Cristalogénesis biológica y cristalografía en la elucidación de la estructura tridimensional de las proteínas. Revisión narrativa

Omar E. Vélasquez-González; Luis Amézquita-Morataya

doi:10.36829/63CTS.v9i2.1032

Autores/as

Omar E. Vélasquez-González Instituto de Química, Universidad Nacional Autónoma de México y Unidad de Química Teórica y Computacional, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos, Guatemala
Luis Amézquita-Morataya Unidad de Química Teórica y Computacional, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos, Guatemala https://orcid.org/0000-0001-5526-3658

DOI:

https://doi.org/10.36829/63CTS.v9i2.1032

Palabras clave:

Estructura tridimensional de las proteínas, cristalogénesis biológica, cristalografía, difracción de rayos X, diseño de fármacos

Resumen

La obtención de información estructural tridimensional de una proteína es de suma importancia en campos tan variados como la bioquímica funcional, las ciencias de materiales o biomédicas. Siendo actualmente la difracción de rayos X de monocristal el estándar de oro para la consecución de este objetivo, la obtención de dicho monocristal sigue siendo un cuello de botella desde el punto de vista práctico, y poco entendido desde el punto de vista teórico. En este artículo se revisa desde la perspectiva estructural de la proteína la forma en que los rayos X permiten obtener la información estructural y las condiciones fisicoquímicas que permiten la formación de un cristal adecuado para estos experimentos.

Descargas

Los datos de descargas todavía no están disponibles.

Biografía del autor/a

Omar E. Vélasquez-González, Instituto de Química, Universidad Nacional Autónoma de México y Unidad de Química Teórica y Computacional, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos, Guatemala

Licenciado en Química USAC, Maestro en Ciencias Químicas UNAM, Profesor Titular Departamento de Fisicoquímica, Facultad de Farmacia, USAC.

Citas

Bagchi, B. (2005). Water dynamics in the hydration layer of biomolecules and self-assembly. Chemical Reviews, 105(9), 3197-3219. https://doi.org/10.1021/cr020661

Békés, M., Langley, D. R., & Crews, C. M. (2022). PROTAC targeted protein degraders: The past is prologue. Nature Reviews Drug Discovery, 21(3), 181-200. https://doi.org/10.1038/s41573-021-00371-6

Berka, K., Hobza, P., & Vondrášek, J. (2009). Analysis of energy stabilization inside the hydrophobic core of rubredoxin. ChemPhysChem, 10(3), 543-548. https://doi.org/10.1002/cphc.200800401

Bonn, D., & Shahidzadeh, N. (2016). Multistep crystallization processes: How notto make perfect single crystals. Proceedings of the National Academy of Sciences of the United States of America, 113(48), 13551-13553. https://doi.org/10.1073/pnas.1616536113

Brett, L., Seunghyon, C., Duilio, C., K., M. D., F., D. W., & David, E. (1993). Crystal structure of a synthetic triple-stranded α-helical bundle. Science, 259(5099), 1288-1293. https://doi.org/10.1126/science.8446897

Burhman, G., de Serrano, V., & Mattos, C. (2003). Organic solvents order the dynamic switch II in Ras crystals. Structure, 11(7), 747-751. https://doi.org/https://doi.org/10.1016/S0969-2126(03)00128-X

Chayen, N. E. (1998). Comparative studies of protein crystallization by vapour-diffusion and microbatch techniques. Acta Crystallographica Section D: Biological Crystallography, 54(1), 8-15. https://doi.org/10.1107/S0907444997005374

Chayen, N. E. (2004). Turning protein crystallisation from an art into a science. In Current Opinion in Structural Biology, 14(5), 577-583. https://doi.org/10.1016/j.sbi.2004.08.002

Curcio, E., Di Profio, G., & Drioli, E. (2008). Probabilistic aspects of polymorph selection by heterogeneous nucleation on microporous hydrophobic membrane surfaces. Journal of Crystal Growth, 310(24), 5364-5369. https://doi.org/10.1016/j.jcrysgro.2008.09.030

Drenth, J. (2007). The Solution of the Phase Problem by the Isomorphous Replacement Method. In Principles of Protein X-Ray Crystallography (pp. 123-171). Springer New York. https://doi.org/10.1007/0-387-33746-6_7

Dror, A., Kanteev, M., Kagan, I., Gihaz, S., Shahar, A., & Fishman, A. (2015). Structural insights into methanol-stable variants of lipase T6 from Geobacillus stearothermophilus. Applied Microbiology and Biotechnology, 99(22), 9449-9461. https://doi.org/https://doi.org/10.1007/s00253-015-6700-4

Emsley, P., & Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta crystallographica section D: biological crystallography, 60(12), 2126-2132.

Frenkel, J. (1939). A general theory of heterophase fluctuations and pretransition phenomena. The Journal of Chemical Physics, 7(7), 538-547. https://doi.org/10.1063/1.1750484

Frye, L., Bhat, S., Akinsanya, K., & Abel, R. (2021). From computer-aided drug discovery to computer-driven drug discovery. Drug Discovery Today: Technologies, 39, 111-117. https://doi.org/10.1016/J.DDTEC.2021.08.001

García-Ruiz, J. M. (2003). Nucleation of protein crystals. Journal of Structural Biology, 142(1), pp. 22-31). Academic Press Inc. https://doi.org/10.1016/S1047-8477(03)00035-2

Gao, K., Wang, R., Chen, J., Tepe, J. J., Huang, F., & Wei, G. W. (2021). Perspectives on SARS-CoV-2 Main Protease Inhibitors. Journal of Medicinal Chemistry, 64(23), 16922-16955. https://doi.org/10.1021/ACS.JMEDCHEM.1C00409

Gavira, J. A., Otálora, F., González-Ramírez, L. A., Melero, E., van Driessche, A. E. S., & García-Ruíz, J. M. (2020). On the quality of protein crystals grown under diffusion mass-transport controlled regime (I). Crystals, 10(2), 1-13. https://doi.org/https://doi.org/10.3390/cryst10020068

Gibbs, J. W. (1878). On the Equilibrium of Heterogeneous Substances. American Journal of Science and Arts, 16(96), 441.

Giegé, R., & Mikol, V. (1989). Crystallogenesis of proteins. Trends in Biotechnology, 7(10), 277-282. https://doi.org/10.1016/0167-7799(89)90047-4

Gihaz, S., Kanteev, M., Pazy, Y., & Fishman, A. (2018). Filling the void: Introducing aromatic interactions into solvent tunnels towards lipase stability in methanol. Applied and Environmental Microbiology, 84(23), Artículo e02143-18. https://doi.org/10.1128/AEM.02143-18

Gomez-Puyou, A., Darzon, A., & Tuena de Gomez-Puyou, M. (1992). Biomolecules in organic solvents. CRC Press.

Grochulski, P., Li, Y., Schrag, J., Bouthillier, F., Smith, P., Harrison, D., Rubin, B., & Cygler, M. (1993). Insights into interfacial activation from an open structure of Candida rugosa lipase. Journal of Biological Chemistry, 268(17), 12843-12847. https://doi.org/10.1016/S0021-9258(18)31464-9

Haas, C., & Drenth, J. (2000). The Interface between a Protein Crystal and an Aqueous Solution and Its Effects on Nucleation and Crystal Growth. Journal of Physical Chemistry B, 104(2), 368-377. https://doi.org/10.1021/jp993210a

Honda, S., Akiba, T., Kato, Y. S., Sawada, Y., Sekijima, M., Ishimura, M., Ooishi, A., Watanabe, H., Odahara, T., & Harata, K. (2008). Crystal structure of a ten-amino acid protein. Journal of the American Chemical Society, 130(46), 15327-15331. https://doi.org/10.1021/ja8030533

Howard, G. C., & Brown, W. E. (2001). Modern protein chemistry: Practical aspects. CRC Press.

Isogai, Y., Imamura, H., Nakae, S., Sumi, T., Takahashi, K. I., Nakagawa, T., ... & Shirai, T. (2018). Tracing whale myoglobin evolution by resurrecting ancient proteins. Scientific reports, 8(1), 1-14. http://dx.doi.org/10.1038/s41598-018-34984-6

Kondrashov, D. A., Zhang, W., Aranda IV, R., Stec, B., & Phillips Jr, G. N. (2008). Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Proteins: Structure, Function, and Bioinformatics, 70(2), 353-362. http://dx.doi.org/10.1002/prot.21499

Konieczny, L., Brylinski, M., & Roterman, I. (2006). Gauss-function-based model of hydrophobicity density in proteins. In Silico Biology, 6(1-2), 15-22.

Kreutzer, A. G., Krumberger, M., Marie, C., Parrocha, T., Morris, M. A., Guaglianone, G., & Nowick, J. S. (2020). Structure-Based Design of a Cyclic Peptide Inhibitor of the SARS-CoV-2 Main Protease. BioRxiv. https://doi.org/10.1101/2020.08.03.234872

Markov, I. (2016). Crystal growth for beginners: Fundamentals of nucleation, crystal growth and epitaxy (3rd ed.). World Scientific Publishing.

McKee, T., McKee, J., Araiza Martínez, M., & Hurtado Chong, A. (2014). Bioquímica: Las bases moleculares de la vida (5th ed.). McGrawHill.

McPherson, A. (2004). Introduction to protein crystallization. Methods, 34(3), 254-265. https://doi.org/10.1016/j.ymeth.2004.03.019

McPherson, A., & Kuznetsov, Y. G. (2014). Mechanisms, kinetics, impurities and defects: Consequences in macromolecular crystallization. Acta Crystallographica Section F: Structural Biology Communications, 70(4), 384-403. https://doi.org/10.1107/S2053230X14004816

Mohtashami, M., Fooladi, J., Haddad-Mashadrizeh, A., Housaindokht, M., & Monhemi, H. (2019). Molecular mechanism of enzyme tolerance against organic solvents: Insights from molecular dynamics simulation. International Journal of Biological Macromolecules, 122(1), 914-923. https://doi.org/10.1016/j.ijbiomac.2018.10.172

Moreno, A., & Mendoza, M. E. (2014). Crystallization in gels. En P. Rudolph (Ed.), Handbook of crystal growth: Bulk crystal growth (2nd ed., pp. 1277-1315). Elsevier. https://doi.org/10.1016/b978-0-444-63303-3.00031-6

Nanev, C. C. (2014). On the elementary processes of protein crystallization: Bond selection mechanism. Journal of Crystal Growth, 402, 195-202. https://doi.org/10.1016/j.jcrysgro.2014.05.030

Nanev, C. C. (2018). Peculiarities of protein crystal nucleation and growth. Crystals, 8(11), Artículo 422. https://doi.org/10.3390/cryst8110422

Nature. (s.f.). Structural Biology. Nature portfolio. https://www.nature.com/subjects/structural-biology

Osipiuk, J., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., & Midwest Center for Structural Genomics. (2011). Crystal structure of ywiB protein from Bacillus subtilis (1R0U; Version 1.2) [Conjunto de datos]. RCSB PDB. https://www.rcsb.org/structure/1R0U

Pace, C. N., Treviño, S., Prabhakaran, E., & Scholtz, J. M. (2004). Protein structure, stability and solubility in water and other solvents. Philosophical Transactions of the Royal Society B: Biological Sciences, 359(1448), 1225-1235. https://doi.org/10.1098/rstb.2004.1500

Parker, M. W. (2003). Protein Structure from X-Ray Diffraction. Journal of Biological Physics, 29(4), 341-362. https://doi.org/10.1023/A:1027310719146

Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of computational chemistry, 25(13), 1605-1612.

Quan, B.-X., Shuai, H., Xia, A.-J., Hou, Y., Zeng, R., Liu, X.-L., Lin, G. F., Qiao, J.-X., Li, W.-P., Wang, F.-L., Wang, K., Zhou, R.-J., Yuen, T. T.-T., Chen, M.-X., Yoon, C., Wu, M., Zhang, S- Y., Huang, C., Wang, Y.-F., … Yang, S. (2022). An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron. Nature Microbiology, 7, 716-725. https://doi.org/10.1038/s41564-022-01119-7

Research Collaboratory for Structural Bioinformatics Protein Data Bank. (2021). PDB statistics: Overall growth of released structures per year [Conjunto de datos]. https://www.rcsb.org/stats/growth/growth-released-structures

Renaud, J.-P. (2020). Structural biology in drug discovery: Methods, techniques, and practices. En J.-P. Renaud (Ed.). John Wiley & Sons. https://doi.org/10.1002/9781118681121

Rhodes, G. (2010). Crystallography made crystal clear (3rd ed.). Elsevier. https://www.elsevier.com/books/crystallography-made-crystal-clear/rhodes/978-0-12-587073-3

Rose, G. D., Fleming, P. J., Banavar, J. R., & Maritan, A. (2006). A backbone-based theory of protein folding. En J. Nathans, Johns Hopkins University School of Medicine & Baltimore (Eds.), Proceedings of the National Academy of Sciences of the United States of America (Vol. 103, Issue 45, pp. 16623-16633). National Academy of Sciences. https://doi.org/10.1073/pnas.0606843103

Saha, D., & Mukherjee, A. (2018). Effect of water and ionic liquids on biomolecules. Biophysical Reviews, 10(3), 795-808. https://doi.org/10.1007/s12551-018-0399-2

Saridakis, E., Dierks, K., Moreno, A., Diekmann, M., & Chayen, N. (2002). Separating nucleation and growth in protein crystallization using dynamic light scattering. Acta Crystallographica Section D: Biological Crystallography, 58(10), 1597-1600. https://doi.org/10.1107/S0907444902014348

Scudellari, M. (2020, 15 May). The sprint to solve coronavirus proteinstructures — and disarm them with drugs. News Feature. https://www.nature.com/articles/d41586-020-01444-z

Smith, R. D. (1999). Correlations between bound N-alkyl isocyanide orientations and pathways for ligand binding in recombinant myoglobins [Tesis doctoral, Rice University].

Subramaniam, S., & Kleywegt, G. J. (2022). A paradigm shift in structural biology. Nature Methods, 19(1), 20-23.

Velásquez-González, O., Campos-Escamilla, C., Flores-Ibarra, A., Esturau-Escofet, N., Arreguin-Espinosa, R., Stojanoff, V., Cuéllar-Cruz, M., & Moreno, A. (2019). Crystal growth in gels from the mechanisms of crystal growth to control of polymorphism: New trends on theoretical and experimental Aspects. Crystals, 9(9), Artículo 443. https://doi.org/10.3390/cryst9090443

Williamson, M. (2011). How proteins work. Garland Science.

Yeats, C. A., & Orengo, C. A. (2007). Evolution of protein domains. In Encyclopedia of Life Sciences. John Wiley & Sons. https://doi.org/10.1002/9780470015902.a0020202

Zhang, S., Krumberger, M., Morris, M. A., Parrocha, C. M. T., Griffin, J. H., Kreutzer, A., & Nowick, J. S. (2020). Structure-Based drug design of an inhibitor of the SARS-CoV-2 (COVID-19) mainprotease using free software: A tutorial for students and scientists. ChemRxiv. https://doi.org/10.26434/chemrxiv.12791954