1
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Saha S, Özden C, Samkutty A, Russi S, Cohen A, Stratton MM, Perry SL. Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature. LAB ON A CHIP 2023; 23:2075-2090. [PMID: 36942575 PMCID: PMC10631519 DOI: 10.1039/d2lc01194h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Proteins are long chains of amino acid residues that perform a myriad of functions in living organisms, including enzymatic reactions, signalling, and maintaining structural integrity. Protein function is determined directly by the protein structure. X-ray crystallography is the primary technique for determining the 3D structure of proteins, and facilitates understanding the effects of protein structure on function. The first step towards structure determination is crystallizing the protein of interest. We have developed a centrifugally-actuated microfluidic device that incorporates the fluid handling and metering necessary for protein crystallization. Liquid handling takes advantage of surface forces to control fluid flow and enable metering, without the need for any fluidic or pump connections. Our approach requires only the simple steps of pipetting the crystallization reagents into the device followed by either spinning or shaking to set up counter-diffusive protein crystallization trials. The use of thin, UV-curable polymers with a high level of X-ray transparency allows for in situ X-ray crystallography, eliminating the manual handling of fragile protein crystals and streamlining the process of protein structure analysis. We demonstrate the utility of our device using hen egg white lysozyme as a model system, followed by the crystallization and in situ, room temperature structural analysis of the hub domain of calcium-calmodulin dependent kinase II (CaMKIIβ).
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Affiliation(s)
- Sarthak Saha
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA.
| | - Can Özden
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Alfred Samkutty
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Silvia Russi
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina Cohen
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Sarah L Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA.
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2
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Vasireddi R, Gardais A, Chavas LMG. Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments. MICROMACHINES 2022; 13:1365. [PMID: 36014287 PMCID: PMC9416059 DOI: 10.3390/mi13081365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Cyclic-olefin-copolymer (COC)-based microfluidic devices are increasingly becoming the center of highly valuable research for in situ X-ray measurements due to their compatibility with X-rays, biological compounds, chemical resistance, optical properties, low cost, and simplified handling. COC microfluidic devices present potential solutions to challenging biological applications such as protein binding, folding, nucleation, growth kinetics, and structural changes. In recent years, the techniques applied to manufacturing and handling these devices have capitalized on enormous progress toward small-scale sample probing. Here, we describe the new and innovative design aspects, fabrication, and experimental implementation of low-cost and micron-sized X-ray-compatible microfluidic sample environments that address diffusion-based crystal formation for crystallographic characterization. The devices appear fully compatible with crystal growth and subsequent X-ray diffraction experiments, resulting in remarkably low background data recording. The results highlighted in this research demonstrate how the engineered microfluidic devices allow the recording of accurate crystallographic data at room temperature and structure determination at high resolution.
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Affiliation(s)
| | - Antonin Gardais
- Synchrotron SOLEIL, L’Orme des Merisier, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Leonard M. G. Chavas
- Department of Applied Physics, Nagoya University, Nagoya 464-8603, Japan
- Synchrotron Radiation Research Center, Nagoya University, Nagoya 464-8603, Japan
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3
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Gilbile D, Shelby ML, Lyubimov AY, Wierman JL, Monteiro DCF, Cohen AE, Russi S, Coleman MA, Frank M, Kuhl TL. Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography. LAB ON A CHIP 2021; 21:4831-4845. [PMID: 34821226 PMCID: PMC8915944 DOI: 10.1039/d1lc00810b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The practice of serial X-ray crystallography (SX) depends on efficient, continuous delivery of hydrated protein crystals while minimizing background scattering. Of the two major types of sample delivery devices, fixed-target devices offer several advantages over widely adopted jet injectors, including: lower sample consumption, clog-free delivery, and the ability to control on-chip crystal density to improve hit rates. Here we present our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial measurements at both synchrotrons and X-ray free electron lasers (XFELs). Our design includes highly X-ray-transparent enclosing thin film layers tuned to minimize scatter background, adaptable sample flow layers tuned to match crystal size, and a large sample area compatible with both raster scanning and rotation based serial data collection. The optically transparent chips can be used both for in situ protein crystallization (to eliminate crystal handling) or crystal slurry loading, with prepared samples stable for weeks in a humidified environment and for several hours in ambient conditions. Serial oscillation crystallography, using a multi-crystal rotational data collection approach, at a microfocus synchrotron beamline (SSRL, beamline 12-1) was used to benchmark the performance of the chips. High-resolution structures (1.3-2.7 Å) were collected from five different proteins - hen egg white lysozyme, thaumatin, bovine liver catalase, concanavalin-A (type VI), and SARS-CoV-2 nonstructural protein NSP5. Overall, our modular fabrication approach enables precise control over the cross-section of materials in the X-ray beam path and facilitates chip adaption to different sample and beamline requirements for user-friendly, straightforward diffraction measurements at room temperature.
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Affiliation(s)
- Deepshika Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
| | - Megan L Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Artem Y Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Diana C F Monteiro
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew A Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Radiation Oncology, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Matthias Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Tonya L Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
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4
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Sui S, Mulichak A, Kulathila R, McGee J, Filiatreault D, Saha S, Cohen A, Song J, Hung H, Selway J, Kirby C, Shrestha OK, Weihofen W, Fodor M, Xu M, Chopra R, Perry SL. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening. J Appl Crystallogr 2021; 54:1034-1046. [PMID: 34429718 PMCID: PMC8366422 DOI: 10.1107/s1600576721004155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/18/2021] [Indexed: 11/10/2022] Open
Abstract
A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and have nine capillary channels per chip. The chip was designed for ease of sample manipulation, sample stability and minimal X-ray background. 3D-printed frames and cassettes conforming to SBS standards are used to house the capillary chips, providing additional mechanical stability and compatibility with automated liquid- and sample-handling robotics. These devices enable an innovative in situ crystal-soaking screening workflow, akin to high-throughput compound screening, such that quantitative electron density maps sufficient to determine weak binding events are efficiently obtained. This work paves the way for adopting a room-temperature microfluidics-based sample delivery method at synchrotron sources to facilitate high-throughput protein-crystallography-based screening of compounds at high concentration with the aim of discovering novel binding events in an automated manner.
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Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Anne Mulichak
- IMCA-CAT, Argonne National Laboratory, Lemont, IL, USA
| | | | - Joshua McGee
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Sarthak Saha
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Aina Cohen
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - Jinhu Song
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | | | - Jonathan Selway
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christina Kirby
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Om K. Shrestha
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Michelle Fodor
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rajiv Chopra
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Sarah L. Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
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5
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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6
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Ren Z, Wang C, Shin H, Bandara S, Kumarapperuma I, Ren MY, Kang W, Yang X. An automated platform for in situ serial crystallography at room temperature. IUCRJ 2020; 7:1009-1018. [PMID: 33209315 PMCID: PMC7642789 DOI: 10.1107/s2052252520011288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Direct observation of functional motions in protein structures is highly desirable for understanding how these nanomachineries of life operate at the molecular level. Because cryogenic temperatures are non-physiological and may prohibit or even alter protein structural dynamics, it is necessary to develop robust X-ray diffraction methods that enable routine data collection at room temperature. We recently reported a crystal-on-crystal device to facilitate in situ diffraction of protein crystals at room temperature devoid of any sample manipulation. Here an automated serial crystallography platform based on this crystal-on-crystal technology is presented. A hardware and software prototype has been implemented, and protocols have been established that allow users to image, recognize and rank hundreds to thousands of protein crystals grown on a chip in optical scanning mode prior to serial introduction of these crystals to an X-ray beam in a programmable and high-throughput manner. This platform has been tested extensively using fragile protein crystals. We demonstrate that with affordable sample consumption, this in situ serial crystallography technology could give rise to room-temperature protein structures of higher resolution and superior map quality for those protein crystals that encounter difficulties during freezing. This serial data collection platform is compatible with both monochromatic oscillation and Laue methods for X-ray diffraction and presents a widely applicable approach for static and dynamic crystallographic studies at room temperature.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
| | - Cong Wang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Sepalika Bandara
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Michael Y. Ren
- A. James Clark School of Engineering, University of Maryland, College Park, MD 20742, USA
| | - Weijia Kang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
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7
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Zhao FZ, Sun B, Yu L, Xiao QJ, Wang ZJ, Chen LL, Liang H, Wang QS, He JH, Yin DC. A novel sample delivery system based on circular motion for in situ serial synchrotron crystallography. LAB ON A CHIP 2020; 20:3888-3898. [PMID: 32966481 DOI: 10.1039/d0lc00443j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A sample delivery system is one of the key parts of serial crystallography. It is the main limiting factor affecting the application of serial crystallography. At present, although a variety of useful sample delivery systems have been developed for serial crystallography, it still remains the focus of the field to further improve the performance and efficiency of sample delivery. In existing sample delivery technologies, samples are usually delivered in linear motion. Here we show that the samples can also be delivered using circular motion, which is a novel motion mode never tested before. In this paper, we report a microfluidic rotating-target sample delivery device, which is characterized by the circular motion of the samples, and verify the performance of the device at a synchrotron radiation facility. The microfluidic rotating-target sample delivery device consists of two parts: a microfluidic sample plate and a motion control system. Sample delivery is realized by rotating the microfluidic sample plate containing in situ grown crystals. This device offers significant advantages, including a very wide adjustable range of delivery speed, low background noise, and low sample consumption. Using the microfluidic rotating-target device, we carried out in situ serial crystallography experiments with lysozyme and proteinase K as model samples at the Shanghai Synchrotron Radiation Facility, and performed structural determination based on the serial crystallographic data. The results showed that the designed device is fully compatible with the synchrotron radiation facility, and the structure determination of proteins is successful using the serial crystallographic data obtained with the device.
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Affiliation(s)
- Feng-Zhu Zhao
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Li Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
| | - Qing-Jie Xiao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China. and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zhi-Jun Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Liang-Liang Chen
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | - Huan Liang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | - Qi-Sheng Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China. and The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Da-Chuan Yin
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China. and Shenzhen Research Institute, Northwestern Polytechnical University, Shenzhen, China
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8
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Gavira JA, Rodriguez-Ruiz I, Martinez-Rodriguez S, Basu S, Teychené S, McCarthy AA, Mueller-Dieckman C. Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips. Acta Crystallogr D Struct Biol 2020; 76:751-758. [PMID: 32744257 DOI: 10.1107/s2059798320008475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Sample handling and manipulation for cryoprotection currently remain critical factors in X-ray structural determination. While several microchips for macromolecular crystallization have been proposed during the last two decades to partially overcome crystal-manipulation issues, increased background noise originating from the scattering of chip-fabrication materials has so far limited the attainable resolution of diffraction data. Here, the conception and use of low-cost, X-ray-transparent microchips for in situ crystallization and direct data collection, and structure determination at atomic resolution close to 1.0 Å, is presented. The chips are fabricated by a combination of either OSTEMER and Kapton or OSTEMER and Mylar materials for the implementation of counter-diffusion crystallization experiments. Both materials produce a sufficiently low scattering background to permit atomic resolution diffraction data collection at room temperature and the generation of 3D structural models of the tested model proteins lysozyme, thaumatin and glucose isomerase. Although the high symmetry of the three model protein crystals produced almost complete data sets at high resolution, the potential of in-line data merging and scaling of the multiple crystals grown along the microfluidic channels is also presented and discussed.
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Affiliation(s)
- Jose A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Spain
| | - Isaac Rodriguez-Ruiz
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INP, INSA, UPS Toulouse, Toulouse, France
| | - Sergio Martinez-Rodriguez
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Spain
| | - Shibom Basu
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Sébastien Teychené
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INP, INSA, UPS Toulouse, Toulouse, France
| | - Andrew A McCarthy
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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9
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Junius N, Jaho S, Sallaz-Damaz Y, Borel F, Salmon JB, Budayova-Spano M. A microfluidic device for both on-chip dialysis protein crystallization and in situ X-ray diffraction. LAB ON A CHIP 2020; 20:296-310. [PMID: 31804643 DOI: 10.1039/c9lc00651f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper reports a versatile microfluidic chip developed for on-chip crystallization of proteins through the dialysis method and in situ X-ray diffraction experiments. A microfabrication process enabling the integration of regenerated cellulose dialysis membranes between two layers of the microchip is thoroughly described. We also describe a rational approach for optimizing on-chip protein crystallization via chemical composition and temperature control, allowing the crystal size, number and quality to be tailored. Combining optically transparent microfluidics and dialysis provides both precise control over the experiment and reversible exploration of the crystallization conditions. In addition, the materials composing the microfluidic chip were tested for their transparency to X-rays in order to assess their compatibility for in situ diffraction data collection. Background scattering was evaluated using a synchrotron X-ray source and the background noise generated by our microfluidic device was compared to that produced by commercial crystallization plates used for diffraction experiments at room temperature. Once crystals of 3 model proteins (lysozyme, IspE, and insulin) were grown on-chip, the microchip was mounted onto the beamline and partial diffraction data sets were collected in situ from several isomorphous crystals and were merged to a complete data set for structure determination. We therefore propose a robust and inexpensive way to fabricate microchips that cover the whole pipeline from crystal growth to the beam and does not require any handling of the protein crystals prior to the diffraction experiment, allowing the collection of crystallographic data at room temperature for solving the three-dimensional structure of the proteins under study. The results presented here allow serial crystallography experiments on synchrotrons and X-ray lasers under dynamically controllable sample conditions to be observed using the developed microchips.
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Affiliation(s)
- Niels Junius
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Sofia Jaho
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Franck Borel
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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10
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Wang JW, Gao J, Wang HF, Jin QH, Rao B, Deng W, Cao Y, Lei M, Ye S, Fang Q. Miniaturization of the Whole Process of Protein Crystallographic Analysis by a Microfluidic Droplet Robot: From Nanoliter-Scale Purified Proteins to Diffraction-Quality Crystals. Anal Chem 2019; 91:10132-10140. [PMID: 31276402 DOI: 10.1021/acs.analchem.9b02138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To obtain diffraction-quality crystals is one of the largest barriers to analyze the protein structure using X-ray crystallography. Here we describe a microfluidic droplet robot that enables successful miniaturization of the whole process of crystallization experiments including large-scale initial crystallization screening, crystallization optimization, and crystal harvesting. The combination of the state-of-the-art droplet-based microfluidic technique with the microbatch crystallization mode dramatically reduces the volumes of droplet crystallization reactors to tens nanoliter range, allowing large-scale initial screening of 1536 crystallization conditions and multifactor crystallization condition optimization with extremely low protein consumption, and on-chip harvesting of diffraction-quality crystals directly from the droplet reactors. We applied the droplet robot in miniaturized crystallization experiments of seven soluble proteins and two membrane proteins, and on-chip crystal harvesting of six proteins. The X-ray diffraction data sets of these crystals were collected using synchrotron radiation for analyzing the structures with similar diffraction qualities as conventional crystallization methods.
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Affiliation(s)
- Jian-Wei Wang
- Institute of Microanalytical Systems, Department of Chemistry , Zhejiang University , Hangzhou , 310058 , China
| | - Jie Gao
- Institute of Microanalytical Systems, Department of Chemistry , Zhejiang University , Hangzhou , 310058 , China
| | - Hui-Feng Wang
- Institute of Microanalytical Systems, Department of Chemistry , Zhejiang University , Hangzhou , 310058 , China
| | - Qiu-Heng Jin
- Life Sciences Institute , Zhejiang University , Hangzhou , 310058 , China
| | - Bing Rao
- State Key Laboratory of Molecular Biology , National Center for Protein Science · Shanghai , Shanghai , 201210 , China
| | - Wei Deng
- State Key Laboratory of Molecular Biology , National Center for Protein Science · Shanghai , Shanghai , 201210 , China
| | - Yu Cao
- State Key Laboratory of Molecular Biology , National Center for Protein Science · Shanghai , Shanghai , 201210 , China
| | - Ming Lei
- State Key Laboratory of Molecular Biology , National Center for Protein Science · Shanghai , Shanghai , 201210 , China
| | - Sheng Ye
- Life Sciences Institute , Zhejiang University , Hangzhou , 310058 , China.,School of Life Sciences , Tianjin University , Tianjin , 300072 , China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry , Zhejiang University , Hangzhou , 310058 , China
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11
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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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12
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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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13
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Thompson S, Shipman PD, Shipman SP, Zurlinden TJ. The counterdiffusion of HCl and NH 3: An experimental and modeling analysis of topochemistry, diffusion, reaction, and phase transitions. J Chem Phys 2019; 150:154306. [DOI: 10.1063/1.5083927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Stephen Thompson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Patrick D. Shipman
- Department of Mathematics, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Stephen P. Shipman
- Department of Mathematics, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Todd J. Zurlinden
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
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14
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Wierman JL, Paré-Labrosse O, Sarracini A, Besaw JE, Cook MJ, Oghbaey S, Daoud H, Mehrabi P, Kriksunov I, Kuo A, Schuller DJ, Smith S, Ernst OP, Szebenyi DME, Gruner SM, Miller RJD, Finke AD. Fixed-target serial oscillation crystallography at room temperature. IUCRJ 2019; 6:305-316. [PMID: 30867928 PMCID: PMC6400179 DOI: 10.1107/s2052252519001453] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/25/2019] [Indexed: 05/18/2023]
Abstract
A fixed-target approach to high-throughput room-temperature serial synchrotron crystallography with oscillation is described. Patterned silicon chips with microwells provide high crystal-loading density with an extremely high hit rate. The microfocus, undulator-fed beamline at CHESS, which has compound refractive optics and a fast-framing detector, was built and optimized for this experiment. The high-throughput oscillation method described here collects 1-5° of data per crystal at room temperature with fast (10° s-1) oscillation rates and translation times, giving a crystal-data collection rate of 2.5 Hz. Partial datasets collected by the oscillation method at a storage-ring source provide more complete data per crystal than still images, dramatically lowering the total number of crystals needed for a complete dataset suitable for structure solution and refinement - up to two orders of magnitude fewer being required. Thus, this method is particularly well suited to instances where crystal quantities are low. It is demonstrated, through comparison of first and last oscillation images of two systems, that dose and the effects of radiation damage can be minimized through fast rotation and low angular sweeps for each crystal.
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Affiliation(s)
| | - Olivier Paré-Labrosse
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Antoine Sarracini
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Jessica E. Besaw
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | | | - Saeed Oghbaey
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Hazem Daoud
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | | | - Anling Kuo
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Scott Smith
- MacCHESS, Cornell University, Ithaca, NY 14853, USA
| | - Oliver P. Ernst
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Sol M. Gruner
- MacCHESS, Cornell University, Ithaca, NY 14853, USA
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - R. J. Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
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15
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Streck S, Hong L, Boyd BJ, McDowell A. Microfluidics for the Production of Nanomedicines: Considerations for Polymer and Lipid-based Systems. Pharm Nanotechnol 2019; 7:423-443. [PMID: 31629401 DOI: 10.2174/2211738507666191019154815] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/30/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Microfluidics is becoming increasingly of interest as a superior technique for the synthesis of nanoparticles, particularly for their use in nanomedicine. In microfluidics, small volumes of liquid reagents are rapidly mixed in a microchannel in a highly controlled manner to form nanoparticles with tunable and reproducible structure that can be tailored for drug delivery. Both polymer and lipid-based nanoparticles are utilized in nanomedicine and both are amenable to preparation by microfluidic approaches. AIM Therefore, the purpose of this review is to collect the current state of knowledge on the microfluidic preparation of polymeric and lipid nanoparticles for pharmaceutical applications, including descriptions of the main synthesis modalities. Of special interest are the mechanisms involved in nanoparticle formation and the options for surface functionalisation to enhance cellular interactions. CONCLUSION The review will conclude with the identification of key considerations for the production of polymeric and lipid nanoparticles using microfluidic approaches.
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Affiliation(s)
- Sarah Streck
- School of Pharmacy, University of Otago, 18 Frederick Street, Dunedin 9054, New Zealand
| | - Linda Hong
- Drug Delivery, Disposition and Dynamics, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Ben J Boyd
- Drug Delivery, Disposition and Dynamics, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Arlene McDowell
- School of Pharmacy, University of Otago, 18 Frederick Street, Dunedin 9054, New Zealand
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16
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Ferreira J, Castro F, Rocha F, Kuhn S. Protein crystallization in a droplet-based microfluidic device: Hydrodynamic analysis and study of the phase behaviour. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2018.06.066] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Ren Z, Ayhan M, Bandara S, Bowatte K, Kumarapperuma I, Gunawardana S, Shin H, Wang C, Zeng X, Yang X. Crystal-on-crystal chips for in situ serial diffraction at room temperature. LAB ON A CHIP 2018; 18:2246-2256. [PMID: 29952383 PMCID: PMC6057835 DOI: 10.1039/c8lc00489g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent developments in serial crystallography at X-ray free electron lasers (XFELs) and synchrotrons have been driven by two scientific goals in structural biology - first, static structure determination from nano or microcrystals of membrane proteins and large complexes that are difficult for conventional cryocrystallography, and second, direct observations of transient structural species in biochemical reactions at near atomic resolution. Since room-temperature diffraction experiments naturally demand a large quantity of purified protein, sample economy is critically important for all steps of serial crystallography from crystallization, crystal delivery to data collection. Here we report the development and applications of "crystal-on-crystal" devices to facilitate large-scale in situ serial diffraction experiments on protein crystals of all sizes - large, small, or microscopic. We show that the monocrystalline quartz as a substrate material prevents vapor loss during crystallization and significantly reduces background X-ray scattering. These devices can be readily adopted at XFEL and synchrotron beamlines, which enable efficient delivery of hundreds to millions of crystals to the X-ray beam, with an overall protein consumption per dataset comparable to that of cryocrystallography.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
- Corresponding authors: and
| | - Medine Ayhan
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sepalika Bandara
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kalinga Bowatte
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Semini Gunawardana
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Cong Wang
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xiaoli Zeng
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Corresponding authors: and
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18
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Lopez CG, Watanabe T, Adamo M, Martel A, Porcar L, Cabral JT. Microfluidic devices for small-angle neutron scattering. J Appl Crystallogr 2018; 51:570-583. [PMID: 29896054 PMCID: PMC5988002 DOI: 10.1107/s1600576718007264] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/14/2018] [Indexed: 12/12/2022] Open
Abstract
A comparative examination is presented of materials and approaches for the fabrication of microfluidic devices for small-angle neutron scattering (SANS). Representative inorganic glasses, metals, and polymer materials and devices are evaluated under typical SANS configurations. Performance criteria include neutron absorption, scattering background and activation, as well as spatial resolution, chemical compatibility and pressure resistance, and also cost, durability and manufacturability. Closed-face polymer photolithography between boron-free glass (or quartz) plates emerges as an attractive approach for rapidly prototyped microfluidic SANS devices, with transmissions up to ∼98% and background similar to a standard liquid cell (I ≃ 10-3 cm-1). For applications requiring higher durability and/or chemical, thermal and pressure resistance, sintered or etched boron-free glass and silicon devices offer superior performance, at the expense of various fabrication requirements, and are increasingly available commercially.
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Affiliation(s)
- Carlos G. Lopez
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Takaichi Watanabe
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Marco Adamo
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Institut Laue–Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Anne Martel
- Institut Laue–Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Lionel Porcar
- Institut Laue–Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - João T. Cabral
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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19
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Mawatari K, Koreeda H, Ohara K, Kohara S, Yoshida K, Yamaguchi T, Kitamori T. Nano X-ray diffractometry device for nanofluidics. LAB ON A CHIP 2018; 18:1259-1264. [PMID: 29594269 DOI: 10.1039/c8lc00077h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanofluidics is gaining attention because it has unique liquid and fluidic properties that are not observed in microfluidics. It has been reported that many liquid properties change when the size of a fluidic channel is reduced below 500-800 nm. To discuss the underlying mechanism, information on the microscopic liquid structure must be obtained (e.g., by X-ray diffractometry). However, the very small volume (attoliters to femtoliters) of a nanochannel and the large volume of its glass substrate prevent measurement of signals from the nanochannel liquid. In this study, we report a novel nanofluidic device that can be used in conjunction with X-ray diffractometry to analyze the structure of water confined in nanochannels. Top-down and bottom-up micro- and nano-fabrication processes were established, and the substrate thickness of the measurement area was reduced to only 2.7 μm, which was almost 1000 times smaller than that of conventional substrates (millimeter scale). With this new device, X-ray diffraction signals were clearly observed in nanochannels 500 nm wide and deep. Based on the X-ray diffraction pattern, the radial distribution function was calculated, which showed a structure nearly similar to that of a bulk sample. Therefore, X-ray diffractometry in nanochannels was realized. This method will provide important information on how a liquid behaves when confined in a nanospace and contribute to chemistry and biology on scales of 10-100 nm (e.g., inter- and intra-cellular spaces). It is also important for designing chemical reactions and fluidic circuits in nanochannels for realizing highly functional devices.
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Affiliation(s)
- Kazuma Mawatari
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan.
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20
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Schieferstein JM, Pawate AS, Varel MJ, Guha S, Astrauskaite I, Gennis RB, Kenis PJA. X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds. LAB ON A CHIP 2018; 18:944-954. [PMID: 29469138 PMCID: PMC5849577 DOI: 10.1039/c7lc01141e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Crystallization of membrane proteins is a critical step for uncovering atomic resolution 3-D structures and elucidating structure-function relationships. Microseeding, the process of transferring sub-microscopic crystal nuclei from initial screens into new crystallization experiments, is an effective, yet underutilized approach to grow crystals suitable for X-ray crystallography. Here, we report simplified methods for crystallization of membrane proteins that utilize microseeding in X-ray transparent microfluidic chips. First, a microfluidic method for introduction of microseed dilutions into metastable crystallization experiments is demonstrated for photoactive yellow protein and cytochrome bo3 oxidase. As microseed concentration decreased, the number of crystals decreased while the average size increased. Second, we demonstrate a microfluidic chip for microseed screening, where many crystallization conditions were formulated on-chip prior to mixing with microseeds. Crystallization composition, crystal size, and diffraction data were collected and mapped on phase diagrams, which revealed that crystals of similar diffraction quality and size typically grow in distinct regions of the phase diagram.
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Affiliation(s)
- Jeremy M Schieferstein
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, USA.
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21
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A Graphene-Based Microfluidic Platform for Electrocrystallization and In Situ X-ray Diffraction. CRYSTALS 2018. [DOI: 10.3390/cryst8020076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Here, we describe a novel microfluidic platform for use in electrocrystallization experiments. The device incorporates ultra-thin graphene-based films as electrodes and as X-ray transparent windows to enable in situ X-ray diffraction analysis. Furthermore, large-area graphene films serve as a gas barrier, creating a stable sample environment over time. We characterize different methods for fabricating graphene electrodes, and validate the electrical capabilities of our device through the use of methyl viologen, a redox-sensitive dye. Proof-of-concept electrocrystallization experiments using an internal electric field at constant potential were performed using hen egg-white lysozyme (HEWL) as a model system. We observed faster nucleation and crystal growth, as well as a higher signal-to-noise for diffraction data obtained from crystals prepared in the presence of an applied electric field. Although this work is focused on the electrocrystallization of proteins for structural biology, we anticipate that this technology should also find utility in a broad range of both X-ray technologies and other applications of microfluidic technology.
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22
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Burton CG, Axford D, Edwards AMJ, Gildea RJ, Morris RH, Newton MI, Orville AM, Prince M, Topham PD, Docker PT. An acoustic on-chip goniometer for room temperature macromolecular crystallography. LAB ON A CHIP 2017; 17:4225-4230. [PMID: 29124258 DOI: 10.1039/c7lc00812k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.
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Affiliation(s)
- C G Burton
- Aston Institute of Material Research, Aston University, Birmingham B4 7ET, UK
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23
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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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24
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Chen W, Pinho B, Hartman RL. Flash crystallization kinetics of methane (sI) hydrate in a thermoelectrically-cooled microreactor. LAB ON A CHIP 2017; 17:3051-3060. [PMID: 28829467 DOI: 10.1039/c7lc00645d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The crystallization kinetics of methane (sI) hydrate were investigated in a thermoelectrically-cooled microreactor with in situ Raman spectroscopy. Step-wise and precise control of the temperature allowed acquisition of reproducible data within minutes, while the nucleation of methane hydrates can take up to 24 h in traditional batch reactors. The propagation rates of methane hydrate (from 3.1-196.3 μm s-1) at the gas-liquid interface were measured for different Reynolds' numbers (0.7-68.9), pressures (30.0-80.9 bar), and sub-cooling temperatures (1.0-4.0 K). The precise measurement of the propagation rates and their subsequent analyses revealed a transition from mixed heat-transfer-crystallization-rate-limited to mixed heat-transfer-mass-transfer-crystallization-rate-limited kinetics. A theoretical model, based on heat transfer, mass transfer, and intrinsic crystallization kinetics, was derived for the first time to understand the non-linear relationship between the propagation rate and sub-cooling temperature. The molecular diffusivity of methane within a stagnant film (ahead of the propagation front) was discovered to follow Stokes-Einstein, while calculated Hatta (0.50-0.68), Lewis (128-207), and beta (0.79-116) numbers also confirmed that the diffusive flux influences crystal growth. Understanding methane hydrate crystal growth is important to the atmospheric, oceanic, and planetary sciences and to energy production, storage, and transportation. Our discoveries could someday advance the science of other multiphase, high-pressure, and sub-cooled crystallizations.
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Affiliation(s)
- Weiqi Chen
- Department of Chemical and Biomolecular Engineering, New York University, Brooklyn, NY 11201, USA.
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25
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Saldanha O, Graceffa R, Hémonnot CYJ, Ranke C, Brehm G, Liebi M, Marmiroli B, Weinhausen B, Burghammer M, Köster S. Rapid Acquisition of X-Ray Scattering Data from Droplet-Encapsulated Protein Systems. Chemphyschem 2017; 18:1220-1223. [DOI: 10.1002/cphc.201700221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Oliva Saldanha
- Institute for X-ray Physics; Georg-August-University Göttingen; 37077 Göttingen Germany
| | - Rita Graceffa
- Institute for X-ray Physics; Georg-August-University Göttingen; 37077 Göttingen Germany
- Current address: European XFEL GmbH; 22869 Schenefeld Germany
| | | | - Christiane Ranke
- Institute for X-ray Physics; Georg-August-University Göttingen; 37077 Göttingen Germany
| | - Gerrit Brehm
- Institute for X-ray Physics; Georg-August-University Göttingen; 37077 Göttingen Germany
| | - Marianne Liebi
- Paul Scherrer Institute; 5232 Villigen Switzerland
- Current address: MAX IV Laboratory; Lund University; 221-00 Lund Sweden
| | - Benedetta Marmiroli
- Institute of Inorganic Chemistry; Graz University of Technology; 8010 Graz Austria
| | - Britta Weinhausen
- European Synchrotron Radiation Facility; 38000 Grenoble France
- Current address: European XFEL GmbH; 22869 Schenefeld Germany
| | - Manfred Burghammer
- European Synchrotron Radiation Facility; 38000 Grenoble France
- Department of Analytical Chemistry; Ghent University; 9000 Ghent Belgium
| | - Sarah Köster
- Institute for X-ray Physics; Georg-August-University Göttingen; 37077 Göttingen Germany
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26
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Schieferstein JM, Pawate AS, Sun C, Wan F, Sheraden PN, Broecker J, Ernst OP, Gennis RB, Kenis PJA. X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization. BIOMICROFLUIDICS 2017; 11:024118. [PMID: 28469762 PMCID: PMC5403737 DOI: 10.1063/1.4981818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/10/2017] [Indexed: 05/10/2023]
Abstract
Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å.
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Affiliation(s)
- Jeremy M Schieferstein
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashtamurthy S Pawate
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Chang Sun
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Frank Wan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paige N Sheraden
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jana Broecker
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S IA8, Canada
| | | | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paul J A Kenis
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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27
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Abstract
Prompted by methodological advances in measurements with X-ray free electron lasers, it was realized in the last two years that traditional (or conventional) methods for data collection from crystals of macromolecular specimens can be complemented by synchrotron measurements on microcrystals that would individually not suffice for a complete data set. Measuring, processing, and merging many partial data sets of this kind requires new techniques which have since been implemented at several third-generation synchrotron facilities, and are described here. Among these, we particularly focus on the possibility of in situ measurements combined with in meso crystal preparations and data analysis with the XDS package and auxiliary programs.
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Affiliation(s)
- Kay Diederichs
- Department of Biology, Universität Konstanz, Box 647, D-78457, Konstanz, Germany.
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
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28
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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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29
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Sui S, Wang Y, Kolewe KW, Srajer V, Henning R, Schiffman JD, Dimitrakopoulos C, Perry SL. Graphene-based microfluidics for serial crystallography. LAB ON A CHIP 2016; 16:3082-96. [PMID: 27241728 PMCID: PMC4970872 DOI: 10.1039/c6lc00451b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.
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Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Yuxi Wang
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Kristopher W Kolewe
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Vukica Srajer
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Robert Henning
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Jessica D Schiffman
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Christos Dimitrakopoulos
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Sarah L Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
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30
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Owen RL, Juanhuix J, Fuchs M. Current advances in synchrotron radiation instrumentation for MX experiments. Arch Biochem Biophys 2016; 602:21-31. [PMID: 27046341 PMCID: PMC5505570 DOI: 10.1016/j.abb.2016.03.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/15/2022]
Abstract
Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.
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Affiliation(s)
- Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Jordi Juanhuix
- Alba Synchrotron, Carrer de la llum 2-26, Cerdanyola, 08192, Spain.
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Lab, Upton, NY, 11973, USA.
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31
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Convert L, Lebel R, Gascon S, Fontaine R, Pratte JF, Charette P, Aimez V, Lecomte R. Real-Time Microfluidic Blood-Counting System for PET and SPECT Preclinical Pharmacokinetic Studies. J Nucl Med 2016; 57:1460-6. [DOI: 10.2967/jnumed.115.162768] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 03/29/2016] [Indexed: 02/03/2023] Open
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32
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Baxter EL, Aguila L, Alonso-Mori R, Barnes CO, Bonagura CA, Brehmer W, Brunger AT, Calero G, Caradoc-Davies TT, Chatterjee R, Degrado WF, Fraser JS, Ibrahim M, Kern J, Kobilka BK, Kruse AC, Larsson KM, Lemke HT, Lyubimov AY, Manglik A, McPhillips SE, Norgren E, Pang SS, Soltis SM, Song J, Thomaston J, Tsai Y, Weis WI, Woldeyes RA, Yachandra V, Yano J, Zouni A, Cohen AE. High-density grids for efficient data collection from multiple crystals. Acta Crystallogr D Struct Biol 2016; 72:2-11. [PMID: 26894529 PMCID: PMC4756618 DOI: 10.1107/s2059798315020847] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/03/2015] [Indexed: 03/01/2023] Open
Abstract
Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice/DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.
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Affiliation(s)
- Elizabeth L. Baxter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Laura Aguila
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christopher O. Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | - Winnie Brehmer
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Tom T. Caradoc-Davies
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria 3800, Australia
- Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, Victoria 3168, Australia
| | - Ruchira Chatterjee
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William F. Degrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Jan Kern
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Andrew C. Kruse
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Karl M. Larsson
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heinrik T. Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Scott E. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Erik Norgren
- Art Robbins Instruments, Sunnyvale, CA 94089, USA
| | - Siew S. Pang
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria 3800, Australia
| | - S. M. Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jessica Thomaston
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yingssu Tsai
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahel A. Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Vittal Yachandra
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Junko Yano
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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33
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Goyal S, Economou AE, Papadopoulos T, Horstman EM, Zhang GGZ, Gong Y, Kenis PJA. Solvent compatible microfluidic platforms for pharmaceutical solid form screening. RSC Adv 2016. [DOI: 10.1039/c5ra26426j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The use of SIFEL in the crystallization fluid layers renders the microfluidic crystallization array compatible with solvents such as tetrahydrofuran, acetonitrile, chloroform, hexane, and toluene.
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Affiliation(s)
- Sachit Goyal
- The Dow Chemical Company
- Polyurethanes R&D
- Freeport
- USA
- Department of Chemical & Biomolecular Engineering
| | - Aristotle E. Economou
- Department of Chemical & Biomolecular Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Theodore Papadopoulos
- Department of Chemical & Biomolecular Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Elizabeth M. Horstman
- Department of Chemical & Biomolecular Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Geoff G. Z. Zhang
- Drug Product Development
- Research and Development
- AbbVie Inc
- North Chicago
- USA
| | - Yuchuan Gong
- Drug Product Development
- Research and Development
- AbbVie Inc
- North Chicago
- USA
| | - Paul J. A. Kenis
- Department of Chemical & Biomolecular Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
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34
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Maeki M, Yamazaki S, Pawate AS, Ishida A, Tani H, Yamashita K, Sugishima M, Watanabe K, Tokeshi M, Kenis PJA, Miyazaki M. A microfluidic-based protein crystallization method in 10 micrometer-sized crystallization space. CrystEngComm 2016. [DOI: 10.1039/c6ce01671e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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35
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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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36
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Murray TD, Lyubimov AY, Ogata CM, Vo H, Uervirojnangkoorn M, Brunger AT, Berger JM. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1987-97. [PMID: 26457423 PMCID: PMC4601365 DOI: 10.1107/s1399004715015011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/11/2015] [Indexed: 11/14/2022]
Abstract
Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10-15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.
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Affiliation(s)
- Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Artem Y. Lyubimov
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Craig M. Ogata
- GM/CA@APS, X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Huy Vo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Monarin Uervirojnangkoorn
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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37
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Boyko KM, Popov VO, Kovalchuk MV. Promising approaches to crystallization of macromolecules suppressing the convective mass transport to the growing crystal. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Beuvier T, Panduro EAC, Kwaśniewski P, Marre S, Lecoutre C, Garrabos Y, Aymonier C, Calvignac B, Gibaud A. Implementation of in situ SAXS/WAXS characterization into silicon/glass microreactors. LAB ON A CHIP 2015; 15:2002-2008. [PMID: 25792250 DOI: 10.1039/c5lc00115c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A successful implementation of in situ X-ray scattering analysis of synthetized particle materials in silicon/glass microreactors is reported. Calcium carbonate (CaCO3) as a model material was precipitated inside the microchannels through the counter-injection of two aqueous solutions, containing carbonate ions and calcium ions, respectively. The synthesized calcite particles were analyzed in situ in aqueous media by combining Small Angle X-ray Scattering (SAXS) and Wide Angle X-ray Scattering (WAXS) techniques at the ESRF ID02 beam line. At high wavevector transfer, WAXS patterns clearly exhibit different scattering features: broad scattering signals originating from the solvent and the glass lid of the chip, and narrow diffraction peaks coming from CaCO3 particles precipitated rapidly inside the microchannel. At low wavevector transfer, SAXS reveals the rhombohedral morphology of the calcite particles together with their micrometer size without any strong background, neither from the chip nor from the water. This study demonstrates that silicon/glass chips are potentially powerful tools for in situ SAXS/WAXS analysis and are promising for studying the structure and morphology of materials in non-conventional conditions like geological materials under high pressure and high temperature.
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Affiliation(s)
- Thomas Beuvier
- LUNAM, Université du Maine, Institut des Molécules et Matériaux du Mans, UMR CNRS 6283, Avenue Olivier Messiaen, 72085 Le Mans Cedex 9, France.
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39
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Lyubimov AY, Murray TD, Koehl A, Araci IE, Uervirojnangkoorn M, Zeldin OB, Cohen AE, Soltis SM, Baxter EL, Brewster AS, Sauter NK, Brunger AT, Berger JM. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:928-40. [PMID: 25849403 PMCID: PMC4388268 DOI: 10.1107/s1399004715002308] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/03/2015] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.
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Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Antoine Koehl
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Ismail Emre Araci
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aina E. Cohen
- SLAC National Accelerator Laboratory, Stanford, CA 94305, USA
| | | | | | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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40
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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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41
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Ielasi FS, Hirtz M, Sekula-Neuner S, Laue T, Fuchs H, Willaert RG. Dip-Pen Nanolithography-Assisted Protein Crystallization. J Am Chem Soc 2014; 137:154-7. [DOI: 10.1021/ja512141k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Francesco S. Ielasi
- Department
of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Michael Hirtz
- Institute
of Nanotechnology and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Sylwia Sekula-Neuner
- Institute
of Nanotechnology and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Thomas Laue
- Institute
of Nanotechnology and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Harald Fuchs
- Institute
of Nanotechnology and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
- Physical
Institute and Center for Nanotechnology, Westfälische Wilhelms-Universität, 48149 Münster, Germany
| | - Ronnie G. Willaert
- Department
of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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42
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Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A 2014; 111:17122-7. [PMID: 25362050 PMCID: PMC4260607 DOI: 10.1073/pnas.1418733111] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.
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Affiliation(s)
| | | | | | | | | | - Christopher O Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | | | | | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Axel T Brunger
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | | | | | | | | | | | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | | | | | - James M Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; and
| | - Stephen Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | | | | | | | | | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Artem Y Lyubimov
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | | | | | | | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | | | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource
| | - Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Yingssu Tsai
- Stanford Synchrotron Radiation Lightsource, Departments of Chemistry
| | - Monarin Uervirojnangkoorn
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | - Soichi Wakatsuki
- Photon Science, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; Structural Biology, and
| | - William I Weis
- Molecular and Cellular Physiology, and Structural Biology, and
| | - Oleg A Zadvornyy
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | - Oliver B Zeldin
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource, Departments of Chemistry,
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43
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Khvostichenko D, Schieferstein JM, Pawate AS, Laible PD, Kenis PJA. X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination. CRYSTAL GROWTH & DESIGN 2014; 14:4886-4890. [PMID: 25285049 PMCID: PMC4181584 DOI: 10.1021/cg5011488] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Indexed: 05/23/2023]
Abstract
Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting of individual crystals. We validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.
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Affiliation(s)
- Daria
S. Khvostichenko
- Department
of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jeremy M. Schieferstein
- Department
of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ashtamurthy S. Pawate
- Department
of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Philip D. Laible
- Biosciences
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Paul J. A. Kenis
- Department
of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Heymann M, Opthalage A, Wierman JL, Akella S, Szebenyi DME, Gruner SM, Fraden S. Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction. IUCRJ 2014; 1:349-60. [PMID: 25295176 PMCID: PMC4174877 DOI: 10.1107/s2052252514016960] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/23/2014] [Indexed: 05/18/2023]
Abstract
An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation.
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Affiliation(s)
- Michael Heymann
- Graduate Program in Biophysics and Structural Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA
- Martin Fisher School of Physics, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Achini Opthalage
- Martin Fisher School of Physics, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | | | - Sathish Akella
- Martin Fisher School of Physics, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Doletha M. E. Szebenyi
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - Seth Fraden
- Martin Fisher School of Physics, Brandeis University, 415 South Street, Waltham, MA 02454, USA
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45
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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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46
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Maeki M, Teshima Y, Yoshizuka S, Yamaguchi H, Yamashita K, Miyazaki M. Controlling Protein Crystal Nucleation by Droplet-Based Microfluidics. Chemistry 2013; 20:1049-56. [DOI: 10.1002/chem.201303270] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Indexed: 11/07/2022]
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47
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Abdallah BG, Kupitz C, Fromme P, Ros A. Crystallization of the large membrane protein complex photosystem I in a microfluidic channel. ACS NANO 2013; 7:10534-43. [PMID: 24191698 PMCID: PMC3940344 DOI: 10.1021/nn402515q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Traditional macroscale protein crystallization is accomplished nontrivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time-consuming and resource-intensive, hindering protein structure determination. Even more difficulties arise when crystallizing large membrane protein complexes such as photosystem I (PSI) due to their large unit cells dominated by solvent and complex characteristics that call for even stricter buffer requirements. Structure determination techniques tailored for these "difficult to crystallize" proteins such as femtosecond nanocrystallography are being developed yet still need specific crystal characteristics. Here, we demonstrate a simple and robust method to screen protein crystallization conditions at low ionic strength in a microfluidic device. This is realized in one microfluidic experiment using low sample amounts, unlike traditional methods where each solution condition is set up separately. Second harmonic generation microscopy via second-order nonlinear imaging of chiral crystals (SONICC) was applied for the detection of nanometer- and micrometer-sized PSI crystals within microchannels. To develop a crystallization phase diagram, crystals imaged with SONICC at specific channel locations were correlated to protein and salt concentrations determined by numerical simulations of the time-dependent diffusion process along the channel. Our method demonstrated that a portion of the PSI crystallization phase diagram could be reconstructed in excellent agreement with crystallization conditions determined by traditional methods. We postulate that this approach could be utilized to efficiently study and optimize crystallization conditions for a wide range of proteins that are poorly understood to date.
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48
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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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49
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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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50
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Rodríguez-Ruiz I, Llobera A, Vila-Planas J, Johnson DW, Gómez-Morales J, García-Ruiz JM. Analysis of the Structural Integrity of SU-8-Based Optofluidic Systems for Small-Molecule Crystallization Studies. Anal Chem 2013; 85:9678-85. [DOI: 10.1021/ac402019x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Isaac Rodríguez-Ruiz
- Laboratorio de
Estudios Cristalográficos, IACT (CSIC-UGR), Avenida de las Palmeras, 4, 18100 Armilla, Granada, Spain
| | - Andreu Llobera
- Institut
de Microelectrónica
de Barcelona (IMB-CNM, CSIC), Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Jordi Vila-Planas
- Institut
de Microelectrónica
de Barcelona (IMB-CNM, CSIC), Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Donald W. Johnson
- DJ DevCorp, 490 Boston Post Road, Sudbury, Massachusetts 01776, United States
| | - Jaime Gómez-Morales
- Laboratorio de
Estudios Cristalográficos, IACT (CSIC-UGR), Avenida de las Palmeras, 4, 18100 Armilla, Granada, Spain
| | - Juan Manuel García-Ruiz
- Laboratorio de
Estudios Cristalográficos, IACT (CSIC-UGR), Avenida de las Palmeras, 4, 18100 Armilla, Granada, Spain
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