Computational Methods for Protein Crystallization Screening
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The goal of protein crystallization screening is to determine the main factors of importance to crystallize a protein under investigation. The protein crystallization screening is often expanded to many hundreds or thousands of conditions to maximize combinatorial chemical space coverage for maximizing the chances of a successful (crystalline) outcome. Available commercial screens may not generate crystalline conditions for some proteins difficult to crystallize. Nevertheless, the previous crystallization trials could be analyzed to recommend screens with crystalline conditions. This chapter presents computational methods for protein crystallization screening.
The the first and second paragraphs (except the first sentences) of Sect. 3.3 are Reprinted from Progress in Biophysics and Molecular Biology, Volume 88, Issue 3, Lawrence J. DeLucas, David Hamrick, Larry Cosenza, Lisa Nagy, Debbie McCombs, Terry Bray, Arnon Chait, Brad Stoops, Alexander Belgovskiy, W. William Wilson, Marc Parham, Nikolai Chernov, Protein crystallization: virtual screening and optimization, Pages 285–309, Copyright (2005) with permission from Elsevier.
The second paragraph (except the first two sentences) and the third paragraph of Sect. 3.4 are Reprinted (adapted) with permission from Crystal Growth and Design 2011 11 (7), Emmanuel Saridakis, Novel Genetic Algorithm-Inspired Concept for Macromolecular Crystal Optimization, 2993–2998. Copyright (2011) American Chemical Society. \(\copyright \)2016 IEEE. Reprinted, with permission, from I. Dinç, M. L. Pusey, and R. S. Aygün, “Optimizing Associative Experimental Design for Protein Crystallization Screening,” in IEEE Transactions on NanoBioscience, vol. 15, no. 2, pp. 101–112, March 2016. doi: https://doi.org/10.1109/TNB.2016.2536030.
- 1.Hampton Research Screen HT. https://hamptonresearch.com/documents/product/hr000783_crystal_screen_2.xls. Accessed 1 November 2015.
- 2.Microlytics MCSG-3 Screen. http://www.microlytic.com/sites/default/files/MCSG3_Formulations_0_0_0.pdf. Accessed 1 November 2015.
- 3.Molecular Dynamics JCGS+ Screen. http://www.moleculardimensions.com/applications/upload/Md1-40%20JCSG%20Plus%20HT-96.pdf. Accessed 1 November 2015.
- 4.Abergel, C., Moulard, M., Moreau, H., Loret, E., Cambillau, C., & Fontecilla-Camps, J. C. (1991). Systematic use of the incomplete factorial approach in the design of protein crystallization experiments. Journal of Biological Chemistry, 266(30), 20131–20138.Google Scholar
- 8.Brodersen, D. E., Andersen, G. R., & Andersen, C. B. F. (2013). Mimer: an automated spreadsheet-based crystallization screening system. Acta Crystallographica Section F, 69(7), 815–820.Google Scholar
- 9.Bruno, A.E., Ruby, A.M., Luft, J.R., Grant, T.D., Seetharaman, J., Montelione, G.T., Hunt, J.F., and Snell, E.H. Comparing chemistry to outcome: the development of a chemical distance metric, coupled with clustering and hierarchal visualization applied to macromolecular crystallography.Google Scholar
- 10.Carter, C. W, Jr., & Carter, C. W. (1979). Protein crystallization using incomplete factorial experiments. The Journal of Biological Chemistry, 254(23), 12219–12223.Google Scholar
- 11.D’Arcy, A., Bergfors, T., Cowan-Jacob, S. W., & Marsh, M. (2014). Microseed matrix screening for optimization in protein crystallization: what have we learned? Acta Crystallographica Section F: Structural Biology Communications, 70(9), 1117–1126.Google Scholar
- 13.Dinc, I. (2016). Associtiave Data Analytics and its Application to Protein Crystallization Analysis. Ph.D dissertation, University of Alabama in Huntsville.Google Scholar
- 14.Dinç, İ., Pusey, M.L., and Aygün, R.S. (2015). Protein crystallization screening using associative experimental design. In Bioinformatics Research and Applications (pp. 84–95). Springer.Google Scholar
- 18.Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., and Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. Springer.Google Scholar
- 28.Pikuta, E. V., Marsic, D., Itoh, T., Bej, A. K., Tang, J., Whitman, W. B., et al. (2007). Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology, 57(7), 1612–1618.CrossRefGoogle Scholar
- 29.Pusey, M., Barcena, J., Morris, M., Singhal, A., Yuan, Q., & Ng, J. (2015). Trace fluorescent labeling for protein crystallization. Structural Biology and Crystallization Communications, 71, 7.Google Scholar