The sample is the single most important variable in the crystallization experiment.9,10 Begin with a pure, homogeneous, stable, active sample. The sample should be as pure as possible, 95 to 98%, assayed by Coomassie stained SDS-PAGE. A homogeneous, active sample, free of contaminants, aggregates, and minimal conformational flexibility is desired. Dynamic Light Scattering (DLS) can be used as a diagnostic for sample homogeneity, measuring the polydispersity of the sample, pointing out aggregation, which can be a deterrent to crystallization.1-4, 10 DLS can be also used to screen and identify sample buffer components such as buffer, pH, ionic strength, excipients, additives, and other chemical variables, as well as temperature, towards optimization of the sample buffer formulation to maximize sample homogeneity. Differential Scanning Fluorimetry (DSF or Thermofluor®) can be used as a diagnostic for sample stability, measuring the temperature stability of the sample in the presence of chemical variables such as pH, buffer, ionic strength, excipients, and additives.5-7
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References and Readings
1. How to Use Dynamic Light Scattering to Improve the Likelihood of Growing Macromolecular Crystals. Gloria E. O. Borgstahl. Methods in Molecular Biology, vol. 363: Macromolecular Crystallography Protocols: Volume 1: Preparation and Crystallization of Macromolecules, Pages 109-129, Edited by: S. Doublié© Humana Press Inc., Totowa, NJ.
2. Light scattering of proteins as a criterion for crystallization. Zulauf, M. and D’Arcy, A. (1992), J. Cryst. Growth 122, 102–106.
3. Dynamic light scattering in evaluating crystallizability of macromolecules. Ferré-D’Amaré, A. R. and Burley, S. K. (1997) Meth. Enzymol. 276, 157–166.
4. Protein Crystallization Techniques, Strategies and, Tips. Bergfors, T. M. (1999) International University Line, La Jolla, CA.
5. Thermofluor-based high-throughput stability optimization of proteins for structural studies. Ericsson, U.B., Hallberg, M.B., DeTitta, G.T., Dekker, N. & Nordlund, P. Anal. Biochem. 357, 289–298 (2006).
6. High-density miniaturized thermal shift assays as a general strategy for drug discovery. Pantoliano, M.W. et al. Journal of Bimolecular Screening, Volume 6, Number 6, 2001.
7. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Niesen, F.H. et al. Nature Protocols, 2212-2221, Volume 2, No. 9, 2007.
8. An improved protocol for rapid freezing of protein samples for longterm storage. Hol, W.G.J. et al, Acta Cryst. (2004). D60, 203-204.
9. The protein as a variable in protein crystallization. Dale GE, Oefner C, D’Arcy A. J Struct Biol. 2003 Apr;142(1):88-97.
10. D’Arcy, A., 1994. Crystallising proteins - A rational approach. Acta Crystallogr. D 50, 469–471.
11. Hydrogen Ion Buffers for Biological Research. Good, Norman E.,Winget, G. Douglas, Winter, Wilhelmina,Connolly, Thomas N.,Izawa, Seikichi, Singh, Raizada M. M. (1966). Biochemistry. 5 (2): 467–477.
12. Hydrogen ion buffers. Good, Norman E.; Izawa, Seikichi (1972). Methods Enzymol. 24: 53–68.
13. Hydrogen Ion Buffers for Biological Research. Ferguson, W. J.,Braunschweiger, K. I., Braunschweiger, W. R., Smith, J. R.; McCormick, J. J., Wasmann, C. C., Jarvis, N. P., Bell, D. H.; Good, N. E. (1980). Anal. Biochem. 104 (2): 300–310.
14. The Biomolecular Crystallization Database version 4: expanded content and new features. Tung, M and Gallagher, DT. 2009 Acta Crystallographica D65, 18-23.
15. Nature Structural Biology 10, 980 (2003).
16. Preparation and analysis of protein crystals. Alexander McPherson. 1982. 75-81. John Wiley & Sons.