Redesign of a four-helix bundle protein by phage display coupled with proteolysis and structural characterization by NMR and X-ray crystallography

Journal of Molecular Biology

Volumn 323, Issue 2, 2002, Pages 253-262

  Chu, Ruiai ^a   Takei, Jiro ^a   Knowlton, J Randolph ^b   Andrykovitch, Michelle ^b   Pei, Wuhong ^a   Kajava, Andrey V ^c   Steinbach, Peter J ^c   Ji, Xinhua ^b   Bai, Yawen ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Four helix bundle protein; NMR structure; Phage display; Proteolysis; X ray structure

Indexed keywords

ARGININE; CYTOCHROME B; HEME; PROTEIN; PROTEINASE; TRYPTOPHAN;

ARTICLE; CRYSTAL STRUCTURE; FLUORESCENCE; HYDROPHOBICITY; LIBRARY; MUTATION; NUCLEAR MAGNETIC RESONANCE; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS; SURFACE PROPERTY; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

EID: 0036405903     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00884-7     Document Type: Article

References (48)

1. DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F. & Lombardi, A. (1999). De novo design and structural characterization of proteins and metalloproteins. Annu. Rev. Biochem. 68, 779-819.
2. Woolfson, D. N. (2001). Core-directed protein design. Curr. Opin. Struct. Biol. 11, 464-471.
3. Walsh, S. T., Cheng, H., Bryson, J. W., Roder, H. & DeGrado, W. F. (1999). Solution structure and dynamics of a de novo designed three-helix bundle protein. Proc. Natl Acad. Sci. USA, 96, 5486-5491.
4. Dahiyat, B. I. & Mayo, S. L. (1997). De novo protein design: Fully automated sequence selection. Science, 278, 82-87.
5. Schafmeister, C. E., LaPorte, S. L., Miercke, L. J. & Stroud, R. M. (1997). A designed four-helix bundle protein with native-like structure. Nature Struct. Biol. 4, 1039-1046.
6. Hill, R. B. & DeGrado, W. F. (1998). Solution structure of a2D, a native-like de novo designed protein. J. Am. Chem. Soc. 120, 1138-1145.
7. Gibney, B. R., Rabanal, F., Skalicky, J. J., Wand, A. J. & Dutton, P. L. (1997). Design of a unique protein scaffold for maquettes. J. Am. Chem. Soc. 119, 2323-2324.
8. Potekhin, S. A., Melnik, T. N., Popov, V., Lanina, N. F., Vazina, A. A., Rigler, P. et al. (2001). De novo design of fibrils made of short alpha-helical coiled coil peptides. Chem. Biol. 8, 1025-1032.
9. Baltzer, L. (1998). Functionalization of designed folded polypeptides. Curr. Opin. Struct. Biol. 8, 466-470.
10. Gibney, B. R., Rabanal, F., Reddy, B. V. & Dutton, P. L. (1998). Effect of four-helix bundle topology on heme binding and redox properties. Biochemistry, 37, 4635-4643.
11. Malakauskas, S. M. & Mayo, S. L. (1998). Design, structure and stability of a hyperthermophilic protein variant. Nature Struct. Biol. 5, 470-475.
12. Betz, S. F., Raleigh, D. P., DeGrado, W. F., Lovejoy, B., Anderson, D., Ogihara, N. & Eisenberg, D. (1995). Crystallization of a designed peptide from a molten globule ensemble. Fold. Des. 1, 57-64.
13. Nautiyal, S., Woolfson, D. N., King, D. S. & Alber, T. (1995). A designed heterotrimeric coiled coil. Biochemistry, 34, 11645-11651.
14. Betz, S. F., Liebman, P. A. & DeGrado, W. F. (1997). De novo design of native proteins: Characterization of proteins intended to fold into antiparallel, ROP-like, four-helix bundles. Biochemistry, 36, 2450-2458.
15. Lumb, K. J. & Kim, P. S. (1995). A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry, 34, 8642-8648.
16. Jiang, X., Farid, H., Pistor, E. & Farid, R. S. (2000). A new approach to the design of uniquely folded thermally stable proteins. Protein Sci. 9, 403-416.
17. Finucane, M. D., Tuna, M., Lees, J. H. & Woolfson, D. N. (1999). Core-directed protein design. I. An experimental method for selecting stable proteins from combinatorial libraries. Biochemistry, 38, 11604-11612.
18. Finucane, M. D. & Woolfson, D. N. (1999). Core-directed protein design. II. Rescue of a multiply mutated and destabilized variant of ubiquitin. Biochemistry, 38, 11613-11623.
19. Scott, J. K. & Smith, G. P. (1990). Searching for peptide ligands with an epitope library. Science, 249, 386-390.
20. Kristensen, P. & Winter, G. (1998). Proteolytic selection for protein folding using filamentous bacteriophages. Fold. Des. 3, 321-328.
21. Sieber, V., Pluckthun, A. & Schmid, F. X. (1998). Selecting proteins with improved stability by a phage-based method. Nature Biotechnol. 16, 955-960.
22. Martin, M., Sieber, V. & Schmid, F. X. (2001). In vitro selection of highly stabilized protein variants with optimized surface. J. Mol. Biol. 309, 717-726.
23. Riechmann, L. & Winter, G. (2000). Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. Proc. Natl Acad. Sci. USA, 97, 10068-10073.
24. 562. Nature Struct. Biol. 1, 30-35.
25. Santoro, M. M. & Bolen, D. W. (1992). A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concentration range. Biochemistry, 31, 4901-4907.
26. 562. Biochemistry, 30, 10150-10155.
27. Jackson, S. E. (1998). How do small single-domain proteins fold? Fold. Des. 3, R81-R91.
28. Hvidt, A. & Nielsen, S. O. (1966). Hydrogen exchange in proteins. Advan. Protein Chem. 21, 287-386.
29. Bai, Y., Milne, J. S., Mayne, L. & Englander, S. W. (1993). Primary structure effects on peptide group hydrogen exchange. Proteins: Struct. Funct. Genet. 17, 75-86.
30. Chu, R. A. & Bai, Y. (2002). Lack of definable nucleation sites in the rate-limiting transition state of Barnase under native conditions. J. Mol. Biol. 315, 761-772.
31. Grzesiek, S., Ikura, M., Gronenborn, A. M., Clore, G. M. & Bax, A. (1992). An efficient experiment for sequential backbone assignment of medium sized isotopically enriched proteins. J. Magn. Reson. 96, 215-221.
32. Wittekind, M. & Mueller, L. (1993). HNCACB, a high-sensitivity 3-D NMR experiment to correlate amide proton and nitrogen resonances with the alpha and beta carbon resonances in proteins. J. Magn. Reson. Ser. B, 101, 201-205.
33. Fesik, S. W. & Zuiderweg, E. R. P. (1988). Heteronuclear three-dimensional NMR spectroscopy. A strategy for the simplification of homonuclear two-dimensional NMR spectra. J. Magn. Reson. 95, 214-220.
34. Vuister, G. W., Bax, A. & correlation:, A. (1993). Quantitative J correlation: A new approach for measuring homonuclear three-bond J(HNHa) coupling constants in 15N-enriched proteins. J. Am. Chem. Soc. 115, 7772-7777.
35. 15N with side-chain Hb resonances. J. Magn. Reson. 95, 636-641.
36. Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J. & Bax, A. (1995). NMR pipe: A multi-dimensional spectral processing system based on UNIX pipes. J. Biomol. NMR, 6, 277-293.
37. Johnson, B. A. & Blevins, R. A. (1994). NMR view: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR, 4, 603-614.
38. Brunger, A. T. (1992). X-PLOR, A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT.
39. Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
40. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W. et al. (1998). Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallog. Sect. D, 54, 905-921.
41. 562 by redetermining the primary structure and using molecular graphics. J. Mol. Biol. 148, 427-448.
42. Jones, T. A. & Kjeldgaard, M. (1997). Electron-density map interpretation. Methods Enzymol. 277, 173-208.
43. 562. Biochemistry, 38, 8657-8670.
44. 562 undergoes fast motions and slow exchange among ordered conformations resembling the folded state. Biochemistry, 41, 5505-5514.
45. Kraulis, P. J. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
46. Merritt, E. A. & Bacon, D. J. (1997). Raster3D: Photo-realistic molecular graphics. Methods Enzymol. 277, 505-524.
47. 562 examined by the dependence of hydrogen exchange on hydrostatic pressure. Biochemistry, 37, 9877-9883.
48. Chu, R., Pei, W., Takei, J. & Bai, Y. (2002). Relationship between the native-state hydrogen exchange and folding pathways of a four-helix bundle protein. Biochemistry, 41, 7998-8003.