Engineering chimaeric proteins from fold fragments: 'Hopeful monsters' in protein design

Biochemical Society Transactions

Volumn 41, Issue 5, 2013, Pages 1137-1140

  Höcker, Birte ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

( )8 barrel; Computational design; Evolution; Flavodoxin like fold; Fold fragments; Protein chimaera

Indexed keywords

CHIMERIC PROTEIN; HYBRID PROTEIN;

ARTICLE; EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN STRUCTURE; SEVERE TERATOID ABNORMALITY;

EVOLUTION, MOLECULAR; FLAVODOXIN; HUMANS; PROTEIN ENGINEERING; PROTEIN FOLDING;

EID: 84884636052     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20130099     Document Type: Article

References (24)

1. Orengo, C.A. and Thornton, J.M. (2005) Protein families and their evolution: a structural perspective. Annu. Rev. Biochem. 74, 867-900
2. Grishin, N.V. (2001) Fold change in evolution of protein structures. J. Struct. Biol. 134, 167-185
3. Söding, J. and Lupas, A.N. (2003) More than the sum of their parts: on the evolution of proteins from peptides. BioEssays 25, 837-846
4. 8-barrel enzyme fold. Chem. Rev. 105, 4038-1055
5. Lee, J. and Blaber, M. (2011) Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc. Natl. Acad. Sci. U.S.A. 108, 126-130
6. Eisenbeis, S. and Höcker, B. (2010) Evolutionary mechanism as a template for protein engineering. J. Pept. Sci. 16, 538-544
7. Ostermeier, M., Shim, J.H. and Benkovic, S.J. (1999) A combinatorial approach to hybrid enzymes independent of DNA homology. Nat. Biotechnol. 17, 1205-1209
8. Lutz, S., Ostermeier, M. and Benkovic, S.J. (2001) Rapid generation of incremental truncation libraries for protein engineering using α-phosphothioate nucleotides. Nucleic Acids Res. 29, E16
9. Otey, C.R., Landwehr, M., Endelman, J.B., Hiraga, K., Bloom, J.D. and Arnold, F.H. (2006) Structure-guided recombination creates an artificial family of cytochromes P450. PLoS Biol. 4, e112
10. Fani, R., Lio, P., Chiarelli, I. and Bazzicalupo, M. (1994) The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the HisA and HisF genes. J. Mol. Evol. 38, 489-495
11. Lang, D., Thoma, R., Henn-Sax, M., Sterner, R. and Wilmanns, M. (2000) Structural evidence for evolution of the βα barrel scaffold by gene duplication and fusion. Science 289, 1546-1550
12. 8-barrel enzyme into two folded halves. Nat. Struct. Biol. 8, 32-36
13. 4-half-barrels. Proc. Natl. Acad. Sci. U.S.A. 101, 16448-16453
14. 8-barrel protein designed from identical half barrels. J. Mol. Biol. 372, 114-129
15. 8 -barrel protein designed from identical half-barrels. Biochemistry 48, 1145-1147
16. Fortenberry, C., Bowman, E.A., Proffitt, W., Dorr, B., Combs, S., Harp, J., Mizoue, L. and Meiler, J. (2011) Exploring symmetry as an avenue to the computational design of large protein domains. J. Am. Chem. Soc. 133, 18026-18029
17. 8 -barrel fold. J. Mol. Biol. 382, 458-466
18. 8 -barrel protein scaffolds. Proc. Natl. Acad. Sci. U.S.A. 106, 3704-3709
19. Höcker, B., Schmidt, S. and Sterner, R. (2002) A common evolutionary origin of two elementary enzyme folds. FEBS Lett. 510, 133-1335
20. Bharat, T.A., Eisenbeis, S., Zeth, K. and Höcker, B. (2008) A βα-barrel built by the combination of fragments from different folds. Proc. Natl. Acad. Sci. U.S.A. 105, 9942-9947
21. Eisenbeis, S., Proffitt, W., Coles, M., Truffault, V., Shanmugaratnam, S., Meiler, J. and Höcker, B. (2012) Potential of fragment recombination for rational design of proteins. J. Am. Chem. Soc. 134, 4019-4022
22. Shanmugaratnam, S., Eisenbeis, S. and Höcker, B. (2012) A highly stable protein chimera built from fragments of different folds. Protein Eng., Des. Sel. 25, 699-703
23. Goldschmidt, R. (1940) The Material Basis of Evolution, Yale University Press, New Haven
24. Farias-Rico, J.A. and Höcker, B. (2013) Design of chimeric proteins by combination of subdomain-sized fragments. Methods Enzymol. 523, 389-405