Rational backbone redesign of a fructosyl peptide oxidase to widen its active site access tunnel.
access tunnel
biosensor
diabetes
fructosyl peptide oxidase
rational enzyme design
Journal
Biotechnology and bioengineering
ISSN: 1097-0290
Titre abrégé: Biotechnol Bioeng
Pays: United States
ID NLM: 7502021
Informations de publication
Date de publication:
12 2020
12 2020
Historique:
received:
18
05
2020
revised:
27
07
2020
accepted:
09
08
2020
pubmed:
17
8
2020
medline:
4
3
2022
entrez:
16
8
2020
Statut:
ppublish
Résumé
Fructosyl peptide oxidases (FPOXs) are enzymes currently used in enzymatic assays to measure the concentration of glycated hemoglobin and albumin in blood samples, which serve as biomarkers of diabetes. However, since FPOX are unable to work directly on glycated proteins, current enzymatic assays are based on a preliminary proteolytic digestion of the target proteins. Herein, to improve the speed and costs of the enzymatic assays for diabetes testing, we applied a rational design approach to engineer a novel enzyme with a wider access tunnel to the catalytic site, using a combination of Rosetta design and molecular dynamics simulations. Our final design, L3_35A, shows a significantly wider and shorter access tunnel, resulting from the deletion of five-amino acids lining the gate structures and from a total of 35 point mutations relative to the wild-type (WT) enzyme. Indeed, upon experimental testing, our engineered enzyme shows good structural stability and maintains significant activity relative to the WT.
Substances chimiques
Amino Acid Oxidoreductases
EC 1.4.-
fructosyl-peptide oxidase
EC 1.5.3.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3688-3698Informations de copyright
© 2020 Wiley Periodicals LLC.
Références
Adams, P. D., Afonine, P. V., Bunkoczi, G., Chen, V. B., Davis, I. W., Echols, N., … Zwart, P. H. (2010). PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica Section D-Biological Crystallography, 66, 213-221.
Battye, T. G. G., Kontogiannis, L., Johnson, O., Powell, H. R., & Leslie, A. G. W. (2011). iMOSFLM: A new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallographica Section D-Biological Crystallography, 67, 271-281.
Capuano, E., Fedele, F., Mennella, C., Visciano, M., Napolitano, A., Lanzuise, S., … Fogliano, V. (2007). Studies on the effect of amadoriase from Aspergillus fumigatus on peptide and protein glycation in vitro. Journal of Agricultural and Food Chemistry, 55, 4189-4195.
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668-1688.
Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., … Damborsky, J. (2012). CAVER 3.0: A tool for the analysis of transport pathways in dynamic protein structures. PLoS Computational Biology, 8, 1002708.
Collard, F., Zhang, J., Nemet, I., Qanungo, K. R., Monnier, V. M., & Yee, V. C. (2008). Crystal structure of the deglycating enzyme fructosamine oxidase (Amadoriase II). Journal of Biological Chemistry, 283, 27007-27016.
DeLano, W. (2002). Pymol: An open-source molecular graphics tool. Newsletter on protein crystallography.
Del Turco, S., & Basta, G. (2012). An update on advanced glycation endproducts and atherosclerosis. Biofactors, 38, 266-274.
Ferri, S., Kim, S., Tsugawa, W., & Sode, K. (2009). Review of fructosyl amino acid oxidase engineering research: A glimpse into the future of hemoglobin A1c biosensing. Journal of Diabetes Science and Technology, 3, 585-592.
Ferri, S., Miyamoto, Y., Sakaguchi-Mikami, A., Tsugawa, W., & Sode, K. (2013). Engineering fructosyl peptide oxidase to improve activity toward the fructosyl hexapeptide standard for HbA1c measurement. Molecular Biotechnology, 54, 939-943.
Gan, W., Gao, F., Xing, K., Jia, M., Liu, H., & Gong, W. (2015). Structural basis of the substrate specificity of the FPOD/FAOD family revealed by fructosyl peptide oxidase from eupenicillium terrenum. Acta Crystallographica Section F: Structural Biology Communications, 71, 381-387.
Gautieri, A., Ionita, M., Silvestri, D., Votta, E., Vesentini, S., Fiore, G. B., … Redaelli, A. (2010). Computer-aided molecular modeling and experimental validation of water permeability properties in biosynthetic materials. Journal of Computational and Theoretical Nanoscience, 7, 1287-1293.
Gautieri, A., Redaelli, A., Buehler, M. J., & Vesentini, S. (2013). Age- and diabetes-related nonenzymatic crosslinks in collagen fibrils: Candidate amino acids involved in advanced glycation end-products. Matrix Biology, 34, 89-95.
Gautieri, A., Vesentini, S., Redaelli, A., & Buehler, M. J. (2009). Intermolecular slip mechanism in tropocollagen nanofibrils. International Journal of Materials Research, 100, 921-925.
Goh, S. Y., & Cooper, M. E. (2008). The role of advanced glycation end products in progression and complications of diabetes. Journal of Clinical Endocrinology and Metabolism, 93, 1143-1152.
Goldenzweig, A., Goldsmith, M., Hill, S. E., Gertman, O., Laurino, P., Ashani, Y., … Fleishman, S. J. (2016). Automated structure- and sequence-based design of proteins for high bacterial expression and stability. Molecular Cell, 63, 337-346.
Hammond, J. B., & Kruger, N. J. (1988). The Bradford method for protein quantitation. Methods in Molecular Biology, 3, 25-32.
Harvey, M. J., Giupponi, G., & De Fabritiis, G. (2009). ACEMD: Accelerating biomolecular dynamics in the microsecond time scale. Journal of Chemical Theory and Computation, 5, 1632-1639.
Hirokawa, K., Nakamura, K., & Kajiyama, N. (2004). Enzymes used for the determination of HbA1C. FEMS Microbiology Letters, 235, 157-62.
Huang, P. S., Ban, Y. E. A., Richter, F., Andre, I., Vernon, R., Schief, W. R., & Baker, D. (2011). RosettaRemodel: A generalized framework for flexible backbone protein design. PLoS One, 6, e24109.
Kaufmann, K. W., Lemmon, G. H., Deluca, S. L., Sheehan, J. H., & Meiler, J. (2010). Practically useful: What the Rosetta protein modeling suite can do for you. Biochemistry, 49, 2987-98.
Kim, S., Ferri, S., Tsugawa, W., Mori, K., & Sode, K. (2010). Motif-based search for a novel fructosyl peptide oxidase from genome databases. Biotechnology and Bioengineering, 106, 358-366.
Kim, S., Miura, S., Ferri, S., Tsugawa, W., & Sode, K. (2009). Cumulative effect of amino acid substitution for the development of fructosyl valine-specific fructosyl amine oxidase. Enzyme and Microbial Technology, 44, 52-56.
Kokkonen, P., Bednar, D., Pinto, G., Prokop, Z., & Damborsky, J. (2019). Engineering enzyme access tunnels. Biotechnology Advances, 37, 107386.
Lin, Z. L., & Zheng, J. (2010). Occurrence, characteristics, and applications of fructosyl amine oxidases (amadoriases). Applied Microbiology and Biotechnology, 86, 1613-1619.
Mandell, D. J., Coutsias, E. A., & Kortemme, T. (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nature Methods, 6, 551-552.
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007). Phaser crystallographic software. Journal of Applied Crystallography, 40, 658-674.
Miura, S., Ferri, S., Tsugawa, W., Kim, S., & Sode, K. (2006). Active site analysis of fructosyl amine oxidase using homology modeling and site-directed mutagenesis. Biotechnology Letters, 28, 1895-1900.
Miura, S., Ferri, S., Tsugawa, W., Kim, S., & Sode, K. (2008). Development of fructosyl amine oxidase specific to fructosyl valine by site-directed mutagenesis. Protein Engineering, Design & Selection, 21, 233-239.
Monnier, V. M., & Wu, X. (2003). Enzymatic deglycation with amadoriase enzymes from Aspergillus sp. as a potential strategy against the complications of diabetes and aging. Biochemical Society Transactions, 31, 1349-1353.
Murshudov, G. N., Skubak, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., … Vagin, A. A. (2011). REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallographica Section D Biological Crystallography, 67, 355-367.
Nagaraj, R. H., Linetsky, M., & Stitt, A. W. (2012). The pathogenic role of Maillard reaction in the aging eye. Amino Acids, 42, 1205-1220.
Nelson, M. T., Humphrey, W., Gursoy, A., Dalke, A., Kale, L. V., Skeel, R. D., & Schulten, K. (1996). NAMD: A parallel, object oriented molecular dynamics program. International Journal of High Performance Computing Applications, 10, 251-268.
Ogawa, N., Kimura, T., Umehara, F., Katayama, Y., Nagai, G., Suzuki, K., … Ichimura, M. (2019). Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Scientific Reports, 9, 942.
Paul, R. G., & Bailey, A. J. (1996). Glycation of collagen: The basis of its central role in the late complications of ageing and diabetes. International Journal of Biochemistry and Cell Biology, 28, 1297-1310.
Qian, Y., Zheng, J., & Lin, Z. L. (2013). Loop engineering of Amadoriase II and mutational cooperativity. Applied Microbiology and Biotechnology, 97, 8599-8607.
Rigoldi, F., Donini, S., Giacomina, F., Sorana, F., Redaelli, A., Bandiera, T., … Gautieri, A. (2018). Thermal stabilization of the deglycating enzyme Amadoriase I by rational design. Scientific Reports, 8, 3042. https://doi.org/10.1038/s41598-018-19991-x
Rigoldi, F., Gautieri, A., Dalle Vedove, A., Lucarelli, A. P., Vesentini, S., & Parisini, E. (2016). Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complex. Proteins Structure Function and Bioinformatics, 84, 744-758.
Rigoldi, F., Spero, L., Dalle Vedove, A., Redaelli, A., Parisini, E., & Gautieri, A. (2016). Molecular dynamics simulations provide insights into the substrate specificity of FAOX family members. Molecular BioSystems, 12, 2622-2633.
Schrödinger. (2017). Pymol. Retrieved from https://pymol.org/2
Sell, D. R., & Monnier, V. M. (2012). Molecular basis of arterial stiffening: Role of glycation-A mini-review. Gerontology, 58, 227-237.
Shahbazmohammadi, H., Sardari, S., Lari, A., & Omidinia, E. (2019). Engineering an efficient mutant of Eupenicillium terrenum fructosyl peptide oxidase for the specific determination of hemoglobin A1c. Applied Microbiology and Biotechnology, 103, 1725-1735.
Shimasaki, T., Yoshida, H., Kamitori, S., & Sode, K. (2017). X-ray structures of fructosyl peptide oxidases revealing residues responsible for gating oxygen access in the oxidative half reaction. Scientific Reports, 7, 2790.
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W. Z., … Higgins, D. G. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Molecular Systems Biology, 7, 539.
Snedeker, J. G., & Gautieri, A. (2014). The role of collagen crosslinks in ageing and diabetes-The good, the bad, and the ugly. Muscles, Ligaments and Tendons Journal, 4, 303-308.
Takahashi, M., Pischetsrieder, M., & Monnier, V. M. (1997). Isolation, purification, and characterization of amadoriase isoenzymes (fructosyl amine-oxygen oxidoreductase EC 1.5.3) from Aspergillus sp. Journal of Biological Chemistry, 272, 3437-3443.
Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., Hung, L. W., … Adams, P. D. (2007). Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallographica Section D: Biological Crystallography, D64, 61-69.
Vincent, A. M., Russell, J. W., Low, P., & Feldman, E. L. (2004). Oxidative stress in the pathogenesis of diabetic neuropathy. Endocrine Reviews, 25, 612-628.
Wang, J. M., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157-1174.
Wu, X. L., Palfey, B. A., Mossine, V. V., & Monnier, V. M. (2001). Kinetic studies, mechanism, and substrate specificity of Amadoriase I from Aspergillus sp. Biochemistry, 40, 12886-12895.
Xing, K., Gan, W., Jia, M., Gao, F., & Gong, W. (2013). Expression, purification, crystallization and preliminary X-ray diffraction analysis of EtFPOX from Eupenicillium terrenum sp. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 69, 666-668.