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Acehan D, Spoth KA, Budziszewski GR, Snell ME, Campomizzi CS, Lynch ML, Bowman SE. Reaching the potential of electron diffraction. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:102007. [PMID: 39055735 PMCID: PMC11271257 DOI: 10.1016/j.xcrp.2024.102007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Microcrystal electron diffraction (MicroED) is an emerging structural technique in which submicron crystals are used to generate diffraction data for structural studies. Structures allow for the study of molecular-level architecture and drive hypotheses about modes of action, mechanisms, dynamics, and interactions with other molecules. Combining cryoelectron microscopy (cryo-EM) instrumentation with crystallographic techniques, MicroED has led to three-dimensional structural models of small molecules, peptides, and proteins and has generated tremendous interest due to its ability to use vanishingly small crystals. In this perspective, we describe the current state of the field for MicroED methodologies, including making and detecting crystals of the appropriate size for the technique, as well as ways to best handle and characterize these crystals. Our perspective provides insight into ways to unlock the full range of potential for MicroED to access previously intractable samples and describes areas of future development.
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Affiliation(s)
- Devrim Acehan
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
- University of Rochester, School of Medicine and Dentistry, Department of Biochemistry and Biophysics, Rochester, NY 14642, USA
| | | | | | | | | | - Miranda L. Lynch
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
| | - Sarah E.J. Bowman
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Biochemistry, Buffalo, NY 14203, USA
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2
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Lynch ML, Snell ME, Potter SA, Snell EH, Bowman SEJ. 20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening. Acta Crystallogr D Struct Biol 2023; 79:198-205. [PMID: 36876429 PMCID: PMC9986797 DOI: 10.1107/s2059798323001274] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 02/11/2023] [Indexed: 03/01/2023] Open
Abstract
Diffraction-based structural methods contribute a large fraction of the biomolecular structural models available, providing a critical understanding of macromolecular architecture. These methods require crystallization of the target molecule, which remains a primary bottleneck in crystal-based structure determination. The National High-Throughput Crystallization Center at Hauptman-Woodward Medical Research Institute has focused on overcoming obstacles to crystallization through a combination of robotics-enabled high-throughput screening and advanced imaging to increase the success of finding crystallization conditions. This paper will describe the lessons learned from over 20 years of operation of our high-throughput crystallization services. The current experimental pipelines, instrumentation, imaging capabilities and software for image viewing and crystal scoring are detailed. New developments in the field and opportunities for further improvements in biomolecular crystallization are reflected on.
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Affiliation(s)
- Miranda L Lynch
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - M Elizabeth Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Stephen A Potter
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Sarah E J Bowman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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3
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Razumtcev A, Li M, Rong J, Teng CC, Pfluegl C, Taylor LS, Simpson GJ. Label-Free Autofluorescence-Detected Mid-Infrared Photothermal Microscopy of Pharmaceutical Materials. Anal Chem 2022; 94:6512-6520. [PMID: 35446548 DOI: 10.1021/acs.analchem.1c05504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Label-free autofluorescence-detected photothermal mid-IR (AF-PTIR) microscopy is demonstrated experimentally and applied to test the distribution of active pharmaceutical ingredients (APIs) in a mixture containing representative pharmaceutical excipients. Two-photon excited UV-fluorescence (TPE-UVF) supports autofluorescence of native aromatic moieties using visible-light optics. Thermal modulation of the fluorescence quantum yield serves to report on infrared absorption, enabling infrared spectroscopy in the fingerprint region with a spatial resolution dictated by fluorescence. AF-PTIR provides high selectivity and sensitivity in image contrast for aromatic APIs, complementing broadly applicable optical photothermal IR (O-PTIR) microscopy based on photothermal modulation of refractive index/scattering. Mapping the API distribution is critical in designing processes for powdered dosage form manufacturing, with high spatial variance potentially producing variability in both delivered dosage and product efficacy. The ubiquity of aromatic moieties within API candidates suggests the viability of AF-PTIR in combination with O-PTIR to improve the confidence of chemical classification in spatially heterogeneous dosage forms.
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Affiliation(s)
- Aleksandr Razumtcev
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Minghe Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jiayue Rong
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chu C Teng
- Pendar Technologies, 30 Spinelli Place, Cambridge, Massachusetts 02138, United States
| | - Christian Pfluegl
- Pendar Technologies, 30 Spinelli Place, Cambridge, Massachusetts 02138, United States
| | - Lynne S Taylor
- Physical and Industrial Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Garth J Simpson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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4
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Klijn ME, Hubbuch J. Application of ultraviolet, visible, and infrared light imaging in protein-based biopharmaceutical formulation characterization and development studies. Eur J Pharm Biopharm 2021; 165:319-336. [PMID: 34052429 DOI: 10.1016/j.ejpb.2021.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/29/2021] [Accepted: 05/12/2021] [Indexed: 01/10/2023]
Abstract
Imaging is increasingly more utilized as analytical technology in biopharmaceutical formulation research, with applications ranging from subvisible particle characterization to thermal stability screening and residual moisture analysis. This review offers a comprehensive overview of analytical imaging for scientists active in biopharmaceutical formulation research and development, where it presents the unique information provided by the ultraviolet (UV), visible (Vis), and infrared (IR) sections in the electromagnetic spectrum. The main body of this review consists of an outline of UV, Vis, and IR imaging techniques for several (bio)physical properties that are commonly determined during protein-based biopharmaceutical formulation characterization and development studies. The review concludes with a future perspective of applied imaging within the field of biopharmaceutical formulation research.
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Affiliation(s)
- Marieke E Klijn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, the Netherlands.
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
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5
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Li C, Ding C, Li M, Rong J, Florian H, Simpson G. Depth-of-field extension in optical imaging for rapid crystal screening. Acta Crystallogr D Struct Biol 2021; 77:463-470. [PMID: 33825707 PMCID: PMC8025887 DOI: 10.1107/s2059798321000097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/04/2021] [Indexed: 11/10/2022] Open
Abstract
The depth of field (DoF) was extended 2.8-fold to achieve rapid crystal screening by retrofitting a custom-designed micro-retarder array (µRA) in the optical beam path of a nonlinear optical microscope. The merits of the proposed strategy for DoF enhancement were assessed in applications of second-harmonic generation imaging of protein crystals. It was found that DoF extension increased the number of crystals detected while simultaneously reducing the number of `z-slices' required for screening. Experimental measurements of the wavelength-dependence of the extended DoF were in excellent agreement with theoretical predictions. These results provide a simple and broadly applicable approach to increase the throughput of existing nonlinear optical imaging methods for protein crystal screening.
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Affiliation(s)
- Chen Li
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Changqin Ding
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Minghe Li
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Jiayue Rong
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Hilary Florian
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Garth Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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6
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Holleman ET, Duguid E, Keefe LJ, Bowman SEJ. Polo: an open-source graphical user interface for crystallization screening. J Appl Crystallogr 2021; 54:673-679. [PMID: 33953660 PMCID: PMC8056757 DOI: 10.1107/s1600576721000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 01/04/2021] [Indexed: 11/29/2022] Open
Abstract
A multi-platform open-source Python-based graphical user interface has been developed to provide access to automated classification and data management tools for biomolecular crystallization screening. Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute (HWI) to efficiently inspect their crystallization experiments. Polo aims to increase efficiency, reducing time spent manually reviewing crystallization images, and to improve the potential of identifying positive crystallization conditions. Polo provides a streamlined one-click graphical interface for the Machine Recognition of Crystallization Outcomes (MARCO) convolutional neural network for automated image classification, as well as powerful tools to view and score crystallization images, to compare crystallization conditions, and to facilitate collaborative review of crystallization screening results. Crystallization images need not have been captured at HWI to utilize Polo’s basic functionality. Polo is free to use and modify for both academic and commercial use under the terms of the copyleft GNU General Public License v3.0.
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Affiliation(s)
- Ethan T Holleman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Erica Duguid
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.,Industrial Macromolecular Crystallography Association Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Lisa J Keefe
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.,Industrial Macromolecular Crystallography Association Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Sarah E J Bowman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.,Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo, Buffalo, NY 14023, USA
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7
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Kato R, Hiraki M, Yamada Y, Tanabe M, Senda T. A fully automated crystallization apparatus for small protein quantities. Acta Crystallogr F Struct Biol Commun 2021; 77:29-36. [PMID: 33439153 PMCID: PMC7805554 DOI: 10.1107/s2053230x20015514] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/23/2020] [Indexed: 12/05/2022] Open
Abstract
In 2003, a fully automated protein crystallization and monitoring system (PXS) was developed to support the structural genomics projects that were initiated in the early 2000s. In PXS, crystallization plates were automatically set up using the vapor-diffusion method, transferred to incubators and automatically observed according to a pre-set schedule. The captured images of each crystallization drop could be monitored through the internet using a web browser. While the screening throughput of PXS was very high, the demands of users have gradually changed over the ensuing years. To study difficult proteins, it has become important to screen crystallization conditions using small amounts of proteins. Moreover, membrane proteins have become one of the main targets for X-ray crystallography. Therefore, to meet the evolving demands of users, PXS was upgraded to PXS2. In PXS2, the minimum volume of the dispenser is reduced to 0.1 µl to minimize the amount of sample, and the resolution of the captured images is increased to five million pixels in order to observe small crystallization drops in detail. In addition to the 20°C incubators, a 4°C incubator was installed in PXS2 because crystallization results may vary with temperature. To support membrane-protein crystallization, PXS2 includes a procedure for the bicelle method. In addition, the system supports a lipidic cubic phase (LCP) method that uses a film sandwich plate and that was specifically designed for PXS2. These improvements expand the applicability of PXS2, reducing the bottleneck of X-ray protein crystallography.
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Affiliation(s)
- Ryuichi Kato
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Masahiko Hiraki
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Yusuke Yamada
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Mikio Tanabe
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
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8
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Polovinkin V, Khakurel K, Babiak M, Angelov B, Schneider B, Dohnalek J, Andreasson J, Hajdu J. Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures. J Appl Crystallogr 2020; 53:1416-1424. [PMID: 33304220 PMCID: PMC7710488 DOI: 10.1107/s1600576720013096] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/27/2020] [Indexed: 12/26/2022] Open
Abstract
Electron diffraction experiments on crystals of membrane proteins grown in lipidic mesophases have not been possible owing to a thick layer of viscous crystallization medium around the crystals. Here it is shown that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can remove the viscous layer, and high-quality electron diffraction on a FIB-milled lamella of a bacteriorhodopsin 3D crystal is demonstrated. Electron crystallography of sub-micrometre-sized 3D protein crystals has emerged recently as a valuable field of structural biology. In meso crystallization methods, utilizing lipidic mesophases, particularly lipidic cubic phases (LCPs), can produce high-quality 3D crystals of membrane proteins (MPs). A major step towards realizing 3D electron crystallography of MP crystals, grown in meso, is to demonstrate electron diffraction from such crystals. The first task is to remove the viscous and sticky lipidic matrix that surrounds the crystals without damaging the crystals. Additionally, the crystals have to be thin enough to let electrons traverse them without significant multiple scattering. In the present work, the concept that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can be used to remove excess host lipidic mesophase matrix is experimentally verified, and then the crystals are thinned to a thickness suitable for electron diffraction. In this study, bacteriorhodopsin (BR) crystals grown in a lipidic cubic mesophase of monoolein were used as a model system. LCP from a part of a hexagon-shaped plate-like BR crystal (∼10 µm in thickness and ∼70 µm in the longest dimension), which was flash-frozen in liquid nitrogen, was milled away with a gallium FIB under cryogenic conditions, and a part of the crystal itself was thinned into a ∼210 nm-thick lamella with the ion beam. The frozen sample was then transferred into an electron cryo-microscope, and a nanovolume of ∼1400 × 1400 × 210 nm of the BR lamella was exposed to 200 kV electrons at a fluence of ∼0.06 e Å−2. The resulting electron diffraction peaks were detected beyond 2.7 Å resolution (with an average peak height to background ratio of >2) by a CMOS-based Ceta 16M camera. The results demonstrate that cryo-FIB milling produces high-quality lamellae from crystals grown in lipidic mesophases and pave the way for 3D electron crystallography on crystals grown or embedded in highly viscous media.
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Affiliation(s)
- Vitaly Polovinkin
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Krishna Khakurel
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Michal Babiak
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/4, 62500 Brno, Czech Republic
| | - Borislav Angelov
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
| | - Jan Dohnalek
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
| | - Jakob Andreasson
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Janos Hajdu
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic.,Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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9
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Cheng QD, Chung HY, Schubert R, Chia SH, Falke S, Mudogo CN, Kärtner FX, Chang G, Betzel C. Protein-crystal detection with a compact multimodal multiphoton microscope. Commun Biol 2020; 3:569. [PMID: 33051587 PMCID: PMC7553921 DOI: 10.1038/s42003-020-01275-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/01/2020] [Indexed: 11/28/2022] Open
Abstract
There is an increasing demand for rapid, effective methods to identify and detect protein micro- and nano-crystal suspensions for serial diffraction data collection at X-ray free-electron lasers or high-intensity micro-focus synchrotron radiation sources. Here, we demonstrate a compact multimodal, multiphoton microscope, driven by a fiber-based ultrafast laser, enabling excitation wavelengths at 775 nm and 1300 nm for nonlinear optical imaging, which simultaneously records second-harmonic generation, third-harmonic generation and three-photon excited ultraviolet fluorescence to identify and detect protein crystals with high sensitivity. The instrument serves as a valuable and important tool supporting sample scoring and sample optimization in biomolecular crystallography, which we hope will increase the capabilities and productivity of serial diffraction data collection in the future.
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Affiliation(s)
- Qing-di Cheng
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
| | - Hsiang-Yu Chung
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Robin Schubert
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
- XFEL Biological Infrastructure Laboratory at the European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Shih-Hsuan Chia
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Celestin Nzanzu Mudogo
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
| | - Franz X Kärtner
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Guoqing Chang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
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10
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Handzlik D, Larson ET, Munschy E, Obmolova G, Collin D, Craig TK. Inexpensive robotic system for standard and fluorescent imaging of protein crystals. Acta Crystallogr F Struct Biol Commun 2019; 75:673-686. [PMID: 31702581 PMCID: PMC6839817 DOI: 10.1107/s2053230x19014730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/31/2019] [Indexed: 11/10/2022] Open
Abstract
Protein-crystallization imaging and classification is a labor-intensive process typically performed either by humans or by instruments that currently cost well over $100 000. This cost puts the use of crystallization-trial imaging outside the reach of most academic laboratories, and also start-up biotechnology firms, where resources are scarce. An imaging system has been designed and prototyped which automatically captures images from multi-well protein-crystallization experiments using both standard and fluorescent imaging techniques at a cost 28 times lower than current market rates. The machine uses a Panowin F1 3D printer as a base and controls it using G-code commands sent from a Python script running on a desktop computer. A graphical user interface (GUI) was developed to enable users to control the machine and facilitate image capture, classification and editing. A 488 nm laser diode and a 525 nm filter were incorporated to allow in situ fluorescent imaging of proteins trace-labeled with a fluorophore, Alexa Fluor 488. The instrument was primarily designed using a 3D printer and augmented using commercially available parts, and this publication aims to serve as a guide for comparable in-laboratory robotics projects.
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Affiliation(s)
| | - Eric T. Larson
- HarkerBIO LLC, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Erika Munschy
- HarkerBIO LLC, 700 Ellicott Street, Buffalo, NY 14203, USA
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11
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Klijn ME, Hubbuch J. Time-Dependent Multi-Light-Source Image Classification Combined With Automated Multidimensional Protein Phase Diagram Construction for Protein Phase Behavior Analysis. J Pharm Sci 2019; 109:331-339. [PMID: 31369742 DOI: 10.1016/j.xphs.2019.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/10/2019] [Accepted: 07/23/2019] [Indexed: 11/29/2022]
Abstract
Image-based protein phase diagram analysis is key for understanding and exploiting protein phase behavior in the biopharmaceutical field. However, required data analysis has become a notorious time-consuming task since high-throughput screening approaches were implemented. A variety of computational tools have been developed to support analysis, but these tools primarily use end point visible light images. This study investigates the combined effect of end point and time-dependent image features obtained from cross-polarized and ultraviolet light features, supplementary to visible light, on protein phase diagram image classification. In addition, external validation was performed to evaluate the classification algorithm's applicability to support protein phase diagram scoring. The predicted protein phase behavior classes were subsequently used to automatically construct multidimensional protein phase diagrams to prevent image information loss without complicating the used image classification algorithm. Combining end point and time-dependent features from 3 light sources resulted in a balanced accuracy of 86.4 ± 4.3%, which is comparable to or better than more complex classifiers reported in literature. External validation resulted in a correct formulation classification rate of 91.7%. Subsequent automated construction of the multidimensional protein phase diagrams, using predicted classes, allowed visualization of details such as crystallization rate and protein phase behavior type coexistence.
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Affiliation(s)
- Marieke E Klijn
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany.
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12
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Ito S, Ueno G, Yamamoto M. DeepCentering: fully automated crystal centering using deep learning for macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1361-1366. [PMID: 31274465 PMCID: PMC6613109 DOI: 10.1107/s160057751900434x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
High-throughput protein crystallography using a synchrotron light source is an important method used in drug discovery. Beamline components for automated experiments including automatic sample changers have been utilized to accelerate the measurement of a number of macromolecular crystals. However, unlike cryo-loop centering, crystal centering involving automated crystal detection is a difficult process to automate fully. Here, DeepCentering, a new automated crystal centering system, is presented. DeepCentering works using a convolutional neural network, which is a deep learning operation. This system achieves fully automated accurate crystal centering without using X-ray irradiation of crystals, and can be used for fully automated data collection in high-throughput macromolecular crystallography.
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Affiliation(s)
- Sho Ito
- ROD (Single Crystal Analysis) Group, Application Laboratories, Rigaku Corporation, 3-9-12 Matubara-cho, Akishima, Tokyo 196-8666, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1205, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1205, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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13
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Mori K, Kuhn B. Imaging Ca 2+ Concentration and pH in Nanopores/Channels of Protein Crystals. J Phys Chem B 2018; 122:9646-9653. [PMID: 30351149 DOI: 10.1021/acs.jpcb.8b07099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein crystals are nanoporous materials. Despite this important characteristic, little is known about the conditions in the pores, also called channels. Here, we describe a method to study the calcium concentration and pH in the nanopores of thaumatin and lysozyme crystals. We load the crystal nanopores with fluorescent indicators and then perfuse the crystals with solutions of different calcium concentrations and pH while reading out the crystal's fluorescence intensity with confocal microscopy. By calibrating the fluorescence signal, we can determine the calcium concentration and pH in the nanopores. For the pH in thaumatin nanopores measured with the ratiometric pH sensor SNARF-1, we find a -0.7 pH shift compared to the bath pH corresponding to a fivefold higher proton concentration. This is similar to the -0.3 pH shift found in lysozyme nanopores. With single-wavelength probes, we find that the calcium concentration in thaumatin crystal nanopores is the same as in the bath, whereas it is 0.24 times lower in lysozyme nanopores. Summarizing, our experiments show that calcium concentration and pH in the nanopores of protein crystals can deviate significantly from that in the bath. In general, the described method can be applied for testing a wide range of ion or small-molecule concentrations in transparent nanoporous materials not only with ratiometric but also with single wavelength fluorescent indicators.
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Affiliation(s)
- Kazuo Mori
- Okinawa Institute of Science and Technology , Graduate University , 1919-1 Tancha , Onna-son, Okinawa 904-0495 , Japan
| | - Bernd Kuhn
- Okinawa Institute of Science and Technology , Graduate University , 1919-1 Tancha , Onna-son, Okinawa 904-0495 , Japan
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14
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Pichlo C, Toelzer C, Chojnacki K, Öcal S, Uthoff M, Ruegenberg S, Hermanns T, Schacherl M, Denzel MS, Hofmann K, Niefind K, Baumann U. Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer. Acta Crystallogr F Struct Biol Commun 2018; 74:307-314. [PMID: 29717999 PMCID: PMC5931144 DOI: 10.1107/s2053230x18005253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/03/2018] [Indexed: 11/10/2022] Open
Abstract
The identification of initial lead conditions for successful protein crystallization is crucial for structural studies using X-ray crystallography. In order to reduce the number of false-negative conditions, an emerging number of fluorescence-based methods have been developed which allow more efficient identification of protein crystals and help to distinguish them from salt crystals. Detection of the native tryptophan fluorescence of protein crystals is one of the most widely used methods. However, this method can fail owing to the properties of the crystallized protein or the chemical composition of the crystallization trials. Here, a simple, fast and cost-efficient method employing 2,2,2-trichloroethanol (TCE) has been developed. It can be performed with a standard UV-light microscope and can be applied to cases in which detection of native tryptophan fluorescence fails. In four test cases this method had no effect on the diffraction properties of the crystals and no structural changes were observed. Further evidence is provided that TCE can be added to crystallization trials during their preparation, making this method compatible with high-throughput approaches.
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Affiliation(s)
- Christian Pichlo
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Christine Toelzer
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Konrad Chojnacki
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
- Faculty of Chemistry, Warsaw University of Technology, ul. Noakowskiego 3, 00-664 Warsaw, Poland
| | - Sinan Öcal
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Matthias Uthoff
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Sabine Ruegenberg
- Max Planck Institute for Biology of Ageing, Research Institute, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - Thomas Hermanns
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674 Cologne, Germany
| | - Magdalena Schacherl
- Structural Dynamics of Proteins, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Martin S. Denzel
- Max Planck Institute for Biology of Ageing, Research Institute, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674 Cologne, Germany
| | - Karsten Niefind
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
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15
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Melnikov I, Svensson O, Bourenkov G, Leonard G, Popov A. The complex analysis of X-ray mesh scans for macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:355-365. [PMID: 29652262 PMCID: PMC6343787 DOI: 10.1107/s2059798318002735] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/15/2018] [Indexed: 12/05/2022]
Abstract
A method and software program, MeshBest, for the detection of individual crystals based on two-dimensional X-ray mesh scans are presented. In macromolecular crystallography, mesh (raster) scans are carried out either as part of X-ray-based crystal-centring routines or to identify positions on the sample holder from which diffraction images can be collected. Here, the methods used in MeshBest, software which automatically analyses diffraction images collected during a mesh scan and produces a two-dimensional crystal map showing estimates of the dimensions, centre positions and diffraction qualities of each crystal contained in the mesh area, are presented. Sample regions producing diffraction images resulting from the superposition of more than one crystal are also distinguished from regions with single-crystal diffraction. The applicability of the method is demonstrated using several cases.
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Affiliation(s)
- Igor Melnikov
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Gordon Leonard
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Alexander Popov
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
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16
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Tarver CL, Pusey M. A low-cost method for visible fluorescence imaging. Acta Crystallogr F Struct Biol Commun 2017; 73:657-663. [PMID: 29199986 PMCID: PMC5713670 DOI: 10.1107/s2053230x17015941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/01/2017] [Indexed: 11/28/2022] Open
Abstract
A wide variety of crystallization solutions are screened to establish conditions that promote the growth of a diffraction-quality crystal. Screening these conditions requires the assessment of many crystallization plates for the presence of crystals. Automated systems for screening and imaging are very expensive. A simple approach to imaging trace fluorescently labeled protein crystals in crystallization plates has been devised, and can be implemented at a cost as low as $50. The proteins β-lactoglobulin B, trypsin and purified concanavalin A (ConA) were trace fluorescently labeled using three different fluorescent probes: Cascade Yellow (CY), Carboxyrhodamine 6G (CR) and Pacific Blue (PB). A crystallization screening plate was set up using β-lactoglobulin B labeled with CR, trypsin labeled with CY, ConA labeled with each probe, and a mixture consisting of 50% PB-labeled ConA and 50% CR-labeled ConA. The wells of these plates were imaged using a commercially available macro-imaging lens attachment for smart devices that have a camera. Several types of macro lens attachments were tested with smartphones and tablets. Images with the highest quality were obtained with an iPhone 6S and an AUKEY Ora 10× macro lens. Depending upon the fluorescent probe employed and its Stokes shift, a light-emitting diode or a laser diode was used for excitation. An emission filter was used for the imaging of protein crystals labeled with CR and crystals with two-color fluorescence. This approach can also be used with microscopy systems commonly used to observe crystallization plates.
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Affiliation(s)
- Crissy L. Tarver
- Department of Biological Science, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Marc Pusey
- Department of Biological Science, University of Alabama in Huntsville, Huntsville, AL 35899, USA
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17
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Locating and Visualizing Crystals for X-Ray Diffraction Experiments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1607:143-164. [PMID: 28573572 DOI: 10.1007/978-1-4939-7000-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.
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18
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Scarborough NM, Godaliyadda GMDP, Ye DH, Kissick DJ, Zhang S, Newman JA, Sheedlo MJ, Chowdhury AU, Fischetti RF, Das C, Buzzard GT, Bouman CA, Simpson GJ. Dynamic X-ray diffraction sampling for protein crystal positioning. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:188-195. [PMID: 28009558 PMCID: PMC5182024 DOI: 10.1107/s160057751601612x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/11/2016] [Indexed: 05/31/2023]
Abstract
A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.
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Affiliation(s)
| | | | - Dong Hye Ye
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - David J. Kissick
- GM/CA@APS, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Shijie Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Justin A. Newman
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Michael J. Sheedlo
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Azhad U. Chowdhury
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Robert F. Fischetti
- GM/CA@APS, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Gregery T. Buzzard
- Department of Mathematics, Purdue University, West Lafayette, IN 47907, USA
| | - Charles A. Bouman
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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19
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Newman JA, Zhang S, Sullivan SZ, Dow XY, Becker M, Sheedlo MJ, Stepanov S, Carlsen MS, Everly RM, Das C, Fischetti RF, Simpson GJ. Guiding synchrotron X-ray diffraction by multimodal video-rate protein crystal imaging. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:959-65. [PMID: 27359145 PMCID: PMC4928651 DOI: 10.1107/s1600577516005919] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/08/2016] [Indexed: 06/01/2023]
Abstract
Synchronous digitization, in which an optical sensor is probed synchronously with the firing of an ultrafast laser, was integrated into an optical imaging station for macromolecular crystal positioning prior to synchrotron X-ray diffraction. Using the synchronous digitization instrument, second-harmonic generation, two-photon-excited fluorescence and bright field by laser transmittance were all acquired simultaneously with perfect image registry at up to video-rate (15 frames s(-1)). A simple change in the incident wavelength enabled simultaneous imaging by two-photon-excited ultraviolet fluorescence, one-photon-excited visible fluorescence and laser transmittance. Development of an analytical model for the signal-to-noise enhancement afforded by synchronous digitization suggests a 15.6-fold improvement over previous photon-counting techniques. This improvement in turn allowed acquisition on nearly an order of magnitude more pixels than the preceding generation of instrumentation and reductions of well over an order of magnitude in image acquisition times. These improvements have allowed detection of protein crystals on the order of 1 µm in thickness under cryogenic conditions in the beamline. These capabilities are well suited to support serial crystallography of crystals approaching 1 µm or less in dimension.
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Affiliation(s)
- Justin A. Newman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Shijie Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Shane Z. Sullivan
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Ximeng Y. Dow
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Michael Becker
- GM/CA@APS, X-Ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Michael J. Sheedlo
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Sergey Stepanov
- GM/CA@APS, X-Ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Mark S. Carlsen
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - R. Michael Everly
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Robert F. Fischetti
- GM/CA@APS, X-Ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
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20
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Lukk T, Gillilan RE, Szebenyi DME, Zipfel WR. A visible-light-excited fluorescence method for imaging protein crystals without added dyes. J Appl Crystallogr 2016; 49:234-240. [PMID: 26937240 PMCID: PMC4762565 DOI: 10.1107/s160057671502419x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/16/2015] [Indexed: 11/10/2022] Open
Abstract
Fluorescence microscopy methods have seen an increase in popularity in recent years for detecting protein crystals in screening trays. The fluorescence-based crystal detection methods have thus far relied on intrinsic UV-inducible tryptophan fluorescence, nonlinear optics or fluorescence in the visible light range dependent on crystals soaked with fluorescent dyes. In this paper data are presented on a novel visible-light-inducible autofluorescence arising from protein crystals as a result of general stabilization of conjugated double-bond systems and increased charge delocalization due to crystal packing. The visible-light-inducible autofluorescence serves as a complementary method to bright-field microscopy in beamline applications where accurate crystal centering about the rotation axis is essential. Owing to temperature-dependent chromophore stabilization, protein crystals exhibit tenfold higher fluorescence intensity at cryogenic temperatures, making the method ideal for experiments where crystals are cooled to 100 K with a cryostream. In addition to the non-damaging excitation wavelength and low laser power required for imaging, the method can also serve a useful role for differentiating protein crystals from salt crystals in screening trays.
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Affiliation(s)
- Tiit Lukk
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Doletha M. E. Szebenyi
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Warren R. Zipfel
- Department of Biomedical Engineering, Cornell University, B41 Weill Hall, Ithaca, NY 14853, USA
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21
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Nonlinear Optical Characterization of Membrane Protein Microcrystals and Nanocrystals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:91-103. [DOI: 10.1007/978-3-319-35072-1_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Gavira JA. Current trends in protein crystallization. Arch Biochem Biophys 2015; 602:3-11. [PMID: 26747744 DOI: 10.1016/j.abb.2015.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/16/2015] [Accepted: 12/22/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. SYNOPSIS Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale.
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Affiliation(s)
- José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT (CSIC-UGR), Avda. de las Palmeras, 4. 18100 Armilla, Granada, Spain
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23
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Luft JR, Wolfley JR, Franks EC, Lauricella AM, Gualtieri EJ, Snell EH, Xiao R, Everett JK, Montelione GT. The detection and subsequent volume optimization of biological nanocrystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041710. [PMID: 26798809 PMCID: PMC4711624 DOI: 10.1063/1.4921199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/05/2015] [Indexed: 06/05/2023]
Abstract
Identifying and then optimizing initial crystallization conditions is a prerequisite for macromolecular structure determination by crystallography. Improved technologies enable data collection on crystals that are difficult if not impossible to detect using visible imaging. The application of second-order nonlinear imaging of chiral crystals and ultraviolet two-photon excited fluorescence detection is shown to be applicable in a high-throughput manner to rapidly verify the presence of nanocrystals in crystallization screening conditions. It is noted that the nanocrystals are rarely seen without also producing microcrystals from other chemical conditions. A crystal volume optimization method is described and associated with a phase diagram for crystallization.
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Affiliation(s)
| | - Jennifer R Wolfley
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Eleanor Cook Franks
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Angela M Lauricella
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Ellen J Gualtieri
- Formulatrix, Inc. , 10 DeAngelo Drive, Bedford, Massachusetts 01730, USA
| | | | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey , 679 Hoes Lane, Piscataway, New Jersey 08854-8021, USA
| | - John K Everett
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey , 679 Hoes Lane, Piscataway, New Jersey 08854-8021, USA
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24
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Newman JA, Scarborough NM, Pogranichniy NR, Shrestha RK, Closser RG, Das C, Simpson GJ. Intercalating dyes for enhanced contrast in second-harmonic generation imaging of protein crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1471-7. [PMID: 26143918 PMCID: PMC4498603 DOI: 10.1107/s1399004715008287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 04/27/2015] [Indexed: 11/10/2022]
Abstract
The second-harmonic generation (SHG) activity of protein crystals was found to be enhanced by up to ∼1000-fold by the intercalation of SHG phores within the crystal lattice. Unlike the intercalation of fluorophores, the SHG phores produced no significant background SHG from solvated dye or from dye intercalated into amorphous aggregates. The polarization-dependent SHG is consistent with the chromophores adopting the symmetry of the crystal lattice. In addition, the degree of enhancement for different symmetries of dyes is consistent with theoretical predictions based on the molecular nonlinear optical response. Kinetics studies indicate that intercalation arises over a timeframe of several minutes in lysozyme, with detectable enhancements within seconds. These results provide a potential means to increase the overall diversity of protein crystals and crystal sizes amenable to characterization by SHG microscopy.
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Affiliation(s)
- Justin A. Newman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Nicole M. Scarborough
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | | | - Rashmi K. Shrestha
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Richard G. Closser
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
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25
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Meyer A, Betzel C, Pusey M. Latest methods of fluorescence-based protein crystal identification. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:121-31. [PMID: 25664782 PMCID: PMC4321462 DOI: 10.1107/s2053230x15000114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/05/2015] [Indexed: 11/21/2022]
Abstract
Fluorescence, whether intrinsic or by using trace fluorescent labeling, can be a powerful aid in macromolecule crystallization. Its use in screening for crystals is discussed here. Successful protein crystallization screening experiments are dependent upon the experimenter being able to identify positive outcomes. The introduction of fluorescence techniques has brought a powerful and versatile tool to the aid of the crystal grower. Trace fluorescent labeling, in which a fluorescent probe is covalently bound to a subpopulation (<0.5%) of the protein, enables the use of visible fluorescence. Alternatively, one can avoid covalent modification and use UV fluorescence, exploiting the intrinsic fluorescent amino acids present in most proteins. By the use of these techniques, crystals that had previously been obscured in the crystallization drop can readily be identified and distinguished from amorphous precipitate or salt crystals. Additionally, lead conditions that may not have been obvious as such under white-light illumination can be identified. In all cases review of the screening plate is considerably accelerated, as the eye can quickly note objects of increased intensity.
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Affiliation(s)
- Arne Meyer
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marc Pusey
- iXpressGenes Inc., 601 Genome Way, Huntsville, AL 35806, USA
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26
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Palczewska G, Salom D. Imaging of rhodopsin crystals with two-photon microscopy. Methods Mol Biol 2015; 1271:55-64. [PMID: 25697516 DOI: 10.1007/978-1-4939-2330-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Two-photon microscopy has been shown to be an invaluable tool for detecting and monitoring protein crystallization trials and characterizing membrane protein crystals. This imaging method has proven especially useful for rhodopsin, because of the dependence of rhodopsin's fluorescence spectra on the isomerization state of its intrinsic chromophore (retinylidene) and, as such, it can provide additional information about the identity and functional state of rhodopsin in crystals. Here, we describe the acquisition of images and two-photon excitation and emission spectra using a commercial two-photon microscope, along with detailed instructions for the handling of rhodopsin crystals and specific examples of rhodopsin data.
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Calero G, Cohen AE, Luft JR, Newman J, Snell EH. Identifying, studying and making good use of macromolecular crystals. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:993-1008. [PMID: 25084371 PMCID: PMC4118793 DOI: 10.1107/s2053230x14016574] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/16/2014] [Indexed: 11/30/2022]
Abstract
As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.
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Affiliation(s)
- Guillermo Calero
- Department of Structural Biology, University of Pittsburgh Medical School, Pittsburgh, PA 15261, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Joseph R Luft
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Janet Newman
- CSIRO Collaborative Crystallisation Centre, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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Deller MC, Rupp B. Approaches to automated protein crystal harvesting. Acta Crystallogr F Struct Biol Commun 2014; 70:133-55. [PMID: 24637746 PMCID: PMC3936438 DOI: 10.1107/s2053230x14000387] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/07/2014] [Indexed: 11/11/2022] Open
Abstract
The harvesting of protein crystals is almost always a necessary step in the determination of a protein structure using X-ray crystallographic techniques. However, protein crystals are usually fragile and susceptible to damage during the harvesting process. For this reason, protein crystal harvesting is the single step that remains entirely dependent on skilled human intervention. Automation has been implemented in the majority of other stages of the structure-determination pipeline, including cloning, expression, purification, crystallization and data collection. The gap in automation between crystallization and data collection results in a bottleneck in throughput and presents unfortunate opportunities for crystal damage. Several automated protein crystal harvesting systems have been developed, including systems utilizing microcapillaries, microtools, microgrippers, acoustic droplet ejection and optical traps. However, these systems have yet to be commonly deployed in the majority of crystallography laboratories owing to a variety of technical and cost-related issues. Automation of protein crystal harvesting remains essential for harnessing the full benefits of fourth-generation synchrotrons, free-electron lasers and microfocus beamlines. Furthermore, automation of protein crystal harvesting offers several benefits when compared with traditional manual approaches, including the ability to harvest microcrystals, improved flash-cooling procedures and increased throughput.
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Affiliation(s)
- Marc C. Deller
- The Joint Center for Structural Genomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Innsbruck Medical University, Schöpfstrasse 41, 6020 Innsbruck, Austria
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29
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Boudes M, Garriga D, Coulibaly F. Reflections on the Many Facets of Protein Microcrystallography. Aust J Chem 2014. [DOI: 10.1071/ch14455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The use of X-ray crystallography for the structure determination of biological macromolecules has experienced a steady expansion over the last 20 years with the Protein Data Bank growing from <1000 deposited structures in 1992 to >100 000 in 2014. The large number of structures determined each year not only reflects the impact of X-ray crystallography on many disciplines in the biological and medical fields but also its accessibility to non-expert laboratories. Thus protein crystallography is now largely a mainstream research technique and is routinely integrated in high-throughput pipelines such as structural genomics projects and structure-based drug design. Yet, significant frontiers remain that continuously require methodological developments. In particular, membrane proteins, large assemblies, and proteins from scarce natural sources still represent challenging targets for which obtaining the large diffracting crystals required for classical crystallography is often difficult. These limitations have fostered the emergence of microcrystallography, novel approaches in structural biology that collectively aim at determining structures from the smallest crystals. Here, we review the state of the art of macromolecular microcrystallography and recent progress achieved in this field.
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Madden JT, Toth SJ, Dettmar CM, Newman JA, Oglesbee RA, Hedderich HG, Everly RM, Becker M, Ronau JA, Buchanan SK, Cherezov V, Morrow ME, Xu S, Ferguson D, Makarov O, Das C, Fischetti R, Simpson GJ. Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:531-40. [PMID: 23765294 PMCID: PMC3682636 DOI: 10.1107/s0909049513007942] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/22/2013] [Indexed: 05/22/2023]
Abstract
Nonlinear optical (NLO) instrumentation has been integrated with synchrotron X-ray diffraction (XRD) for combined single-platform analysis, initially targeting applications for automated crystal centering. Second-harmonic-generation microscopy and two-photon-excited ultraviolet fluorescence microscopy were evaluated for crystal detection and assessed by X-ray raster scanning. Two optical designs were constructed and characterized; one positioned downstream of the sample and one integrated into the upstream optical path of the diffractometer. Both instruments enabled protein crystal identification with integration times between 80 and 150 µs per pixel, representing a ∼10(3)-10(4)-fold reduction in the per-pixel exposure time relative to X-ray raster scanning. Quantitative centering and analysis of phenylalanine hydroxylase from Chromobacterium violaceum cPAH, Trichinella spiralis deubiquitinating enzyme TsUCH37, human κ-opioid receptor complex kOR-T4L produced in lipidic cubic phase (LCP), intimin prepared in LCP, and α-cellulose samples were performed by collecting multiple NLO images. The crystalline samples were characterized by single-crystal diffraction patterns, while α-cellulose was characterized by fiber diffraction. Good agreement was observed between the sample positions identified by NLO and XRD raster measurements for all samples studied.
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Affiliation(s)
- Jeremy T. Madden
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Scott J. Toth
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Christopher M. Dettmar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Justin A. Newman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Robert A. Oglesbee
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Hartmut G. Hedderich
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - R. Michael Everly
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Michael Becker
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Judith A. Ronau
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Susan K. Buchanan
- NIDDK, National Institutes of Health, Building 50, Room 4503, 50 South Drive, Bethesda, MD 20814, USA
| | - Vadim Cherezov
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Marie E. Morrow
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Shenglan Xu
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Dale Ferguson
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Oleg Makarov
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Robert Fischetti
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
- Correspondence e-mail:
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Krauss IR, Merlino A, Vergara A, Sica F. An overview of biological macromolecule crystallization. Int J Mol Sci 2013; 14:11643-91. [PMID: 23727935 PMCID: PMC3709751 DOI: 10.3390/ijms140611643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/11/2022] Open
Abstract
The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-81-674-479; Fax: +39-81-674-090
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Kissick DJ, Dettmar CM, Becker M, Mulichak AM, Cherezov V, Ginell SL, Battaile KP, Keefe LJ, Fischetti RF, Simpson GJ. Towards protein-crystal centering using second-harmonic generation (SHG) microscopy. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:843-51. [PMID: 23633594 PMCID: PMC3640472 DOI: 10.1107/s0907444913002746] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 01/28/2013] [Indexed: 11/10/2022]
Abstract
The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals was explored. These studies included (i) comparison of microcrystal positions in cryoloops as determined by SHG imaging and by X-ray diffraction rastering and (ii) X-ray structure determinations of selected proteins to investigate the potential for laser-induced damage from SHG imaging. In studies using β2 adrenergic receptor membrane-protein crystals prepared in lipidic mesophase, the crystal locations identified by SHG images obtained in transmission mode were found to correlate well with the crystal locations identified by raster scanning using an X-ray minibeam. SHG imaging was found to provide about 2 µm spatial resolution and shorter image-acquisition times. The general insensitivity of SHG images to optical scatter enabled the reliable identification of microcrystals within opaque cryocooled lipidic mesophases that were not identified by conventional bright-field imaging. The potential impact of extended exposure of protein crystals to five times a typical imaging dose from an ultrafast laser source was also assessed. Measurements of myoglobin and thaumatin crystals resulted in no statistically significant differences between structures obtained from diffraction data acquired from exposed and unexposed regions of single crystals. Practical constraints for integrating SHG imaging into an active beamline for routine automated crystal centering are discussed.
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Affiliation(s)
- David J. Kissick
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Michael Becker
- GM/CA-CAT at the APS, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Anne M. Mulichak
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, Argonne, IL 60439, USA
| | | | - Stephan L. Ginell
- SBC-CAT at the APS, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, Argonne, IL 60439, USA
| | - Lisa J. Keefe
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, Argonne, IL 60439, USA
| | - Robert F. Fischetti
- GM/CA-CAT at the APS, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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Abstract
Oligomerization is one of several mechanisms that can regulate the activity of G protein-coupled receptors (GPCRs), but little is known about the structure of GPCR oligomers. Crystallography and NMR are the only methods able to reveal the details of receptor-receptor interactions at an atomic level, and several GPCR homodimers already have been described from crystal structures. Two clusters of symmetric interfaces have been identified from these structures that concur with biochemical data, one involving helices I, II, and VIII and the other formed mainly by helices V and VI. In this chapter, we describe the protocols used in our laboratory for the crystallization of rhodopsin and the β2-adrenergic receptor (β2-AR). For bovine rhodopsin, we developed a new purification strategy including a (NH4)2SO4-induced phase separation that proved essential to obtain crystals of photoactivated rhodopsin containing parallel dimers. Crystallization of native bovine rhodopsin was achieved by the classic vapor-diffusion technique. For β2-AR, we developed a purification strategy based on previously published protocols employing a lipidic cubic phase to obtain diffracting crystals of a β2-AR/T4-lysozyme chimera bound to the antagonist carazolol.
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Haupert LM, DeWalt EL, Simpson GJ. Modeling the SHG activities of diverse protein crystals. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1513-21. [PMID: 23090400 DOI: 10.1107/s0907444912037638] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 08/31/2012] [Indexed: 11/10/2022]
Abstract
A symmetry-additive ab initio model for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine point-group symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much of the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within the crystal lattice. Two or more orders-of-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of ~84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices.
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Affiliation(s)
- Levi M Haupert
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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35
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Khan I, Gillilan R, Kriksunov I, Williams R, Zipfel WR, Englich U. Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning. J Appl Crystallogr 2012; 45:936-943. [PMID: 22997474 DOI: 10.1107/s002188981203470x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 08/04/2012] [Indexed: 11/10/2022] Open
Abstract
Confocal microscopy, a technique that has been extensively applied in cellular biological studies, may also be applied to the visualization and three-dimensional imaging of protein crystals at high resolution on synchrotron beamlines. Protein crystal samples are examined using a commercially available confocal microscope adapted for cryogenic use. A preliminary test using a custom confocal design adapted for beamline use is also presented. The confocal optics configuration is compatible with nonlinear imaging techniques such as two-photon excited fluorescence imaging and second harmonic generation. The possibilities of this method are explored using two modes: fluorescence and reflection confocal. In fluorescence mode, small amounts of dye are introduced into the crystal through soaking or growth conditions. Under such conditions, protein crystals are easily resolved from salts and amorphous precipitates, which do not generally take up dye. Reflection mode, which does not require dye, still exhibits greater resolution and sensitivity to surface detail than conventional wide-field microscopy as a result of the confocal optics configuration. The inherent three-dimensional nature of the method means that on-axis sample views (along the direction of the X-ray beam) can be reconstructed from an off-axis configuration, simplifying the beamline setup and providing uniquely detailed views of cryogenically cooled crystals.
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Affiliation(s)
- I Khan
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, Ithaca, NY 14853, USA
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36
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Gasecka A, Tauc P, Lewit-Bentley A, Brasselet S. Investigation of molecular and protein crystals by three photon polarization resolved microscopy. PHYSICAL REVIEW LETTERS 2012; 108:263901. [PMID: 23004978 DOI: 10.1103/physrevlett.108.263901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Indexed: 06/01/2023]
Abstract
We implement three photon fluorescence polarization resolved microscopy to optically investigate molecular and protein crystals. The availability of UV transitions using IR pulses allows analyses without fluorescence staining. Polarization resolved studies indicate that high-order symmetry structures can be revealed and that strong fluorescent energy transfer occurs between molecules. We show how this permits identification of a monocrystalline nature for a sample at the subwavelength resolution scale.
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Affiliation(s)
- Alicja Gasecka
- Institut Fresnel, CNRS, Aix-Marseille Université, Ecole Centrale Marseille, Campus de St Jérôme, 13013 Marseille, France
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Padayatti P, Palczewska G, Sun W, Palczewski K, Salom D. Imaging of protein crystals with two-photon microscopy. Biochemistry 2012; 51:1625-37. [PMID: 22324807 DOI: 10.1021/bi201682q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Second-order nonlinear optical imaging of chiral crystals (SONICC), which portrays second-harmonic generation (SHG) by noncentrosymmetric crystals, is emerging as a powerful imaging technique for protein crystals in media opaque to visible light because of its high signal-to-noise ratio. Here we report the incorporation of both SONICC and two-photon excited fluorescence (TPEF) into one imaging system that allows visualization of crystals as small as ~10 μm in their longest dimension. Using this system, we then documented an inverse correlation between the level of symmetry in examined crystals and the intensity of their SHG. Moreover, because of blue-green TPEF exhibited by most tested protein crystals, we also could identify and image SHG-silent protein crystals. Our experimental data suggest that the TPEF in protein crystals is mainly caused by the oxidation of tryptophan residues. Additionally, we found that unspecific fluorescent dyes are able to bind to lysozyme crystals and enhance their detection by TPEF. We finally confirmed that the observed fluorescence was generated by a two-photon rather than a three-photon process. The capability for imaging small protein crystals in turbid or opaque media with nondamaging infrared light in a single system makes the combination of SHG and intrinsic visible TPEF a powerful tool for nondestructive protein crystal identification and characterization during crystallization trials.
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