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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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Talreja S, Perry SL, Guha S, Bhamidi V, Zukoski CF, Kenis PJA. Determination of the phase diagram for soluble and membrane proteins. J Phys Chem B 2010; 114:4432-41. [PMID: 20235520 PMCID: PMC2848416 DOI: 10.1021/jp911780z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Revised: 02/23/2010] [Indexed: 12/01/2022]
Abstract
Methods to efficiently determine the phase behavior of novel proteins have the potential to significantly benefit structural biology efforts. Here, we present protocols to determine both the solubility boundary and the supersolubility boundary for protein/precipitant systems using an evaporation-based crystallization platform. This strategy takes advantage of the well-defined rates of evaporation that occur in this platform to determine the state of the droplet at any point in time without relying on an equilibrium-based end point. The dynamic nature of this method efficiently traverses phase space along a known path, such that a solubility diagram can be mapped out for both soluble and membrane proteins while using a smaller amount of protein than what is typically used in optimization screens. Furthermore, a variation on this method can be used to decouple crystal nucleation and growth events, so fewer and larger crystals can be obtained within a given droplet. The latter protocol can be used to rescue a crystallization trial where showers of tiny crystals were observed. We validated both of the protocols to determine the phase behavior and the protocol to optimize crystal quality using the soluble proteins lysozyme and ribonuclease A as well as the membrane protein bacteriorhodopsin.
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Affiliation(s)
- Sameer Talreja
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Sarah L. Perry
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Sudipto Guha
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Venkateswarlu Bhamidi
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Charles F. Zukoski
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Paul J. A. Kenis
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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Solubility of lysozyme in polyethylene glycol-electrolyte mixtures: the depletion interaction and ion-specific effects. Biophys J 2008; 95:1285-94. [PMID: 18441020 DOI: 10.1529/biophysj.108.128694] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The solubility of aqueous solutions of lysozyme in the presence of polyethylene glycol and various alkaline salts was studied experimentally. The protein-electrolyte mixture was titrated with polyethylene glycol, and when precipitation of the protein occurred, a strong increase of the absorbance at 340 nm was observed. The solubility data were obtained as a function of experimental variables such as protein and electrolyte concentrations, electrolyte type, degree of polymerization of polyethylene glycol, and pH of the solution; the last defines the net charge of the lysozyme. The results indicate that the solubility of lysozyme decreases with the addition of polyethylene glycol; the solubility is lower for a polyethylene glycol with a higher degree of polymerization. Further, the logarithm of the protein solubility is a linear function of the polyethylene glycol concentration. The process is reversible and the protein remains in its native form. An increase of the electrolyte (NaCl) concentration decreases the solubility of lysozyme in the presence and absence of polyethylene glycol. The effect can be explained by the screening of the charged amino residues of the protein. The solubility experiments were performed at two different pH values (pH = 4.0 and 6.0), where the lysozyme net charge was +11 and +8, respectively. Ion-specific effects were systematically investigated. Anions such as Br(-), Cl(-), F(-), and H(2)PO(4)(-) (all in combination with Na(+)), when acting as counterions to a protein with positive net charge, exhibit a strong effect on the lysozyme solubility. The differences in protein solubility for chloride solutions with different cations Cs(+), K(+), and Na(+) (coions) were much smaller. The results at pH = 4.0 show that anions decrease the lysozyme solubility in the order F(-) < H(2)PO(4)(-) < Cl(-) < Br(-) (the inverse Hofmeister series), whereas cations follow the direct Hofmeister series (Cs(+) < K(+) < Na(+)) in this situation.
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Grouazel S, Bonneté F, Astier JP, Ferté N, Perez J, Veesler S. Exploring bovine pancreatic trypsin inhibitor phase transitions. J Phys Chem B 2007; 110:19664-70. [PMID: 17004835 DOI: 10.1021/jp0627123] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper presents an investigation of the phase diagram of BPTI (bovine pancreatic trypsin inhibitor)/350 mM KSCN at pH 4.9 by direct observation and numerical simulations. We report optical microscopy and light and X-ray scattering experiments coupled with theoretical data analysis using numerical tools. The phase diagram is thoroughly determined, as a function of temperature. Two polymorphs are observed by video microscopy and their solubility measured. In this phase diagram, the liquid-liquid phase separation (LLPS) is metastable with respect to the solid-liquid phase separation. Above the T(L-L) boundary curve, solutions are composed of a mixture of BPTI monomers and decamers. Attractive interactions are stronger between decamers than between monomers. Below the T(L-L) boundary curve, the dense phase is highly concentrated in protein and composed of BPTI decamers alone. Thus, the driving force for liquid-liquid or liquid-solid phase separation is the attraction between decamers at low pH. The structure factors of the dense phases are characteristic of repulsive dense phases because of a hard sphere repulsion core, meaning that in the dense phase proteins are actually in contact (interparticle distance of 53 A). In agreement with the Oswald rule of stages, LLPS occurs prior to and impedes the solid nucleation.
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Affiliation(s)
- Sylvain Grouazel
- Centre de Recherche en Matière Condensée et Nanosciences, CRMCN-CNRS, Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France
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Abstract
The physical chemistry of crystal growth can help to identify directions in which to look for improved crystal properties. In this chapter, we summarize how crystal growth depends on parameters that can be controlled experimentally, and relate them to the tools available for optimizing a particular crystal form for crystal shape, volume, and diffraction quality. Our purpose is to sketch the conceptual basis of optimization and to provide sample protocols derived from those foundations. We hope to assist even those who chose not to use systematic methods by enabling them to carry out rudimentary optimization searches armed with a better understanding of how the underlying physical chemistry operates.
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Affiliation(s)
- Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Anderson MJ, Hansen CL, Quake SR. Phase knowledge enables rational screens for protein crystallization. Proc Natl Acad Sci U S A 2006; 103:16746-51. [PMID: 17075056 PMCID: PMC1636526 DOI: 10.1073/pnas.0605293103] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We show that knowledge of the phase behavior of a protein allows one to create a rational screen that increases the success rate of crystallizing challenging proteins. The strategy is based on using microfluidics to perform large numbers of protein solubility experiments across many different chemical conditions to identify reagents for crystallization experiments. Phase diagrams were generated for the identified reagents and used to design customized crystallization screens for every protein. This strategy was applied with a 75% success rate to the crystallization of 12 diverse proteins, most of which failed to crystallize when using traditional techniques. The overall diffraction success rate was 33%, about double what was achieved with conventional automation in large-scale protein structure consortia. The higher diffraction success rates are achieved by designing customized crystallization screens using the phase behavior information for each target. The identification of reagents based on an understanding of protein solubility and the use of phase diagrams in the design of individualized crystallization screens therefore promotes high crystallization rates and the production of diffraction-quality crystals.
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Affiliation(s)
- Megan J. Anderson
- *Department of Biochemistry and Molecular Biophysics, California Institute of Technology, MS 128-95, Pasadena, CA 91125
| | - Carl L. Hansen
- Departments of Physics and Astronomy and Electrical and Computer Engineering, Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4; and
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, 318 Campus Drive, Room E300, Stanford, CA 94305
- To whom correspondence should be addressed. E-mail:
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Saijo S, Sato T, Tanaka N, Ichiyanagi A, Sugano Y, Shoda M. Precipitation diagram and optimization of crystallization conditions at low ionic strength for deglycosylated dye-decolorizing peroxidase from a basidiomycete. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:729-32. [PMID: 16511141 PMCID: PMC1952364 DOI: 10.1107/s1744309105019469] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Accepted: 06/21/2005] [Indexed: 11/10/2022]
Abstract
The growth of suitably sized protein crystals is essential for protein structure determination by X-ray crystallography. In general, crystals are grown using a trial-and-error method. However, these methods have been modified with the advent of microlitre dispensing-robot technology and of protocols that rapidly screen for crystal nucleation conditions. The use of one such automatic dispenser for mixing protein drops (1.3-2.0 microl in volume) of known concentration and pH with precipitating solutions (ejecting 2.0 microl droplets) containing salt is described here. The results of the experiments are relevant to a crystallization approach based on a two-step procedure: screening for the crystal nucleation step employing robotics followed by optimization of the crystallization conditions using incomplete factorial experimental design. Large crystals have successfully been obtained using quantities as small as 3.52 mg protein.
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Affiliation(s)
- Shinya Saijo
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-10 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Takao Sato
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-10 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Nobuo Tanaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-10 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Atsushi Ichiyanagi
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Yasushi Sugano
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Makoto Shoda
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-10 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- Correspondence e-mail:
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Vivarès D, Bonneté F. Liquid−Liquid Phase Separations in Urate Oxidase/PEG Mixtures: Characterization and Implications for Protein Crystallization. J Phys Chem B 2004; 108:6498-507. [DOI: 10.1021/jp037502u] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- D. Vivarès
- CRMCN-CNRS, Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France, and LMCP-UMR7590, Case 115, 4 place Jussieu, F-75252 Paris Cedex 05, France
| | - F. Bonneté
- CRMCN-CNRS, Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France, and LMCP-UMR7590, Case 115, 4 place Jussieu, F-75252 Paris Cedex 05, France
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Odahara T. Stability and solubility of integral membrane proteins from photosynthetic bacteria solubilized in different detergents. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1660:80-92. [PMID: 14757223 DOI: 10.1016/j.bbamem.2003.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
As a first step toward the establishment of practical guidelines for the search for crystallization conditions, stability and solubility were examined for integral membrane proteins from photosynthetic bacteria in the presence of different detergents. The results obtained from their stability provided practical information on the proper choice of detergent type in the preparation process and the subsequent crystallization experiment. In addition, the determination of a solubility diagram provided a practical method for quantifying the correct choice of detergent concentration and for setting up the suitable precipitant concentration in the crystallization experiment.
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Affiliation(s)
- Takayuki Odahara
- National Institute of Advanced Industrial Science and Technology, Tsukuba Central-6, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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Finet S, Vivarès D, Bonneté F, Tardieu A. Controlling Biomolecular Crystallization by Understanding the Distinct Effects of PEGs and Salts on Solubility. Methods Enzymol 2003; 368:105-29. [PMID: 14674271 DOI: 10.1016/s0076-6879(03)68007-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Stéphanie Finet
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP200 F38043 Grenoble, France
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Quantitative evaluation of the near-C2 symmetry of the bacterial photosynthetic reaction center. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(98)01203-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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