An affibody in complex with a target protein: Structure and coupled folding
10.1073/pnas.0436086100
Crossref journal-article
Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences (341)
Abstract

Combinatorial protein engineering provides powerful means for functional selection of novel binding proteins. One class of engineered binding proteins, denoted affibodies, is based on the three-helix scaffold of the Z domain derived from staphylococcal protein A. The Z SPA-1 affibody has been selected from a phage-displayed library as a binder to protein A. Z SPA-1 also binds with micromolar affinity to its own ancestor, the Z domain. We have characterized the Z SPA-1 affibody in its uncomplexed state and determined the solution structure of a Z:Z SPA-1 protein–protein complex. Uncomplexed Z SPA-1 behaves as an aggregation-prone molten globule, but folding occurs on binding, and the original (Z) three-helix bundle scaffold is fully formed in the complex. The structural basis for selection and strong binding is a large interaction interface with tight steric and polar/nonpolar complementarity that directly involves 10 of 13 mutated amino acid residues on Z SPA-1 . We also note similarities in how the surface of the Z domain responds by induced fit to binding of Z SPA-1 and Ig Fc, respectively, suggesting that the Z SPA-1 affibody is capable of mimicking the morphology of the natural binding partner for the Z domain.

Bibliography

Wahlberg, E., Lendel, C., Helgstrand, M., Allard, P., Dincbas-Renqvist, V., Hedqvist, A., Berglund, H., Nygren, P.-Åke, & Härd, T. (2003). An affibody in complex with a target protein: Structure and coupled folding. Proceedings of the National Academy of Sciences, 100(6), 3185–3190.

Authors 9
  1. Elisabet Wahlberg (first)
  2. Christofer Lendel (additional)
  3. Magnus Helgstrand (additional)
  4. Peter Allard (additional)
  5. Vildan Dincbas-Renqvist (additional)
  6. Anders Hedqvist (additional)
  7. Helena Berglund (additional)
  8. Per-Åke Nygren (additional)
  9. Torleif Härd (additional)
References 32 Referenced 94
  1. B Nilsson, T Moks, B Jansson, L Abrahmsén, A Elmblad, E Holmgren, C Henrichson, T A Jones, M Uhlén Protein Eng 1, 107–113 (1987). (10.1093/protein/1.2.107) / Protein Eng by Nilsson B (1987)
  2. J Deisenhofer Biochemistry 20, 2361–2370 (1981). (10.1021/bi00512a001) / Biochemistry by Deisenhofer J (1981)
  3. K Nord, E Gunneriusson, J Ringdahl, S Stål, M Uhlén, P-Å Nygren Nat Biotechnol 15, 772–777 (1997). (10.1038/nbt0897-772) / Nat Biotechnol by Nord K (1997)
  4. K Nord, E Gunneriusson, M Uhlén, P-Å Nygren J Biotechnol 80, 45–54 (2000). (10.1016/S0168-1656(00)00232-7) / J Biotechnol by Nord K (2000)
  5. M Hansson, J Ringdahl, A Robert, U Power, L Goetsch, T Nguyen, M Uhlén, S Ståhl, P-Å Nygren Immunotechnology 4, 237–252 (1999). (10.1016/S1380-2933(98)00026-8) / Immunotechnology by Hansson M (1999)
  6. K Nord, O Nord, M Uhlén, B Kelley, C Ljungqvist, P-Å Nygren Eur J Biochem 268, 4269–4277 (2001). (10.1046/j.1432-1327.2001.02344.x) / Eur J Biochem by Nord K (2001)
  7. J Rönnmark, H Grönlund, M Uhlén, P-Å Nygren Eur J Biochem 269, 2647–2655 (2002). (10.1046/j.1432-1033.2002.02926.x) / Eur J Biochem by Rönnmark J (2002)
  8. M Eklund, L Axelsson, M Uhlén, P-Å Nygren Proteins Struct Funct Genet 48, 454–462 (2002). (10.1002/prot.10169) / Proteins Struct Funct Genet by Eklund M (2002)
  9. C Lendel, E Wahlberg, H Berglund, M Eklund, P-Å Nygren, T Härd J Biomol NMR 24, 271–272 (2002). (10.1023/A:1021664710731) / J Biomol NMR by Lendel C (2002)
  10. G Wagner, S G Hyberts, T F Havel Annu Rev Biophys Biomol Struct 21, 167–198 (1992). (10.1146/annurev.bb.21.060192.001123) / Annu Rev Biophys Biomol Struct by Wagner G (1992)
  11. G W Vuister, S-J Kim, C Wu, A Bax J Am Chem Soc 116, 9206–9210 (1994). (10.1021/ja00099a041) / J Am Chem Soc by Vuister G W (1994)
  12. J Cavanagh, W J Fairbrother, A G Palmer, N J Skelton Protein NMR Spectroscopy: Principles and Practice (Academic, New York, 1996). / Protein NMR Spectroscopy: Principles and Practice by Cavanagh J (1996)
  13. M Helgstrand, P Kraulis, P Allard, T Härd J Biomol NMR 18, 329–336 (2000). (10.1023/A:1026729404698) / J Biomol NMR by Helgstrand M (2000)
  14. K Wüthrich NMR of Proteins and Nucleic Acids (Wiley, New York, 1986). / NMR of Proteins and Nucleic Acids by Wüthrich K (1986)
  15. C M Fletcher, D N M Jones, R Diamond, D Neuhaus J Biomol NMR 8, 292–310 (1996). (10.1007/BF00410328) / J Biomol NMR by Fletcher C M (1996)
  16. G Cornilescu, F Delaglio, A Bax J Biomol NMR 13, 289–302 (1999). (10.1023/A:1008392405740) / J Biomol NMR by Cornilescu G (1999)
  17. S Ludvigsen, F M Poulsen J Biomol NMR 2, 227–233 (1992). (10.1007/BF01875318) / J Biomol NMR by Ludvigsen S (1992)
  18. G A Jeffrey, W Saenger Hydrogen Bonding in Biological Structures (Springer, Berlin, 1991). (10.1007/978-3-642-85135-3) / Hydrogen Bonding in Biological Structures by Jeffrey G A (1991)
  19. A T Brünger, G M Clore, A M Gronenborn, M Karplus Proc Natl Acad Sci USA 83, 3801–3805 (1986). (10.1073/pnas.83.11.3801) / Proc Natl Acad Sci USA by Brünger A T (1986)
  20. J Kuszewski, A M Gronenborn, G M Clore J Am Chem Soc 121, 2337–2338 (1999). (10.1021/ja9843730) / J Am Chem Soc by Kuszewski J (1999)
  21. J Kuszewski, A M Gronenborn, G M Clore J Magn Reson 125, 171–177 (1997). (10.1006/jmre.1997.1116) / J Magn Reson by Kuszewski J (1997)
  22. R Koradi, M Billeter, K Wüthrich J Mol Graphics 14, 51–55 (1996). (10.1016/0263-7855(96)00009-4) / J Mol Graphics by Koradi R (1996)
  23. R A Laskowski, J A C Rullmann, M W MacArthur, R Kaptein, J M Thornton J Biomol NMR 8, 477–486 (1996). (10.1007/BF00228148) / J Biomol NMR by Laskowski R A (1996)
  24. R Rodriguez, G Chinea, N Lopez, T Pons, G Vriend CABIOS 14, 523–528 (1998). / CABIOS by Rodriguez R (1998)
  25. G Semisotnov, N Rodionova, O Razgulyaev, V Uversky, A Gripas, R Gilmanshin Biopolymers 31, 119–128 (1991). (10.1002/bip.360310111) / Biopolymers by Semisotnov G (1991)
  26. C Dobson Curr Biol 4, 636–640 (1994). (10.1016/S0960-9822(00)00141-X) / Curr Biol by Dobson C (1994)
  27. O Ptitsyn Trends Biochem Sci 20, 376–379 (1995). (10.1016/S0968-0004(00)89081-7) / Trends Biochem Sci by Ptitsyn O (1995)
  28. M Tashiro, R Tejero, D E Zimmerman, B Celda, B Nilsson, G T Montelione J Mol Biol 272, 573–590 (1997). (10.1006/jmbi.1997.1265) / J Mol Biol by Tashiro M (1997)
  29. M Högbom, M Eklund, P-Å Nygren, P Nordlund Proc Natl Acad Sci USA 100, 3191–3196 (2003). (10.1073/pnas.0436100100) / Proc Natl Acad Sci USA by Högbom M (2003)
  30. I Aphasizheva, D Dolgikh, Z Abdullaev, V Uversky, M Kirpichnikov, O Ptitsyn FEBS Lett 425, 101–104 (1998). (10.1016/S0014-5793(98)00201-4) / FEBS Lett by Aphasizheva I (1998)
  31. J Lecomte, C Matthews Protein Eng 6, 1–10 (1993). (10.1093/protein/6.1.1) / Protein Eng by Lecomte J (1993)
  32. D C Tahmassebi, T Sasaki J Org Chem 63, 728–731 (1998). (10.1021/jo970812m) / J Org Chem by Tahmassebi D C (1998)
Dates
Type When
Created 22 years, 5 months ago (March 18, 2003, 6:15 p.m.)
Deposited 3 years, 2 months ago (June 7, 2022, 2:06 a.m.)
Indexed 3 months, 2 weeks ago (May 21, 2025, 6:06 a.m.)
Issued 22 years, 6 months ago (Feb. 19, 2003)
Published 22 years, 6 months ago (Feb. 19, 2003)
Published Online 22 years, 6 months ago (Feb. 19, 2003)
Published Print 22 years, 5 months ago (March 18, 2003)
Funders 0

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@article{Wahlberg_2003, title={An affibody in complex with a target protein: Structure and coupled folding}, volume={100}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0436086100}, DOI={10.1073/pnas.0436086100}, number={6}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Wahlberg, Elisabet and Lendel, Christofer and Helgstrand, Magnus and Allard, Peter and Dincbas-Renqvist, Vildan and Hedqvist, Anders and Berglund, Helena and Nygren, Per-Åke and Härd, Torleif}, year={2003}, month=feb, pages={3185–3190} }