling material, well suited to level off small irregularities of the shell growth surface. We hypothesize that the exceptional ability of laths to change their direction may be promoted by the mode of growth of biogenic calcite, from a precursor liquid phase induced by organic molecules.
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Affiliation(s)
- Antonio G Checa
- Departamento de Estratigrafía y Paleontología, Universidad de Granada, 18071 Granada, Spain; Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, 18100 Armilla, Spain.
| | - María E Yáñez-Ávila
- Departamento de Estratigrafía y Paleontología, Universidad de Granada, 18071 Granada, Spain
| | | | - Francisco Varela-Feria
- Centro de Investigación, Tecnología e Innovación, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Erika Griesshaber
- Department für Geo- und Umweltwissenschaften, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Wolfgang W Schmahl
- Department für Geo- und Umweltwissenschaften, Ludwig-Maximilians-Universität München, 80333 München, Germany
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27
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Oh J, Xu J, Chong J, Wang D. Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest. Methods 2019; 159-160:29-34. [PMID: 30797902 DOI: 10.1016/j.ymeth.2019.02.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 11/16/2022] Open
Abstract
Transcription, catalyzed by RNA polymerase II (Pol II) in eukaryotes, is the first step in gene expression. RNA Pol II is a 12-subunit enzyme complex regulated by many different transcription factors during transcription initiation, elongation, and termination. During elongation, Pol II encounters various types of obstacles that can cause transcriptional pausing and arrest. Through decades of research on transcriptional pausing, it is widely known that Pol II can distinguish between different types of obstacles by its active site. A major class of obstacles is DNA lesions. While some DNA lesions can cause transient transcriptional pausing, which can be bypassed by Pol II itself or with the help from other elongation factors, bulky DNA damage can cause prolonged transcriptional pausing and arrest, which signals for transcription coupled repair. Using biochemical and structural biology approaches, the outcomes of many different types of DNA lesions, DNA modifications, and DNA binding molecules to transcription were studied. In this mini review, we will describe the in vitro transcription assays with Pol II to investigate the impacts of various DNA lesions on transcriptional outcomes and the crystallization method of lesion-arrested Pol II complex. These methods can provide a general platform for the structural and biochemical analysis of Pol II transcriptional pausing and bypass mechanisms.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States.
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28
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Zheng P, Zhang M, Khan MH, Liu H, Jin Y, Yue J, Gao Y, Teng M, Zhu Z, Niu L. Crystallographic Analysis of the Catalytic Mechanism of Phosphopantothenoylcysteine Synthetase from Saccharomyces cerevisiae. J Mol Biol 2019; 431:764-776. [PMID: 30653991 DOI: 10.1016/j.jmb.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 11/20/2022]
Abstract
Phosphopantothenoylcysteine (PPC) synthetase (PPCS) catalyzes nucleoside triphosphate-dependent condensation reaction between 4'-phosphopantothenate (PPA) and l-cysteine to form PPC in CoA biosynthesis. The catalytic mechanism of PPCS has not been resolved yet. Coenzyme A biosynthesis protein 2 (Cab2) possesses activity of PPCS in Saccharomyces cerevisiae. Our enzymatic assays suggest that Cab2 could utilize both ATP and CTP to activate PPA in vitro. The results of isothermal titration calorimetry indicate that PPA, CTP, and ATP could bind to Cab2 individually, with PPA having the highest binding affinity. To provide further insight into the catalytic mechanism of Cab2, we determined the crystal structures of Cab2 and its complex with PPA, the reaction intermediate 4'-phosphopantothenoyl-CMP, the final reaction product PPC, and the product analogue phosphopantothenoylcystine. Except for PPA, all other ligands were generated in situ and present in the active-site pocket of Cab2. Structures of Cab2 in complex with ligands provide insight into substrates binding and its catalytic mechanism. Analysis of structures indicates that the carboxyl of PPA-moiety of ligands and the γ-amino group of Asn97 possess different conformations in these complex structures. The cysteine/cystine/serine selectivity assays for Cab2 indicate that the amino group rather than the thiol group of l-cysteine attacks the carbonyl of 4'-phosphopantothenoyl-CMP to form PPC. Based on structural and biochemical data, the catalytic mechanism of Cab2 was proposed for the first time.
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Affiliation(s)
- Peiyi Zheng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Mengying Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.
| | - Muhammad Hidayatullah Khan
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Hejun Liu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yuping Jin
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jian Yue
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yongxiang Gao
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.
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29
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Clabbers MTB, Gruene T, van Genderen E, Abrahams JP. Reducing dynamical electron scattering reveals hydrogen atoms. Acta Crystallogr A Found Adv 2019; 75:82-93. [PMID: 30575586 PMCID: PMC6302931 DOI: 10.1107/s2053273318013918] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/02/2018] [Indexed: 11/26/2022] Open
Abstract
Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure solution and its effects can only be modelled in specific cases. Dynamical scattering can be reduced experimentally by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometre-sized crystals from organic pharmaceuticals allow positional refinement of the hydrogen atoms, even whilst ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resolution.
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Affiliation(s)
- Max T. B. Clabbers
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Tim Gruene
- Paul Scherrer Institut (PSI), CH-5232 Villigen PSI, Switzerland
| | | | - Jan Pieter Abrahams
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Paul Scherrer Institut (PSI), CH-5232 Villigen PSI, Switzerland
- Leiden Institute of Biology, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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30
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Doak RB, Nass Kovacs G, Gorel A, Foucar L, Barends TRM, Grünbein ML, Hilpert M, Kloos M, Roome CM, Shoeman RL, Stricker M, Tono K, You D, Ueda K, Sherrell DA, Owen RL, Schlichting I. Crystallography on a chip - without the chip: sheet-on-sheet sandwich. Acta Crystallogr D Struct Biol 2018; 74:1000-1007. [PMID: 30289410 PMCID: PMC6173051 DOI: 10.1107/s2059798318011634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/16/2018] [Indexed: 11/29/2022] Open
Abstract
Crystallography chips are fixed-target supports consisting of a film (for example Kapton) or wafer (for example silicon) that is processed using semiconductor-microfabrication techniques to yield an array of wells or through-holes in which single microcrystals can be lodged for raster-scan probing. Although relatively expensive to fabricate, chips offer an efficient means of high-throughput sample presentation for serial diffraction data collection at synchrotron or X-ray free-electron laser (XFEL) sources. Truly efficient loading of a chip (one microcrystal per well and no wastage during loading) is nonetheless challenging. The wells or holes must match the microcrystal size of interest, requiring that a large stock of chips be maintained. Raster scanning requires special mechanical drives to step the chip rapidly and with micrometre precision from well to well. Here, a `chip-less' adaptation is described that essentially eliminates the challenges of loading and precision scanning, albeit with increased, yet still relatively frugal, sample usage. The device consists simply of two sheets of Mylar with the crystal solution sandwiched between them. This sheet-on-sheet (SOS) sandwich structure has been employed for serial femtosecond crystallography data collection with micrometre-sized crystals at an XFEL. The approach is also well suited to time-resolved pump-probe experiments, in particular for long time delays. The SOS sandwich enables measurements under XFEL beam conditions that would damage conventional chips, as documented here. The SOS sheets hermetically seal the sample, avoiding desiccation of the sample provided that the X-ray beam does not puncture the sheets. This is the case with a synchrotron beam but not with an XFEL beam. In the latter case, desiccation, setting radially outwards from each punched hole, sets lower limits on the speed and line spacing of the raster scan. It is shown that these constraints are easily accommodated.
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Affiliation(s)
- R. Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Alexander Gorel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Lutz Foucar
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marie Luise Grünbein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Mario Hilpert
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marco Kloos
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Christopher M. Roome
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Miriam Stricker
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Daehyun You
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, England
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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Tanaka I, Komatsuzaki N, Yue WX, Chatake T, Kusaka K, Niimura N, Miura D, Iwata T, Miyachi Y, Nukazuka G, Matsuda H. Cryoprotectant-free high-pressure cooling and dynamic nuclear polarization for more sensitive detection of hydrogen in neutron protein crystallography. Acta Crystallogr D Struct Biol 2018; 74:787-791. [PMID: 30082514 PMCID: PMC6079630 DOI: 10.1107/s2059798318005028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/27/2018] [Indexed: 11/21/2022] Open
Abstract
To improve the sensitivity of hydrogen detection using neutrons, a proton-polarization technique together with a high-pressure cooling method is necessary. The highest pressure (200 MPa) used in the experiment described here enabled relatively large protein crystals to be cooled without any cryoprotectants while retaining the protein structure, and it was confirmed that high-pressure-cooled crystals diffracted to nearly the same resolution as flash-cooled small crystals soaked with cryoprotectants. Dynamic nuclear polarization was used as a proton-polarization technique for protein crystals, and ∼300 mg polycrystalline protein doped with TEMPOL gave a maximum proton polarization of 22.3% at a temperature of 0.5 K in a 2.5 T magnetic field.
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Affiliation(s)
- Ichiro Tanaka
- College of Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan
| | - Naoya Komatsuzaki
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Wen-Xue Yue
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Toshiyuki Chatake
- Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan
| | - Daisuke Miura
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
| | - Takahiro Iwata
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
| | - Yoshiyuki Miyachi
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
| | - Genki Nukazuka
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
| | - Hiroki Matsuda
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
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Agirre J, van Raaij MJ. Carbohydrate structure hits the groove. Acta Crystallogr F Struct Biol Commun 2018; 74:441-442. [PMID: 30084392 PMCID: PMC6096480 DOI: 10.1107/s2053230x18010853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An introduction to the Acta Cryst. F special issue on glycoproteins and protein–carbohydrate complexes in which the contents, the current state of the field and the future of glycan structural biology are briefly discussed.
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Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Mark J. van Raaij
- Department of Molecular Structure, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, E-28049 Madrid, Spain
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Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol 2018; 74:531-544. [PMID: 29872004 PMCID: PMC6096492 DOI: 10.1107/s2059798318006551] [Citation(s) in RCA: 1486] [Impact Index Per Article: 247.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/27/2018] [Indexed: 02/23/2023] Open
Abstract
This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
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Affiliation(s)
- Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People’s Republic of China
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Randy J. Read
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Alexandre Urzhumtsev
- Faculté des Sciences et Technologies, Université de Lorraine, BP 239, 54506 Vandoeuvre-les-Nancy, France
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, California, USA
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Buss M, Geerds C, Patschkowski T, Niehaus K, Niemann HH. Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris. Acta Crystallogr F Struct Biol Commun 2018; 74:345-350. [PMID: 29870018 PMCID: PMC5987742 DOI: 10.1107/s2053230x18006933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/06/2018] [Indexed: 03/27/2024] Open
Abstract
Flavin-dependent halogenases can be used as biocatalysts because they regioselectively halogenate their substrates under mild reaction conditions. New halogenases with novel substrate specificities will add to the toolbox of enzymes available to organic chemists. HalX, the product of the xcc-b100_4193 gene, is a putative flavin-dependent halogenase from Xanthomonas campestris. The enzyme was recombinantly expressed and crystallized in order to aid in identifying its hitherto unknown substrate. Native data collected to a resolution of 2.5 Å showed indications of merohedral twinning in a hexagonal lattice. Attempts to solve the phase problem by molecular replacement failed. Here, a detailed analysis of the suspected twinning is presented. It is most likely that the crystals are trigonal (point group 3) and exhibit perfect hemihedral twinning so that they appear to be hexagonal (point group 6). As there are several molecules in the asymmetric unit, noncrystallographic symmetry may complicate twinning analysis and structure determination.
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Affiliation(s)
- Maren Buss
- Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Christina Geerds
- Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Thomas Patschkowski
- Faculty of Biology, Proteome and Metabolome Research, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Centre of Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Faculty of Biology, Proteome and Metabolome Research, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Centre of Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Hartmut H. Niemann
- Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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Clabbers MTB, Gruene T, Parkhurst JM, Abrahams JP, Waterman DG. Electron diffraction data processing with DIALS. Acta Crystallogr D Struct Biol 2018; 74:506-518. [PMID: 29872002 PMCID: PMC6096487 DOI: 10.1107/s2059798318007726] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/23/2018] [Indexed: 03/28/2023] Open
Abstract
Electron diffraction is a relatively novel alternative to X-ray crystallography for the structure determination of macromolecules from three-dimensional nanometre-sized crystals. The continuous-rotation method of data collection has been adapted for the electron microscope. However, there are important differences in geometry that must be considered for successful data integration. The wavelength of electrons in a TEM is typically around 40 times shorter than that of X-rays, implying a nearly flat Ewald sphere, and consequently low diffraction angles and a high effective sample-to-detector distance. Nevertheless, the DIALS software package can, with specific adaptations, successfully process continuous-rotation electron diffraction data. Pathologies encountered specifically in electron diffraction make data integration more challenging. Errors can arise from instrumentation, such as beam drift or distorted diffraction patterns from lens imperfections. The diffraction geometry brings additional challenges such as strong correlation between lattice parameters and detector distance. These issues are compounded if calibration is incomplete, leading to uncertainty in experimental geometry, such as the effective detector distance and the rotation rate or direction. Dynamic scattering, absorption, radiation damage and incomplete wedges of data are additional factors that complicate data processing. Here, recent features of DIALS as adapted to electron diffraction processing are shown, including diagnostics for problematic diffraction geometry refinement, refinement of a smoothly varying beam model and corrections for distorted diffraction images. These novel features, combined with the existing tools in DIALS, make data integration and refinement feasible for electron crystallography, even in difficult cases.
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Affiliation(s)
- Max T. B. Clabbers
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tim Gruene
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - James M. Parkhurst
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Jan Pieter Abrahams
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - David G. Waterman
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
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Liu CH, Chen YT, Hou MH, Hu NJ, Chen CS, Shaw JF. Crystallographic analysis of the Staphylococcus epidermidis lipase involved in esterification in aqueous solution. Acta Crystallogr F Struct Biol Commun 2018; 74:351-354. [PMID: 29870019 PMCID: PMC5987743 DOI: 10.1107/s2053230x18006775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/03/2018] [Indexed: 11/10/2022] Open
Abstract
The Staphylococcus epidermidis lipase (SeLip, GehC) can be used in flavour-compound production via esterification in aqueous solution. This study reports the crystallization and crystallographic analysis of recombinant GehC (rGehC; Lys303-Lys688) with a molecular weight of 43 kDa. rGehC was crystallized at 293 K using PEG 10 000 as a precipitant, and a 99.9% complete native data set was collected from a cooled crystal at 77 K to a resolution of 1.9 Å with an overall Rmerge value of 7.3%. The crystals were orthorhombic and belonged to space group P212121, with unit-cell parameters a = 42.07, b = 59.31, c = 171.30 Å, α = β = γ = 90°. Solvent-content calculations suggest that there is likely to be one lipase subunit in the asymmetric unit.
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Affiliation(s)
- Cheng-Huan Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Road, South District, Taichung City 402, Taiwan
| | - Yu-Ting Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 145 Xingda Road, South District, Taichung City 402, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 145 Xingda Road, South District, Taichung City 402, Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, 145 Xingda Road, South District, Taichung City 402, Taiwan
| | - Chin-Shuh Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Road, South District, Taichung City 402, Taiwan
| | - Jei-Fu Shaw
- Department of Biological Science and Technology, I-Shou University, No. 1, Section 1, Syuecheng Road, Dashu District, Kaohsiung City 84001, Taiwan
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Abstract
G protein-coupled receptors (GPCRs) represent a large superfamily of membrane proteins that mediate cell signaling and regulate a variety of physiological processes in the human body. Structure-function studies of this superfamily were enabled a decade ago by multiple breakthroughs in technology that included receptor stabilization, crystallization in a membrane environment, and microcrystallography. The recent emergence of X-ray free-electron lasers (XFELs) has further accelerated structural studies of GPCRs and other challenging proteins by overcoming radiation damage and providing access to high-resolution structures and dynamics using micrometer-sized crystals. Here, we summarize key technology advancements and major milestones of GPCR research using XFELs and provide a brief outlook on future developments in the field.
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Affiliation(s)
- Benjamin Stauch
- Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; ,
| | - Vadim Cherezov
- Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; ,
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Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B. Detect, correct, retract: How to manage incorrect structural models. FEBS J 2018; 285:444-466. [PMID: 29113027 PMCID: PMC5799025 DOI: 10.1111/febs.14320] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022]
Abstract
The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe. The occurrence of severe errors or gross misinterpretations raises fundamental questions: Why do such aberrations emerge in the first place? How did they evade the sophisticated validation procedures which often produce clear and dire warnings, and why were severe errors not noticed by the depositors themselves, their supervisors, referees and editors? Once detected, what can be done to either correct, improve or eliminate such models? How do incorrect models affect the underlying claims or biomedical hypotheses they were intended, but failed, to support? What is the long-range effect of the propagation of such errors? And finally, what mechanisms can be envisioned to restore the validity of the scientific record and, if necessary, retract publications that are clearly invalidated by the lack of experimental evidence? We suggest that cognitive bias and flawed epistemology are likely at the root of the problem. By using examples from the published literature and from public repositories such as the Protein Data Bank, we provide case summaries to guide correction or improvement of structural models. When strong claims are unsustainable because of a deficient crystallographic model, removal of such a model and even retraction of the affected publication are necessary to restore the integrity of the scientific record.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Robyn Stanfield
- Department of Structural and Computational Biology, BCC206, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, Poznan, 61-614, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, 61-704, Poland
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Bernhard Rupp
- CVMO, k.-k.Hofkristallamt, 991 Audrey Place, Vista, CA, 92084, USA
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstr. 41, Innsbruck, 6020, Austria
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Shen Y, Dana H, Abdelfattah AS, Patel R, Shea J, Molina RS, Rawal B, Rancic V, Chang YF, Wu L, Chen Y, Qian Y, Wiens MD, Hambleton N, Ballanyi K, Hughes TE, Drobizhev M, Kim DS, Koyama M, Schreiter ER, Campbell RE. A genetically encoded Ca 2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578. BMC Biol 2018; 16:9. [PMID: 29338710 PMCID: PMC5771076 DOI: 10.1186/s12915-018-0480-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/03/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetically encoded calcium ion (Ca2+) indicators (GECIs) are indispensable tools for measuring Ca2+ dynamics and neuronal activities in vitro and in vivo. Red fluorescent protein (RFP)-based GECIs have inherent advantages relative to green fluorescent protein-based GECIs due to the longer wavelength light used for excitation. Longer wavelength light is associated with decreased phototoxicity and deeper penetration through tissue. Red GECI can also enable multicolor visualization with blue- or cyan-excitable fluorophores. RESULTS Here we report the development, structure, and validation of a new RFP-based GECI, K-GECO1, based on a circularly permutated RFP derived from the sea anemone Entacmaea quadricolor. We have characterized the performance of K-GECO1 in cultured HeLa cells, dissociated neurons, stem-cell-derived cardiomyocytes, organotypic brain slices, zebrafish spinal cord in vivo, and mouse brain in vivo. CONCLUSION K-GECO1 is the archetype of a new lineage of GECIs based on the RFP eqFP578 scaffold. It offers high sensitivity and fast kinetics, similar or better than those of current state-of-the-art indicators, with diminished lysosomal accumulation and minimal blue-light photoactivation. Further refinements of the K-GECO1 lineage could lead to further improved variants with overall performance that exceeds that of the most highly optimized red GECIs.
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Affiliation(s)
- Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Hod Dana
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
- Present address: Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 4195, USA
| | - Ahmed S Abdelfattah
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Present address: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Ronak Patel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Jamien Shea
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Rosana S Molina
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Bijal Rawal
- Department of Physiology, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Vladimir Rancic
- Department of Physiology, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Yu-Fen Chang
- LumiSTAR Biotechnology Incorporation, Nangang District, Taipei City, 115, Taiwan
| | - Lanshi Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yingche Chen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yong Qian
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Matthew D Wiens
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Nathan Hambleton
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Thomas E Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Mikhail Drobizhev
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Douglas S Kim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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Inokoshi M, Shimizu H, Nozaki K, Takagaki T, Yoshihara K, Nagaoka N, Zhang F, Vleugels J, Van Meerbeek B, Minakuchi S. Crystallographic and morphological analysis of sandblasted highly translucent dental zirconia. Dent Mater 2018; 34:508-518. [PMID: 29325861 DOI: 10.1016/j.dental.2017.12.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/22/2017] [Accepted: 12/20/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To assess the influence of alumina sandblasting on four highly translucent dental zirconia grades. METHODS Fully sintered zirconia disk-shaped specimens (15-mm diameter; 0.5-mm thickness) of four highly translucent yttria partially stabilized zirconia (Y-PSZ) grades (KATANA HT, KATANA STML, KATANA UTML, Kuraray Noritake; Zpex Smile, Tosoh) were sandblasted with 50-μm alumina (Al2O3) sand (Kulzer) or left 'as-sintered' (control) (n=5). For each zirconia grade, the translucency was measured using a colorimeter. Surface roughness was assessed using 3D confocal laser microscopy, upon which the zirconia grades were statistically compared for surface roughness using a Kruskal-Wallis test (n=10). X-ray diffraction (XRD) with Rietveld analysis was used to assess the zirconia-phase composition. Micro-Raman spectroscopy was used to assess the potentially induced residual stress. RESULTS The translucency of KATANA UTML was the highest (36.7±1.8), whereas that of KATANA HT was the lowest (29.5±0.9). The 'Al2O3-sandblasted' and 'as-sintered' zirconia revealed comparable surface-roughness Sa values. Regarding zirconia-phase composition, XRD with Rietveld analysis revealed that the 'as-sintered' KATANA UTML contained the highest amount of cubic zirconia (c-ZrO2) phase (71wt%), while KATANA HT had the lowest amount of c-ZrO2 phase (41wt%). KATANA STML and Zpex Smile had a comparable zirconia-phase composition (60wt% c-ZrO2 phase). After Al2O3-sandblasting, a significant amount (over 25wt%) of rhombohedral zirconia (r-ZrO2) phase was detected for all highly translucent zirconia grades. SIGNIFICANCE Al2O3-sandblasting did not affect the surface roughness of the three highly translucent Y-PSZ zirconia grades, but it changed its phase composition.
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Affiliation(s)
- Masanao Inokoshi
- Gerodontology and Oral Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan.
| | - Haruki Shimizu
- Gerodontology and Oral Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Kosuke Nozaki
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Japan
| | - Tomohiro Takagaki
- Department of Cariology and Operative Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Kumiko Yoshihara
- Center for Innovative Clinical Medicine, Okayama University Hospital, Japan
| | - Noriyuki Nagaoka
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Japan
| | - Fei Zhang
- KU Leuven (University of Leuven), Department of Materials Engineering, Belgium; KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven, Dentistry, Belgium
| | - Jozef Vleugels
- KU Leuven (University of Leuven), Department of Materials Engineering, Belgium
| | - Bart Van Meerbeek
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven, Dentistry, Belgium
| | - Shunsuke Minakuchi
- Gerodontology and Oral Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
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Shao YT, Zuo JM. Nanoscale symmetry fluctuations in ferroelectric barium titanate, BaTiO 3. Acta Crystallogr B Struct Sci Cryst Eng Mater 2017; 73:708-714. [PMID: 28762980 DOI: 10.1107/s2052520617008496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
Crystal charge density is a ground-state electronic property. In ferroelectrics, charge is strongly influenced by lattice and vice versa, leading to a range of interesting temperature-dependent physical properties. However, experimental determination of charge in ferroelectrics is challenging because of the formation of ferroelectric domains. Demonstrated here is the scanning convergent-beam electron diffraction (SCBED) technique that can be simultaneously used for imaging ferroelectric domains and identifying crystal symmetry and its fluctuations. Results from SCBED confirm the acentric tetragonal, orthorhombic and rhombohedral symmetry for the ferroelectric phases of BaTiO3. However, the symmetry is not homogeneous; regions of a few tens of nanometres retaining almost perfect symmetry are interspersed in regions of lower symmetry. While the observed highest symmetry is consistent with the displacive model of ferroelectric phase transitions in BaTiO3, the observed nanoscale symmetry fluctuations are consistent with the predictions of the order-disorder phase-transition mechanism.
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Affiliation(s)
- Yu Tsun Shao
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jian Min Zuo
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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42
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Naitow H, Matsuura Y, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Tanaka R, Tanaka T, Sugahara M, Kobayashi J, Nango E, Iwata S, Kunishima N. Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation. Acta Crystallogr D Struct Biol 2017; 73:702-709. [PMID: 28777085 PMCID: PMC5571745 DOI: 10.1107/s2059798317008919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/14/2017] [Indexed: 01/09/2023] Open
Abstract
Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.
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Affiliation(s)
- Hisashi Naitow
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- XFEL Research and Development Division, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yasumasa Joti
- XFEL Research and Development Division, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Kameshima
- XFEL Research and Development Division, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takaki Hatsui
- XFEL Research and Development Division, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makina Yabashi
- XFEL Research and Development Division, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- SACLA Science Research Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tomoyuki Tanaka
- SACLA Science Research Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Michihiro Sugahara
- SACLA Science Research Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Jun Kobayashi
- SACLA Science Research Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Eriko Nango
- SACLA Science Research Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - So Iwata
- SACLA Science Research Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Naoki Kunishima
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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43
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Johansson LC, Stauch B, Ishchenko A, Cherezov V. A Bright Future for Serial Femtosecond Crystallography with XFELs. Trends Biochem Sci 2017; 42:749-762. [PMID: 28733116 DOI: 10.1016/j.tibs.2017.06.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022]
Abstract
X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies. Here, we review the latest developments in instrumentation, sample delivery, data analysis, crystallization methods, and applications of SFX to important biological questions, and conclude with brief insights into the bright future of structural biology using XFELs.
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Affiliation(s)
- Linda C Johansson
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Benjamin Stauch
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA.
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44
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Greenwood AI, Clay MC, Rienstra CM. 31P-dephased, 13C-detected REDOR for NMR crystallography at natural isotopic abundance. J Magn Reson 2017; 278:8-17. [PMID: 28319851 PMCID: PMC5478420 DOI: 10.1016/j.jmr.2017.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/21/2017] [Accepted: 02/26/2017] [Indexed: 05/14/2023]
Abstract
Typically, the process of NMR-based structure determination relies on accurately measuring a large number of internuclear distances to serve as restraints for simulated annealing calculations. In solids, the rotational-echo double-resonance (REDOR) experiment is a widely used approach to determine heteronuclear dipolar couplings corresponding to distances usually in the range of 1.5-8Å. A challenge in the interpretation of REDOR data is the degeneracy of symmetric subunits in an oligomer or equivalent molecules in a crystal lattice, which produce REDOR trajectories that depend explicitly on two or more distances instead of one. This degeneracy cannot be overcome by either spin dilution (for molecules containing 31P, 19F and other highly abundant nuclei) or selective pulses (in the case where there is chemical shift degeneracy). For small, crystalline molecules, such as phosphoserine, we demonstrate that as many as five inter-molecular distances must be considered to model 31P-dephased REDOR data accurately. We report excellent agreement between simulation and experiment once lattice couplings, 31P chemical shift anisotropy, and radio-frequency field inhomogeneity are all taken into account. We also discuss the systematic inaccuracies that may result from approximations that consider only the initial slope of the REDOR trajectory and/or that utilize a two- or three-spin system. Furthermore, we demonstrate the applicability of 31P-dephased REDOR for validation or refinement of candidate crystal structures and show that this approach is especially informative for NMR crystallography of 31P-containing molecules.
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Affiliation(s)
- Alexander I Greenwood
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mary C Clay
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chad M Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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45
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McGregor N, Yin V, Tung CC, Van Petegem F, Brumer H. Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases. Plant J 2017; 89:651-670. [PMID: 27859885 PMCID: PMC5315667 DOI: 10.1111/tpj.13421] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/14/2016] [Accepted: 11/04/2016] [Indexed: 05/22/2023]
Abstract
The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species.
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Affiliation(s)
- Nicholas McGregor
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Victor Yin
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ching-Chieh Tung
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
- Department of Botany, University of British Columbia, 6270
University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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Abstract
This chapter provides a review of different advanced methods that help to increase the success rate of a crystallization project, by producing larger and higher quality single crystals for determination of macromolecular structures by crystallographic methods. For this purpose, the chapter is divided into three parts. The first part deals with the fundamentals for understanding the crystallization process through different strategies based on physical and chemical approaches. The second part presents new approaches involved in more sophisticated methods not only for growing protein crystals but also for controlling the size and orientation of crystals through utilization of electromagnetic fields and other advanced techniques. The last section deals with three different aspects: the importance of microgravity, the use of ligands to stabilize proteins, and the use of microfluidics to obtain protein crystals. All these advanced methods will allow the readers to obtain suitable crystalline samples for high-resolution X-ray and neutron crystallography.
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Affiliation(s)
- Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Cd.Mx., Mexico City, 04510, Mexico.
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47
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Larsen AS, Rantanen J, Johansson KE. Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations. J Pharm Sci 2016; 106:348-355. [PMID: 27863805 DOI: 10.1016/j.xphs.2016.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/27/2016] [Accepted: 10/11/2016] [Indexed: 11/20/2022]
Abstract
Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration rate, different dehydrated structures were observed. Removing all water molecules immediately and removing water relatively fast (10 water molecules/10 ps) resulted in an amorphous system, whereas relatively slow computational dehydration (3 water molecules/10 ps) resulted in a crystalline anhydrate. The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure could represent a kinetically trapped dehydration intermediate.
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Affiliation(s)
- Anders S Larsen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Jukka Rantanen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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48
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Axenopoulos A, Rafailidis D, Papadopoulos G, Houstis EN, Daras P. Similarity Search of Flexible 3D Molecules Combining Local and Global Shape Descriptors. IEEE/ACM Trans Comput Biol Bioinform 2016; 13:954-970. [PMID: 26561479 DOI: 10.1109/tcbb.2015.2498553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this paper, a framework for shape-based similarity search of 3D molecular structures is presented. The proposed framework exploits simultaneously the discriminative capabilities of a global, a local, and a hybrid local-global shape feature to produce a geometric descriptor that achieves higher retrieval accuracy than each feature does separately. Global and hybrid features are extracted using pairwise computations of diffusion distances between the points of the molecular surface, while the local feature is based on accumulating pairwise relations among oriented surface points into local histograms. The local features are integrated into a global descriptor vector using the bag-of-features approach. Due to the intrinsic property of its constituting shape features to be invariant to articulations of the 3D objects, the framework is appropriate for similarity search of flexible 3D molecules, while at the same time it is also accurate in retrieving rigid 3D molecules. The proposed framework is evaluated in flexible and rigid shape matching of 3D protein structures as well as in shape-based virtual screening of large ligand databases with quite promising results.
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49
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Ginn HM, Roedig P, Kuo A, Evans G, Sauter NK, Ernst O, Meents A, Mueller-Werkmeister H, Miller RJD, Stuart DI. TakeTwo: an indexing algorithm suited to still images with known crystal parameters. Acta Crystallogr D Struct Biol 2016; 72:956-65. [PMID: 27487826 PMCID: PMC4973211 DOI: 10.1107/s2059798316010706] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/01/2016] [Indexed: 11/10/2022] Open
Abstract
The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information. On the other hand, shots from both X-ray free-electron lasers and serial synchrotron crystallography experiments are still images, in which the few three-dimensional data available arise only from the curvature of the Ewald sphere. Traditional synchrotron crystallography methods are thus less well suited to still image data processing. Here, a new indexing method is presented with the aim of maximizing information use from a still image given the known unit-cell dimensions and space group. Efficacy for cubic, hexagonal and orthorhombic space groups is shown, and for those showing some evidence of diffraction the indexing rate ranged from 90% (hexagonal space group) to 151% (cubic space group). Here, the indexing rate refers to the number of lattices indexed per image.
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Affiliation(s)
- Helen Mary Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, England
| | - Philip Roedig
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anling Kuo
- Department of Biochemistry, University of Toronto, King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Gwyndaf Evans
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, England
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Oliver Ernst
- Department of Biochemistry, University of Toronto, King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Alke Meents
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henrike Mueller-Werkmeister
- Department of Biochemistry, University of Toronto, King’s College Circle, Toronto, ON M5S 1A8, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
- Departments of Physics and Chemistry, University of Toronto, 80 St George Street, Toronto, ON M5S 1H6, Canada
| | - R. J. Dwayne Miller
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
- Departments of Physics and Chemistry, University of Toronto, 80 St George Street, Toronto, ON M5S 1H6, Canada
| | - David Ian Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, England
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50
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Abstract
Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015; Shi et al., 2016; Shi, Nannenga, Iadanza, & Gonen, 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment.
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Affiliation(s)
- J A Rodriguez
- UCLA-DOE Institute, University of California, Los Angeles CA, United States
| | - T Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn VA, United States.
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