1
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Henkel A, Galchenkova M, Maracke J, Yefanov O, Klopprogge B, Hakanpää J, Mesters JR, Chapman HN, Oberthuer D. JINXED: just in time crystallization for easy structure determination of biological macromolecules. IUCRJ 2023; 10:253-260. [PMID: 36892542 PMCID: PMC10161778 DOI: 10.1107/s2052252523001653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/23/2023] [Indexed: 05/06/2023]
Abstract
Macromolecular crystallography is a well established method in the field of structural biology and has led to the majority of known protein structures to date. After focusing on static structures, the method is now under development towards the investigation of protein dynamics through time-resolved methods. These experiments often require multiple handling steps of the sensitive protein crystals, e.g. for ligand-soaking and cryo-protection. These handling steps can cause significant crystal damage, and hence reduce data quality. Furthermore, in time-resolved experiments based on serial crystallography, which use micrometre-sized crystals for short diffusion times of ligands, certain crystal morphologies with small solvent channels can prevent sufficient ligand diffusion. Described here is a method that combines protein crystallization and data collection in a novel one-step process. Corresponding experiments were successfully performed as a proof-of-principle using hen egg-white lysozyme and crystallization times of only a few seconds. This method, called JINXED (Just IN time Crystallization for Easy structure Determination), promises high-quality data due to the avoidance of crystal handling and has the potential to enable time-resolved experiments with crystals containing small solvent channels by adding potential ligands to the crystallization buffer, simulating traditional co-crystallization approaches.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jeroen R Mesters
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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2
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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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3
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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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4
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Microfluidic Protein Imaging Platform: Study of Tau Protein Aggregation and Alzheimer's Drug Response. Bioengineering (Basel) 2020; 7:bioengineering7040162. [PMID: 33322166 PMCID: PMC7763324 DOI: 10.3390/bioengineering7040162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 11/23/2022] Open
Abstract
Tau protein aggregation is identified as one of the key phenomena associated with the onset and progression of Alzheimer’s disease. In the present study, we performed on-chip confocal imaging of tau protein aggregation and tau–drug interactions using a spiral-shaped passive micromixing platform. Numerical simulations and experiments were performed in order to validate the performance of the micromixer design. We performed molecular modeling of adenosine triphosphate (ATP)-induced tau aggregation in order to successfully validate the concept of helical tau filament formation. Tau aggregation and native tau restoration were realized using an immunofluorescence antibody assay. The dose–response behavior of an Alzheimer’s drug, methylthioninium chloride (MTC), was monitored on-chip for defining the optimum concentration of the drug. The proposed device was tested for reliability and repeatability of on-chip tau imaging. The amount of the tau protein sample used in our experiments was significantly less than the usage for conventional techniques, and the whole protein–drug assay was realized in less than two hours. We identified that intensity-based tau imaging could be used to study Alzheimer’s drug response. In addition, it was demonstrated that cell-free, microfluidic tau protein assays could be used as potential on-chip drug evaluation tools for Alzheimer’s disease.
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5
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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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6
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Levenstein MA, Kim YY, Hunter L, Anduix-Canto C, González Niño C, Day SJ, Li S, Marchant WJ, Lee PA, Tang CC, Burghammer M, Meldrum FC, Kapur N. Evaluation of microflow configurations for scale inhibition and serial X-ray diffraction analysis of crystallization processes. LAB ON A CHIP 2020; 20:2954-2964. [PMID: 32666988 DOI: 10.1039/d0lc00239a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The clean and reproducible conditions provided by microfluidic devices are ideal sample environments for in situ analyses of chemical and biochemical reactions and assembly processes. However, the small size of microchannels makes investigating the crystallization of poorly soluble materials on-chip challenging due to crystal nucleation and growth that result in channel fouling and blockage. Here, we demonstrate a reusable insert-based microfluidic platform for serial X-ray diffraction analysis and examine scale formation in response to continuous and segmented flow configurations across a range of temperatures. Under continuous flow, scale formation on the reactor walls begins almost immediately on mixing of the crystallizing species, which over time results in occlusion of the channel. Depletion of ions at the start of the channel results in reduced crystallization towards the end of the channel. Conversely, segmented flow can control crystallization, so it occurs entirely within the droplet. Consequently, the spatial location within the channel represents a temporal point in the crystallization process. Whilst each method can provide useful crystallographic information, time-resolved information is lost when reactor fouling occurs and changes the solution conditions with time. The flow within a single device can be manipulated to give a broad range of information addressing surface interaction or solution crystallization.
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Affiliation(s)
- Mark A Levenstein
- School of Mechanical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
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7
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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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8
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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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9
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Górzny M, Opara N, Guzenko V, Cadarso V, Schift H, Li X, Padeste C. Microfabricated silicon chip as lipid membrane sample holder for serial protein crystallography. MICRO AND NANO ENGINEERING 2019. [DOI: 10.1016/j.mne.2019.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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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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11
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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: 25] [Impact Index Per Article: 5.0] [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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12
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Grünbein ML, Nass Kovacs G. Sample delivery for serial crystallography at free-electron lasers and synchrotrons. Acta Crystallogr D Struct Biol 2019; 75:178-191. [PMID: 30821706 PMCID: PMC6400261 DOI: 10.1107/s205979831801567x] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022] Open
Abstract
The high peak brilliance and femtosecond pulse duration of X-ray free-electron lasers (XFELs) provide new scientific opportunities for experiments in physics, chemistry and biology. In structural biology, one of the major applications is serial femtosecond crystallography. The intense XFEL pulse results in the destruction of any exposed microcrystal, making serial data collection mandatory. This requires a high-throughput serial approach to sample delivery. To this end, a number of such sample-delivery techniques have been developed, some of which have been ported to synchrotron sources, where they allow convenient low-dose data collection at room temperature. Here, the current sample-delivery techniques used at XFEL and synchrotron sources are reviewed, with an emphasis on liquid injection and high-viscosity extrusion, including their application for time-resolved experiments. The challenges associated with sample delivery at megahertz repetition-rate XFELs are also outlined.
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Affiliation(s)
- Marie Luise Grünbein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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13
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Gicquel Y, Schubert R, Kapis S, Bourenkov G, Schneider T, Perbandt M, Betzel C, Chapman HN, Heymann M. Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography. J Vis Exp 2018. [PMID: 29757285 PMCID: PMC6100780 DOI: 10.3791/57133] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 µm grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.
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Affiliation(s)
- Yannig Gicquel
- Center for Free Electron Laser Science, DESY; Department of Physics, University of Hamburg
| | - Robin Schubert
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg; The Hamburg Center for Ultrafast Imaging, University of Hamburg; Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI)
| | - Svetlana Kapis
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg
| | | | | | - Markus Perbandt
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg; The Hamburg Center for Ultrafast Imaging, University of Hamburg
| | - Christian Betzel
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg; The Hamburg Center for Ultrafast Imaging, University of Hamburg; Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI)
| | - Henry N Chapman
- Center for Free Electron Laser Science, DESY; Department of Physics, University of Hamburg; The Hamburg Center for Ultrafast Imaging, University of Hamburg
| | - Michael Heymann
- Center for Free Electron Laser Science, DESY; Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry;
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14
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Silva BFB. SAXS on a chip: from dynamics of phase transitions to alignment phenomena at interfaces studied with microfluidic devices. Phys Chem Chem Phys 2018; 19:23690-23703. [PMID: 28828415 DOI: 10.1039/c7cp02736b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field of microfluidics offers attractive possibilities to perform novel experiments that are difficult (or even impossible) to perform using conventional bulk and surface-based methods. Such attractiveness comes from several important aspects inherent to these miniaturized devices. First, the flow of fluids under submillimeter confinement typically leads to a drop of inertial forces, meaning that turbulence is practically suppressed. This leads to predictable and controllable flow profiles, along with well-defined chemical gradients and stress fields that can be used for controlled mixing and actuation on the micro and nanoscale. Secondly, intricate microfluidic device designs can be fabricated using cleanroom standard procedures. Such intricate geometries can take diverse forms, designed by researchers to perform complex tasks, that require exquisite control of flow of several components and gradients, or to mimic real world examples, facilitating the establishment of more realistic models. Thirdly, microfluidic devices are usually compatible with in situ or integrated characterization methods that allow constant real-time monitoring of the processes occurring inside the microchannels. This is very different from typical bulk-based methods, where usually one can only observe the final result, or otherwise, take quick snapshots of the evolving process or take aliquots to be analyzed separately. Altogether, these characteristics inherent to microfluidic devices provide researchers with a set of tools that allow not only exquisite control and manipulation of materials at the micro and nanoscale, but also observation of these effects. In this review, we will focus on the use and prospects of combining microfluidic devices with in situ small-angle X-ray scattering (and related techniques such as small-angle neutron scattering and X-ray photon correlation spectroscopy), and their enormous potential for physical-chemical research, mainly in self-assembly and phase-transitions, and surface characterization.
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Affiliation(s)
- Bruno F B Silva
- Department of Life Sciences, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga, Braga 4715-330, Portugal.
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15
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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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16
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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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17
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Li S, Zeng M, Gaule T, McPherson MJ, Meldrum FC. Passive Picoinjection Enables Controlled Crystallization in a Droplet Microfluidic Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1702154. [PMID: 28873281 DOI: 10.1002/smll.201702154] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Indexed: 06/07/2023]
Abstract
Segmented flow microfluidic devices offer an attractive means of studying crystallization processes. However, while they are widely employed for protein crystallization, there are few examples of their use for sparingly soluble compounds due to problems with rapid device fouling and irreproducibility over longer run-times. This article presents a microfluidic device which overcomes these issues, as this is constructed around a novel design of "picoinjector" that facilitates direct injection into flowing droplets. Exploiting a Venturi junction to reduce the pressure within the droplet, it is shown that passive injection of solution from a side-capillary can be achieved in the absence of an applied electric field. The operation of this device is demonstrated for calcium carbonate, where highly reproducible results are obtained over long run-times at high supersaturations. This compares with conventional devices that use a Y-junction to achieve solution loading, where in-channel precipitation of calcium carbonate occurs even at low supersaturations. This work not only opens the door to the use of microfluidics to study the crystallization of low solubility compounds, but the simple design of a passive picoinjector will find wide utility in areas including multistep reactions and investigation of reaction dynamics.
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Affiliation(s)
- Shunbo Li
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Muling Zeng
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Thembaninkosi Gaule
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael J McPherson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Fiona C Meldrum
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
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18
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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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19
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Schubert R, Kapis S, Gicquel Y, Bourenkov G, Schneider TR, Heymann M, Betzel C, Perbandt M. A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution. IUCRJ 2016; 3:393-401. [PMID: 27840678 PMCID: PMC5094441 DOI: 10.1107/s2052252516016304] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/13/2016] [Indexed: 05/20/2023]
Abstract
Many biochemical processes take place on timescales ranging from femto-seconds to seconds. Accordingly, any time-resolved experiment must be matched to the speed of the structural changes of interest. Therefore, the timescale of interest defines the requirements of the X-ray source, instrumentation and data-collection strategy. In this study, a minimalistic approach for in situ crystallization is presented that requires only a few microlitres of sample solution containing a few hundred crystals. It is demonstrated that complete diffraction data sets, merged from multiple crystals, can be recorded within only a few minutes of beamtime and allow high-resolution structural information of high quality to be obtained with a temporal resolution of 40 ms. Global and site-specific radiation damage can be avoided by limiting the maximal dose per crystal to 400 kGy. Moreover, analysis of the data collected at higher doses allows the time-resolved observation of site-specific radiation damage. Therefore, our approach is well suited to observe structural changes and possibly enzymatic reactions in the low-millisecond regime.
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Affiliation(s)
- Robin Schubert
- University of Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging c/o DESY, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Svetlana Kapis
- University of Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Yannig Gicquel
- Center for Free Electron Laser Science c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | - Michael Heymann
- Center for Free Electron Laser Science c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian Betzel
- University of Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Markus Perbandt
- University of Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging c/o DESY, Luruper Chaussee 149, 22761 Hamburg, Germany
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20
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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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21
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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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22
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MAEKI M, YAMAGUCHI H, TOKESHI M, MIYAZAKI M. Microfluidic Approaches for Protein Crystal Structure Analysis. ANAL SCI 2016; 32:3-9. [DOI: 10.2116/analsci.32.3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Masatoshi MAEKI
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University
- Advanced Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology
| | | | - Manabu TOKESHI
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University
| | - Masaya MIYAZAKI
- Advanced Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology
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23
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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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24
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Michalska K, Tan K, Chang C, Li H, Hatzos-Skintges C, Molitsky M, Alkire R, Joachimiak A. In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1386-95. [PMID: 26524303 PMCID: PMC4629866 DOI: 10.1107/s1600577515016598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/05/2015] [Indexed: 05/22/2023]
Abstract
A prototype of a 96-well plate scanner for in situ data collection has been developed at the Structural Biology Center (SBC) beamline 19-ID, located at the Advanced Photon Source, USA. The applicability of this instrument for protein crystal diffraction screening and data collection at ambient temperature has been demonstrated. Several different protein crystals, including selenium-labeled, were used for data collection and successful SAD phasing. Without the common procedure of crystal handling and subsequent cryo-cooling for data collection at T = 100 K, crystals in a crystallization buffer show remarkably low mosaicity (<0.1°) until deterioration by radiation damage occurs. Data presented here show that cryo-cooling can cause some unexpected structural changes. Based on the results of this study, the integration of the plate scanner into the 19-ID end-station with automated controls is being prepared. With improvement of hardware and software, in situ data collection will become available for the SBC user program including remote access.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Kemin Tan
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Changsoo Chang
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Hui Li
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | | | - Michael Molitsky
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Randy Alkire
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, USA
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25
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Fabrication of Microfluidic Valves Using a Hydrogel Molding Method. Sci Rep 2015; 5:13375. [PMID: 26300303 PMCID: PMC4547104 DOI: 10.1038/srep13375] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/24/2015] [Indexed: 02/07/2023] Open
Abstract
In this paper, a method for fabricating a microfluidic valve made of polydimethylsiloxane (PDMS) using a rapid prototyping method for microchannels through hydrogel cast molding is discussed. Currently, the valves in microchannels play an important role in various microfluidic devices. The technology to prototype microfluidic valves rapidly is actively being developed. For the rapid prototyping of PDMS microchannels, a method that uses a hydrogel as the casting mold has been recently developed. This technique can be used to prepare a three-dimensional structure through simple and uncomplicated methods. In this study, we were able to fabricate microfluidic valves easily using this rapid prototyping method that utilizes hydrogel cast molding. In addition, we confirmed that the valve displacement could be predicted within a range of constant pressures. Moreover, because microfluidic valves fabricated using this method can be directly observed from a cross-sectional direction, we anticipate that this technology will significantly contribute to clarifying fluid behavior and other phenomena in microchannels and microfluidic valves with complex structures.
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26
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Pawate AS, Šrajer V, Schieferstein J, Guha S, Henning R, Kosheleva I, Schmidt M, Ren Z, Kenis PJA, Perry SL. Towards time-resolved serial crystallography in a microfluidic device. Acta Crystallogr F Struct Biol Commun 2015; 71:823-30. [PMID: 26144226 PMCID: PMC4498702 DOI: 10.1107/s2053230x15009061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/11/2015] [Indexed: 11/10/2022] Open
Abstract
Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction initiation. This work utilizes a microfluidic crystallization platform for the serial time-resolved Laue diffraction analysis of macroscopic crystals of photoactive yellow protein (PYP). Reaction initiation was achieved via pulsed laser illumination, and the resultant electron-density difference maps clearly depict the expected pR(1)/pR(E46Q) and pR(2)/pR(CW) states at 10 µs and the pB1 intermediate at 1 ms. The strategies presented here have tremendous potential for extension to chemical triggering methods for reaction initiation and for extension to dynamic, multivariable analyses.
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Affiliation(s)
- Ashtamurthy S. Pawate
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Jeremy Schieferstein
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sudipto Guha
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Marius Schmidt
- Department of Physics, The University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
| | - Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
- Renz Research Inc., Westmont, Illinois, USA
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sarah L. Perry
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, Massachusetts, USA
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27
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Maeki M, Pawate AS, Yamashita K, Kawamoto M, Tokeshi M, Kenis PJA, Miyazaki M. A Method of Cryoprotection for Protein Crystallography by Using a Microfluidic Chip and Its Application for in Situ X-ray Diffraction Measurements. Anal Chem 2015; 87:4194-200. [DOI: 10.1021/acs.analchem.5b00151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Masatoshi Maeki
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Division
of Biotechnology and Macromolecular Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
| | - Ashtamurthy S. Pawate
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Kenichi Yamashita
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
| | - Masahide Kawamoto
- Kyushu Synchrotron
Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841−0051, Japan
| | - Manabu Tokeshi
- Division
of Biotechnology and Macromolecular Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Paul J. A. Kenis
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Masaya Miyazaki
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
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28
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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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29
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Abstract
Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is a growing realization that serial microcrystallography and certain cutting-edge solution scattering experiments can be performed at existing storage ring sources by utilizing new technology. In this sense, next-generation sources are serving two distinct functions, namely, provision of new capabilities that require the newer sources and inspiration of new methods that can be performed at existing sources.
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30
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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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31
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Perry SL, Guha S, Pawate AS, Henning R, Kosheleva I, Srajer V, Kenis PJA, Ren Z. In situ serial Laue diffraction on a microfluidic crystallization device. J Appl Crystallogr 2014; 47:1975-1982. [PMID: 25484843 PMCID: PMC4248567 DOI: 10.1107/s1600576714023322] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/22/2014] [Indexed: 11/10/2022] Open
Abstract
Renewed interest in room-temperature diffraction has been prompted by the desire to observe structural dynamics of proteins as they function. Serial crystallography, an experimental strategy that aggregates small pieces of data from a large uniform pool of crystals, has been demonstrated at synchrotrons and X-ray free-electron lasers. This work utilizes a microfluidic crystallization platform for serial Laue diffraction from macroscopic crystals and proposes that a collection of small slices of Laue data from many individual crystals is a realistic solution to the difficulties in dynamic studies of irreversible biochemical reactions.
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Affiliation(s)
- Sarah L. Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA, USA
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Sudipto Guha
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Ashtamurthy S. Pawate
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Vukica Srajer
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
- Renz Research Inc., Westmont, IL, USA
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32
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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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