1
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Henkel A, Galchenkova M, Maracke J, Yefanov O, Klopprogge B, Hakanpää J, Mesters JR, Chapman HN, Oberthuer D. JINXED: just in time crystallization for easy structure determination of biological macromolecules. IUCRJ 2023; 10:253-260. [PMID: 36892542 PMCID: PMC10161778 DOI: 10.1107/s2052252523001653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/23/2023] [Indexed: 05/06/2023]
Abstract
Macromolecular crystallography is a well established method in the field of structural biology and has led to the majority of known protein structures to date. After focusing on static structures, the method is now under development towards the investigation of protein dynamics through time-resolved methods. These experiments often require multiple handling steps of the sensitive protein crystals, e.g. for ligand-soaking and cryo-protection. These handling steps can cause significant crystal damage, and hence reduce data quality. Furthermore, in time-resolved experiments based on serial crystallography, which use micrometre-sized crystals for short diffusion times of ligands, certain crystal morphologies with small solvent channels can prevent sufficient ligand diffusion. Described here is a method that combines protein crystallization and data collection in a novel one-step process. Corresponding experiments were successfully performed as a proof-of-principle using hen egg-white lysozyme and crystallization times of only a few seconds. This method, called JINXED (Just IN time Crystallization for Easy structure Determination), promises high-quality data due to the avoidance of crystal handling and has the potential to enable time-resolved experiments with crystals containing small solvent channels by adding potential ligands to the crystallization buffer, simulating traditional co-crystallization approaches.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jeroen R. Mesters
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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2
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Nazari H, Heirani-Tabasi A, Ghorbani S, Eyni H, Razavi Bazaz S, Khayati M, Gheidari F, Moradpour K, Kehtari M, Ahmadi Tafti SM, Ahmadi Tafti SH, Ebrahimi Warkiani M. Microfluidic-Based Droplets for Advanced Regenerative Medicine: Current Challenges and Future Trends. BIOSENSORS 2021; 12:20. [PMID: 35049648 PMCID: PMC8773546 DOI: 10.3390/bios12010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
Microfluidics is a promising approach for the facile and large-scale fabrication of monodispersed droplets for various applications in biomedicine. This technology has demonstrated great potential to address the limitations of regenerative medicine. Microfluidics provides safe, accurate, reliable, and cost-effective methods for encapsulating different stem cells, gametes, biomaterials, biomolecules, reagents, genes, and nanoparticles inside picoliter-sized droplets or droplet-derived microgels for different applications. Moreover, microenvironments made using such droplets can mimic niches of stem cells for cell therapy purposes, simulate native extracellular matrix (ECM) for tissue engineering applications, and remove challenges in cell encapsulation and three-dimensional (3D) culture methods. The fabrication of droplets using microfluidics also provides controllable microenvironments for manipulating gametes, fertilization, and embryo cultures for reproductive medicine. This review focuses on the relevant studies, and the latest progress in applying droplets in stem cell therapy, tissue engineering, reproductive biology, and gene therapy are separately evaluated. In the end, we discuss the challenges ahead in the field of microfluidics-based droplets for advanced regenerative medicine.
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Affiliation(s)
- Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
| | - Asieh Heirani-Tabasi
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center Hospital, Tehran University of Medical Sciences, Tehran 14535, Iran; (A.H.-T.); (S.H.A.T.)
- Department of Cell Therapy and Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14535, Iran
| | - Sadegh Ghorbani
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark;
| | - Hossein Eyni
- Cellular and Molecular Research Center, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran;
- Department of Anatomical Sciences, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
| | - Maryam Khayati
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan 45371, Iran;
| | - Fatemeh Gheidari
- Department of Biotechnology, University of Tehran, Tehran 14535, Iran;
| | - Keyvan Moradpour
- Department of Chemical Engineering, Sharif University of Technology, Tehran 14535, Iran;
| | - Mousa Kehtari
- Department of Biology, Faculty of Science, University of Tehran, Tehran 14535, Iran;
| | - Seyed Mohsen Ahmadi Tafti
- Colorectal Surgery Research Center, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran 14535, Iran;
| | - Seyed Hossein Ahmadi Tafti
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center Hospital, Tehran University of Medical Sciences, Tehran 14535, Iran; (A.H.-T.); (S.H.A.T.)
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
- Institute of Molecular Medicine, Sechenov University, 119991 Moscow, Russia
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3
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Huang CY, Olieric V, Caffrey M, Wang M. In Meso In Situ Serial X-Ray Crystallography (IMISX): A Protocol for Membrane Protein Structure Determination at the Swiss Light Source. Methods Mol Biol 2020; 2127:293-319. [PMID: 32112330 DOI: 10.1007/978-1-0716-0373-4_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lipid cubic phases (LCP) have enabled the determination of many important high-resolution structures of membrane proteins such as G-protein-coupled receptors, photosensitive proteins, enzymes, channels, and transporters. However, harvesting the crystals from the glass or plastic plates in which crystals grow is challenging. The in meso in situ serial X-ray crystallography (IMISX) method uses thin plastic windowed plates that minimize LCP crystal manipulation. The method, which is compatible with high-throughput in situ measurements, allows systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without direct crystal harvesting. In this chapter, we describe an IMISX protocol for in situ serial X-ray data collection of LCP-grown crystals at both cryogenic and room temperatures which includes the crystallization setup, sample delivery, automated serial diffraction data collection, and experimental phasing. We also detail how the IMISX method was applied successfully for the structure determination of two novel targets-the undecaprenyl-pyrophosphate phosphatase BacA and the chemokine G-protein-coupled receptor CCR2A.
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Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland.
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
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4
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Cheng R, Huang C, Hennig M, Nar H, Schnapp G. In situ
crystallography as an emerging method for structure solution of membrane proteins: the case of CCR2A. FEBS J 2019; 287:866-873. [DOI: 10.1111/febs.15098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/10/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022]
Affiliation(s)
| | - Chia‐Ying Huang
- Swiss Light Source Paul Scherrer Institute Villigen Switzerland
| | | | - Herbert Nar
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Gisela Schnapp
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
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5
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Candoni N, Grossier R, Lagaize M, Veesler S. Advances in the Use of Microfluidics to Study Crystallization Fundamentals. Annu Rev Chem Biomol Eng 2019; 10:59-83. [PMID: 31018097 DOI: 10.1146/annurev-chembioeng-060718-030312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review compares droplet-based microfluidic systems used to study crystallization fundamentals in chemistry and biology. An original high-throughput droplet-based microfluidic platform is presented. It uses nanoliter droplets, generates a chemical library, and directly solubilizes powder, thus economizing both material and time. It is compatible with all solvents without the need for surfactant. Its flexibility permits phase diagram determination and crystallization studies (screening and optimizing experiments) and makes it easy to use for nonspecialists in microfluidics. Moreover, it allows concentration measurement via ultraviolet spectroscopy and solid characterization via X-ray diffraction analysis.
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Affiliation(s)
- Nadine Candoni
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288 Marseille, France; , , ,
| | - Romain Grossier
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288 Marseille, France; , , ,
| | - Mehdi Lagaize
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288 Marseille, France; , , ,
| | - Stéphane Veesler
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288 Marseille, France; , , ,
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6
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de Wijn R, Hennig O, Roche J, Engilberge S, Rollet K, Fernandez-Millan P, Brillet K, Betat H, Mörl M, Roussel A, Girard E, Mueller-Dieckmann C, Fox GC, Olieric V, Gavira JA, Lorber B, Sauter C. A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography. IUCRJ 2019; 6:454-464. [PMID: 31098026 PMCID: PMC6503916 DOI: 10.1107/s2052252519003622] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/14/2019] [Indexed: 05/15/2023]
Abstract
Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.
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Affiliation(s)
- Raphaël de Wijn
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Oliver Hennig
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Jennifer Roche
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS–Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France
| | | | - Kevin Rollet
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Pablo Fernandez-Millan
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Karl Brillet
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS–Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France
| | - Eric Girard
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Gavin C. Fox
- PROXIMA 2A beamline, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Vincent Olieric
- Paul Scherrer Institute, Swiss Light Source, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos, IACT, CSIC–Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Bernard Lorber
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
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7
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Keedy DA. Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography. Acta Crystallogr D Struct Biol 2019; 75:123-137. [PMID: 30821702 PMCID: PMC6400254 DOI: 10.1107/s2059798318017941] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023] Open
Abstract
Proteins inherently fluctuate between conformations to perform functions in the cell. For example, they sample product-binding, transition-state-stabilizing and product-release states during catalysis, and they integrate signals from remote regions of the structure for allosteric regulation. However, there is a lack of understanding of how these dynamic processes occur at the basic atomic level. This gap can be at least partially addressed by combining variable-temperature (instead of traditional cryogenic temperature) X-ray crystallography with algorithms for modeling alternative conformations based on electron-density maps, in an approach called multitemperature multiconformer X-ray crystallography (MMX). Here, the use of MMX to reveal alternative conformations at different sites in a protein structure and to estimate the degree of energetic coupling between them is discussed. These insights can suggest testable hypotheses about allosteric mechanisms. Temperature is an easily manipulated experimental parameter, so the MMX approach is widely applicable to any protein that yields well diffracting crystals. Moreover, the general principles of MMX are extensible to other perturbations such as pH, pressure, ligand concentration etc. Future work will explore strategies for leveraging X-ray data across such perturbation series to more quantitatively measure how different parts of a protein structure are coupled to each other, and the consequences thereof for allostery and other aspects of protein function.
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Affiliation(s)
- Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, USA
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8
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The Study of the Mechanism of Protein Crystallization in Space by Using Microchannel to Simulate Microgravity Environment. CRYSTALS 2018. [DOI: 10.3390/cryst8110400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Space is expected to be a convection-free, quiescent environment for the production of large-size and high-quality protein crystals. However, the mechanisms by which the diffusion environment in space improves the quality of the protein crystals are not fully understood. The interior of a microfluidic device can be used to simulate a microgravity environment to investigate the protein crystallization mechanism that occurs in space. In the present study, lysozyme crystals were grown in a prototype microchannel device with a height of 50 μm in a glass-polydimethylsiloxane (PDMS)-glass sandwich structure. Comparative experiments were also conducted in a sample pool with a height of 2 mm under the same growth conditions. We compared the crystal morphologies and growth rates of the grown crystals in the two sample pools. The experimental results showed that at very low initial supersaturation, the morphology and growth rates of lysozyme crystals under the simulated microgravity conditions is similar to that on Earth. With increasing initial supersaturation, a convection-free, quiescent environment is better for lysozyme crystal growth. When the initial supersaturation exceeded a threshold, the growth of the lysozyme crystal surface under the simulated microgravity conditions never completely transform from isotropic to anisotropic. The experimental results showed that the convection may have a dual effect on the crystal morphology. Convection can increase the roughness of the crystal surface and promote the transformation of the crystal form from circular to tetragonal during the crystallization process.
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9
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High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Nat Protoc 2018; 13:260-292. [PMID: 29300389 DOI: 10.1038/nprot.2017.135] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein crystallography has significantly advanced in recent years, with in situ data collection, in which crystals are placed in the X-ray beam within their growth medium, being a major point of focus. In situ methods eliminate the need to harvest crystals, a previously unavoidable drawback, particularly for often small membrane-protein crystals. Here, we present a protocol for the high-throughput in situ X-ray screening of and data collection from soluble and membrane-protein crystals at room temperature (20-25°C) and under cryogenic conditions. The Mylar in situ method uses Mylar-based film sandwich plates that are inexpensive, easy to make, and compatible with automated imaging, and that show very low background scattering. They support crystallization in microbatch and vapor-diffusion modes, as well as in lipidic cubic phases (LCPs). A set of 3D-printed holders for differently sized patches of Mylar sandwich films makes the method robust and versatile, allows for storage and shipping of crystals, and enables automated mounting at synchrotrons, as well as goniometer-based screening and data collection. The protocol covers preparation of in situ plates and setup of crystallization trials; 3D printing and assembly of holders; opening of plates, isolation of film patches containing crystals, and loading them onto holders; basic screening and data-collection guidelines; and unloading of holders, as well as reuse and recycling of them. In situ plates are prepared and assembled in 1 h; holders are 3D-printed and assembled in ≤90 min; and an in situ plate is opened, and a film patch containing crystals is isolated and loaded onto a holder in 5 min.
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10
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Gerard CJJ, Ferry G, Vuillard LM, Boutin JA, Chavas LMG, Huet T, Ferte N, Grossier R, Candoni N, Veesler S. Crystallization via tubing microfluidics permits both in situ and ex situ X-ray diffraction. Acta Crystallogr F Struct Biol Commun 2017; 73:574-578. [PMID: 28994406 PMCID: PMC5633925 DOI: 10.1107/s2053230x17013826] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/25/2017] [Indexed: 11/10/2022] Open
Abstract
A microfluidic platform was used to address the problems of obtaining diffraction-quality crystals and crystal handling during transfer to the X-ray diffractometer. Crystallization conditions of a protein of pharmaceutical interest were optimized and X-ray data were collected both in situ and ex situ.
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Affiliation(s)
- Charline J. J. Gerard
- CINaM–CNRS, Aix-Marseille Université, Campus de Luminy, Case 913, 13288 Marseille CEDEX 09, France
| | - Gilles Ferry
- Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Laurent M. Vuillard
- Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean A. Boutin
- Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | | | - Tiphaine Huet
- PROXIMA-1, Synchrotron SOLEIL, Gif-sur-Yvette, France
| | - Nathalie Ferte
- CINaM–CNRS, Aix-Marseille Université, Campus de Luminy, Case 913, 13288 Marseille CEDEX 09, France
| | - Romain Grossier
- CINaM–CNRS, Aix-Marseille Université, Campus de Luminy, Case 913, 13288 Marseille CEDEX 09, France
| | - Nadine Candoni
- CINaM–CNRS, Aix-Marseille Université, Campus de Luminy, Case 913, 13288 Marseille CEDEX 09, France
| | - Stéphane Veesler
- CINaM–CNRS, Aix-Marseille Université, Campus de Luminy, Case 913, 13288 Marseille CEDEX 09, France
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11
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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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12
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Broecker J, Klingel V, Ou WL, Balo AR, Kissick D, Ogata CM, Kuo A, Ernst OP. A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. CRYSTAL GROWTH & DESIGN 2016; 16:6318-6326. [PMID: 28261000 PMCID: PMC5328415 DOI: 10.1021/acs.cgd.6b00950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/30/2016] [Indexed: 05/20/2023]
Abstract
In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometer-based X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi. In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.
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Affiliation(s)
- Jana Broecker
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- E-mail:
| | - Viviane Klingel
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Aidin R. Balo
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David
J. Kissick
- GM/CA
at Advanced Photon Source, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Craig M. Ogata
- GM/CA
at Advanced Photon Source, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Anling Kuo
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Oliver P. Ernst
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- E-mail:
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13
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Ghazal A, Lafleur JP, Mortensen K, Kutter JP, Arleth L, Jensen GV. Recent advances in X-ray compatible microfluidics for applications in soft materials and life sciences. LAB ON A CHIP 2016; 16:4263-4295. [PMID: 27731448 DOI: 10.1039/c6lc00888g] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The increasingly narrow and brilliant beams at X-ray facilities reduce the requirements for both sample volume and data acquisition time. This creates new possibilities for the types and number of sample conditions that can be examined but simultaneously increases the demands in terms of sample preparation. Microfluidic-based sample preparation techniques have emerged as elegant alternatives that can be integrated directly into the experimental X-ray setup remedying several shortcomings of more traditional methods. We review the use of microfluidic devices in conjunction with X-ray measurements at synchrotron facilities in the context of 1) mapping large parameter spaces, 2) performing time resolved studies of mixing-induced kinetics, and 3) manipulating/processing samples in ways which are more demanding or not accessible on the macroscale. The review covers the past 15 years and focuses on applications where synchrotron data collection is performed in situ, i.e. directly on the microfluidic platform or on a sample jet from the microfluidic device. Considerations such as the choice of materials and microfluidic designs are addressed. The combination of microfluidic devices and measurements at large scale X-ray facilities is still emerging and far from mature, but it definitely offers an exciting array of new possibilities.
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Affiliation(s)
- Aghiad Ghazal
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
| | - Josiane P Lafleur
- Dept. of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kell Mortensen
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
| | - Jörg P Kutter
- Dept. of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
| | - Grethe V Jensen
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
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14
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Sanchez-Weatherby J, Moraes I. Crystal Dehydration in Membrane Protein Crystallography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:73-89. [PMID: 27553236 PMCID: PMC6126552 DOI: 10.1007/978-3-319-35072-1_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Crystal dehydration has been successfully implemented to facilitate the structural solution of a number of soluble and membrane protein structures over the years. This chapter will present the currently available tools to undertake controlled crystal dehydration, focusing on some successful membrane protein cases. Also discussed here will be some practical considerations regarding membrane protein crystals and the relationship between different techniques in order to help researchers to select the most suitable technique for their projects.
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Affiliation(s)
| | - Isabel Moraes
- Membrane Protein Laboratory, Diamond Light Source/Imperial College London, Harwell Campus, Didcot, Oxfordshire UK
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15
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Michalska K, Tan K, Chang C, Li H, Hatzos-Skintges C, Molitsky M, Alkire R, Joachimiak A. In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1386-95. [PMID: 26524303 PMCID: PMC4629866 DOI: 10.1107/s1600577515016598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/05/2015] [Indexed: 05/22/2023]
Abstract
A prototype of a 96-well plate scanner for in situ data collection has been developed at the Structural Biology Center (SBC) beamline 19-ID, located at the Advanced Photon Source, USA. The applicability of this instrument for protein crystal diffraction screening and data collection at ambient temperature has been demonstrated. Several different protein crystals, including selenium-labeled, were used for data collection and successful SAD phasing. Without the common procedure of crystal handling and subsequent cryo-cooling for data collection at T = 100 K, crystals in a crystallization buffer show remarkably low mosaicity (<0.1°) until deterioration by radiation damage occurs. Data presented here show that cryo-cooling can cause some unexpected structural changes. Based on the results of this study, the integration of the plate scanner into the 19-ID end-station with automated controls is being prepared. With improvement of hardware and software, in situ data collection will become available for the SBC user program including remote access.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Kemin Tan
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Changsoo Chang
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Hui Li
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | | | - Michael Molitsky
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Randy Alkire
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, USA
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16
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Application of in situ diffraction in high-throughput structure determination platforms. Methods Mol Biol 2015; 1261:233-53. [PMID: 25502203 DOI: 10.1007/978-1-4939-2230-7_13] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.
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17
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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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18
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Márquez JA, Cipriani F. CrystalDirect™: a novel approach for automated crystal harvesting based on photoablation of thin films. Methods Mol Biol 2014; 1091:197-203. [PMID: 24203334 DOI: 10.1007/978-1-62703-691-7_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The last years have seen a major development in automation for protein production, crystallization, and X-ray diffraction data collection, which has contributed to accelerate the pace of structure solution and to facilitate the study of ever more challenging targets through macromolecular crystallography. This has led to a considerable increase in the numbers of crystals produced and analyzed. However the process of recovering crystals from crystallization supports and mounting them in X-ray data collection pins remains a manual and delicate operation. Here we present a novel approach enabling full automation of the crystal mounting process and describe the operation of the first-automated CrystalDirect harvesting unit. Implications for crystallography applications and for the future operational integration of automated crystallization and data collection resources are discussed.
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Affiliation(s)
- José A Márquez
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
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19
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Trastoy B, Lomino JV, Wang LX, Sundberg EJ. Liquid-liquid diffusion crystallization improves the X-ray diffraction of EndoS, an endo-β-N-acetylglucosaminidase from Streptococcus pyogenes with activity on human IgG. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1405-10. [PMID: 24316841 DOI: 10.1107/s1744309113030650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/08/2013] [Indexed: 11/10/2022]
Abstract
Endoglycosidase S (EndoS) is an enzyme secreted by Streptococcus pyogenes that specifically hydrolyzes the β-1,4-di-N-acetylchitobiose core glycan on immunoglobulin G (IgG) antibodies. One of the most common human pathogens and the cause of group A streptococcal infections, S. pyogenes secretes EndoS in order to evade the host immune system by rendering IgG effector mechanisms dysfunctional. On account of its specificity for IgG, EndoS has also been used extensively for chemoenzymatic synthesis of homogeneous IgG glycoprotein preparations and is being developed as a novel therapeutic for a wide range of autoimmune diseases. The structural basis of its enzymatic activity and substrate specificity, however, remains unknown. Here, the purification and crystallization of EndoS are reported. Using traditional hanging-drop and sitting-drop vapor-diffusion crystallization, crystals of EndoS were grown that diffracted to a maximum of 3.5 Å resolution but suffered from severe anisotropy, the data from which could only be reasonably processed to 7.5 Å resolution. When EndoS was crystallized by liquid-liquid diffusion, it was possible to grow crystals with a different space group to those obtained by vapor diffusion. Crystals of wild-type endoglycosidase and glycosynthase constructs of EndoS grown by liquid-liquid diffusion diffracted to 2.6 and 1.9 Å resolution, respectively, with a greatly diminished anisotropy. Despite extensive efforts, the failure to reproduce these liquid-liquid diffusion-grown crystals by vapor diffusion suggests that these crystallization methods each sample a distinct crystallization space.
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Affiliation(s)
- Beatriz Trastoy
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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20
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Giegé R. A historical perspective on protein crystallization from 1840 to the present day. FEBS J 2013; 280:6456-97. [DOI: 10.1111/febs.12580] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/27/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire; Université de Strasourg et CNRS; France
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21
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Roessler CG, Kuczewski A, Stearns R, Ellson R, Olechno J, Orville AM, Allaire M, Soares AS, Héroux A. Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:805-8. [PMID: 23955046 PMCID: PMC3747951 DOI: 10.1107/s0909049513020372] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/23/2013] [Indexed: 05/21/2023]
Abstract
To take full advantage of advanced data collection techniques and high beam flux at next-generation macromolecular crystallography beamlines, rapid and reliable methods will be needed to mount and align many samples per second. One approach is to use an acoustic ejector to eject crystal-containing droplets onto a solid X-ray transparent surface, which can then be positioned and rotated for data collection. Proof-of-concept experiments were conducted at the National Synchrotron Light Source on thermolysin crystals acoustically ejected onto a polyimide `conveyor belt'. Small wedges of data were collected on each crystal, and a complete dataset was assembled from a well diffracting subset of these crystals. Future developments and implementation will focus on achieving ejection and translation of single droplets at a rate of over one hundred per second.
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Affiliation(s)
| | - Anthony Kuczewski
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Richard Stearns
- Labcyte Inc., 1190 Borregas Avenue, Sunnyvale, CA 94089, USA
| | - Richard Ellson
- Labcyte Inc., 1190 Borregas Avenue, Sunnyvale, CA 94089, USA
| | - Joseph Olechno
- Labcyte Inc., 1190 Borregas Avenue, Sunnyvale, CA 94089, USA
| | - Allen M. Orville
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Marc Allaire
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Annie Héroux
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
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22
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Abstract
Droplet-based microfluidics or digital microfluidics is a subclass of microfluidic devices, wherein droplets are generated using active or passive methods. The active method for generation of droplets involves the use of an external factor such as an electric field for droplet generation. Two techniques that fall in this category are dielectrophoresis (DEP) and electrowetting on dielectric (EWOD). In passive methods, the droplet generation depends on the geometry and dimensions of the device. T-junction and flow focusing methods are examples of passive methods used for generation of droplets. In this chapter the methods used for droplet generation, mixing of contents of droplets, and the manipulation of droplets are described in brief. A review of the applications of digital microfluidics with emphasis on the last decade is presented.
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Affiliation(s)
- Sanjiv Sharma
- Institute of Biomedical Engineering & Department of Chemistry, Imperial College, London, UK.
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23
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Cipriani F, Röwer M, Landret C, Zander U, Felisaz F, Márquez JA. CrystalDirect: a new method for automated crystal harvesting based on laser-induced photoablation of thin films. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1393-9. [DOI: 10.1107/s0907444912031459] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/10/2012] [Indexed: 11/10/2022]
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24
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Kurz M, Blattmann B, Kaech A, Briand C, Reardon P, Ziegler U, Gruetter MG. High-throughput counter-diffusion capillary crystallization andin situdiffraction using high-pressure freezing in protein crystallography. J Appl Crystallogr 2012. [DOI: 10.1107/s0021889812034061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Post-crystallization treatments such as manual fishing of crystals and soaking in cryoprotectant solutions, especially of large macromolecular complexes and membrane proteins, are cumbersome and often lead to crystal damage and reduced diffraction data quality. Here, a capillary crystallization plate is presented that simultaneously allows counter-diffusion crystallization at the nanolitre scale in a high-throughput screening mode, low-temperaturein situdiffraction data collection from crystals after cryoprotection and low-temperaturein situdata collection of crystals without the addition of any cryoprotectant after high-pressure (HP) freezing. The development of this plate and plunge cooling of crystals in the capillaries is a major step towards implementing automatedin situhigh-throughput crystal diffraction data collection at a synchrotron beamline. In combination with HP freezing this offers a new opportunity to obtain structural information from fragile crystals of supramolecular complexes that might otherwise not be feasible.
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25
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Ildefonso M, Candoni N, Veesler S. A Cheap, Easy Microfluidic Crystallization Device Ensuring Universal Solvent Compatibility. Org Process Res Dev 2012. [DOI: 10.1021/op200291z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Ildefonso
- Centre Interdisciplinaire
de Nanosciences de Marseille CINAM-CNRS, Aix-Marseille Université, Campus de Luminy, F-13288 Marseille,
France
| | - Nadine Candoni
- Centre Interdisciplinaire
de Nanosciences de Marseille CINAM-CNRS, Aix-Marseille Université, Campus de Luminy, F-13288 Marseille,
France
| | - Stéphane Veesler
- Centre Interdisciplinaire
de Nanosciences de Marseille CINAM-CNRS, Aix-Marseille Université, Campus de Luminy, F-13288 Marseille,
France
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26
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Sørensen HO, Schmidt S, Wright JP, Vaughan GBM, Techert S, Garman EF, Oddershede J, Davaasambuu J, Paithankar KS, Gundlach C, Poulsen HF. Multigrain crystallography. ACTA ACUST UNITED AC 2012. [DOI: 10.1524/zkri.2012.1438] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Nitahara S, Maeki M, Yamaguchi H, Yamashita K, Miyazaki M, Maeda H. Three-dimensional Raman spectroscopic imaging of protein crystals deposited on a nanodroplet. Analyst 2012; 137:5730-5. [DOI: 10.1039/c2an35942a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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28
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Yu Y, Wang X, Oberthür D, Meyer A, Perbandt M, Duan L, Kang Q. Design and application of a microfluidic device for protein crystallization using an evaporation-based crystallization technique. J Appl Crystallogr 2011. [DOI: 10.1107/s0021889811048047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new crystallization system is described, which makes it possible to use an evaporation-based microfluidic crystallization technique for protein crystallization. The gas and water permeability of the used polydimethylsiloxane (PDMS) material enables evaporation of the protein solution in the microfluidic device. The rates of evaporation are controlled by the relative humidity conditions, which are adjusted in a precise and stable way by using saturated solutions of different reagents. The protein crystals could nucleate and grow under different relative humidity conditions. Using this method, crystal growth could be improved so that approximately 1 mm-sized lysozyme crystals were obtained more successfully than using standard methods. The largest lysozyme crystal obtained reached 1.57 mm in size. The disadvantage of the good gas permeability in PDMS microfluidic devices becomes an advantage for protein crystallization. The radius distributions of aggregrates in the solutions inside the described microfluidic devices were derived fromin situdynamic light scattering measurements. The experiments showed that the environment inside of the microfluidic device is more stable than that of conventional crystallization techniques. However, the morphological results showed that the protein crystals grown in the microfluidic device could lose their morphological stability. Air bubbles in microfluidic devices play an important role in the evaporation progress. A model was constructed to analyze the relationship of the rates of evaporation and the growth of air bubbles to the relative humidity.
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29
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Christensen J, Gerdts CJ, Clifton MC, Stewart L. Salvage and storage of infectious disease protein targets in the SSGCID high-throughput crystallization pathway using microfluidics. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1022-6. [PMID: 21904044 PMCID: PMC3169396 DOI: 10.1107/s1744309111023232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 06/14/2011] [Indexed: 12/03/2022]
Abstract
SSGCID protein crystals were salvaged and stored using the MPCS Plug Maker and CrystalCards when high-throughput traditional sitting-drop vapor diffusion initially failed. The MPCS Plug Maker is a microcapillary-based protein-crystallization system for generating diffraction-ready crystals from nanovolumes of protein. Crystallization screening using the Plug Maker was used as a salvage pathway for proteins that failed to crystallize during the initial observation period using the traditional sitting-drop vapor-diffusion method. Furthermore, the CrystalCards used to store the crystallization experiments set up by the Plug Maker are shown be a viable container for long-term storage of protein crystals without a discernable loss of diffraction quality with time. Use of the Plug Maker with SSGCID proteins is demonstrated to be an effective crystal-salvage and storage method.
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30
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Guild K, Zhang Y, Stacy R, Mundt E, Benbow S, Green A, Myler PJ. Wheat germ cell-free expression system as a pathway to improve protein yield and solubility for the SSGCID pipeline. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1027-31. [PMID: 21904045 PMCID: PMC3169397 DOI: 10.1107/s1744309111032143] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 08/08/2011] [Indexed: 02/03/2023]
Abstract
Recombinant expression of proteins of interest in Escherichia coli is an important tool in the determination of protein structure. However, lack of expression and insolubility remain significant challenges to the expression and crystallization of these proteins. The SSGCID program uses a wheat germ cell-free expression system as a rescue pathway for proteins that are either not expressed or insoluble when produced in E. coli. Testing indicates that the system is a valuable tool for these protein targets. Further increases in solubility were obtained by the addition of the NVoy polymer reagent to the reaction mixture. These data indicate that this eukaryotic cell-free expression system has a high success rate and that the addition of specific reagents can increase the yield of soluble protein.
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Affiliation(s)
- Katherine Guild
- Seattle Biomedical Research Institute, USA
- Department of Global Health, University of Washington, USA
| | - Yang Zhang
- Seattle Biomedical Research Institute, USA
| | | | | | | | | | - Peter J. Myler
- Seattle Biomedical Research Institute, USA
- Department of Global Health, University of Washington, USA
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31
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Stojanoff V, Jakoncic J, Oren DA, Nagarajan V, Navarro Poulsen JC, Adams-Cioaba MA, Bergfors T, Sommer MOA. From screen to structure with a harvestable microfluidic device. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:971-5. [PMID: 21821908 PMCID: PMC3151141 DOI: 10.1107/s1744309111024456] [Citation(s) in RCA: 19] [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: 03/22/2011] [Accepted: 06/21/2011] [Indexed: 11/11/2022]
Abstract
Advances in automation have facilitated the widespread adoption of high-throughput vapour-diffusion methods for initial crystallization screening. However, for many proteins, screening thousands of crystallization conditions fails to yield crystals of sufficient quality for structural characterization. Here, the rates of crystal identification for thaumatin, catalase and myoglobin using microfluidic Crystal Former devices and sitting-drop vapour-diffusion plates are compared. It is shown that the Crystal Former results in a greater number of identified initial crystallization conditions compared with vapour diffusion. Furthermore, crystals of thaumatin and lysozyme obtained in the Crystal Former were used directly for structure determination both in situ and upon harvesting and cryocooling. On the basis of these results, a crystallization strategy is proposed that uses multiple methods with distinct kinetic trajectories through the protein phase diagram to increase the output of crystallization pipelines.
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Affiliation(s)
- Vivian Stojanoff
- National Synchrotron Light Source, Brookhaven National Laboratories, Upton, NY 11973, USA
| | - Jean Jakoncic
- National Synchrotron Light Source, Brookhaven National Laboratories, Upton, NY 11973, USA
| | - Deena A. Oren
- Structural Biology Resource Center, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - V. Nagarajan
- JAN Scientific Inc., 4726 Eleventh Avenue NE, Suite 101, Seattle, WA 98105, USA
| | - Jens-Christian Navarro Poulsen
- Department of Chemistry, Biophysical Chemistry Group, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | | | - Terese Bergfors
- Department of Cell and Molecular Biology, Uppsala University, SE-75 124 Uppsala, Sweden
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32
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Paithankar KS, Sørensen HO, Wright JP, Schmidt S, Poulsen HF, Garman EF. Simultaneous X-ray diffraction from multiple single crystals of macromolecules. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:608-18. [DOI: 10.1107/s0907444911015617] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/25/2011] [Indexed: 11/11/2022]
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33
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Soliman ASM, Warkentin M, Apker B, Thorne RE. Development of high-performance X-ray transparent crystallization plates for in situ protein crystal screening and analysis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:646-56. [PMID: 21697603 DOI: 10.1107/s090744491101883x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/17/2011] [Indexed: 11/10/2022]
Abstract
X-ray transparent crystallization plates based upon a novel drop-pinning technology provide a flexible, simple and inexpensive approach to protein crystallization and screening. The plates consist of open cells sealed top and bottom by thin optically, UV and X-ray transparent films. The plates do not need wells or depressions to contain liquids. Instead, protein drops and reservoir solution are held in place by rings with micrometre dimensions that are patterned onto the bottom film. These rings strongly pin the liquid contact lines, thereby improving drop shape and position uniformity, and thus crystallization reproducibility, and simplifying automated image analysis of drop contents. The same rings effectively pin solutions containing salts, proteins, cryoprotectants, oils, alcohols and detergents. Strong pinning by rings allows the plates to be rotated without liquid mixing to 90° for X-ray data collection or to be inverted for hanging-drop crystallization. The plates have the standard SBS format and are compatible with standard liquid-handling robots.
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Luft JR, Snell EH, Detitta GT. Lessons from high-throughput protein crystallization screening: 10 years of practical experience. Expert Opin Drug Discov 2011; 6:465-80. [PMID: 22646073 DOI: 10.1517/17460441.2011.566857] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION X-ray crystallography provides the majority of our structural biological knowledge at a molecular level and, in terms of pharmaceutical design, is a valuable tool to accelerate discovery. It is the premier technique in the field, but its usefulness is significantly limited by the need to grow well-diffracting crystals. It is for this reason that high-throughput crystallization has become a key technology that has matured over the past 10 years through the field of structural genomics. Areas covered : The authors describe their experiences in high-throughput crystallization screening in the context of structural genomics and the general biomedical community. They focus on the lessons learnt from the operation of a high-throughput crystallization-screening laboratory, which to date has screened over 12,500 biological macromolecules. They also describe the approaches taken to maximize the success while minimizing the effort. Through this, the authors hope that the reader will gain an insight into the efficient design of a laboratory and protocols to accomplish high-throughput crystallization on a single-, multiuser laboratory or industrial scale. Expert opinion : High-throughput crystallization screening is readily available but, despite the power of the crystallographic technique, getting crystals is still not a solved problem. High-throughput approaches can help when used skillfully; however, they still require human input in the detailed analysis and interpretation of results to be more successful.
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Affiliation(s)
- Joseph R Luft
- Hauptman-Woodward Medical Research Institute , 700 Ellicott St., Buffalo, NY 14203 , USA +1 716 898 8623 ; +1 716 898 8660 ;
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Zeng S, Liu X, Xie H, Lin B. Basic Technologies for Droplet Microfluidics. MICROFLUIDICS 2011; 304:69-90. [DOI: 10.1007/128_2011_149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Berger MA, Decker JH, Mathews II. Diffraction study of protein crystals grown in cryoloops and micromounts. J Appl Crystallogr 2010; 43:1513-1518. [PMID: 22477781 PMCID: PMC3253742 DOI: 10.1107/s0021889810040409] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Accepted: 10/08/2010] [Indexed: 11/11/2022] Open
Abstract
Protein crystals are usually grown in hanging or sitting drops and generally get transferred to a loop or micromount for cryocooling and data collection. This paper describes a method for growing crystals on cryoloops for easier manipulation of the crystals for data collection. This study also investigates the steps for the automation of this process and describes the design of a new tray for the method. The diffraction patterns and the structures of three proteins grown by both the new method and the conventional hanging-drop method are compared. The new setup is optimized for the automation of the crystal mounting process. Researchers could prepare nanolitre drops under ordinary laboratory conditions by growing the crystals directly in loops or micromounts. As has been pointed out before, higher levels of supersaturation can be obtained in very small volumes, and the new method may help in the exploration of additional crystallization conditions.
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Affiliation(s)
- Michael A. Berger
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, SSRL MS 99, Menlo Park, CA 94025, USA
| | - Johannes H. Decker
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, SSRL MS 99, Menlo Park, CA 94025, USA
| | - Irimpan I. Mathews
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, SSRL MS 99, Menlo Park, CA 94025, USA
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Sauter NK, Poon BK. Autoindexing with outlier rejection and identification of superimposed lattices. J Appl Crystallogr 2010; 43:611-616. [PMID: 20502598 PMCID: PMC2875182 DOI: 10.1107/s0021889810010782] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 03/22/2010] [Indexed: 11/11/2022] Open
Abstract
Constructing a model lattice to fit the observed Bragg diffraction pattern is straightforward for perfect samples, but indexing can be challenging when artifacts are present, such as poorly shaped spots, split crystals giving multiple closely aligned lattices and outright superposition of patterns from aggregated microcrystals. To optimize the lattice model against marginal data, refinement can be performed using a subset of the observations from which the poorly fitting spots have been discarded. Outliers are identified by assuming a Gaussian error distribution for the best-fitting spots and points diverging from this distribution are culled. The set of remaining observations produces a superior lattice model, while the rejected observations can be used to identify a second crystal lattice, if one is present. The prevalence of outliers provides a potentially useful measure of sample quality. The described procedures are implemented for macromolecular crystallography within the autoindexing program labelit.index (http://cci.lbl.gov/labelit).
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Affiliation(s)
- Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
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Choi JH, Lee SK, Lim JM, Yang SM, Yi GR. Designed pneumatic valve actuators for controlled droplet breakup and generation. LAB ON A CHIP 2010; 10:456-461. [PMID: 20126685 DOI: 10.1039/b915596a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The dynamic breakup of emulsion droplets was demonstrated in double-layered microfluidic devices equipped with designed pneumatic actuators. Uniform emulsion droplets, produced by shearing at a T-junction, were broken into smaller droplets when they passed downstream through constrictions formed by a pneumatically actuated valve in the upper control layer. The valve-assisted droplet breakup was significantly affected by the shape and layout of the control valves on the emulsion flow channel. Interestingly, by actuating the pneumatic valve immediately above the T-junction, the sizes of the emulsion droplets were controlled precisely in a programmatic manner that produced arrays of uniform emulsion droplets in various sizes and dynamic patterns.
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Affiliation(s)
- Jae-Hoon Choi
- National Creative Research Initiative Center for Integrated Optofluidic Systems, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea
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Mark D, Haeberle S, Roth G, Von Stetten F, Zengerle R. Microfluidic Lab-on-a-Chip Platforms: Requirements, Characteristics and Applications. MICROFLUIDICS BASED MICROSYSTEMS 2010. [DOI: 10.1007/978-90-481-9029-4_17] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Mark D, Haeberle S, Roth G, von Stetten F, Zengerle R. Microfluidic lab-on-a-chip platforms: requirements, characteristics and applications. Chem Soc Rev 2010; 39:1153-82. [PMID: 20179830 DOI: 10.1039/b820557b] [Citation(s) in RCA: 765] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel Mark
- HSG-IMIT-Institut für Mikro- und Informationstechnik, Wilhelm-Schickard-Strasse 10, 78052 Villingen-Schwenningen, Germany
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41
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Srisa-Art M, Bonzani IC, Williams A, Stevens MM, deMello AJ, Edel JB. Identification of rare progenitor cells from human periosteal tissue using droplet microfluidics. Analyst 2009; 134:2239-45. [PMID: 19838410 DOI: 10.1039/b910472k] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The isolation and characterisation of single cells from a heterogeneous population are important processes in cell biology, immunology, stem cell research, and cancer research. In the development of novel cell-based therapies, there is a considerable need to target specific cell types to allow for further analysis and amplification ex vivo. We introduce, herein, the use of droplet-based microfluidics as a platform technology for the identification and quantification of distinct cell phenotypes. Using molecular labelling of specific cell populations by antibodies and fluorescent dyes, detection of single cells encapsulated within picolitre-sized aqueous droplets can be performed using high-sensitivity confocal fluorescence detection. Specifically, rare progenitor cells were immunodetected within a heterogeneous population of cells isolated from human periosteal tissue. Using this model human cell population, the accuracy and reproducibility of the droplet system were tested and the results were verified using conventional flow cytometry. It was found that the quantitation of phenotypic subpopulations measured using both techniques is directly comparable. Accordingly, this study demonstrates the biological capacity of droplet-based microfluidics for cellular analysis and provides a necessary first step towards the development of a novel cell sorting technology.
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Affiliation(s)
- Monpichar Srisa-Art
- Department of Chemistry, Imperial College London, South Kensington, London, UK SW7 2AZ
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Chen YF, Tate MW, Gruner SM. Facilitating protein crystal cryoprotection in thick-walled plastic capillaries by high-pressure cryocooling. J Appl Crystallogr 2009; 42:525-530. [PMID: 19529790 PMCID: PMC2684497 DOI: 10.1107/s0021889809011315] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 03/26/2009] [Indexed: 11/10/2022] Open
Abstract
Many steps in the X-ray crystallographic solution of protein structures have been automated. However, the harvesting and cryocooling of crystals still rely primarily on manual handling, frequently with consequent mechanical damage. An attractive alternative is to grow crystals directly inside robust plastic capillaries that may be cryocooled and mounted on the beamline goniometer. In this case, it is still desirable to devise a way to cryoprotect the crystals, which is difficult owing to the poor thermal conductivity of thick plastic capillary walls and the large thermal mass of the capillary and internal mother liquor. A method is described to circumvent these difficulties. It is shown that high-pressure cryocooling substantially reduced the minimal concentrations of cryoprotectants required to cryocool water inside capillaries without formation of ice crystals. The minimal concentrations of PEG 200, PEG 400 and glycerol necessary for complete vitrification under pressure cryocooling were determined.
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Affiliation(s)
- Yi-Fan Chen
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
- Cornell High Energy Synchrotron Source (CHESS), Ithaca, NY 14853, USA
| | - Mark W. Tate
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
- Cornell High Energy Synchrotron Source (CHESS), Ithaca, NY 14853, USA
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Dhouib K, Khan Malek C, Pfleging W, Gauthier-Manuel B, Duffait R, Thuillier G, Ferrigno R, Jacquamet L, Ohana J, Ferrer JL, Théobald-Dietrich A, Giegé R, Lorber B, Sauter C. Microfluidic chips for the crystallization of biomacromolecules by counter-diffusion and on-chip crystal X-ray analysis. LAB ON A CHIP 2009; 9:1412-21. [PMID: 19417908 DOI: 10.1039/b819362b] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microfluidic devices were designed to perform on micromoles of biological macromolecules and viruses the search and the optimization of crystallization conditions by counter-diffusion, as well as the on-chip analysis of crystals by X-ray diffraction. Chips composed of microchannels were fabricated in poly-dimethylsiloxane (PDMS), poly-methyl-methacrylate (PMMA) and cyclo-olefin-copolymer (COC) by three distinct methods, namely replica casting, laser ablation and hot embossing. The geometry of the channels was chosen to ensure that crystallization occurs in a convection-free environment. The transparency of the materials is compatible with crystal growth monitoring by optical microscopy. The quality of the protein 3D structures derived from on-chip crystal analysis by X-ray diffraction using a synchrotron radiation was used to identify the most appropriate polymers. Altogether the results demonstrate that for a novel biomolecule, all steps from the initial search of crystallization conditions to X-ray diffraction data collection for 3D structure determination can be performed in a single chip.
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Affiliation(s)
- Kaouthar Dhouib
- Architecture et réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084, Strasbourg, France
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Courtois F, Olguin LF, Whyte G, Theberge AB, Huck WTS, Hollfelder F, Abell C. Controlling the Retention of Small Molecules in Emulsion Microdroplets for Use in Cell-Based Assays. Anal Chem 2009; 81:3008-16. [DOI: 10.1021/ac802658n] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fabienne Courtois
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Luis F. Olguin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Graeme Whyte
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Ashleigh B. Theberge
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Wilhelm T. S. Huck
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Chris Abell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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Abstract
Microfluidics offers a wide range of new tools that permit one to revisit the formation of crystals in solution and yield insights into crystallization processes. We review such recent microfluidic devices and particularly emphasize lab-on-chips dedicated to the high-throughput screening of crystallization conditions of proteins with nanolitre consumption. We also thoroughly discuss the possibilities offered by the microfluidic tools to acquire thermodynamic and kinetic data that may improve industrial processes and shed a new light on nucleation and growth mechanisms.
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Affiliation(s)
- Jacques Leng
- Université Bordeaux-1, Laboratoire du Futur, Pessac cedex, France
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Chapter 8 Advances in Microfluidic Membrane Protein Crystallization Techniques. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Gerdts CJ, Elliott M, Lovell S, Mixon MB, Napuli AJ, Staker BL, Nollert P, Stewart L. The plug-based nanovolume Microcapillary Protein Crystallization System (MPCS). ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2008; 64:1116-22. [PMID: 19020349 PMCID: PMC2585160 DOI: 10.1107/s0907444908028060] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 09/02/2008] [Indexed: 12/01/2022]
Abstract
The Microcapillary Protein Crystallization System (MPCS) is a new protein-crystallization technology used to generate nanolitre-sized crystallization experiments for crystal screening and optimization. Using the MPCS, diffraction-ready crystals were grown in the plastic MPCS CrystalCard and were used to solve the structure of methionine-R-sulfoxide reductase. The Microcapillary Protein Crystallization System (MPCS) embodies a new semi-automated plug-based crystallization technology which enables nanolitre-volume screening of crystallization conditions in a plasticware format that allows crystals to be easily removed for traditional cryoprotection and X-ray diffraction data collection. Protein crystals grown in these plastic devices can be directly subjected to in situ X-ray diffraction studies. The MPCS integrates the formulation of crystallization cocktails with the preparation of the crystallization experiments. Within microfluidic Teflon tubing or the microfluidic circuitry of a plastic CrystalCard, ∼10–20 nl volume droplets are generated, each representing a microbatch-style crystallization experiment with a different chemical composition. The entire protein sample is utilized in crystallization experiments. Sparse-matrix screening and chemical gradient screening can be combined in one comprehensive ‘hybrid’ crystallization trial. The technology lends itself well to optimization by high-granularity gradient screening using optimization reagents such as precipitation agents, ligands or cryoprotectants.
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Affiliation(s)
- Cory J Gerdts
- Accelerated Technologies Center for Gene to 3D Structure, USA
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Srisa-Art M, Dyson EC, deMello AJ, Edel JB. Monitoring of Real-Time Streptavidin−Biotin Binding Kinetics Using Droplet Microfluidics. Anal Chem 2008; 80:7063-7. [DOI: 10.1021/ac801199k] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Monpichar Srisa-Art
- Department of Chemistry, and Institute of Biomedical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Emily C. Dyson
- Department of Chemistry, and Institute of Biomedical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Andrew J. deMello
- Department of Chemistry, and Institute of Biomedical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Joshua B. Edel
- Department of Chemistry, and Institute of Biomedical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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Protein crystallization in restricted geometry: advancing old ideas for modern times in structural proteomics. Methods Mol Biol 2008; 426:363-76. [PMID: 18542876 DOI: 10.1007/978-1-60327-058-8_23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
In the structural genomics period traditional methods for protein crystallization have been eclipsed by automation using batch or vapor diffusion equilibration to find conditions conducive for protein crystal growth. Although many globular and soluble proteins predominantly from prokaryotes have been crystallized and their structures solved by high throughput approaches, the remaining difficult proteins require more systematic and reflective methods combining miniaturization and integration of modern and traditional crystallography techniques. One of these conventional methods is growing crystals in restricted geometry, which is a historically well-known concept and a practical technique under-used by today's crystallographers. This chapter presents practical guidelines to use capillaries for microbatch crystallization screening and counter-diffusion crystallization as valuable techniques to obtain protein crystals in confined volumes. The emphasis in the authors' application is to perform broad-based screening with a microgram amount of protein, optimize crystal growth in a supersaturation gradient, and undergo in situ x-ray data analysis for x-ray crystallography without invasive manipulation. Applications and concepts presented here bring to light future prerequisites for the next generation of automation for structural genomics.
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Huebner A, Sharma S, Srisa-Art M, Hollfelder F, Edel JB, Demello AJ. Microdroplets: a sea of applications? LAB ON A CHIP 2008; 8:1244-54. [PMID: 18651063 DOI: 10.1039/b806405a] [Citation(s) in RCA: 375] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The exploitation of microdroplets produced within microfluidic environments has recently emerged as a new and exciting technological platform for applications within the chemical and biological sciences. Interest in microfluidic systems has been stimulated by a range of fundamental features that accompany system miniaturization. Such features include the ability to process and handle small volumes of fluid, improved analytical performance when compared to macroscale analogues, reduced instrumental footprints, low unit cost, facile integration of functional components and the exploitation of atypical fluid dynamics to control molecules in both time and space. Moreover, microfluidic systems that generate and utilize a stream of sub-nanolitre droplets dispersed within an immiscible continuous phase have the added advantage of allowing ultra-high throughput experimentation and being able to mimic conditions similar to that of a single cell (in terms of volume, pH, and salt concentration) thereby compartmentalizing biological and chemical reactions. This review provides an overview of methods for generating, controlling and manipulating droplets. Furthermore, we discuss key fields of use in which such systems may make a significant impact, with particular emphasis on novel applications in the biological and physical sciences.
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Affiliation(s)
- Ansgar Huebner
- Department of Chemistry, Lensfield Road, Cambridge, UKCB2 1EW.
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