Repeat proteins challenge the concept of structural domains
Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For ma...
Guardado en:
| Autor principal: | |
|---|---|
| Otros Autores: | , , , , |
| Formato: | Capítulo de libro |
| Lenguaje: | Inglés |
| Publicado: |
Portland Press Ltd
2015
|
| Acceso en línea: | Registro en Scopus DOI Handle Registro en la Biblioteca Digital |
| Aporte de: | Registro referencial: Solicitar el recurso aquí |
| Sumario: | Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For many natural repeat-proteins, it has been shown that weak energetic links between repeats lead to the breakdown of co-operativity and the appearance of folding sub-domains within an apparently regular repeat array. The quasi-1D architecture of repeat-proteins is crucial in detailing how the local energetic balances can modulate the folding dynamics of these proteins, which can be related to the physiological behaviour of these ubiquitous biological systems. © 2015 Authors; published by Portland Press Limited. |
|---|---|
| Bibliografía: | Wetlaufer, D.B., Nucleation, rapid folding, and globular intrachain regions in proteins (1973) Proc. Natl. Acad. Sci. U.S.A., 70, pp. 697-701. , CrossRef PubMed Nasir, A., Kim, K.M., Caetano-Anollés, G., Global patterns of protein domain gain and loss in superkingdoms (2014) PLoS Comput. Biol., 10, p. e1003452. , CrossRef PubMed Jacob, F., Evolution and tinkering (1977) Science, 196, pp. 1161-1166. , CrossRef PubMed Marcotte, E.M., Pellegrini, M., Yeates, T.O., Eisenberg, D., A census of protein repeats (1999) J. Mol. Biol., 293, pp. 151-160. , CrossRef PubMed Ferreiro, D.U., Walczak, A.M., Komives, E.A., Wolynes, P.G., The energy landscapes of repeat-containing proteins: Topology, cooperativity, and the folding funnels of one-dimensional architectures (2008) PLoS Comput. Biol., 4, p. e1000070. , CrossRef PubMed Luo, H., Nijveen, H., Understanding and identifying amino acid repeats (2014) Brief. Bioinform., 15, pp. 582-591. , CrossRef PubMed Shih, E.S., Hwang, M.J., Alternative alignments from comparison of protein structures (2004) Proteins, 56, pp. 519-527. , CrossRef PubMed Abraham, A.L., Rocha, E.P., Pothier, J., Swelfe: A detector of internal repeats in sequences and structures (2008) Bioinformatics, 24, pp. 1536-1537. , CrossRef PubMed Walsh, I., Sirocco, F.G., Minervini, G., Di Domenico, T., Ferrari, C., Tosatto, S.C., RAPHAEL: Recognition, periodicity and insertion assignment of solenoid protein structures (2012) Bioinformatics, 28, pp. 3257-3264. , CrossRef PubMed Di Domenico, T., Potenza, E., Walsh, I., Parra, R.G., Giollo, M., Minervini, G., Tosatto, S.C., RepeatsDB: A database of tandem repeat protein structures (2014) Nucleic Acids Res., 42, pp. D352-D357. , CrossRef PubMed Kajava, A.V., Tandem repeats in proteins: From sequence to structure (2012) J. Struct. Biol., 179, pp. 279-288. , CrossRef PubMed Schaper, E., Kajava, A.V., Hauser, A., Anisimova, M., Repeat or not repeat? - Statistical validation of tandem repeat prediction in genomic sequences (2012) Nucleic Acids Res., 40, pp. 10005-10017. , CrossRef PubMed Parra, R.G., Espada, R., Sánchez, I.E., Sippl, M.J., Ferreiro, D.U., Detecting repetitions and periodicities in proteins by tiling the structural space (2013) J. Phys. Chem. B, 117, pp. 12887-12897. , CrossRef PubMed Sippl, M.J., Wiederstein, M., A note on difficult structure alignment problems (2008) Bioinformatics, 24, pp. 426-427. , CrossRef PubMed Sippl, M.J., On distance and similarity in fold space (2008) Bioinformatics, 24, pp. 872-873. , CrossRef PubMed Tang, K.S., Fersht, A.R., Itzhaki, L.S., Sequential unfolding of ankyrin repeats in tumor suppressor p16 (2003) Structure, 11, pp. 67-73. , CrossRef PubMed Lowe, A.R., Itzhaki, L.S., Biophysical characterisation of the small ankyrin repeat protein myotrophin (2007) J. Mol. Biol., 365, pp. 1245-1255. , CrossRef PubMed Zeeb, M., Rosner, H., Zeslawski, W., Canet, D., Holak, T.A., Balbach, J., Protein folding and stability of human CDK inhibitor p19 INK4d (2002) J. Mol. Biol., 315, pp. 447-457. , CrossRef PubMed Bradley, C.M., Barrick, D., Limits of cooperativity in a structurally modular protein: Response of the Notch ankyrin domain to analogous alanine substitutions in each repeat (2002) J. Mol. Biol., 324, pp. 373-386. , CrossRef PubMed Ferreiro, D.U., Cervantes, C.F., Truhlar, S.M., Cho, S.S., Wolynes, P.G., Komives, E.A., Stabilizing IκBα by consensus design (2007) J. Mol. Biol., 365, pp. 1201-1216. , CrossRef PubMed Ferreiro, D.U., Komives, E.A., Molecular mechanisms of system control of NF-κB signaling by IκBα (2010) Biochemistry, 49, pp. 1560-1567. , CrossRef PubMed Truhlar, S.M., Mathes, E., Cervantes, C.F., Ghosh, G., Komives, E.A., Pre-folding IκBα alters control of NF-κB signaling (2008) J. Mol. Biol., 380, pp. 67-82. , CrossRef PubMed Werbeck, N.D., Rowling, P.J., Chellamuthu, V.R., Itzhaki, L.S., Shifting transition states in the unfolding of a large ankyrin repeat protein (2008) Proc. Natl. Acad. Sci. U.S.A., 105, pp. 9982-9987. , CrossRef PubMed Itzhaki, L.S., Lowe, A.R., From artificial antibodies to nanosprings: The biophysical properties of repeat proteins (2012) Adv. Exp. Med. Biol., 747, pp. 153-166. , CrossRef PubMed Aksel, T., Barrick, D., Direct observation of parallel folding pathways revealed using a symmetric repeat protein system (2014) Biophys. J., 107, pp. 220-232. , CrossRef PubMed Wetzel, S.K., Settanni, G., Kenig, M., Binz, H.K., Plückthun, A., Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins (2008) J. Mol. Biol., 376, pp. 241-257. , CrossRef PubMed Ferreiro, D.U., Cho, S.S., Komives, E.A., Wolynes, P.G., The energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family (2005) J. Mol. Biol., 354, pp. 679-692. , CrossRef PubMed Hagai, T., Azia, A., Trizac, E., Levy, Y., Modulation of folding kinetics of repeat proteins: Interplay between intra and interdomain interactions (2012) Biophys. J., 103, pp. 1555-1565. , CrossRef PubMed Javadi, Y., Main, E.R., Exploring the folding energy landscape of a series of designed consensus tetratricopeptide repeat proteins (2009) Proc. Natl. Acad. Sci. U. S. A., 106, pp. 17383-17388. , CrossRef PubMed Tripp, K.W., Barrick, D., Rerouting the folding pathway of the Notch ankyrin domain by reshaping the energy landscape (2008) J. Am. Chem. Soc., 130, pp. 5681-5688. , CrossRef PubMed Street, T.O., Barrick, D., Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape (2009) Protein Sci., 18, pp. 58-68. , PubMed Aksel, T., Barrick, D., Analysis of repeat protein folding using nearest neighbor statistical mechanical models (2009) Methods Enzymol., 455, pp. 95-125. , CrossRef PubMed Ferreiro, D.U., Komives, E.A., The plastic landscape of repeat proteins (2007) Proc. Natl. Acad. Sci. U.S.A., 104, pp. 7735-7736. , CrossRef PubMed Schafer, N.P., Hoffman, R.M., Burger, A., Craig, P.O., Komives, E.A., Wolynes, P.G., Discrete kinetic models from funneled energy landscape simulations (2012) PLoS One, 7, p. e50635. , CrossRef PubMed Ferreiro, D.U., Komives, E.A., Wolynes, P.G., Frustration in biomolecules (2014) Q. Rev. Biophys., 47, pp. 285-363. , CrossRef PubMed Ferreiro, D.U., Hegler, J.A., Komives, E.A., Wolynes, P.G., Localizing frustration in native proteins and protein assemblies (2007) Proc. Natl. Acad. Sci. U.S.A., 104, pp. 19819-19824. , CrossRef PubMed Panchenko, A.R., Luthey-Schulten, Z., Wolynes, P.G., Foldons, protein structural modules, and exons (1996) Proc. Natl. Acad. Sci. U.S.A., 93, pp. 2008-2013. , CrossRef PubMed Schafer, N.P., Kim, B.L., Zheng, W., Wolynes, P.G., Learning to fold proteins using energy landscape theory (2014) Isr. J. Chem., 54, pp. 1311-1337. , CrossRef PubMed Tsai, C.J., Maizel, J.V., Nussinov, R., Anatomy of protein structures: Visualizing how a one-dimensional protein chain folds into a three-dimensional shape (2000) Proc. Natl. Acad. Sci. U.S.A., 97, pp. 12038-12043. , CrossRef PubMed Lamboy, J.A., Kim, H., Dembinski, H., Ha, T., Komives, E.A., Single-molecule FRET reveals the native-state dynamics of the IκBα ankyrin repeat domain (2013) J. Mol. Biol., 425, pp. 2578-2590. , CrossRef PubMed Sivanandan, S., Naganathan, A.N., A disorder-induced domino-like destabilization mechanism governs the folding and functional dynamics of the repeat protein iκbα (2013) PLoS Comput Biol., 9, p. e1003403. , CrossRef PubMed Neher, E., How frequent are correlated changes in families of protein sequences? (1994) Proc. Natl. Acad. Sci. U.S.A., 91, pp. 98-102. , CrossRef PubMed Weigt, M., White, R.A., Szurmant, H., Hoch, J.A., Hwa, T., Identification of direct residue contacts in protein-protein interaction by message passing (2009) Proc. Natl. Acad. Sci. U.S.A., 106, pp. 67-72. , CrossRef PubMed Mora, T., Walczak, A.M., Bialek, W., Callan, C.G., Maximum entropy models for antibody diversity (2010) Proc. Natl. Acad. Sci. U.S.A., 107, pp. 5405-5410. , CrossRef PubMed Morcos, F., Hwa, T., Onuchic, J.N., Weigt, M., Direct coupling analysis for protein contact prediction (2014) Methods Mol. Biol., 1137, pp. 55-70. , CrossRef PubMed Sulkowska, J.I., Morcos, F., Weigt, M., Hwa, T., Onuchic, J.N., Genomics-aided structure prediction (2012) Proc. Natl. Acad. Sci. U.S.A., 109, pp. 10340-10345. , CrossRef PubMed Marks, D.S., Colwell, L.J., Sheridan, R., Hopf, T.A., Pagnani, A., Zecchina, R., Sander, C., Protein 3D structure computed from evolutionary sequence variation (2011) PLoS One, 6, p. e28766. , CrossRef PubMed Cheng, R.R., Morcos, F., Levine, H., Onuchic, J.N., Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information (2014) Proc. Natl. Acad. Sci. U.S.A., 111, pp. E563-E571. , CrossRef PubMed Lui, S., Tiana, G., The network of stabilizing contacts in proteins studied by coevolutionary data (2013) J. Chem. Phys., 139, p. 155103. , CrossRef PubMed Espada, R., Parra, R.G., Mora, T., Walczak, A.M., Ferreiro, D.U., Capturing coevolutionary signals in repeat proteins (2015) BMC Bioinformatics Morcos, F., Schafer, N.P., Cheng, R.R., Onuchic, J.N., Wolynes, P.G., Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection (2014) Proc. Natl. Acad. Sci. U.S.A., 111, pp. 12408-12413. , CrossRef PubMed |
| ISSN: | 03005127 |
| DOI: | 10.1042/BST20150083 |