Short peptides self-assemble to produce catalytic amyloids

Nature Chemistry

Volumn 6, Issue 4, 2014, Pages 303-309

  Rufo, Caroline M ^a   Moroz, Yurii S ^a   Moroz, Olesia V ^a   Stöhr, Jan ^b   Smith, Tyler A ^a   Hu, Xiaozhen ^c   Degrado, William F ^c   Korendovych, Ivan V ^a  

^a SYRACUSE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID; CARBONATE DEHYDRATASE; PEPTIDE; ZINC;

ARTICLE; CATALYSIS; CHEMISTRY; HUMAN; HYDROLYSIS; PROTEIN CONFORMATION; SYNTHESIS; TRANSMISSION ELECTRON MICROSCOPY;

AMYLOID; CARBONIC ANHYDRASES; CATALYSIS; HUMANS; HYDROLYSIS; MICROSCOPY, ELECTRON, TRANSMISSION; PEPTIDES; PROTEIN CONFORMATION; ZINC;

EID: 84896925534     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.1894     Document Type: Article

References (37)

1. Greenwald, J. & Riek, R. On the possible amyloid origin of protein folds. J. Mol. Biol. 421, 417-426 (2012).
2. Carny, O. & Gazit, E. A model for the role of short self-Assembled peptides in the very early stages of the origin of life. FASEB J. 19, 1051-1055 (2005).
3. DeGrado, W. F. & Lear, J. D. Induction of peptide conformation at apolar/water interfaces: A study with model peptides of defined hydrophobic periodicity. J. Am. Chem. Soc. 107, 7684-7689 (1985).
4. Eisenberg, D. & Jucker, M. The amyloid state of proteins in human diseases. Cell 148, 1188-1203 (2012).
5. Colletier, J. P. et al. Molecular basis for amyloid-beta polymorphism. Proc. Natl Acad. Sci. USA 108, 16938-16943 (2011).
6. Nowick, J. S. Exploring b-sheet structure and interactions with chemical model systems. Acc. Chem. Res. 41, 1319-1330 (2008).
7. Wachtershauser, G. Before enzymes and templates: Theory of surface metabolism. Microbiol. Rev. 52, 452-484 (1988).
8. Rode, B. M., Son, H. L., Suwannachot, Y. & Bujdak, J. The combination of salt induced peptide formation reaction and clay catalysis: A way to higher peptides under primitive earth conditions. Orig. Life Evol. Biosph. 29, 273-286 (1999).
9. Christianson, D. W. & Fierke, C. A. Carbonic anhydrase: Evolution of a zinc binding site by nature and by design. Acc. Chem. Res. 29, 331-339 (1996).
10. Iverson, T. M., Alber, B. E., Kisker, C., Ferry, J. G. & Rees, D. C. A closer look at the active site of gamma-class carbonic anhydrases: High-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39, 9222-9231 (2000).
11. West, M. W. et al. De novo amyloid proteins from designed combinatorial libraries. Proc. Natl Acad. Sci. USA 96, 11211-11216 (1999).
12. DeGrado, W. F., Wasserman, Z. R. & Lear, J. D. Protein design, a minimalist approach. Science 243, 622-628 (1989).
13. Schneider, J. P. et al. Responsive hydrogels from the intramolecular folding and self-Assembly of a designed peptide. J. Am. Chem. Soc. 124, 15030-15037 (2002).
14. Zhang, S., Marini, D. M., Hwang, W. & Santoso, S. Design of nanostructured biological materials through self-Assembly of peptides and proteins. Curr. Opin. Chem. Biol. 6, 865-871 (2002).
15. Minor, D. L. & Kim, P. S. Measurement of the b-sheet-forming propensities of amino acids. Nature 367, 660-663 (1994).
16. Smith, C. K., Withka, J. M. & Regan, L. A thermodynamic scale for the b-sheet forming tendencies of the amino acids. Biochemistry 33, 5510-5517 (1994).
17. Krattiger, P., Kovasy, R., Revell, J. D., Ivan, S. & Wennemers, H. Increased structural complexity leads to higher activity: Peptides as efficient and versatile catalysts for asymmetric aldol reactions. Org. Lett. 7, 1101-1103 (2005).
18. Tang, Z. et al. Small peptides catalyze highly enantioselective direct aldol reactions of aldehydes with hydroxyacetone: Unprecedented regiocontrol in aqueous media. Org. Lett. 6, 2285-2287 (2004).
19. Kodaka, M. Hydrolysis of p-nitrophenyl esters by histidine-containing linear and cyclic peptides. Bull. Chem. Soc. Jpn 56, 3857-3858 (1983).
20. Bolon, D. N. & Mayo, S. Enzyme-like proteins by computational design. Proc. Natl Acad. Sci. USA 98, 14272-14279 (2001).
21. Wei, Y. & Hecht, M. H. Enzyme-like proteins from an unselected library of designed amino acid sequences. Protein Eng. Des. Sel. 17, 67-75 (2004).
22. Patel, S. C., Bradley, L. H., Jinadasa, S. P. & Hecht, M. H. Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4-helix bundle proteins. Protein Sci. 18, 1388-1400 (2009).
23. Broo, K. S., Brive, L., Ahlberg, P. & Baltzer, L. Catalysis of hydrolysis and transesterification reactions of p-nitrophenyl esters by a designed helix-loop-helix dimer. J. Am. Chem. Soc. 119, 11362-11372 (1997).
24. Zastrow, M. L., Peacock, A. F. A., Stuckey, J. A. & Pecoraro, V. L. Hydrolytic catalysis and structural stabilization in a designed metalloprotein. Nature Chem. 4, 118-123 (2012).
25. Der, B. S., Edwards, D. R. & Kuhlman, B. Catalysis by a de novo zinc-mediated protein interface: Implications for natural enzyme evolution and rational enzyme engineering. Biochemistry 51, 3933-3940 (2012).
26. Verpoort, J. A., Mehta, S. & Edsall, J. T. Esterase activities of human carbonic anhydrases B and C. J. Biol. Chem. 242, 4221-4229 (1967).
27. Calero, M. & Gasset, M. Fourier transform infrared and circular dichroism spectroscopies for amyloid studies. Methods Mol. Biol. 299, 129-151 (2005).
28. Yamaguchi, K., Kamatari, Y. O., Fukuoka, M., Miyaji, R. & Kuwata, K. Nearly reversible conformational change of amyloid fibrils as revealed by pH-jump experiments. Biochemistry 52, 6797-6806 (2013).
29. Yamaguchi, K., Matsumoto, T. & Kuwata, K. Critical region for amyloid fibril formation of mouse prion protein: Unusual amyloidogenic properties of the helix 2 peptide. Biochemistry 47, 13242-13251 (2008).
30. Coleman, J. E. & Coleman, R. V. Magnetic circular dichroism of Co(II) carbonic anhydrase. J. Biol. Chem. 247, 4718-4728 (1972).
31. Spevacek, A. R. et al. Zinc drives a tertiary fold in the prion protein with familial disease mutation sites at the interface. Structure 21, 236-246 (2013).
32. Walter, E. D., Stevens, D. J., Visconte,M. P. &Millhauser, G. L. The prion protein is a combined zinc and copper binding protein: Zn2+ alters the distribution of Cu2+ coordination modes. J. Am. Chem. Soc. 129, 15440-15441 (2007).
33. Donnelly, P. S., Xiao, Z. & Wedd, A. G. Copper and Alzheimer's disease. Curr. Opin. Chem. Biol. 11, 128-133 (2007).
34. Chassaing, S. et al. Copper and heme-mediated Ab toxicity: Redox chemistry, Ab oxidations and anti-ROS compounds. Curr. Top. Med. Chem. 12, 2573-2595 (2012).
35. Cassagnes, L-E. et al. The catalytically active copper-Amyloid-beta state: Coordination site responsible for reactive oxygen species production. Angew. Chem. Int. Ed. 52, 11110-11113 (2013).
36. Korendovych, I. V. et al. Computational design of a self-Assembling b-peptide oligomer. Org. Lett. 12, 5142-5145 (2010).
37. Kuipers, B. J. H. & Gruppen, H. Prediction of molar extinction coefficients of proteins and peptides using UV absorption of the constituent amino acids at 214 nm to enable quantitative reverse phase high-performance liquid chromatography-mass spectrometry analysis. J. Agricult. Food Chem. 55, 5445-5451 (2007).