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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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2
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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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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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Schieferstein JM, Pawate AS, Varel MJ, Guha S, Astrauskaite I, Gennis RB, Kenis PJA. X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds. LAB ON A CHIP 2018; 18:944-954. [PMID: 29469138 PMCID: PMC5849577 DOI: 10.1039/c7lc01141e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Crystallization of membrane proteins is a critical step for uncovering atomic resolution 3-D structures and elucidating structure-function relationships. Microseeding, the process of transferring sub-microscopic crystal nuclei from initial screens into new crystallization experiments, is an effective, yet underutilized approach to grow crystals suitable for X-ray crystallography. Here, we report simplified methods for crystallization of membrane proteins that utilize microseeding in X-ray transparent microfluidic chips. First, a microfluidic method for introduction of microseed dilutions into metastable crystallization experiments is demonstrated for photoactive yellow protein and cytochrome bo3 oxidase. As microseed concentration decreased, the number of crystals decreased while the average size increased. Second, we demonstrate a microfluidic chip for microseed screening, where many crystallization conditions were formulated on-chip prior to mixing with microseeds. Crystallization composition, crystal size, and diffraction data were collected and mapped on phase diagrams, which revealed that crystals of similar diffraction quality and size typically grow in distinct regions of the phase diagram.
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Affiliation(s)
- Jeremy M Schieferstein
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, USA.
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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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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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7
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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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8
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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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9
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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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10
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Luft JR, Newman J, Snell EH. Crystallization screening: the influence of history on current practice. Acta Crystallogr F Struct Biol Commun 2014; 70:835-53. [PMID: 25005076 PMCID: PMC4089519 DOI: 10.1107/s2053230x1401262x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 05/30/2014] [Indexed: 11/17/2022] Open
Abstract
While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed.
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Affiliation(s)
- Joseph R. Luft
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Janet Newman
- CSIRO Collaborative Crystallisation Centre, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Structural Biology, SUNY Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
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11
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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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12
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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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13
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Moraes I, Evans G, Sanchez-Weatherby J, Newstead S, Stewart PDS. Membrane protein structure determination - the next generation. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:78-87. [PMID: 23860256 PMCID: PMC3898769 DOI: 10.1016/j.bbamem.2013.07.010] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/28/2013] [Accepted: 07/07/2013] [Indexed: 11/19/2022]
Abstract
The field of Membrane Protein Structural Biology has grown significantly since its first landmark in 1985 with the first three-dimensional atomic resolution structure of a membrane protein. Nearly twenty-six years later, the crystal structure of the beta2 adrenergic receptor in complex with G protein has contributed to another landmark in the field leading to the 2012 Nobel Prize in Chemistry. At present, more than 350 unique membrane protein structures solved by X-ray crystallography (http://blanco.biomol.uci.edu/mpstruc/exp/list, Stephen White Lab at UC Irvine) are available in the Protein Data Bank. The advent of genomics and proteomics initiatives combined with high-throughput technologies, such as automation, miniaturization, integration and third-generation synchrotrons, has enhanced membrane protein structure determination rate. X-ray crystallography is still the only method capable of providing detailed information on how ligands, cofactors, and ions interact with proteins, and is therefore a powerful tool in biochemistry and drug discovery. Yet the growth of membrane protein crystals suitable for X-ray diffraction studies amazingly remains a fine art and a major bottleneck in the field. It is often necessary to apply as many innovative approaches as possible. In this review we draw attention to the latest methods and strategies for the production of suitable crystals for membrane protein structure determination. In addition we also highlight the impact that third-generation synchrotron radiation has made in the field, summarizing the latest strategies used at synchrotron beamlines for screening and data collection from such demanding crystals. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Isabel Moraes
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
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14
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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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15
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Till M, Robson A, Byrne MJ, Nair AV, Kolek SA, Shaw Stewart PD, Race PR. Improving the success rate of protein crystallization by random microseed matrix screening. J Vis Exp 2013. [PMID: 24022545 DOI: 10.3791/50548] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Random microseed matrix screening (rMMS) is a protein crystallization technique in which seed crystals are added to random screens. By increasing the likelihood that crystals will grow in the metastable zone of a protein's phase diagram, extra crystallization leads are often obtained, the quality of crystals produced may be increased, and a good supply of crystals for data collection and soaking experiments is provided. Here we describe a general method for rMMS that may be applied to either sitting drop or hanging drop vapor diffusion experiments, established either by hand or using liquid handling robotics, in 96-well or 24-well tray format.
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Affiliation(s)
- Marisa Till
- School of Biochemistry, University of Bristol
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16
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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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17
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Soares AS, Engel MA, Stearns R, Datwani S, Olechno J, Ellson R, Skinner JM, Allaire M, Orville AM. Acoustically mounted microcrystals yield high-resolution X-ray structures. Biochemistry 2011; 50:4399-401. [PMID: 21542590 PMCID: PMC3144476 DOI: 10.1021/bi200549x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate a general strategy for determining structures from showers of microcrystals. It uses acoustic droplet ejection to transfer 2.5 nL droplets from the surface of microcrystal slurries, through the air, onto mounting micromesh pins. Individual microcrystals are located by raster-scanning a several-micrometer X-ray beam across the cryocooled micromeshes. X-ray diffraction data sets merged from several micrometer-sized crystals are used to determine 1.8 Ǻ resolution crystal structures.
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Affiliation(s)
- Alexei S. Soares
- Biology Department, Brookhaven National Laboratory, Upton NY 11973-5000
| | - Matthew A. Engel
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton NY 11973-5000
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794-2580
| | - Richard Stearns
- Labcyte Inc. 1190 Borregas Avenue, Sunnyvale, California 94089
| | - Sammy Datwani
- Labcyte Inc. 1190 Borregas Avenue, Sunnyvale, California 94089
| | - Joe Olechno
- Labcyte Inc. 1190 Borregas Avenue, Sunnyvale, California 94089
| | - Richard Ellson
- Labcyte Inc. 1190 Borregas Avenue, Sunnyvale, California 94089
| | - John M. Skinner
- Biology Department, Brookhaven National Laboratory, Upton NY 11973-5000
| | - Marc Allaire
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton NY 11973-5000
| | - Allen M. Orville
- Biology Department, Brookhaven National Laboratory, Upton NY 11973-5000
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18
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Crespo R, Martins PM, Gales L, Rocha F, Damas AM. Potential use of ultrasound to promote protein crystallization. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810040951] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This work shows promising applications of ultrasound in promoting protein crystallization, which is important for structure determination by X-ray crystallography. It was observed that ultrasound can be used as a nucleation promoter as it decreases the energy barrier for crystal formation. Crystallization experiments on egg-white lysozyme were carried out with and without ultrasonic irradiation using commercial crystallization plates placed in temperature-controlled water baths. The nucleation-promoting effect introduced by ultrasound is illustrated by the reduction of the metastable zone width, as measured by the isothermal microbatch technique. The same effect was confirmed by the increased number of conditions leading to the formation of crystals when vapour diffusion techniques were carried out in the presence of ultrasound. By inducing faster nucleation, ultrasound leads to protein crystals grown at low supersaturation levels, which are known to have better diffraction properties. In fact, X-ray diffraction data sets collected using 13 lysozyme crystals (seven grown with ultrasound and six without) show an average 0.1 Å improvement in the resolution limit when ultrasound was used (p< 0.10). Besides the immediate application of ultrasound in nucleation promotion, the preliminary diffraction results also suggest a promising application in crystal quality enhancement.
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19
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Kutach AK, Villaseñor AG, Lam D, Belunis C, Janson C, Lok S, Hong LN, Liu CM, Deval J, Novak TJ, Barnett JW, Chu W, Shaw D, Kuglstatter A. Crystal Structures of IL-2-inducible T cell Kinase Complexed with Inhibitors: Insights into Rational Drug Design and Activity Regulation. Chem Biol Drug Des 2010; 76:154-63. [DOI: 10.1111/j.1747-0285.2010.00993.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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