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Boyko KM, Timofeev VI, Samygina VR, Kuranova IP, Popov VO, Koval’chuk MV. Protein crystallization under microgravity conditions. Analysis of the results of Russian experiments performed on the International Space Station in 2005−2015. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516050059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boyko KM, Popov VO, Kovalchuk MV. Promising approaches to crystallization of macromolecules suppressing the convective mass transport to the growing crystal. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ng JD, Baird JK, Coates L, Garcia-Ruiz JM, Hodge TA, Huang S. Large-volume protein crystal growth for neutron macromolecular crystallography. Acta Crystallogr F Struct Biol Commun 2015; 71:358-70. [PMID: 25849493 PMCID: PMC4388167 DOI: 10.1107/s2053230x15005348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/15/2015] [Indexed: 11/10/2022] Open
Abstract
Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.
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Affiliation(s)
- Joseph D. Ng
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
- iXpressGenes Inc., Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - James K. Baird
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, MS6475, Oak Ridge, TN 37831, USA
| | - Juan M. Garcia-Ruiz
- Laboratorio de Estudios Cristalográficos (IACT), CSIC–Universidad de Granada, Avenida de la Innovación s/n, Armilla (Granada), Spain
| | - Teresa A. Hodge
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Sijay Huang
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, 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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Carruthers Jr CW, Gerdts C, Johnson MD, Webb P. A microfluidic, high throughput protein crystal growth method for microgravity. PLoS One 2013; 8:e82298. [PMID: 24278480 PMCID: PMC3836816 DOI: 10.1371/journal.pone.0082298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/31/2013] [Indexed: 11/18/2022] Open
Abstract
The attenuation of sedimentation and convection in microgravity can sometimes decrease irregularities formed during macromolecular crystal growth. Current terrestrial protein crystal growth (PCG) capabilities are very different than those used during the Shuttle era and that are currently on the International Space Station (ISS). The focus of this experiment was to demonstrate the use of a commercial off-the-shelf, high throughput, PCG method in microgravity. Using Protein BioSolutions' microfluidic Plug Maker™/CrystalCard™ system, we tested the ability to grow crystals of the regulator of glucose metabolism and adipogenesis: peroxisome proliferator-activated receptor gamma (apo-hPPAR-γ LBD), as well as several PCG standards. Overall, we sent 25 CrystalCards™ to the ISS, containing ~10,000 individual microgravity PCG experiments in a 3U NanoRacks NanoLab (1U = 10(3) cm.). After 70 days on the ISS, our samples were returned with 16 of 25 (64%) microgravity cards having crystals, compared to 12 of 25 (48%) of the ground controls. Encouragingly, there were more apo-hPPAR-γ LBD crystals in the microgravity PCG cards than the 1g controls. These positive results hope to introduce the use of the PCG standard of low sample volume and large experimental density to the microgravity environment and provide new opportunities for macromolecular samples that may crystallize poorly in standard laboratories.
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Affiliation(s)
- Carl W. Carruthers Jr
- Houston Methodist Research Institute, Department of Genomic Medicine, Houston, Texas, United States of America
- * E-mail:
| | - Cory Gerdts
- Protein BioSolutions, Inc., Gaithersburg, Maryland, United States of America
| | | | - Paul Webb
- Houston Methodist Research Institute, Department of Genomic Medicine, Houston, Texas, United States of America
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Kantardjieff KA, Lind C, Ng J, Santarsiero BD. Efforts to enhance coverage of crystallography in United States secondary education. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810034333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
Ultra-high-resolution X-ray crystallography of macromolecules (i.e. resolution better than 0.8 Angstroms) is a rising field that promises to provide new insight into the structure-function relationships of biomacromolecules. The picture emerging from macromolecular structures at this resolution is far more complex than previously understood, requiring for its study improved tools for structure refinement, analysis and annotation. Some of these problems were highlighted during the recent High Resolution Drug Design Meeting (Bischenberg-Strasbourg, France, 13-16 May 2004). We will review here some of the results and discussions that took place during that meeting and elaborate on the trends and challenges ahead in this emerging new field of research.
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Han Y, Cang HX, Zhou JX, Wang YP, Bi RC, Colelesage J, Delbaere LTJ, Nahoum V, Shi R, Zhou M, Zhu DW, Lin SX. Protein crystal growth on board Shenzhou 3: a concerted effort improves crystal diffraction quality and facilitates structure determination. Biochem Biophys Res Commun 2004; 324:1081-6. [PMID: 15485665 DOI: 10.1016/j.bbrc.2004.09.166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Indexed: 10/26/2022]
Abstract
The crystallization of 16 proteins was carried out using 60 wells on board Shenzhou 3 in 2002. Although the mission was only 7 days, careful and concerted planning at all stages made it possible to obtain crystals of improved quality compared to their ground controls for some of the proteins. Significantly improved resolutions were obtained from diffracted crystals of 4 proteins. A complete data set from a space crystal of the PEP carboxykinase yielded significantly higher resolution (1.46A vs. 1.87A), I/sigma (22.4 vs. 15.5), and a lower average temperature factor (29.2A(2) vs. 42.9A(2)) than the best ground-based control crystal. The 3-D structure of the enzyme is well improved with significant ligand density. It has been postulated that the reduced convection and absence of macromolecule sedimentation under microgravity have advantages/benefits for protein crystal growth. Improvements in experimental design for protein crystal growth in microgravity are ongoing.
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Affiliation(s)
- Y Han
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Abstract
The need for high-resolution structure information on membrane proteins is immediate and growing. Currently, the only reliable way to get it is crystallographically. The rate-limiting step from protein to structure is crystal production. An overview of the current ideas and experimental approaches prevailing in the area of membrane protein crystallization is presented. The long-established surfactant-based method has been reviewed extensively and is not examined in detail here. The focus instead is on the latest methods, all of which exploit the spontaneous self-assembling properties of lipids and detergent as vesicles (vesicle-fusion method), discoidal micelles (bicelle method), and liquid crystals or mesophases (in meso or cubic-phase method). In the belief that a knowledge of the underlying phase science is integral to understanding the molecular basis of these assorted crystallization strategies, the article begins with a brief primer on lipids, mesophases, and phase science, and the related issue of form and function as applied to lipids is addressed. The experimental challenges associated with and the solutions for procuring adequate amounts of homogeneous membrane proteins, or parts thereof, are examined. The cubic-phase method is described from the following perspectives: how it is done in practice, its general applicability and successes to date, and the nature of the mesophases integral to the process. Practical aspects of the method are examined with regard to salt, detergent, and screen solution effects; crystallization at low temperatures; tailoring the cubic phase to suit the target protein; different cubic-phase types; dealing with low-protein samples, colorless proteins, microcrystals, and radiation damage; transport within the cubic phase for drug design, cofactor retention, and phasing; using spectroscopy for quality control; harvesting crystals; and miniaturization and robotization for high-throughput screening. The section ends with a hypothesis for nucleation and growth of membrane protein crystals in meso. Thus far, the bicelle and vesicle-fusion methods have produced crystals of one membrane protein, bacteriorhodopsin. The experimental details of both methods are reviewed and their general applicability in the future is commented on. The three new methods are rationalized by analogy to crystallization in microgravity and with respect to epitaxy. A list of Web resources in the area of membrane protein crystallogenesis is included.
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