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Structural and biochemical characterization of the novel serpin Iripin-5 from Ixodes ricinus

. 2021 Sep 01 ; 77 (Pt 9) : 1183-1196. [epub] 20210823

Language English Country United States Media print-electronic

Document type Journal Article

Grant support
CZ.02.1.01/0.0/0.0/15_003/00004 European Regional Development Fund, MEYS
19-14704Y Grantová Agentura České Republiky
105/2019/P Jihočeská Univerzita v Českých Budějovicích
04-039/2019/P Jihočeská Univerzita v Českých Budějovicích

Links

PubMed 34473088
PubMed Central PMC8573701
DOI 10.1107/s2059798321007920
PII: S2059798321007920
Knihovny.cz E-resources

Iripin-5 is the main Ixodes ricinus salivary serpin, which acts as a modulator of host defence mechanisms by impairing neutrophil migration, suppressing nitric oxide production by macrophages and altering complement functions. Iripin-5 influences host immunity and shows high expression in the salivary glands. Here, the crystal structure of Iripin-5 in the most thermodynamically stable state of serpins is described. In the reactive-centre loop, the main substrate-recognition site of Iripin-5 is likely to be represented by Arg342, which implies the targeting of trypsin-like proteases. Furthermore, a computational structural analysis of selected Iripin-5-protease complexes together with interface analysis revealed the most probable residues of Iripin-5 involved in complex formation.

See more in PubMed

Barrett, A. J., Rawlings, N. D. & Woessner, J. F. (2004). Handbook of Proteolytic Enzymes, 2nd ed, Vol. 1. London: Academic Press.

Belorgey, D., Hägglöf, P., Karlsson-Li, S. & Lomas, D. A. (2007). Prion, 1, 15–20. PubMed PMC

Berendsen, H. J. C., Grigera, J. R. & Straatsma, T. P. (1987). J. Phys. Chem. 91, 6269–6271.

Berendsen, H. J. C., van der Spoel, D. & van Drunen, R. (1995). Comput. Phys. Commun. 91, 43–56.

Berman, H., Henrick, K. & Nakamura, H. (2003). Nat. Struct. Mol. Biol. 10, 980. PubMed

Bos, I. G. A., Hack, C. E. & Abrahams, J. P. (2002). Immunobiology, 205, 518–533. PubMed

Chlastáková, A., Kotál, J., Beránková, Z., Kaščáková, B., Martins, L. A., Langhansová, H., Prudnikova, T., Ederová, M., Kutá Smatanová, I., Kotsyfakis, M. & Chmelař, J. (2021). Front. Immunol. 12, 626200. PubMed PMC

Chmelař, J., Kotál, J., Kopecký, J., Pedra, J. H. F. & Kotsyfakis, M. (2016). Trends Parasitol. 32, 368–377. PubMed PMC

Chmelař, J., Kotál, J., Langhansová, H. & Kotsyfakis, M. (2017). Front. Cell. Infect. Microbiol. 7, 216. PubMed PMC

Chmelar, J., Oliveira, C. J., Rezacova, P., Francischetti, I. M. B., Kovarova, Z., Pejler, G., Kopacek, P., Ribeiro, J. M. C., Mares, M., Kopecky, J. & Kotsyfakis, M. (2011). Blood, 117, 736–744. PubMed PMC

Cox, J. & Mann, M. (2008). Nat. Biotechnol. 26, 1367–1372. PubMed

Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V. & Mann, M. (2011). J. Proteome Res. 10, 1794–1805. PubMed

Daix, V., Schroeder, H., Praet, N., Georgin, J.-P., Chiappino, I., Gillet, L., de Fays, K., Decrem, Y., Leboulle, G., Godfroid, E., Bollen, A., Pastoret, P.-P., Gern, L., Sharp, P. M. & Vanderplasschen, A. (2007). Insect Mol. Biol. 16, 155–166. PubMed

DeLano, W. L. (2002). PyMOL. http://www.pymol.org.

Dunstone, M. A. & Whisstock, J. C. (2011). Methods Enzymol. 501, 63–87. PubMed

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501. PubMed PMC

Feller, S. E. & MacKerell, A. D. (2000). J. Phys. Chem. B, 104, 7510–7515.

Francischetti, I. M. B., Sa-Nunes, A., Mans, B. J., Santos, I. M. & Ribeiro, J. M. C. (2009). Front. Biosci. 14 2051–2088. PubMed PMC

Fujinaga, M., Chernaia, M. M., Halenbeck, R., Koths, K. & James, M. N. G. (1996). J. Mol. Biol. 261, 267–278. PubMed

Gettins, P. G. W. (2002). Chem. Rev. 102, 4751–4804. PubMed

Gettins, P. G. W. & Olson, S. T. (2016). Biochem. J. 473, 2273–2293. PubMed PMC

Hansen, G., Gielen-Haertwig, H., Reinemer, P., Schomburg, D., Harrenga, A. & Niefind, K. (2011). J. Mol. Biol. 409, 681–691. PubMed

Humphrey, W., Dalke, A. & Schulten, K. (1996). J. Mol. Graph. 14, 33–38. PubMed

Huntington, J. A. (2011). J. Thromb. Haemost. 9, Suppl. 1, 26–34. PubMed

Kabsch, W. (2010). Acta Cryst. D66, 133–144. PubMed PMC

Katona, G., Berglund, G. I., Hajdu, J., Gráf, L. & Szilágyi, L. (2002). J. Mol. Biol. 315, 1209–1218. PubMed

Kervinen, J., Crysler, C., Bayoumy, S., Abad, M. C., Spurlino, J., Deckman, I., Greco, M. N., Maryanoff, B. E. & de Garavilla, L. (2010). Biochem. Pharmacol. 80, 1033–1041. PubMed

Klauda, J. B., Brooks, B. R., MacKerell, A. D., Venable, R. M. & Pastor, R. W. (2005). J. Phys. Chem. B, 109, 5300–5311. PubMed

Kotál, J., Langhansová, H., Lieskovská, J., Andersen, J. F., Francischetti, I. M. B., Chavakis, T., Kopecký, J., Pedra, J. H. F., Kotsyfakis, M. & Chmelař, J. (2015). J. Proteomics, 128, 58–68. PubMed PMC

Kovářová, Z., Chmelař, J., Šanda, M., Brynda, J., Mareš, M. & Řezáčová, P. (2010). Acta Cryst. F66, 1453–1457. PubMed PMC

Krissinel, E. & Henrick, K. (2007). J. Mol. Biol. 372, 774–797. PubMed

Kýčková, K. & Kopecký, J. (2006). J. Med. Entomol. 43, 1208–1214. PubMed

Laroux, F. S., Pavlick, K. P., Hines, I. N., Kawachi, S., Harada, H., Bharwani, S., Hoffman, J. M. & Grisham, M. B. (2001). Acta Physiol. Scand. 173, 113–118. PubMed

Law, R. H. P., Zhang, Q., McGowan, S., Buckle, A. M., Silverman, G. A., Wong, W., Rosado, C. J., Langendorf, C. G., Pike, R. N., Bird, P. I. & Whisstock, J. C. (2006). Genome Biol. 7, 216. PubMed PMC

Leboulle, G., Crippa, M., Decrem, Y., Mejri, N., Brossard, M., Bollen, A. & Godfroid, E. (2002). J. Biol. Chem. 277, 10083–10089. PubMed

Livak, K. J. & Schmittgen, T. D. (2001). Methods, 25, 402–408. PubMed

Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D. & Lopez, R. (2019). Nucleic Acids Res. 47, W636–W641. PubMed PMC

Marijanovic, E. M., Fodor, J., Riley, B. T., Porebski, B. T., Costa, M. G. S., Kass, I., Hoke, D. E., McGowan, S. & Buckle, A. M. (2019). Sci. Rep. 9, 3870. PubMed PMC

Mellet, P., Michels, B. & Bieth, J. G. (1996). J. Biol. Chem. 271, 30311–30314. PubMed

Mueller, U., Darowski, N., Fuchs, M. R., Förster, R., Hellmig, M., Paithankar, K. S., Pühringer, S., Steffien, M., Zocher, G. & Weiss, M. S. (2012). J. Synchrotron Rad. 19, 442–449. PubMed PMC

Mulenga, A., Khumthong, R. & Chalaire, K. C. (2009). BMC Genomics, 10, 217. PubMed PMC

Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355–367. PubMed PMC

Nagata, K. (1996). Trends Biochem. Sci. 21, 23–26. PubMed

Páleníková, J., Lieskovská, J., Langhansová, H., Kotsyfakis, M., Chmelař, J. & Kopecký, J. (2015). Infect. Immun. 83, 1949–1956. PubMed PMC

Pemberton, P. A., Stein, P. E., Pepys, M. B., Potter, J. M. & Carrell, R. W. (1988). Nature, 336, 257–258. PubMed

Porter, L., Radulović, Ž., Kim, T., Braz, G. R. C., Da Silva Vaz, I. & Mulenga, A. (2015). Ticks Tick Borne Dis. 6, 16–30. PubMed PMC

Prevot, P.-P., Adam, B., Boudjeltia, K. Z., Brossard, M., Lins, L., Cauchie, P., Brasseur, R., Vanhaeverbeek, M., Vanhamme, L. & Godfroid, E. (2006). J. Biol. Chem. 281, 26361–26369. PubMed

Prevot, P.-P., Beschin, A., Lins, L., Beaufays, J., Grosjean, A., Bruys, L., Adam, B., Brossard, M., Brasseur, R., Zouaoui Boudjeltia, K., Vanhamme, L. & Godfroid, E. (2009). FEBS J. 276, 3235–3246. PubMed

Prevot, P.-P., Couvreur, B., Denis, V., Brossard, M., Vanhamme, L. & Godfroid, E. (2007). Vaccine, 25, 3284–3292. PubMed

Rappsilber, J., Mann, M. & Ishihama, Y. (2007). Nat. Protoc. 2, 1896–1906. PubMed

Rashid, Q., Kapil, C., Singh, P., Kumari, V. & Jairajpuri, M. A. (2015). J. Biomol. Struct. Dyn. 33, 1352–1362. PubMed

Robert, X. & Gouet, P. (2014). Nucleic Acids Res. 42, W320–W324. PubMed PMC

Schlee, S., Straub, K., Schwab, T., Kinateder, T., Merkl, R. & Sterner, R. (2019). Proteins, 87, 815–825. PubMed

Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V. & Mann, M. (2006). Nat. Protoc. 1, 2856–2860. PubMed

Silverman, G. A., Bird, P. I., Carrell, R. W., Church, F. C., Coughlin, P. B., Gettins, P. G., Irving, J. A., Lomas, D. A., Luke, C. J., Moyer, R. W., Pemberton, P. A., Remold-O’Donnell, E., Salvesen, G. S., Travis, J. & Whisstock, J. C. (2001). J. Biol. Chem. 276, 33293–33296. PubMed

Sparta, K. M., Krug, M., Heinemann, U., Mueller, U. & Weiss, M. S. (2016). J. Appl. Cryst. 49, 1085–1092.

Spence, M. A., Mortimer, M. D., Buckle, A. M., Minh, B. Q. & Jackson, C. J. (2021). Mol. Biol. Evol. 38, 2915–2929. PubMed PMC

Sprong, H., Azagi, T., Hoornstra, D., Nijhof, A. M., Knorr, S., Baarsma, M. E. & Hovius, J. W. (2018). Parasites Vectors, 11, 145. PubMed PMC

Tirloni, L., Seixas, A., Mulenga, A., da Silva Vaz, I. Jr & Termignoni, C. (2014). Exp. Parasitol. 137, 25–34. PubMed

Tsukada, H. & Blow, D. M. (1985). J. Mol. Biol. 184, 703–711. PubMed

Tyson, K. R., Elkins, C. & de Silva, A. M. (2008). J. Immunol. 180, 3964–3968. PubMed

Vagin, A. & Teplyakov, A. (2010). Acta Cryst. D66, 22–25. PubMed

Vangone, A., Spinelli, R., Scarano, V., Cavallo, L. & Oliva, R. (2011). Bioinformatics, 27, 2915–2916. PubMed

Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., Jain, S., Lewis, S. M., Arendall, W. B., Snoeyink, J., Adams, P. D., Lovell, S. C., Richardson, J. S. & Richardson, D. C. (2018). Protein Sci. 27, 293–315. PubMed PMC

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S. (2011). Acta Cryst. D67, 235–242. PubMed PMC

Yamasaki, M., Arii, Y., Mikami, B. & Hirose, M. (2002). J. Mol. Biol. 315, 113–120. PubMed

Zou, Z., Anisowicz, A., Hendrix, M. J., Thor, A., Neveu, M., Sheng, S., Rafidi, K., Seftor, E. & Sager, R. (1994). Science, 263, 526–529. PubMed

Zundert, G. C. P. van, Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J. & Bonvin, A. M. J. J. (2016). J. Mol. Biol. 428, 720–725. PubMed

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