リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion

Tamura-Sakaguchi, Risako Aruga, Rie Hirose, Mika Ekimoto, Toru Miyake, Takuya Hizukuri, Yohei Oi, Rika Kaneko, Mika K. Kato, Yukinari Akiyama, Yoshinori Ikeguchi, Mitsunori Iwasaki, Kenji Nogi, Terukazu 京都大学 DOI:10.1107/S2059798321002527

2021.05

概要

Antibody labeling has been conducted extensively for structure determination using both X-ray crystallography and electron microscopy (EM). However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, an alternative method has been developed to prepare an antibody complex by inserting an exogenous epitope into the target. It has already been demonstrated that the Fab of the NZ-1 monoclonal antibody can form a stable complex with a target containing a PA12 tag as an inserted epitope. Nevertheless, it was also found that complex formation through the inserted PA12 tag inevitably caused structural changes around the insertion site on the target. Here, an attempt was made to improve the tag-insertion method, and it was consequently discovered that an alternate tag (PA14) could replace various loops on the target without inducing large structural changes. Crystallographic analysis demonstrated that the inserted PA14 tag adopts a loop-like conformation with closed ends in the antigen-binding pocket of the NZ-1 Fab. Due to proximity of the termini in the bound conformation, the more optimal PA14 tag had only a minor impact on the target structure. In fact, the PA14 tag could also be inserted into a sterically hindered loop for labeling. Molecular-dynamics simulations also showed a rigid structure for the target regardless of PA14 insertion and complex formation with the NZ-1 Fab. Using this improved labeling technique, negative-stain EM was performed on a bacterial site-2 protease, which enabled an approximation of the domain arrangement based on the docking mode of the NZ-1 Fab.

この論文で使われている画像

参考文献

Abraham, M. J., Murtola, T., Schulz, R., Pa´ll, S., Smith, J. C., Hess, B. & Lindahl, E. (2015). SoftwareX, 1–2, 19–25.

Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352–367. Akiyama, K., Mizuno, S., Hizukuri, Y., Mori, H., Nogi, T. & Akiyama,

Y. (2015). eLife, 4, e08928.

Akiyama, Y., Kanehara, K. & Ito, K. (2004). EMBO J. 23, 4434–4442.

Alba, B. M., Leeds, J. A., Onufryk, C., Lu, C. Z. & Gross, C. A. (2002). Genes Dev. 16, 2156–2168.

Boisset, N., Penczek, P., Taveau, J.-C., Lamy, J., Frank, J. & Lamy, J. (1995). J. Struct. Biol. 115, 16–29.

Boisset, N., Radermacher, M., Grassucci, R., Taveau, J.-C., Liu, W., Lamy, J., Frank, J. & Lamy, J. N. (1993). J. Struct. Biol. 111, 234–244. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino,

R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12–21.

Coleman, J. A., Yang, D., Zhao, Z., Wen, P. C., Yoshioka, C., Tajkhorshid, E. & Gouaux, E. (2019). Nature, 569, 141–145.

Day, P. W., Rasmussen, S. G. F., Parnot, C., Fung, J. J., Masood, A., Kobilka, T. S., Yao, X.-J., Choi, H.-J., Weis, W. I., Rohrer, D. K. & Kobilka, B. K. (2007). Nat. Methods, 4, 927–929.

Deckert, G., Warren, P. V., Gaasterland, T., Young, W. G., Lenox, A. L., Graham, D. E., Overbeek, R., Snead, M. A., Keller, M., Aujay, M., Huber, R., Feldman, R. A., Short, J. M., Olsen, G. J. & Swanson, R. V. (1998). Nature, 392, 353–358.

Dolinsky, T. J., Nielsen, J. E., McCammon, J. A. & Baker, N. A. (2004). Nucleic Acids Res. 32, W665–W667.

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

Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H. & Pedersen, L. G. (1995). J. Chem. Phys. 103, 8577–8593.

Evans, P. R. & Murshudov, G. N. (2013). Acta Cryst. D69, 1204–1214. Feig, M., Karanicolas, J. & Brooks, C. L. (2004). J. Mol. Graph. Model. 22, 377–395.

Fujii, Y., Kaneko, M., Neyazaki, M., Nogi, T., Kato, Y. & Takagi, J. (2014). Protein Expr. Purif. 95, 240–247.

Fujii, Y., Matsunaga, Y., Arimori, T., Kitago, Y., Ogasawara, S., Kaneko, M. K., Kato, Y. & Takagi, J. (2016). J. Cell Sci. 129, 1512– 1522.

Hess, B. (2008). J. Chem. Theory Comput. 4, 116–122.

Hino, T., Iwata, S. & Murata, T. (2013). Curr. Opin. Struct. Biol. 23, 563–568.

Hizukuri, Y., Akiyama, K. & Akiyama, Y. (2017). Methods Enzymol. 584, 1–33.

Hizukuri, Y. & Akiyama, Y. (2012). Mol. Microbiol. 86, 1232–1245. Hizukuri, Y., Oda, T., Tabata, S., Tamura-Kawakami, K., Oi, R., Sato,

M., Takagi, J., Akiyama, Y. & Nogi, T. (2014). Structure, 22, 326– 336.

Hoover, W. G. (1985). Phys. Rev. A, 31, 1695–1697.

Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmu¨ ller, H. & MacKerell, A. D. Jr (2017). Nat. Methods, 14, 71–73.

Hunte, C. & Michel, H. (2002). Curr. Opin. Struct. Biol. 12, 503–508. Jo, S., Kim, T., Iyer, V. G. & Im, W. (2008). J. Comput. Chem. 29, 1859–1865.

Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. (1983). J. Chem. Phys. 79, 926–935.

Kabsch, W. (1976). Acta Cryst. A32, 922–923. Kabsch, W. (2010). Acta Cryst. D66, 125–132.

Kanehara, K., Akiyama, Y. & Ito, K. (2001). Gene, 281, 71–79. Kanehara, K., Ito, K. & Akiyama, Y. (2002). Genes Dev. 16, 2147–2155.

Kato, Y., Kaneko, M. K., Kuno, A., Uchiyama, N., Amano, K., Chiba, Y., Hasegawa, Y., Hirabayashi, J., Narimatsu, H., Mishima, K. & Osawa, M. (2006). Biochem. Biophys. Res. Commun. 349, 1301–1307.

Kim, J., Tan, Y. Z., Wicht, K. J., Erramilli, S. K., Dhingra, S. K., Okombo, J., Vendome, J., Hagenah, L. M., Giacometti, S. I., Warren, A. L., Nosol, K., Roepe, P. D., Potter, C. S., Carragher, B., Kossiakoff, A. A., Quick, M., Fidock, D. A. & Mancia, F. (2019). Nature, 576, 315–320.

Koide, S. (2009). Curr. Opin. Struct. Biol. 19, 449–457.

Ku¨ hlbrandt, W. (2014). Science, 343, 1443–1444.

Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D. Jr, Klauda, J. B. & Im, W. (2016). J. Chem. Theory Comput. 12, 405–413.

MacKerell, A. D. Jr, Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wio´rkiewicz-Kuczera, J., Yin, D. & Karplus, M. (1998). J. Phys. Chem. B, 102, 3586–3616.

MacKerell, A. D. Jr, Feig, M. & Brooks, C. L. (2004). J. Am. Chem. Soc. 126, 698–699.

Miller, J. H. (1972). Experiments in Molecular Genetics. New York: Cold Spring Harbor Laboratory Press. Miyagi, H., Asada, H., Suzuki, M., Takahashi, Y., Yasunaga, M., Suno, C., Iwata, S. & Saito, J. I. (2020). Sci. Rep. 10, 11669.

Miyake, T., Hizukuri, Y. & Akiyama, Y. (2020). Front. Microbiol. 11, 607381.

Mukherjee, S., Erramilli, S. K., Ammirati, M., Alvarez, F. J. D., Fennell, K. F., Purdy, M. D., Skrobek, B. M., Radziwon, K., Coukos, J., Kang, Y., Dutka, P., Gao, X., Qiu, X., Yeager, M., Xu, H. E., Han, S. & Kossiakoff, A. A. (2020). Nat. Commun. 11, 1598. Nose´, S. (1984). Mol. Phys. 52, 255–268.

Nose´, S. & Klein, M. L. (1983). Mol. Phys. 50, 1055–1076.

Olsson, M. H., Søndergaard, C. R., Rostkowski, M. & Jensen, J. H. (2011). J. Chem. Theory Comput. 7, 525–537.

Ostermeier, C., Iwata, S., Ludwig, B. & Michel, H. (1995). Nat. Struct. Mol. Biol. 2, 842–846.

Parrinello, M. & Rahman, A. (1981). J. Appl. Phys. 52, 7182–7190. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). J. Comput. Chem. 25, 1605–1612.

Pronk, S., Pa´ll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B. & Lindahl, E. (2013). Bioinformatics, 29, 845–854.

Rasmussen, S. G. F., Choi, H.-J., Rosenbaum, D. M., Kobilka, T. S., Thian, F. S., Edwards, P. C., Burghammer, M., Ratnala, V. R. P., Sanishvili, R., Fischetti, R. F., Schertler, G. F. X., Weis, W. I. & Kobilka, B. K. (2007). Nature, 450, 383–387.

Rubinstein, J. L. (2007). Methods, 41, 409–416.

Sˇali, A. & Blundell, T. L. (1993). J. Mol. Biol. 234, 779–815.

Søndergaard, C. R., Olsson, M. H., Rostkowski, M. & Jensen, J. H. (2011). J. Chem. Theory Comput. 7, 2284–2295.

Tamura, R., Oi, R., Akashi, S., Kaneko, M. K., Kato, Y. & Nogi, T. (2019). Protein Sci. 28, 823–836.

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

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.

Wu, S., Avila-Sakar, A., Kim, J., Booth, D. S., Greenberg, C. H., Rossi, A., Liao, M., Li, X., Alian, A., Griner, S. L., Juge, N., Yu, Y., Mergel, C. M., Chaparro-Riggers, J., Strop, P., Tampe´, R., Edwards, R. H., Stroud, R. M., Craik, C. S. & Cheng, Y. (2012). Structure, 20, 582– 592.

Zhang, K. (2016). J. Struct. Biol. 193, 1–12.

Zheng, S. Q., Palovcak, E., Armache, J.-P., Verba, K. A., Cheng, Y. & Agard, D. A. (2017). Nat. Methods, 14, 331–332.

Zhou, Y., Morais-Cabral, J. H., Kaufman, A. & MacKinnon, R. (2001). Nature, 414, 43–48.

Zivanov, J., Nakane, T., Forsberg, B. O., Kimanius, D., Hagen, W. J., Lindahl, E. & Scheres, S. H. W. (2018). eLife, 7, e42166.

参考文献をもっと見る

全国の大学の
卒論・修論・学位論文

一発検索!

この論文の関連論文を見る