Peptide binding affinity redistributes preassembled repeat protein fragments.
NMR spectroscopy
peptide binding
protein design
protein fragment complementation
repeat protein
Journal
Biological chemistry
ISSN: 1437-4315
Titre abrégé: Biol Chem
Pays: Germany
ID NLM: 9700112
Informations de publication
Date de publication:
25 02 2019
25 02 2019
Historique:
received:
24
08
2018
accepted:
21
11
2018
pubmed:
6
12
2018
medline:
2
11
2019
entrez:
6
12
2018
Statut:
ppublish
Résumé
Designed armadillo repeat proteins (dArmRPs) are modular peptide binders composed of N- and C-terminal capping repeats Y and A and a variable number of internal modules M that each specifically recognize two amino acids of the target peptide. Complementary fragments of dArmRPs obtained by splitting the protein between helices H1 and H2 of an internal module show conditional and specific assembly only in the presence of a target peptide (Michel, E., Plückthun, A., and Zerbe, O. (2018). Peptide-guided assembly of repeat protein fragments. Angew. Chem. Int. Ed. 57, 4576-4579). Here, we investigate dArmRP fragments that already spontaneously assemble with high affinity, e.g. those obtained from splits between entire modules or between helices H2 and H3. We find that the interaction of the peptide with the assembled fragments induces distal conformational rearrangements that suggest an induced fit on a global protein level. A population analysis of an equimolar mixture of an N-terminal and three C-terminal fragments with various affinities for the target peptide revealed predominant assembly of the weakest peptide binder. However, adding a target peptide to this mixture altered the population of the protein complexes such that the combination with the highest affinity for the peptide increased and becomes predominant when adding excess of peptide, highlighting the feasibility of peptide-induced enrichment of best binders from inter-modular fragment mixtures.
Identifiants
pubmed: 30517075
doi: 10.1515/hsz-2018-0355
pii: hsz-2018-0355
doi:
Substances chimiques
Armadillo Domain Proteins
0
Peptides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
395-404Références
Alfarano, P., Varadamsetty, G., Ewald, C., Parmeggiani, F., Pellarin, R., Zerbe, O., Plückthun, A., and Caflisch, A. (2012). Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Sci. 21, 1298–1314.
Alford, R.F., Leaver-Fay, A., Jeliazko, J.R., O’Meara, M.J., DiMaio, F.P., Park, H., Shapovalov, M.V., Renfrew, P.D., Mulligan, V.M., Kappel, K., et al. (2017). The Rosetta all-atom energy function for macromolecular modeling and design. J. Chem. Theory Comput. 13, 3031–3038.
Binz, H.K., Amstutz, P., and Plückthun, A. (2005). Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 23, 1257–1268.
Conti, E., Uy, M., Leighton, L., Blobel, G., and Kuriyan, J. (1998). Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Cell. 94, 193–204.
Gebauer, M. and Skerra, A. (2009). Engineered protein scaffolds as next-generation antibody therapeutics. Curr. Opin. Chem. Biol. 13, 245–255.
Hansen, S., Tremmel, D., Madhurantakam, C., Reichen, C., Mittl, P.R., and Plückthun, A. (2016). Structure and energetic contributions of a designed modular peptide-binding protein with picomolar affinity. J. Am. Chem. Soc. 138, 3526–3532.
Kang, A.S., Jones, T.M., and Burton, D.R. (1991). Antibody redesign by chain shuffling from random combinatorial immunoglobulin libraries. Proc. Natl. Acad. Sci. USA 88, 11120–11123.
Kay, L.E., Torchia, D.A., and Bax, A. (1989). Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry. 28, 8972–8979.
Kuriyan, J. and Cowburn, D. (1997). Modular peptide recognition domains in eukaryotic signaling. Annu. Rev. Biophys. Biomol. Struct. 26, 259–288.
McCafferty, J. and Schofield, D. (2015). Identification of optimal protein binders through the use of large genetically encoded display libraries. Curr. Opin. Chem. Biol. 26, 16–24.
Michel, E. and Wüthrich, K. (2012a). High-yield Escherichia coli-based cell-free expression of human proteins. J. Biomol. NMR. 53, 43–51.
Michel, E. and Wüthrich, K. (2012b). Cell-free expression of disulfide-containing eukaryotic proteins for structural biology. FEBS J. 279, 3176–3184.
Michel, E. and Allain, F.H. (2015). Selective amino acid segmental labeling of multi-domain proteins. Methods Enzymol. 565, 389–422.
Michel, E., Skrisovska, L., Wüthrich, K., and Allain, F.H. (2013). Amino acid-selective segmental isotope labeling of multidomain proteins for structural biology. ChemBioChem. 14, 457–466.
Michel, E., Plückthun, A., and Zerbe, O. (2018). Peptide-guided assembly of repeat protein fragments. Angew. Chem. Int. Ed. 57, 4576–4579.
Noggle, J.H. and Schirmer, R.E. (1971). The Nuclear Overhauser Effect: Chemical Applications (New York: Academic Press).
Palmer, A.G. (2015). Enzyme dynamics from NMR spectroscopy. Acc. Chem. Res. 48, 457–465.
Parmeggiani, F., Pellarin, R., Larsen, A.P., Varadamsetty, G., Stumpp, M.T., Zerbe, O., Caflisch, A., and Plückthun, A. (2008). Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. J. Mol. Biol. 376, 1282–1304.
Plückthun, A. (2015). Designed ankyrin repeat proteins (DARPins): binding proteins for research, diagnostics, and therapy. Annu. Rev. Pharmacol. Toxicol. 55, 489–511.
Reichen, C., Hansen, S., Forzani, C., Honegger, A., Fleishman, S.J., Zhou, T., Parmeggiani, F., Ernst, P., Madhurantakam, C., Ewald, C., et al. (2016). Computationally designed Armadillo repeat proteins for modular peptide recognition. J. Mol. Biol. 428, 4467–4489.
Sattler, M., Schleucher, J., and Griesinger, C. (1999). Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. Nucl. Magn. Reson. Spectrosc. 34, 93–158.
Ueda, H., Tsumoto, K., Kubota, K., Suzuki, E., Nagamune, T., Nishimura, H., Schueler, P.A., Winter, G., Kumagai, I., and Mohoney, W.C. (1996). Open sandwich ELISA: a novel immunoassay based on the interchain interaction of antibody variable region. Nat. Biotechnol. 14, 1714-1718.
Watson, R.P., Christen, M.T., Ewald, C., Bumbak, F., Reichen, C., Mihajlovic, M., Schmidt, E., Güntert, P., Caflisch, A., Plückthun, A., et al. (2014). Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure. Structure 22, 985–995.
Wishart, D.S. and Sykes, B.D. (1994). The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J. Biomol. NMR 4, 171–180.