RNA grooves can accommodate disulfide-bridged bundles of α-helical peptides

ChemBioChem

Volumn 11, Issue 6, 2010, Pages 767-770

  Hyun, Soonsil ^a   Na, Jiyoung ^a   Lee, Su Jin ^a   Park, Sangeun ^a   Yu, Jaehoon ^a  

^a Seoul National University   (South Korea)

Author keywords

Disulfide bonds; Peptide bundles; Peptides protein design; RNA

Indexed keywords

AMPHOPHILE; DISULFIDE; LEUCINE; LYSINE; PEPTIDE; RNA;

ALPHA HELIX; ANISOTROPY; ARTICLE; BINDING AFFINITY; CIRCULAR DICHROISM; COVALENT BOND; DIMERIZATION; DISULFIDE BOND; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CIRCULAR DICHROISM; CYSTEINE; DIMERIZATION; DISULFIDES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; RNA;

EID: 77950661674     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.201000072     Document Type: Article

References (36)

1. T. Hermann, Curr. Opin. Struct. Biol. 2005, 15, 355-366.
2. T. C. Chang, J. T. Mendell, Annu. Rev. Genomics Hum. Genet. 2007, 8, 215-239.
3. J. L. Battiste, H. Mao, N. S. Rao, R. Tan, D. R. Muhandiram, L. E. Kay, A. D. Frankel, J. R. Williamson, Science 1996, 273, 1547-1551.
4. a) Y. Tor, ChemBioChem 2003, 4, 998 -1007;
5. b) S. Renner, V. Ludwig, O. Boden, U. Scheffer, M. Gabel, G. Schneider, ChemBioChem 2005, 6, 1119- 1125;
6. c) E. S. DeJong, C. E. Chang, M. K. Gilson, J. P. Marino, Biochemistry 2003, 42, 8035-8046.
7. a) J. R. Thomas, P. J. Hergenother, Chem. Rev. 2008, 108, 1171 -1224;
8. b) L. P. Kotra, J. Haddad, S. Mobashery, Antimicrob. Agents Chemother. 2000, 44, 3249-3256.
9. C. Das, A. D. Frankel, Biopolymers 2003, 70, 80-85.
10. a) S. Hyun, H. J. Kim, N. J. Lee, K. H. Lee, Y. Lee, D. R. Ahn, K. Kim, S. Jeong, J. Yu, J. Am. Chem. Soc. 2007, 129, 4514- 4515;
11. b) Y. Lee, S. Hyun, H. J. Kim, J. Yu, Angew. Chem. 2008, 120, 140 -143;
12. Angew. Chem. Int. Ed. 2008, 47, 134- 137;
13. c) S. J. Lee, S. Hyun, J. S. Kieft, J. Yu, J. Am. Chem. Soc. 2009, 131, 2224-2230.
14. N. L. Mills, M. D. Daugherty, A. D. Frankel, R. K. Guy, J. Am. Chem. Soc. 2006, 128, 3496-3497.
15. S. K. Sia, P. A. Carr, A. G. Cochran, V. N. Malashkevich, P. S. Kim, Proc. Natl. Acad. Sci. USA 2002, 99, 14664-14669.
16. a) D. R. Eyre, Science 1980, 207, 1315 - 1322;
17. b) P. Barthe, S. Rochette, C. Vita, C. Roumestand, Protein Sci. 2000, 9, 942-955.
18. C. E. Schafmeister, J. Po, G. L. Verdine, J. Am. Chem. Soc. 2000, 122, 5891-5892.
19. A. Davidson, T. C. Leeper, Z. Athanassiou, K. Patora-Komisarska, J. Karn, J. A. Robinson, G. Varani, Proc. Natl. Acad. Sci. USA 2009, 106, 11931-11936.
20. J. A. Cox, M. Comte, J. E. Fitton, W. F. DeGrado, J. Biol. Chem. 1985, 260, 2527-2534.
21. See reviews; a) L. K. Henchey, A. L. Jochim, P. S. Arora, Curr. Opin. Chem. Biol. 2008, 12, 692 -697;
22. b) J. Garner, M. M. Harding, Org. Biomol. Chem. 2007, 5, 3577-3585;
23. c) J. Venkatraman, S. C. Shankaramma, P. Balaram, Chem. Rev. 2001, 101, 3131-3152.
24. a) C. E. Schafmeister, J. Po, G. L. Verdine, J. Am. Chem. Soc. 2000, 122, 5891-5892;
25. b) D. Y. Jackson, D. S. King, J. Chmielewski, S. Singh, P. G. Schultz, J. Am. Chem. Soc. 1991, 113, 9391- 9392;
26. c) J. C. Phelan, N. J. Skelton, A. C. Braisted, R. S. McDowell, J. Am. Chem. Soc. 1997, 119, 455-460.
27. Hydrocarbon-stapled peptides have been synthesized through a ringclosing metathesis with Grubbs' catalyst and subsequent hydrogenation. But, the thio-Lys derivative was used. Both cases need the unnatural amino acids; a) L. D. Walensky, A. L. Kung, I. Escher, T. J. Malia, S. Barbuto, R. D. Wright, G. Wagner, G. L. Verdine, S. J. Korsmeyer, Science 2004, 305, 1466-1470;
28. b) P. S. Kutchukian, J. S. Yang, G. L. Verdine, E. I. Shakhnovich, J. Am. Chem. Soc. 2009, 131, 4622-4627.
29. The reactions were carried out in organic solvent in order to dissolve the linker derivatives. Under these conditions, the peptide could not form the proper conformation, and thus aggregated.
30. For the initial oxidation condition, peptide was dissolved in DMSO and formed a substantial amount of a kinetically favourable kink peptide. Peptide in ammonium bicarbonate and long-time oxidation in air reduced formation of the kink peptide.
31. +: calcd 1839.2, found 1839.0. Helicity was calculated to be 12 and 13% in water and 50% TFE in buffer, respectively.
32. See the Supporting Information.
33. The half lives of dimer D and monomer D are 540 and 180 min, respectively, in reductive cytoplasmic condition. Those of dimer D and kink peptide are 170 and less than 60 min, respectively, in human serum. See the Supporting Information.
34. mix gave 300-times and 70-times weaker affinities, respectively. This observation suggests that the dimer does not interact strongly in cases in which the groove is shallow (DNA) or the structure of the RNA is too rigid (tRNA). See the Supporting Information.
35. A. V. Filikov, V. Mohan, T. A. Vickers, R. H. Griffey, P. D. Cook, R. A. Abagyan, T. L. James, J. Comput.-Aided Mol. Des. 2000, 14, 593-610.
36. N. W. Luedtke, Q. Liu, Y. Tor, Biochemistry 2003, 42, 11391-11403.