Folding of a designed simple ankyrin repeat protein

Protein Science

Volumn 13, Issue 11, 2004, Pages 2864-2870

  Devi, V Sathya ^a   Binz, H Kaspar ^a   Stumpp, Michael T ^a   Plückthun, Andreas ^a   Bosshard, Hans Rudolf ^a   Jelesarov, Ilian ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Ankyrin repeat; Calorimetry; Protein design; Protein folding; Protein stability

Indexed keywords

ANKYRIN;

ARTICLE; DIFFERENTIAL SCANNING CALORIMETRY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

ANKYRIN REPEAT; DRUG DESIGN; MODELS, MOLECULAR; PEPTIDE LIBRARY; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN RENATURATION; TEMPERATURE; UREA;

EID: 7244238411     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.04935704     Document Type: Article

References (35)

1. Batchelor, A.H., Piper, D.E., de la Brousse, F.C., McKnight, S.L., and Wolberger, C. 1998. The structure of GABP α/β: An ETS domain ankyrin repeat heterodimer bound to DNA. Science 279: 1037-1041.
2. Binz, H.K., Stumpp, M.T., Forrer, P., Amstutz, P., and Pluckthun, A. 2003. Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J. Mol. Biol. 332: 489-503.
3. Binz, H.K., Amstutz, P., Kohl, A., Stumpp, M.T., Briand, C., Forrer, P., Grutter, M.G., and Pluckthun, A. 2004. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 22: 575-582.
4. Bork, P. 1993. Hundreds of ankyrin-like repeats in functionally diverse proteins - Mobile modules that cross phyla horizontally. Proteins 17: 363-374.
5. Bradley, C.M. and Barrick, D. 2002. Limits of cooperativity in a structurally modular protein: Response of the notch ankyrin domain to analogous alanine substitutions in each repeat. J. Mol. Biol. 324: 373-386.
6. Edelhoch, H. 1967. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6: 1948-1954.
7. Fersht, A.R. 1999. Structure and mechanism in protein science: A guide to enzyme and protein folding, p. 543. W.H. Freeman and Company, New York.
8. Forrer, P., Stumpp, M.T., Binz, H.K., and Pluckthun, A. 2003. A novel strategy to design binding molecules harnessing the modular nature of repeat proteins. FEBS Lett. 539: 2-6.
9. Forrer, P., Binz, H.K., Stumpp, M.T., and Pluckthun, A. 2004. Consensus design of repeat proteins. Chem. Biochem. 5: 183-189.
10. Gomez, J., Hilser, V.J., Xie, D., and Freire, E. 1995. The heat-capacity of proteins. Proteins 22: 404-412.
11. Groves, M.R. and Barford, D. 1999. Topological characteristics of helical repeat proteins. Curr. Opin. Struct. Biol. 9: 383-389.
12. John, D.M. and Weeks, K.M. 2000. Van't Hoff enthalpies without baselines. Protein Sci. 9: 1416-1419.
13. Kohl, A., Binz, H.K., Forrer, P., Stumpp, M.T., Pluckthun, A., and Grutter, M.G. 2003. Designed to be stable: Crystal structure of a consensus ankyrin repeat protein. Proc. Natl. Acad. Sci. 100: 1700-1705.
14. Koradi, R., Billeter, M., and Wuthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14: 51-55.
15. Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P., and Bork, P. 2002. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30: 242-244.
16. Main, E.R.G., Jackson, S.E., and Regan, L. 2003. The folding and design of repeat proteins: Reaching a consensus. Curr. Opin. Struct. Biol. 13: 482-489.
17. Makhatadze, G.I. and Privalov, P.L. 1995. Energetics of protein structure. Adv. Protein Chem. 47: 307-425.
18. Makhatadze, G.I., Lopez, M.M., and Privalov, P.L. 1997. Heat capacities of protein functional groups. Biophys. Chem. 64: 93-101.
19. Marcotte, E.M., Pellegrini, M., Yeates, T.O., and Eisenberg, D. 1999. A census of protein repeats. J. Mol. Biol. 293: 151-160.
20. McDonald, N.Q. and Peters, G. 1998. Ankyrin for clues about the function of p16(INK4a). Nat. Struct. Biol. 5: 85-88.
21. Michaely, P., Tomchick, D.R., Machius, M., and Anderson, R.G.W. 2002. Crystal structure of a 12 ANK repeat stack from human ankyrinR. EMBO J. 21: 6387-6396.
22. Milev, S., Gorfe, A.A., Karshikoff, A., Clubb, R.T., Bosshard, H.R., and Jelesarov, I. 2003. Energetics of sequence-specific protein-DNA association: Conformational stability of the DNA binding domain of integrase Tn916 and its cognate DNA duplex. Biochemistry 42: 3492-3502.
23. Mosavi, L.K. and Peng, Z.Y. 2003. Structure-based substitutions for increased solubility of a designed protein. Protein Eng. 16: 739-745.
24. Mosavi, L.K., Minor, D.L., and Peng, Z.Y. 2002. Consensus-derived structural determinants of the ankyrin repeat motif. Proc. Natl. Acad. Sci. 99: 16029-16034.
25. Plotnikov, V.V., Brandts, J.M., Lin, L.N., and Brandts, J.F. 1997. A new ultrasensitive scanning calorimeter. Anal. Biochem. 250: 237-244.
26. Robinson, N.E. and Robinson, A.B. 2001. Prediction of protein deamidation rates from primary and three-dimensional structure. Proc. Natl. Acad. Sci. 98: 4367-4372.
27. Sedgwick, S.G. and Smerdon, S.J. 1999. The ankyrin repeat: A diversity of interactions on a common structural framework. Trends Biochem. Sci. 24: 311-316.
28. Tang, K.S., Guralnick, B.J., Wang, W.K., Fersht, A.R., and Itzhaki, L.S. 1999. Stability and folding of the tumour suppressor protein p16. J. Mol. Biol. 285: 1869-1886.
29. Tang, K.S., Fersht, A.R., and Itzhaki, L.S. 2003. Sequential unfolding of ankyrin repeats in tumor suppressor p16. Structure 11: 67-73.
30. Walker, R.G., Willingham, A.T., and Zuker, C.S. 2000. A Drosophila mechanosensory transduction channel. Science 287: 2229-2234.
31. Zeeb, M., Rosner, H., Zeslawski, W., Canet, D., Holak, T.A., and Balbach, J. 2002. Protein folding and stability of human CDK inhibitor p19(INK4d). J. Mol. Biol. 315: 447-457.
32. Zhang, B. and Peng, Z.Y. 2000. A minimum folding unit in the ankyrin repeat protein p16(INK4). J. Mol. Biol. 299: 1121-1132.
33. Zweifel, M.E. and Barrick, D. 2001a. Studies of the ankyrin repeats of the Drosophila melanogaster Notch receptor. 1. Solution conformational and hydrodynamic properties. Biochemistry 40: 14344-14356.
34. _. 2001b. Studies of the ankyrin repeats of the Drosophila melanogaster Notch receptor. 2. Solution stability and cooperativity of unfolding. Biochemistry 40: 14357-14367.
35. Zweifel, M.E., Leahy, D.J., Hughson, F.M., and Barrick, D. 2003. Structure and stability of the ankyrin domain of the Drosophila Notch receptor. Protein Sci. 12: 2622-2632.