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Schwardmann LS, Benninghaus L, Lindner SN, Wendisch VF. Prospects of formamide as nitrogen source in biotechnological production processes. Appl Microbiol Biotechnol 2024; 108:105. [PMID: 38204134 PMCID: PMC10781810 DOI: 10.1007/s00253-023-12962-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 01/12/2024]
Abstract
This review presents an analysis of formamide, focussing on its occurrence in nature, its functional roles, and its promising applications in the context of the bioeconomy. We discuss the utilization of formamide as an innovative nitrogen source achieved through metabolic engineering. These approaches underscore formamide's potential in supporting growth and production in biotechnological processes. Furthermore, our review illuminates formamide's role as a nitrogen source capable of safeguarding cultivation systems against contamination in non-sterile conditions. This attribute adds an extra layer of practicality to its application, rendering it an attractive candidate for sustainable and resilient industrial practices. Additionally, the article unveils the versatility of formamide as a potential carbon source that could be combined with formate or CO2 assimilation pathways. However, its attributes, i.e., enriched nitrogen content and comparatively limited energy content, led to conclude that formamide is more suitable as a co-substrate and that its use as a sole source of carbon for biomass and bio-production is limited. Through our exploration of formamide's properties and its applications, this review underscores the significance of formamide as valuable resource for a large spectrum of industrial applications. KEY POINTS: • Formidases enable access to formamide as source of nitrogen, carbon, and energy • The formamide/formamidase system supports non-sterile fermentation • The nitrogen source formamide supports production of nitrogenous compounds.
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Affiliation(s)
- Lynn S Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
- , Aminoverse B.V., Daelderweg 9, 6361 HK, Nuth, Beekdaelen, The Netherlands
| | - Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Steffen N Lindner
- Department of Biochemistry, Charite Universitatsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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2
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Round A, Jungcheng E, Fortmann-Grote C, Giewekemeyer K, Graceffa R, Kim C, Kirkwood H, Mills G, Round E, Sato T, Pascarelli S, Mancuso A. Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:141-162. [PMID: 38507205 DOI: 10.1007/978-3-031-52193-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.
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Affiliation(s)
| | | | | | | | | | - Chan Kim
- European XFEL, Schenefeld, Germany
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3
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Makita H, Zhang M, Yano J, Kern J. Room temperature crystallography and X-ray spectroscopy of metalloenzymes. Methods Enzymol 2023; 688:307-348. [PMID: 37748830 PMCID: PMC10799221 DOI: 10.1016/bs.mie.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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Soares AS, Yamada Y, Jakoncic J, McSweeney S, Sweet RM, Skinner J, Foadi J, Fuchs MR, Schneider DK, Shi W, Andi B, Andrews LC, Bernstein HJ. Serial crystallography with multi-stage merging of thousands of images. Acta Crystallogr F Struct Biol Commun 2022; 78:281-288. [PMID: 35787556 PMCID: PMC9254899 DOI: 10.1107/s2053230x22006422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
The effectiveness of clustering in merging data sets from large numbers of crystals in serial crystallography can be improved by combining multiple clustering techniques using unit-cell parameter-based clustering for very incomplete sets and switching to reflection-based clustering once the preliminary merging has increased the completeness. KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer ‘distances’ among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences.
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5
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
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Davy B, Axford D, Beale JH, Butryn A, Docker P, Ebrahim A, Leen G, Orville AM, Owen RL, Aller P. Reducing sample consumption for serial crystallography using acoustic drop ejection. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1820-1825. [PMID: 31490175 PMCID: PMC6730619 DOI: 10.1107/s1600577519009329] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/28/2019] [Indexed: 05/18/2023]
Abstract
Efficient sample delivery is an essential aspect of serial crystallography at both synchrotrons and X-ray free-electron lasers. Rastering fixed target chips through the X-ray beam is an efficient method for serial delivery from the perspectives of both sample consumption and beam time usage. Here, an approach for loading fixed targets using acoustic drop ejection is presented that does not compromise crystal quality, can reduce sample consumption by more than an order of magnitude and allows serial diffraction to be collected from a larger proportion of the crystals in the slurry.
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Affiliation(s)
- Bradley Davy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Peter Docker
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Ali Ebrahim
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Gabriel Leen
- PolyPico Technologies Ltd, Unit 10, Airways Technology Park, Rathmacullig Wes, Ballygarvan, Cork T12 DY95, Ireland
- Department of Electronic and Computer Engineering, University of Limerick, Ireland
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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Samara YN, Brennan HM, McCarthy L, Bollard MT, Laspina D, Wlodek JM, Campos SL, Natarajan R, Gofron K, McSweeney S, Soares AS, Leroy L. Using sound pulses to solve the crystal-harvesting bottleneck. Acta Crystallogr D Struct Biol 2018; 74:986-999. [PMID: 30289409 PMCID: PMC6173054 DOI: 10.1107/s2059798318011506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/14/2018] [Indexed: 01/16/2023] Open
Abstract
Crystal harvesting has proven to be difficult to automate and remains the rate-limiting step for many structure-determination and high-throughput screening projects. This has resulted in crystals being prepared more rapidly than they can be harvested for X-ray data collection. Fourth-generation synchrotrons will support extraordinarily rapid rates of data acquisition, putting further pressure on the crystal-harvesting bottleneck. Here, a simple solution is reported in which crystals can be acoustically harvested from slightly modified MiTeGen In Situ-1 crystallization plates. This technique uses an acoustic pulse to eject each crystal out of its crystallization well, through a short air column and onto a micro-mesh (improving on previous work, which required separately grown crystals to be transferred before harvesting). Crystals can be individually harvested or can be serially combined with a chemical library such as a fragment library.
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Affiliation(s)
- Yasmin N. Samara
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Universidade Federal de Santa Maria, 97105-900 Santa Maria-RS, Brazil
| | - Haley M. Brennan
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Liam McCarthy
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, Stony Brook University, New York, NY 11794-5215, USA
| | - Mary T. Bollard
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, York College of Pennsylvania, York, PA 17403, USA
| | - Denise Laspina
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, Stony Brook University, New York, NY 11794-5215, USA
| | - Jakub M. Wlodek
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Computer Science, Stony Brook University, New York, NY 11794-5215, USA
| | - Stefanie L. Campos
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Clinical Nutrition, Stony Brook University, New York, NY 11794-5215, USA
| | - Ramya Natarajan
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kazimierz Gofron
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Sean McSweeney
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Ludmila Leroy
- Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
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9
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High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Nat Protoc 2018; 13:260-292. [PMID: 29300389 DOI: 10.1038/nprot.2017.135] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein crystallography has significantly advanced in recent years, with in situ data collection, in which crystals are placed in the X-ray beam within their growth medium, being a major point of focus. In situ methods eliminate the need to harvest crystals, a previously unavoidable drawback, particularly for often small membrane-protein crystals. Here, we present a protocol for the high-throughput in situ X-ray screening of and data collection from soluble and membrane-protein crystals at room temperature (20-25°C) and under cryogenic conditions. The Mylar in situ method uses Mylar-based film sandwich plates that are inexpensive, easy to make, and compatible with automated imaging, and that show very low background scattering. They support crystallization in microbatch and vapor-diffusion modes, as well as in lipidic cubic phases (LCPs). A set of 3D-printed holders for differently sized patches of Mylar sandwich films makes the method robust and versatile, allows for storage and shipping of crystals, and enables automated mounting at synchrotrons, as well as goniometer-based screening and data collection. The protocol covers preparation of in situ plates and setup of crystallization trials; 3D printing and assembly of holders; opening of plates, isolation of film patches containing crystals, and loading them onto holders; basic screening and data-collection guidelines; and unloading of holders, as well as reuse and recycling of them. In situ plates are prepared and assembled in 1 h; holders are 3D-printed and assembled in ≤90 min; and an in situ plate is opened, and a film patch containing crystals is isolated and loaded onto a holder in 5 min.
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Abstract
Micro-diffraction tools for macromolecular crystallography, first developed at the end of 1990s and now an integral part of many synchrotron beamlines, enable some of the experiments which were not feasible just a decade or so ago. These include data collection from very small samples, just a few micrometers in size; from larger, but severely inhomogeneous samples; and from samples which are optically invisible. Improved micro-diffraction tools led to improved signal-to-noise ratio, to mitigation of radiation damage in some cases, and to better-designed diffraction experiments. Small, micron-scale beams can be attained in different ways and knowing the details of the implementation is important in order to design the diffraction experiment properly. Similarly, precision, reproducibility and stability of the goniometry, and caveats of detection systems need to be taken into account. Lastly, to make micro-diffraction widely applicable, the sophistication, robustness, and user-friendliness of these tools are just as important as the technical capabilities.
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Affiliation(s)
- Ruslan Sanishvili
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA.
| | - Robert F Fischetti
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
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Broecker J, Klingel V, Ou WL, Balo AR, Kissick D, Ogata CM, Kuo A, Ernst OP. A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. CRYSTAL GROWTH & DESIGN 2016; 16:6318-6326. [PMID: 28261000 PMCID: PMC5328415 DOI: 10.1021/acs.cgd.6b00950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/30/2016] [Indexed: 05/20/2023]
Abstract
In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometer-based X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi. In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.
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Affiliation(s)
- Jana Broecker
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- E-mail:
| | - Viviane Klingel
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Aidin R. Balo
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David
J. Kissick
- GM/CA
at Advanced Photon Source, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Craig M. Ogata
- GM/CA
at Advanced Photon Source, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Anling Kuo
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Oliver P. Ernst
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- E-mail:
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Hirata K, Foadi J, Evans G, Hasegawa K, Zeldin OB. Structural Biology with Microfocus Beamlines. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-4-431-56030-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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13
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Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature. Sci Rep 2016; 6:25558. [PMID: 27150272 PMCID: PMC4858681 DOI: 10.1038/srep25558] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/18/2016] [Indexed: 12/27/2022] Open
Abstract
Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.
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14
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Martin-Garcia JM, Conrad CE, Coe J, Roy-Chowdhury S, Fromme P. Serial femtosecond crystallography: A revolution in structural biology. Arch Biochem Biophys 2016; 602:32-47. [PMID: 27143509 DOI: 10.1016/j.abb.2016.03.036] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022]
Abstract
Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein.
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Affiliation(s)
- Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Chelsie E Conrad
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA.
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15
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Gorrec F. Protein crystallization screens developed at the MRC Laboratory of Molecular Biology. Drug Discov Today 2016; 21:819-25. [PMID: 27032894 PMCID: PMC4911435 DOI: 10.1016/j.drudis.2016.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/04/2016] [Accepted: 03/08/2016] [Indexed: 12/12/2022]
Abstract
In order to solve increasingly challenging protein structures with crystallography, crystallization reagents and screen formulations are regularly investigated. Here, we briefly describe 96-condition screens developed at the MRC Laboratory of Molecular Biology: the LMB sparse matrix screen, Pi incomplete factorial screens, the MORPHEUS grid screens and the ANGSTROM optimization screen. In this short review, we also discuss the difficulties and advantages associated with the development of protein crystallization screens.
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Affiliation(s)
- Fabrice Gorrec
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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16
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Roessler CG, Agarwal R, Allaire M, Alonso-Mori R, Andi B, Bachega JFR, Bommer M, Brewster AS, Browne MC, Chatterjee R, Cho E, Cohen AE, Cowan M, Datwani S, Davidson VL, Defever J, Eaton B, Ellson R, Feng Y, Ghislain LP, Glownia JM, Han G, Hattne J, Hellmich J, Héroux A, Ibrahim M, Kern J, Kuczewski A, Lemke HT, Liu P, Majlof L, McClintock WM, Myers S, Nelsen S, Olechno J, Orville AM, Sauter NK, Soares AS, Soltis SM, Song H, Stearns RG, Tran R, Tsai Y, Uervirojnangkoorn M, Wilmot CM, Yachandra V, Yano J, Yukl ET, Zhu D, Zouni A. Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography. Structure 2016; 24:631-640. [PMID: 26996959 DOI: 10.1016/j.str.2016.02.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/25/2015] [Accepted: 02/17/2016] [Indexed: 02/01/2023]
Abstract
X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.
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Affiliation(s)
- Christian G Roessler
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Rakhi Agarwal
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Marc Allaire
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Babak Andi
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - José F R Bachega
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos, CEP: 13560-970, Brazil
| | - Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Michael C Browne
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruchira Chatterjee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Eunsun Cho
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew Cowan
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | | | - Victor L Davidson
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816-2364, USA
| | - Jim Defever
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | | | - Yiping Feng
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Guangye Han
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Julia Hellmich
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Annie Héroux
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anthony Kuczewski
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Henrik T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | | | | | - Stuart Myers
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Silke Nelsen
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Allen M Orville
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Alexei S Soares
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Heng Song
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | | | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Yingssu Tsai
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Chemistry, Stanford University, Stanford, CA 94305-4401, USA
| | | | - Carrie M Wilmot
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vittal Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Erik T Yukl
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
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17
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Ericson DL, Yin X, Scalia A, Samara YN, Stearns R, Vlahos H, Ellson R, Sweet RM, Soares AS. Acoustic Methods to Monitor Protein Crystallization and to Detect Protein Crystals in Suspensions of Agarose and Lipidic Cubic Phase. ACTA ACUST UNITED AC 2016; 21:107-14. [DOI: 10.1177/2211068215616365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/16/2022]
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18
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Foley BJ, Drozd AM, Bollard MT, Laspina D, Podobedov N, Zeniou N, Rao AS, Andi B, Jackimowicz R, Sweet RM, McSweeney S, Soares AS. Maintaining Microclimates during Nanoliter Chemical Dispensations Using Custom-Designed Source Plate Lids. JOURNAL OF LABORATORY AUTOMATION 2015; 21:115-24. [PMID: 26564917 DOI: 10.1177/2211068215616072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 11/17/2022]
Abstract
A method is described for using custom snap-on lids to protect chemicals in microtiter plates from evaporation and contamination. The lids contain apertures (diameter 1.5, 1.0, or 0.5 mm) through which the chemical building blocks can be transferred. The lid with 0.5 mm apertures was tested using a noncontact acoustic liquid handler; the 1.0 and 1.5 mm lids were tested using two tip-based liquid handlers. All of the lids reduced the rate at which solvents evaporated to room air, and greatly reduced the rate of contamination by water and oxygen from room air. In steady-state measurements, the lids reduced the rate of evaporation of methanol, 1-hexene, and water by 33% to 248%. In cycled experiments, the contamination of aqueous solvent with oxygen was reduced below detectability and the rate at which DMSO engorged atmospheric water was reduced by 81%. Our results demonstrate that the lids preserve the integrity of air-sensitive reagents during the time needed for different types of liquid handlers to perform dispensations. Controlling degradation and evaporation of chemical building blocks exposed to the atmosphere is increasingly useful as the reagent volume is reduced by advances in liquid handling technology, such as acoustic droplet ejection.
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Affiliation(s)
- Bryan J Foley
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY, USA Fairmont State University, Fairmont, WV, USA
| | - Ashley M Drozd
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY, USA Long Island University, Brooklyn, NY, USA
| | - Mary T Bollard
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY, USA York College of Pennsylvania, York, PA, USA
| | - Denise Laspina
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY, USA Department of Biology, Stony Brook University, Stony Brook, NY, USA
| | - Nikita Podobedov
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY, USA Ward Melville High School, Setauket-East Setauket, NY, USA
| | - Nicholas Zeniou
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY, USA St. Anthony's High School, Huntington Station, NY, USA
| | - Anjali S Rao
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY, USA Department of Mechanical Engineering, Stony Brook University, Stony Brook, NY, USA
| | - Babak Andi
- Energy Sciences Directorate, NSLS-II, Brookhaven National Laboratory, Upton, NY, USA
| | - Rick Jackimowicz
- Energy Sciences Directorate, NSLS-II, Brookhaven National Laboratory, Upton, NY, USA
| | - Robert M Sweet
- Energy Sciences Directorate, NSLS-II, Brookhaven National Laboratory, Upton, NY, USA Biosciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Sean McSweeney
- Energy Sciences Directorate, NSLS-II, Brookhaven National Laboratory, Upton, NY, USA Biosciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Alexei S Soares
- Energy Sciences Directorate, NSLS-II, Brookhaven National Laboratory, Upton, NY, USA
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19
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Sackmann EK, Majlof L, Hahn-Windgassen A, Eaton B, Bandzava T, Daulton J, Vandenbroucke A, Mock M, Stearns RG, Hinkson S, Datwani SS. Technologies That Enable Accurate and Precise Nano- to Milliliter-Scale Liquid Dispensing of Aqueous Reagents Using Acoustic Droplet Ejection. ACTA ACUST UNITED AC 2015; 21:166-77. [PMID: 26341100 DOI: 10.1177/2211068215602191] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 11/16/2022]
Abstract
Acoustic liquid handling uses high-frequency acoustic signals that are focused on the surface of a fluid to eject droplets with high accuracy and precision for various life science applications. Here we present a multiwell source plate, the Echo Qualified Reservoir (ER), which can acoustically transfer over 2.5 mL of fluid per well in 25-nL increments using an Echo 525 liquid handler. We demonstrate two Labcyte technologies-Dynamic Fluid Analysis (DFA) methods and a high-voltage (HV) grid-that are required to maintain accurate and precise fluid transfers from the ER at this volume scale. DFA methods were employed to dynamically assess the energy requirements of the fluid and adjust the acoustic ejection parameters to maintain a constant velocity droplet. Furthermore, we demonstrate that the HV grid enhances droplet velocity and coalescence at the destination plate. These technologies enabled 5-µL per destination well transfers to a 384-well plate, with accuracy and precision values better than 4%. Last, we used the ER and Echo 525 liquid handler to perform a quantitative polymerase chain reaction (qPCR) assay to demonstrate an application that benefits from the flexibility and larger volume capabilities of the ER.
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20
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Wu P, Noland C, Ultsch M, Edwards B, Harris D, Mayer R, Harris SF. Developments in the Implementation of Acoustic Droplet Ejection for Protein Crystallography. ACTA ACUST UNITED AC 2015; 21:97-106. [PMID: 26275619 DOI: 10.1177/2211068215598938] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 11/16/2022]
Abstract
Acoustic droplet ejection (ADE) enables crystallization experiments at the low-nanoliter scale, resulting in rapid vapor diffusion equilibration dynamics and efficient reagent usage in the empirical discovery of structure-enabling protein crystallization conditions. We extend our validation of this technology applied to the diverse physicochemical property space of aqueous crystallization reagents where dynamic fluid analysis coupled to ADE aids in accurate and precise dispensations. Addition of crystallization seed stocks, chemical additives, or small-molecule ligands effectively modulates crystallization, and we here provide examples in optimization of crystal morphology and diffraction quality by the acoustic delivery of ultra-small volumes of these cofactors. Additional applications are discussed, including set up of in situ proteolysis and alternate geometries of crystallization that leverage the small scale afforded by acoustic delivery. Finally, we describe parameters of a system of automation in which the acoustic liquid handler is integrated with a robotic arm, plate centrifuge, peeler, sealer, and stacks, which allows unattended high-throughput crystallization experimentation.
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Affiliation(s)
- Ping Wu
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | - Cameron Noland
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | - Mark Ultsch
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | | | | | - Robert Mayer
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | - Seth F Harris
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
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21
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Guo F, Zhou W, Li P, Mao Z, Yennawar N, French JB, Jun Huang T. Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:2733-7. [PMID: 25641793 PMCID: PMC4478196 DOI: 10.1002/smll.201403262] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/19/2014] [Indexed: 05/20/2023]
Abstract
Advances in modern X-ray sources and detector technology have made it possible for crystallographers to collect usable data on crystals of only a few micrometers or less in size. Despite these developments, sample handling techniques have significantly lagged behind and often prevent the full realization of current beamline capabilities. In order to address this shortcoming, a surface acoustic wave-based method for manipulating and patterning crystals is developed. This method, which does not damage the fragile protein crystals, can precisely manipulate and pattern micrometer and submicrometer-sized crystals for data collection and screening. The technique is robust, inexpensive, and easy to implement. This method not only promises to significantly increase efficiency and throughput of both conventional and serial crystallography experiments, but will also make it possible to collect data on samples that were previously intractable.
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Affiliation(s)
- Feng Guo
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Weijie Zhou
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Peng Li
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Zhangming Mao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neela Yennawar
- Huck Institutes for Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jarrod B. French
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tony Jun Huang
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
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22
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Teplitsky E, Joshi K, Ericson DL, Scalia A, Mullen JD, Sweet RM, Soares AS. High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density. J Struct Biol 2015; 191:49-58. [PMID: 26027487 DOI: 10.1016/j.jsb.2015.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 05/21/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
We describe a high throughput method for screening up to 1728 distinct chemicals with protein crystals on a single microplate. Acoustic droplet ejection (ADE) was used to co-position 2.5nL of protein, precipitant, and chemicals on a MiTeGen in situ-1 crystallization plate™ for screening by co-crystallization or soaking. ADE-transferred droplets follow a precise trajectory which allows all components to be transferred through small apertures in the microplate lid. The apertures were large enough for 2.5nL droplets to pass through them, but small enough so that they did not disrupt the internal environment created by the mother liquor. Using this system, thermolysin and trypsin crystals were efficiently screened for binding to a heavy-metal mini-library. Fluorescence and X-ray diffraction were used to confirm that each chemical in the heavy-metal library was correctly paired with the intended protein crystal. A fragment mini-library was screened to observe two known lysozyme ligands using both co-crystallization and soaking. A similar approach was used to identify multiple, novel thaumatin binding sites for ascorbic acid. This technology pushes towards a faster, automated, and more flexible strategy for high throughput screening of chemical libraries (such as fragment libraries) using as little as 2.5nL of each component.
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Affiliation(s)
- Ella Teplitsky
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biochemistry and Cell Biology, Stony Brook University, NY 11794-5215, USA
| | - Karan Joshi
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Electronics and Electrical Communication Engineering, PEC University of Technology, Chandigarh, India
| | - Daniel L Ericson
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biomedical Engineering, University at Buffalo, SUNY, 12 Capen Hall, Buffalo, NY 14260, USA
| | - Alexander Scalia
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biological Sciences, 4400 Vestal Parkway East, Binghamton University, NY 13902, USA
| | - Jeffrey D Mullen
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Physics Department, University of Oregon, Eugene, OR 97403-1274, USA
| | - Robert M Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
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23
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Coquelle N, Brewster AS, Kapp U, Shilova A, Weinhausen B, Burghammer M, Colletier JP. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1184-96. [PMID: 25945583 PMCID: PMC4427202 DOI: 10.1107/s1399004715004514] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 03/04/2015] [Indexed: 01/30/2023]
Abstract
High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.
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Affiliation(s)
- Nicolas Coquelle
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ulrike Kapp
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Anastasya Shilova
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Britta Weinhausen
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Manfred Burghammer
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
- Department of Analytical Chemistry, Ghent University, Ghent B-9000, Belgium
| | - Jacques-Philippe Colletier
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
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24
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Schlichting I. Serial femtosecond crystallography: the first five years. IUCRJ 2015; 2:246-55. [PMID: 25866661 PMCID: PMC4392417 DOI: 10.1107/s205225251402702x] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/09/2014] [Indexed: 05/18/2023]
Abstract
Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.
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Affiliation(s)
- Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
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25
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Cuttitta CM, Ericson DL, Scalia A, Roessler CG, Teplitsky E, Joshi K, Campos O, Agarwal R, Allaire M, Orville AM, Sweet RM, Soares AS. Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:94-103. [PMID: 25615864 PMCID: PMC4304690 DOI: 10.1107/s1399004714013728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 06/12/2014] [Indexed: 12/03/2022]
Abstract
Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s(-1)) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.
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Affiliation(s)
- Christina M. Cuttitta
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Center for Developmental Neuroscience and Department of Biology, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA
| | - Daniel L. Ericson
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biomedical Engineering, University at Buffalo, SUNY, 12 Capen Hall, Buffalo, NY 14260, USA
| | - Alexander Scalia
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biological Sciences, Binghamton University, 4400 Vestal Parkway East, Binghamton, NY 11973-5000, USA
| | - Christian G. Roessler
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Ella Teplitsky
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Karan Joshi
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Electronics and Electrical Communication Engineering, PEC University of Technology, Chandigarh, India
| | - Olven Campos
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biological Science, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33414, USA
| | - Rakhi Agarwal
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Marc Allaire
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Allen M. Orville
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Robert M. Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
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26
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Zipper LE, Aristide X, Bishop DP, Joshi I, Kharzeev J, Patel KB, Santiago BM, Joshi K, Dorsinvil K, Sweet RM, Soares AS. A simple technique to reduce evaporation of crystallization droplets by using plate lids with apertures for adding liquids. Acta Crystallogr F Struct Biol Commun 2014; 70:1707-13. [PMID: 25484231 PMCID: PMC4259245 DOI: 10.1107/s2053230x14025126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/16/2014] [Indexed: 11/17/2022] Open
Abstract
A method is described for using plate lids to reduce evaporation in low-volume vapor-diffusion crystallization experiments. The plate lids contain apertures through which the protein and precipitants were added to different crystallization microplates (the reservoir was filled before fitting the lids). Plate lids were designed for each of these commonly used crystallization microplates. This system minimizes the dehydration of crystallization droplets containing just a few nanolitres of protein and precipitant, and results in more reproducible diffraction from the crystals. For each lid design, changes in the weight of the plates were used to deduce the rate of evaporation under different conditions of temperature, air movement, droplet size and precipitant. For comparison, the state of dehydration was also visually assessed throughout the experiment. Finally, X-ray diffraction methods were used to compare the diffraction of protein crystals that were conventionally prepared against those that were prepared on plates with plate lids. The measurements revealed that the plate lids reduced the rate of evaporation by 63-82%. Crystals grown in 5 nl drops that were set up with plate lids diffracted to higher resolution than similar crystals from drops that were set up without plate lids. The results demonstrate that plate lids can be instrumental for improving few-nanolitre crystallizations.
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Affiliation(s)
- Lauren E. Zipper
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Mechanical Engineering, Binghamton University, 4400 Vestal Parkway East, Vestal, NY 13902, USA
| | - Xavier Aristide
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- North Babylon High School, 1 Phelps Lane North, Babylon, NY 11703, USA
| | - Dylan P. Bishop
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Northport High School, 154 Laurel Hill Road, Northport, NY 11768, USA
| | - Ishita Joshi
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- St Augustine Catholic High School, 2188 Rodick Road, Markham, ON L6C 1S3, Canada
| | - Julia Kharzeev
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Earl L. Vandermeulen High School, 350 Old Post Road, Port Jefferson, NY 11777, USA
| | - Krishna B. Patel
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- John P. Stevens High School, 855 Grove Avenue, Edison, NJ 08820, USA
| | - Brianna M. Santiago
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Connetquot High School, 190 7th Street, Bohemia, NY 11716, USA
| | - Karan Joshi
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Electronics and Electrical Communication Engineering, PEC University of Technology, Chandigarh, India
| | - Kahille Dorsinvil
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Robert M. Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
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Soares AS, Mullen JD, Parekh RM, McCarthy GS, Roessler CG, Jackimowicz R, Skinner JM, Orville AM, Allaire M, Sweet RM. Solvent minimization induces preferential orientation and crystal clustering in serial micro-crystallography on micro-meshes, in situ plates and on a movable crystal conveyor belt. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1231-9. [PMID: 25343789 PMCID: PMC4211130 DOI: 10.1107/s1600577514017731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 08/01/2014] [Indexed: 05/21/2023]
Abstract
X-ray diffraction data were obtained at the National Synchrotron Light Source from insulin and lysozyme crystals that were densely deposited on three types of surfaces suitable for serial micro-crystallography: MiTeGen MicroMeshes™, Greiner Bio-One Ltd in situ micro-plates, and a moving kapton crystal conveyor belt that is used to deliver crystals directly into the X-ray beam. 6° wedges of data were taken from ∼100 crystals mounted on each material, and these individual data sets were merged to form nine complete data sets (six from insulin crystals and three from lysozyme crystals). Insulin crystals have a parallelepiped habit with an extended flat face that preferentially aligned with the mounting surfaces, impacting the data collection strategy and the design of the serial crystallography apparatus. Lysozyme crystals had a cuboidal habit and showed no preferential orientation. Preferential orientation occluded regions of reciprocal space when the X-ray beam was incident normal to the data-collection medium surface, requiring a second pass of data collection with the apparatus inclined away from the orthogonal. In addition, crystals measuring less than 20 µm were observed to clump together into clusters of crystals. Clustering required that the X-ray beam be adjusted to match the crystal size to prevent overlapping diffraction patterns. No additional problems were encountered with the serial crystallography strategy of combining small randomly oriented wedges of data from a large number of specimens. High-quality data able to support a realistic molecular replacement solution were readily obtained from both crystal types using all three serial crystallography strategies.
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Affiliation(s)
- Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jeffrey D. Mullen
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973, USA
- Physics Department, University of Oregon, Eugene, OR 97403-1274, USA
| | - Ruchi M. Parekh
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973, USA
- Suffolk County Community College, Selden, NY 11784, USA
| | - Grace S. McCarthy
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Rick Jackimowicz
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - John M. Skinner
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Allen M. Orville
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Marc Allaire
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Robert M. Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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28
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Gorrec F. Progress in macromolecular crystallography depends on further miniaturization of crystallization experiments. Drug Discov Today 2014; 19:1505-7. [PMID: 25048082 DOI: 10.1016/j.drudis.2014.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Fabrice Gorrec
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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29
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Cole K, Roessler CG, Mulé EA, Benson-Xu EJ, Mullen JD, Le BA, Tieman AM, Birone C, Brown M, Hernandez J, Neff S, Williams D, Allaire M, Orville AM, Sweet RM, Soares AS. A linear relationship between crystal size and fragment binding time observed crystallographically: implications for fragment library screening using acoustic droplet ejection. PLoS One 2014; 9:e101036. [PMID: 24988328 PMCID: PMC4079544 DOI: 10.1371/journal.pone.0101036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
High throughput screening technologies such as acoustic droplet ejection (ADE) greatly increase the rate at which X-ray diffraction data can be acquired from crystals. One promising high throughput screening application of ADE is to rapidly combine protein crystals with fragment libraries. In this approach, each fragment soaks into a protein crystal either directly on data collection media or on a moving conveyor belt which then delivers the crystals to the X-ray beam. By simultaneously handling multiple crystals combined with fragment specimens, these techniques relax the automounter duty-cycle bottleneck that currently prevents optimal exploitation of third generation synchrotrons. Two factors limit the speed and scope of projects that are suitable for fragment screening using techniques such as ADE. Firstly, in applications where the high throughput screening apparatus is located inside the X-ray station (such as the conveyor belt system described above), the speed of data acquisition is limited by the time required for each fragment to soak into its protein crystal. Secondly, in applications where crystals are combined with fragments directly on data acquisition media (including both of the ADE methods described above), the maximum time that fragments have to soak into crystals is limited by evaporative dehydration of the protein crystals during the fragment soak. Here we demonstrate that both of these problems can be minimized by using small crystals, because the soak time required for a fragment hit to attain high occupancy depends approximately linearly on crystal size.
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Affiliation(s)
- Krystal Cole
- Office of Educational Programs, Brookhaven National Laboratory, Upton, New York, United States of America
- Purchase College, State University of New York, Purchase, New York, United States of America
| | - Christian G. Roessler
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Elizabeth A. Mulé
- Office of Educational Programs, Brookhaven National Laboratory, Upton, New York, United States of America
- Freeport High School, Freeport, New York, United States of America
| | - Emma J. Benson-Xu
- Office of Educational Programs, Brookhaven National Laboratory, Upton, New York, United States of America
- Georgetown Day School, Washington, DC, United States of America
| | - Jeffrey D. Mullen
- Office of Educational Programs, Brookhaven National Laboratory, Upton, New York, United States of America
- Physics Department, University of Oregon, Eugene, Oregon, United States of America
| | - Benjamin A. Le
- Office of Educational Programs, Brookhaven National Laboratory, Upton, New York, United States of America
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Alanna M. Tieman
- Office of Educational Programs, Brookhaven National Laboratory, Upton, New York, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Claire Birone
- Babylon Junior-Senior High School, Babylon, New York, United States of America
| | - Maria Brown
- Sayville High School, West Sayville, New York, United States of America
| | - Jesus Hernandez
- Queens Metropolitan High School, Forest Hills, New York, United States of America
| | - Sherry Neff
- Shoreham-Wading River High School, Shoreham, New York, United States of America
| | - Daniel Williams
- Shelter Island High School, Shelter Island, New York, United States of America
| | - Marc Allaire
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Allen M. Orville
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York, United States of America
- Biosciences Department, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Robert M. Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York, United States of America
- Biosciences Department, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York, United States of America
- * E-mail:
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30
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Accardo A, Di Fabrizio E, Limongi T, Marinaro G, Riekel C. Probing droplets on superhydrophobic surfaces by synchrotron radiation scattering techniques. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:643-53. [PMID: 24971957 PMCID: PMC4073955 DOI: 10.1107/s1600577514009849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 05/01/2014] [Indexed: 06/03/2023]
Abstract
Droplets on artificially structured superhydrophobic surfaces represent quasi contact-free sample environments which can be probed by X-ray microbeams and nanobeams in the absence of obstructing walls. This review will discuss basic surface wettability concepts and introduce the technology of structuring surfaces. Quasi contact-free droplets are compared with contact-free droplets; processes related to deposition and evaporation on solid surfaces are discussed. Droplet coalescence based on the electrowetting effect allows the probing of short-time mixing and reaction processes. The review will show for several materials of biological interest that structural processes related to conformational changes, nucleation and assembly during droplet evaporation can be spatially and temporally resolved by raster-scan diffraction techniques. Orientational ordering of anisotropic materials deposited during solidification at pinning sites facilitates the interpretation of structural data.
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Affiliation(s)
- Angelo Accardo
- Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Enzo Di Fabrizio
- Physical Science and Engineering Divisions, KAUST (King Abdullah University of Science and Technology), Jeddah, Saudi Arabia
- Department of Clinical and Experimental Medicine, BIONEM Lab at University Magna Graecia, Campus Salvatore Venuta, Viale Europa 88100, Germaneto-Catanzaro, Italy
| | - Tania Limongi
- Physical Science and Engineering Divisions, KAUST (King Abdullah University of Science and Technology), Jeddah, Saudi Arabia
| | - Giovanni Marinaro
- Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex, France
| | - Christian Riekel
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex, France
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31
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Héroux A, Allaire M, Buono R, Cowan ML, Dvorak J, Flaks L, LaMarra S, Myers SF, Orville AM, Robinson HH, Roessler CG, Schneider DK, Shea-McCarthy G, Skinner JM, Skinner M, Soares AS, Sweet RM, Berman LE. Macromolecular crystallography beamline X25 at the NSLS. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:627-32. [PMID: 24763654 PMCID: PMC3998817 DOI: 10.1107/s1600577514003415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 02/14/2014] [Indexed: 05/05/2023]
Abstract
Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community.
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Affiliation(s)
- Annie Héroux
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Marc Allaire
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Richard Buono
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Matthew L. Cowan
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Joseph Dvorak
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Leon Flaks
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Steven LaMarra
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Stuart F. Myers
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Allen M. Orville
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Howard H. Robinson
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Christian G. Roessler
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Dieter K. Schneider
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Grace Shea-McCarthy
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - John M. Skinner
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Michael Skinner
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Robert M. Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Lonny E. Berman
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
- Correspondence e-mail:
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32
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Yin X, Scalia A, Leroy L, Cuttitta CM, Polizzo GM, Ericson DL, Roessler CG, Campos O, Ma MY, Agarwal R, Jackimowicz R, Allaire M, Orville AM, Sweet RM, Soares AS. Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1177-89. [PMID: 24816088 PMCID: PMC4014116 DOI: 10.1107/s1399004713034603] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/24/2013] [Indexed: 11/17/2022]
Abstract
Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.
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Affiliation(s)
- Xingyu Yin
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, NY 11794-5215, USA
- Nanjing University, Nanjing, Jiangsu, People’s Republic of China
| | - Alexander Scalia
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biological Sciences, Binghamton University, 4400 Vestal Parkway East, NY 13902, USA
| | - Ludmila Leroy
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- CAPES Foundation, Ministry of Education of Brazil, 70040-020 Brasilia-DF, Brazil
- Universidade Federal de Minas Gerais, 6627 Av. Antonio Carlos, 31270-901 Belo Horizonte-MG, Brazil
| | - Christina M. Cuttitta
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Center for Developmental Neuroscience and Department of Biology, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA
| | - Gina M. Polizzo
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- St Joseph’s College, 155 West Roe Boulevard, East Patchogue, NY 11772, USA
| | - Daniel L. Ericson
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biomedical Engineering, University at Buffalo, SUNY, 12 Capen Hall, Buffalo, NY 14260, USA
| | - Christian G. Roessler
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Olven Campos
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biological Science, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33414, USA
| | - Millie Y. Ma
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Comsewogue High School, 565 Bicycle Path, Port Jefferson Station, NY 11776, USA
| | - Rakhi Agarwal
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Rick Jackimowicz
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Marc Allaire
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Allen M. Orville
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Robert M. Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
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Deller MC, Rupp B. Approaches to automated protein crystal harvesting. Acta Crystallogr F Struct Biol Commun 2014; 70:133-55. [PMID: 24637746 PMCID: PMC3936438 DOI: 10.1107/s2053230x14000387] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/07/2014] [Indexed: 11/11/2022] Open
Abstract
The harvesting of protein crystals is almost always a necessary step in the determination of a protein structure using X-ray crystallographic techniques. However, protein crystals are usually fragile and susceptible to damage during the harvesting process. For this reason, protein crystal harvesting is the single step that remains entirely dependent on skilled human intervention. Automation has been implemented in the majority of other stages of the structure-determination pipeline, including cloning, expression, purification, crystallization and data collection. The gap in automation between crystallization and data collection results in a bottleneck in throughput and presents unfortunate opportunities for crystal damage. Several automated protein crystal harvesting systems have been developed, including systems utilizing microcapillaries, microtools, microgrippers, acoustic droplet ejection and optical traps. However, these systems have yet to be commonly deployed in the majority of crystallography laboratories owing to a variety of technical and cost-related issues. Automation of protein crystal harvesting remains essential for harnessing the full benefits of fourth-generation synchrotrons, free-electron lasers and microfocus beamlines. Furthermore, automation of protein crystal harvesting offers several benefits when compared with traditional manual approaches, including the ability to harvest microcrystals, improved flash-cooling procedures and increased throughput.
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Affiliation(s)
- Marc C. Deller
- The Joint Center for Structural Genomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Innsbruck Medical University, Schöpfstrasse 41, 6020 Innsbruck, Austria
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Roessler CG, Kuczewski A, Stearns R, Ellson R, Olechno J, Orville AM, Allaire M, Soares AS, Héroux A. Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:805-8. [PMID: 23955046 PMCID: PMC3747951 DOI: 10.1107/s0909049513020372] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/23/2013] [Indexed: 05/21/2023]
Abstract
To take full advantage of advanced data collection techniques and high beam flux at next-generation macromolecular crystallography beamlines, rapid and reliable methods will be needed to mount and align many samples per second. One approach is to use an acoustic ejector to eject crystal-containing droplets onto a solid X-ray transparent surface, which can then be positioned and rotated for data collection. Proof-of-concept experiments were conducted at the National Synchrotron Light Source on thermolysin crystals acoustically ejected onto a polyimide `conveyor belt'. Small wedges of data were collected on each crystal, and a complete dataset was assembled from a well diffracting subset of these crystals. Future developments and implementation will focus on achieving ejection and translation of single droplets at a rate of over one hundred per second.
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Affiliation(s)
| | - Anthony Kuczewski
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Richard Stearns
- Labcyte Inc., 1190 Borregas Avenue, Sunnyvale, CA 94089, USA
| | - Richard Ellson
- Labcyte Inc., 1190 Borregas Avenue, Sunnyvale, CA 94089, USA
| | - Joseph Olechno
- Labcyte Inc., 1190 Borregas Avenue, Sunnyvale, CA 94089, USA
| | - Allen M. Orville
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Marc Allaire
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Annie Héroux
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA
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35
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Wagner A, Duman R, Stevens B, Ward A. Microcrystal manipulation with laser tweezers. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1297-302. [PMID: 23793156 PMCID: PMC3689533 DOI: 10.1107/s090744491300958x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 04/08/2013] [Indexed: 11/14/2022]
Abstract
X-ray crystallography is the method of choice to deduce atomic resolution structural information from macromolecules. In recent years, significant investments in structural genomics initiatives have been undertaken to automate all steps in X-ray crystallography from protein expression to structure solution. Robotic systems are widely used to prepare crystallization screens and change samples on synchrotron beamlines for macromolecular crystallography. The only remaining manual handling step is the transfer of the crystal from the mother liquor onto the crystal holder. Manual mounting is relatively straightforward for crystals with dimensions of >25 µm; however, this step is nontrivial for smaller crystals. The mounting of microcrystals is becoming increasingly important as advances in microfocus synchrotron beamlines now allow data collection from crystals with dimensions of only a few micrometres. To make optimal usage of these beamlines, new approaches have to be taken to facilitate and automate this last manual handling step. Optical tweezers, which are routinely used for the manipulation of micrometre-sized objects, have successfully been applied to sort and mount macromolecular crystals on newly designed crystal holders. Diffraction data from CPV type 1 polyhedrin microcrystals mounted with laser tweezers are presented.
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Affiliation(s)
- Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, England.
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Villaseñor AG, Wong A, Shao A, Garg A, Donohue TJ, Kuglstatter A, Harris SF. Nanolitre-scale crystallization using acoustic liquid-transfer technology. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:893-900. [PMID: 22868754 PMCID: PMC3413209 DOI: 10.1107/s0907444912016617] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/16/2012] [Indexed: 11/11/2022]
Abstract
Focused acoustic energy allows accurate and precise liquid transfer on scales from picolitre to microlitre volumes. This technology was applied in protein crystallization, successfully transferring a diverse set of proteins as well as hundreds of precipitant solutions from custom and commercial crystallization screens and achieving crystallization in drop volumes as small as 20 nl. Only higher concentrations (>50%) of 2-methyl-2,4-pentanediol (MPD) appeared to be systematically problematic in delivery. The acoustic technology was implemented in a workflow, successfully reproducing active crystallization systems and leading to the discovery of crystallization conditions for previously uncharacterized proteins. The technology offers compelling advantages in low-nanolitre crystallization trials by providing significant reagent savings and presenting seamless scalability for those crystals that require larger volume optimization experiments using the same vapor-diffusion format.
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Affiliation(s)
- Armando G Villaseñor
- Department of Discovery Technologies, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA
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