Crystallization of Cellobiohydrolase in the Presence of Cellulose-Degraded Cellobiose: Analysis of Intermolecular Interactions and Association Dynamics

Abstract

Crystallization of enzymes in presence of impurities is important for clarifying the role of enzymes in natural world. Although it is proposed that impurities inhibit nucleation of enzyme crystallization, details are unclear. In this study, crystallization of cellobiohydrolase from Aspergillus niger was investigated by dynamic and time-resolved static light scattering using cellobiose as an impurity. We aimed to clarify how cellobiose inhibits cellobiohydrolase crystallization and to crystallize cellobiohydrolase in concentrated cellobiose without using seeds. The contribution of attractive forces to total intermolecular interactions of cellobiohydrolase monomers increased with the molar ratio of cellobiose/cellobiohydrolase (R(cb/ce)). Association dynamics of cellobiohydrolase using lithium sulfate, however, showed that the initial aggregation rate decreased with an increase in R(cb/ce). Because binding sites of cellobioses to cellobiohydrolase molecules differed from those for the growth of protein crystals, the binding of cellobioses would increase the chemical potential of the cellobiohydrolase monomers, which gradually reduced supersaturation for growth as the aggregate size increased. This result was in contrast with the conventional idea that cellobiose inhibits the nucleation of cellobiohydrolase crystals. Gentle agitation of cellobiose-containing cellobiohydrolase solutions during sitting-drop vapor-diffusion growth resulted in the growth of cellobiohydrolase single crystals for all R(cb/ce) conditions without using seeds.

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K. Onuma, N. Furubayashi, F. Shibata, Y. Kobayashi, S. Kaito, Y. Ohnishi and K. Inaka, "Crystallization of Cellobiohydrolase in the Presence of Cellulose-Degraded Cellobiose: Analysis of Intermolecular Interactions and Association Dynamics," Journal of Crystallization Process and Technology, Vol. 4 No. 1, 2014, pp. 1-13. doi: 10.4236/jcpt.2014.41001.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] T. Bergfors, “Seeds to Crystals,” Journal of Structural Biology, Vol. 142, No. 1, 2003, pp. 66-76.
http://dx.doi.org/10.1016/S1047-8477(03)00039-X
[2] S. M. Roberts and G. J. Davies, “The Crystallization and Structural Analysis of Cellulases (and Other Glycoside Hydrolases): Strategies and Tactics,” In: H. J. Gilbert, Ed., Methods in Enzymology, Cellulase, Vol. 510, Elsevier, 2012, pp. 141-167.
[3] R. Sims, M. Taylor, J. Saddler and W. Mabee, “From 1st - and 2nd -Generation Biofuels Technologies: An Overview of Current Industry and RD&D Activities,” International Energy Agency Bioenergy, OECD/IEA, Paris, 2008, p. 124.
[4] R. Wolfenden and M. Snider, “The Depth of Chemical and the Power of Enzymes a Catalysis,” Accounts of Chemical Research, Vol. 34, No. 12, 2001, pp. 938-945.
http://dx.doi.org/10.1021/ar000058i
[5] R. Berner, “The Long-Term Caobon Cycle, Fossil Fuels and Atmospheric Composition,” Nature, Vol. 426, 2003, pp. 323-326.
[6] Y. S. Liu, Y. Zeng, Y. Luo, Q. Xu, M. E. Himmel, S. J. Smith and S. Y. Ding, “Does the Cellulose-Binding Module Move on the Cellulose Surface?” Cellulose, Vol. 16, No. 4, 2009, pp. 587-597.
http://dx.doi.org/10.1007/s10570-009-9306-0
[7] M. Juy, A. G. Amit, P. M. Alzari, R. J. Poljak, M. Claeyssens, P. Beguin and J. P. Aubert, “3-Dimensionla Atructure of a Thermostable Bacterial Cellulase,” Nature, Vol. 357, 1992, pp. 89-91.
[8] Y. Hata, K. Natori, Y. Katsube, T. Ooi, M. Arai and H. Okada, “Crystallization and Preliminary-X-Ray Diffraction Studies of an Endoglucanase from Aspergillus-aculeatus,” Journal of Molecular Biology, Vol. 241, No. 2, 1994, pp. 278-280.
http://dx.doi.org/10.1006/jmbi.1994.1499
[9] J. H. Pereira, R. Sapra, J. V. Volponi, C. L. Kozina, B. Simmons and P. D. Adams, “Structure of Endoglucanase Cel9A from the Tehrmoacidophilic Alicyclobacillus acidocaldarius,” Acta Crystallographica Section D, Vol. 65, No. 8, 2009, pp. 744-750.
http://dx.doi.org/10.1107/S0907444909012773
[10] M. V. Liberato, W. Generoso, W. Malago Jr., F. Henrique-Silva and I. Polikarpov, “Crystallization and Preliminary X-Ray Diffraction Analysis of Endoglukanase III from Trichoderma harzianum,” Acta Crystallographica Section F, Vol. 68, No. 3, 2012, pp. 306-309.
http://dx.doi.org/10.1107/S1744309112000838
[11] E. T. Prates, I. Stankovic, R. L. Silveira, M. V. Liberato, F. Henrique-Silva, N. Pereira Jr., I. Polikarpov and M. S. Skaf, “X-Ray Structure and Molecular Dynamic Simulations of Endoglucanase 3 from Trichoderma harzianum: Structure Organization and Substrate Recognition by Endoglucanase That Lack Cellulose Binding Module,” PLOS ONE, 2013.
http://www.plosone.orgpath=10.1371/journal.pone.0059069
[12] T. Bergfors, J. Rouvinen, P. Lehtovaara, X. Cladentey, P. Tomme, M. Claeyssens, G. Pettersson, T. Teeri, J. Knowles and T. A. Jones, “Crystallization of the Core Protein of Cellobiohydrolase-II from Trichoderma-reesei,” Journal of Molecular Biology, Vol. 209, No. 1, 1989, pp. 167-169.
http://dx.doi.org/10.1016/0022-2836(89)90179-4
[13] J. Rouvinen, T. Bergfors, T. Teeri, J. K. Knowles and T. A. Jones, “Three-Dimensional Structure of Cellobiohydrolase II from Trichoderma Reesei,” Science, Vol. 249, 1990, pp. 380-386.
[14] A. Grassick, G. Birrane, M. Tuohy, P. Murray and T. Higgins, “Crystallization and Preliminary Crystallographic Analysis of the Catalytic Domain Cellobiohydrolase I from Talaromyces emersonii,” Acta Crystallographica Section D, Vol. 59, No. 7, 2003, pp. 1283-1284.
http://dx.doi.org/10.1107/S0907444903009843
[15] T. Parkkinen, A. Koivula, J. Vehmaanpera and J. Rouvinen, “Preliminary X-Ray Analysis of Cellobiohydrolase Cel7B from Melanocarpus albomyces,” Acta Crystallographica Section F, Vol. 63, No. 9, 2007, pp. 754-757.
[16] S. Jindou, S. Petkun, L. Shimon, E. A. Bayer and R. Lamed, “Crystallization and Preliminary Diffraction Studies of CBM3b of Cellobiohydrolase 9A from Clostridium thermocellum,” Acta Crystallographica Section F, Vol. 63, No. 12, 2007, pp. 1044-1047.
http://dx.doi.org/10.1107/S1744309107054644
[17] F. Colussi, L. C. Textor, V. Serpa, R. N. Maeda, N. Pereira and I. Polikarpov, “Purification, Crystallization and Preliminary Crystallographic Analysis of the Catalytic Domain of the Extracellular Cellulase CGHI from Trichoderma harzianum,” Acta Crystallographica Section F, Vol. 66, No. 9, 2010, pp. 1041-1044.
http://dx.doi.org/10.1107/S1744309110026886
[18] A. Varrot, T. P. Frandsen, I. von Ossowski, V. Boyer, S. Cottaz, H. Driguez, M. Schulein and G. J. Davis, “Struc- tural Basis for Ligand Binding and Processivity in Cellobiohydrolase Cel6A from Humicola insolens,” Structure, Vol. 11, No. 7, 2003, pp. 855-864.
http://dx.doi.org/10.1016/S0969-2126(03)00124-2
[19] K. Eckert, A. Vigouroux, L. Lo Leggio and S. Morera, “Crystal Structures of A. acidocaldarius Endogulucanase Cel9A Complex with Cello-Oligosaccharides,” Journal of Molecular Biology, Vol. 394, No. 1, 2009, pp. 61-70.
http://dx.doi.org/10.1016/j.jmb.2009.08.060
[20] W. Ubhayasekera, I. G. Munoz, A. Vasella, J. Stahlberg and S. L. Mowbray, “Structure of Phanerochaete chrysosporium Cel7D in Complex with Products and Inhibitors,” FEBS Journal, Vol. 272, No. 8, 2005, pp. 1952-1964.
http://dx.doi.org/10.1111/j.1742-4658.2005.04625.x
[21] B. R. Thomas, P. G. Vekilov and F. Rosenberger, “Effects of Microheterongeneity in Hen-Egg White Lysozyme Crystallization,” Acta Crystallographica Section D, Vol. 54, No. 2, 1998, pp. 226-236.
http://dx.doi.org/10.1107/S0907444997010676
[22] W. Eberstein, Y. Georgalis and W. Saenger, “Molecular Interactions in Crystalling Lysozyme Solutions Studied by Photon Correlation Spectroscopy,” Journal of Crystal Growth, Vol. 143, No. 1-2, 1994, pp. 71-78.
http://dx.doi.org/10.1016/0022-0248(94)90369-7
[23] S. Tanaka, M. Ataka, K. Onuma and T. Kubota, “Rationalization of Membrane Protein Crystallization with Polyehtylene Glycol Using a Simple Depletion Model,” Biophysical Journal, Vol. 84, No. 5, 2003, pp. 3299-3306.
http://dx.doi.org/10.1016/S0006-3495(03)70054-X
[24] K. Onuma and N. Kanzaki, “Size Distribution and Intermolecular Interaction of Laminin-1 in Physiological Solution,” Journal of Physical Chemistry B, Vol. 107, No. 42, 2003, pp. 11799-11804.
http://dx.doi.org/10.1021/jp0355298
[25] D. L. Zechel, A. B. Boraston, T. M. Gloster, C. M. Boraston, J. M. Macdonald, D. Matthew, G. Tilbrook, R. V. Stick and G. J. Davis, “Iminosugar Glycosidase Inhibitors: Structural and Thermodynamic Dissection of the Binding of Isofagomine and-Glucosidases 1-Deoxynojirimycin to Two,” Journal of American Chemical Society, Vol. 125, No. 47, 2003, pp. 14313-14323.
http://dx.doi.org/10.1021/ja036833h
[26] N. Kanzaki, T. Ueda and K. Onuma, “Intermolecular Interaction of Actin Revealed by Dynamic Light Scattering Technique,” Journal of Physical Chemistry B, Vol. 110, No. 6, 2006, pp. 2881-2887.
http://dx.doi.org/10.1021/jp054865g
[27] S. W. Provencher, “A Constrained Regularization Method for Inverting Data Represented by Linear Agebraic or In- tegral Equations,” Computer Physics Communications, Vol. 27, No. 3, 1982, pp. 213-227.
http://dx.doi.org/10.1016/0010-4655(82)90173-4
[28] S. E. Ingles, A. Katzenstein, W. Schlenker and K. Huber, “Time-Resolved Recording of Ionic Dyestuff Aggregation by Static Light Scattering,” Langmuir, Vol. 16, No. 7, 2000, pp. 3010-3018.
http://dx.doi.org/10.1021/la9903649
[29] K. Onuma, A. Oyane, K. Tsutsui, K. Tanaka, G. Treboux, N. Kanzaki and A. Ito, “Precipitation Kinetics of Hydroxyapatite Revealed by Continuous-Angle Laser Light Scattering Technique,” Journal of Physical Chemistry B, Vol. 104, No. 45, 2000, pp. 10563-10568.
http://dx.doi.org/10.1021/jp002697g
[30] T. Witte, B. Decker, J. Mattay and K. Huber, “Formation of Branched Callxarene Aggregates-A Time-Resolved Static Scattering Study,” Journal of American Chemical Society, Vol. 126, No. 30, 2004, pp. 9276-9282.
http://dx.doi.org/10.1021/ja0493291
[31] K. Onuma, A. Watanabe, N. Kanzaki and T. Kubota, “Association Kinetics of Wild-And Mutant-Type Ynd1p in Relation to Quality of Grown Crystals,” Journal of Physical Chemistry B, Vol. 110, No. 49, 2006, pp. 24876- 24883. http://dx.doi.org/10.1021/jp0643146
[32] K. Onuma, N. Furubayashi, F. Shibata, Y. Kobayashi, S. Kaito, Y. Ohnishi and K. Inaka, “Anomalous Effect of Poly(ethylene)glycol on Intermolecular Interaction and Protein Association,” Crystal Growth & Design, Vol. 9, No. 5, 2009, pp. 2517-2524.
http://dx.doi.org/10.1021/cg900019e
[33] P. N. Pusey and R. J. A. Tough, “Particle Interactions,” In: R. Pecora, Ed., Dynamic Light Scattering, Plenum, New York, 1985, pp. 85-179.
http://dx.doi.org/10.1007/978-1-4613-2389-1_4
[34] D. N. Petsev and P. G. Vekilov, “Evidence of Non-DLVO Hydration Interactions in Solutions of the Protein Apoferritin,” Physical Review Letters, Vol. 84, No. 6, 2000, pp. 1339-1342.
http://dx.doi.org/10.1103/PhysRevLett.84.1339
[35] J. Narayanan and X. Y. Liu, “Protein Interactions in Undersaturated and Supersaturated Solutions: A Study Using Light and X-Ray Scattering,” Biophysical Journal, Vol. 84, No. 1, 2003, pp. 523-532.
http://dx.doi.org/10.1016/S0006-3495(03)74871-1
[36] K. C. Holmes, W. Gebhard, D. Popp and W. Kabsch, “Atomic Model of the Actin Filament,” Nature, Vol. 347, 1990, pp. 44-49.
[37] X. Chen, R. K. Cook and P. A. Rubenstein, “Yeast Actin with a Mutation in the “Hydrophobic Plug” between Subdomains 3 and 4 (L266D) Displays a Cold-Sensitive Polymerization,” Journal of Cell Biology, Vol. 123, 1993, pp. 1185-1195. http://dx.doi.org/10.1083/jcb.123.5.1185

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