Abstract
Protein crystallization remains a highly empirical process. The purpose of protein crystallization screening is the determination of the main factors of importance leading to protein crystallization. One of the major problems about determining these factors is that screening is often expanded to many hundreds or thousands of conditions to maximize combinatorial chemical space coverage for a successful (crystalline) outcome. In this paper, we propose a new experimental design method called “Associative Experimental Design (AED)” that provides a list of screening factors that are likely to lead to higher scoring outcomes or crystals by analyzing preliminary experimental results. We have tested AED on Nucleoside diphosphate kinase, HAD superfamily hydrolase, and nucleoside kinase proteins derived from the hyperthermophile Thermococcus thioreducens [1]. After obtaining the candidate novel conditions, we have confirmed that AED method yielded high scoring crystals after experimenting in a wet lab.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Pikuta, E.V., Marsic, D., Itoh, T., Bej, A.K., Tang, J., Whitman, W.B., Ng, J.D., Garriott, O.K., Hoover, R.B.: 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 (2007)
McPherson, A., Gavira, J.A.: Introduction to protein crystallization. Acta Crystallographica Section F: Structural Biology Communications 70(1), 2–20 (2014)
Jancarik, J., Kim, S.-H.: Sparse matrix sampling: a screening method for crystallization of proteins. Journal of Applied Crystallography 24(4), 409–411 (1991)
McPherson, A.: Crystallization of Biological Macromolecules. Cold Spring Harbor Laboratory Press (1999), http://books.google.com/books?id=EDNRAAAAMAAJ
Asherie, N.: Protein crystallization and phase diagrams. Methods 34(3), 266–272 (2004)
Stevens, R.C.: High-throughput protein crystallization. Current Opinion in Structural Biology 10(5), 558–563 (2000)
Brodersen, D.E., Andersen, G.R., Andersen, C.B.F.: Mimer: an automated spreadsheet-based crystallization screening system. Acta Crystallographica Section F 69(7), 815–820 (2013), http://dx.doi.org/10.1107/S1744309113014425 , doi:10.1107/S1744309113014425
Carter Jr., C.W., Carter, C.W.: Protein crystallization using incomplete factorial experiments. J. Biol. Chem. 254(23), 12219–12223 (1979)
Abergel, C., Moulard, M., Moreau, H., Loret, E., Cambillau, C., Fontecilla-Camps, J.C.: Systematic use of the incomplete factorial approach in the design of protein crystallization experiments. Journal of Biological Chemistry 266(30), 20131–20138 (1991)
Doudna, J.A., Grosshans, C., Gooding, A., Kundrot, C.E.: Crystallization of ribozymes and small rna motifs by a sparse matrix approach. Proceedings of the National Academy of Sciences 90(16), 7829–7833 (1993)
Cox, M.J., Weber, P.C.: An investigation of protein crystallization parameters using successive automated grid searches (sags). Journal of Crystal Growth 90(1), 318–324 (1988)
Luft, J.R., Newman, J., Snell, E.H.: Crystallization screening: the influence of history on current practice. Structural Biology and Crystallization Communications 70(7), 835–853 (2014)
Snell, E.H., Nagel, R.M., Wojtaszcyk, A., O’Neill, H., Wolfley, J.L., Luft, J.R.: The application and use of chemical space mapping to interpret crystallization screening results. Acta Crystallographica Section D: Biological Crystallography 64(12), 1240–1249 (2008)
McPherson, A., Cudney, B.: Optimization of crystallization conditions for biological macromolecules. Acta Crystallographica Section F 70(11), 1445–1467 (2014), http://dx.doi.org/10.1107/S2053230X14019670 , doi:10.1107/S2053230X14019670
Yang, H., Rasmuson, Å.C.: Phase equilibrium and mechanisms of crystallization in liquid–liquid phase separating system. Fluid Phase Equilibria 385, 120–128 (2015)
Baumgartner, K., Galm, L., Nötzold, J., Sigloch, H., Morgenstern, J., Schleining, K., Suhm, S., Oelmeier, S.A., Hubbuch, J.: Determination of protein phase diagrams by microbatch experiments: Exploring the influence of precipitants and ph. International Journal of Pharmaceutics 479(1), 28–40 (2015)
Forsythe, E., Achari, A., Pusey, M.L.: Trace fluorescent labeling for high-throughput crystallography. Acta Crystallographica Section D: Biological Crystallography 62(3), 339–346 (2006)
Newman, J., Fazio, V.J., Lawson, B., Peat, T.S.: The c6 web tool: a resource for the rational selection of crystallization conditions. Crystal Growth & Design 10(6), 2785–2792 (2010)
Pusey, M.L., Paley, M.S., Turner, M.B., Rogers, R.D.: Protein crystallization using room temperature ionic liquids. Crystal Growth & Design 7(4), 787–793 (2007)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Dinç, İ., Pusey, M.L., Aygün, R.S. (2015). Protein Crystallization Screening Using Associative Experimental Design. In: Harrison, R., Li, Y., Măndoiu, I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science(), vol 9096. Springer, Cham. https://doi.org/10.1007/978-3-319-19048-8_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-19048-8_8
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-19047-1
Online ISBN: 978-3-319-19048-8
eBook Packages: Computer ScienceComputer Science (R0)