All-cis helical polypeptides

Journal of Organic Chemistry

Volumn 72, Issue 22, 2007, Pages 8251-8258

  Poteau, Romuald ^a   Trinquier, Georges ^a  

^a UNIVERSITÉ PAUL SABATIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; EXOTHERMIC REACTIONS; HYDROGEN BONDS; PLASTICITY; PROTEINS; QUANTUM CHEMISTRY; THERMODYNAMIC STABILITY;

ALANINE TRIDECAMERS; HELICAL POLYPEPTIDES; INTRAMOLECULAR HYDROGEN BONDS; PEPTIDE BONDS;

POLYPEPTIDES;

ALANINE; POLYPEPTIDE;

ARTICLE; CALCULATION; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; HYDROGEN BOND; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN STABILITY; PROTEIN STRUCTURE; QUANTUM CHEMISTRY; STRUCTURE ANALYSIS; THERMODYNAMICS;

COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; STEREOISOMERISM;

EID: 35548957867     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo0711790     Document Type: Article

References (78)

1. Giraldo, O.; Brock, S. L.; Marquez, M.; Suib, S. L.; Hillhouse, H.; Tsapatsis, M. Nature 2000, 405, 38.
2. Piguet, C.; Borkovec, M.; Hamacek, J.; Zeckert, K. Coord. Chem. Rev. 2005, 249, 705.
3. Bai, J.; Wang, J.; Zeng, X. C. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 19664.
4. Weaver, T. M. Protein Sci. 2000, 9, 201.
5. (a) Stapley, B. J.; Creamer, T. P. Protein Sci. 1999, 8, 587.
6. (b) Rucker, A. L.; Creamer, T. P. Protein Sci. 2002, 11, 980.
7. (c) Pappu, R. V.; Rose, G. D. Protein Sci. 2002, 11, 2437.
8. (d) Ma, K.; Wang, K. Biochem. J. 2003, 374, 687.
9. (e) Ferreon, J. C.; Hilser, V. J. Protein Sci. 2003, 12, 447.
10. (f) Whittington, S. J.; Creamer, T. P. Biochemistry 2003, 42, 14690.
11. (g) Chellgren, B. W.; Creamer, T. P. J. Am. Chem. Soc. 2004, 126, 14734.
12. (h) Chen, K.; Liu, Z.; Kallenbach, N. R. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15352.
13. (i) Hamburger, J. B.; Ferreon, J. C.; Whitten, S. T.; Hilser, V. J. Biochemistry 2004, 43, 9790.
14. (j) Bochicchio, B.; Aït-Ali, A.; Tamburro, A. M.; Alix, A. J. P. Biopolymers 2004, 73, 484.
15. (k) Mezei, M.; Fleming, P. J.; Srinivasan, R.; Rose, G. D. Proteins: Struct., Funct., Bioinf. 2004, 55, 502.
16. (l) Vila, J. A.; Baldoni, H. A.; Ripoll, D. R.; Ghosh, A.; Scheraga, H. A. Biophys. J. 2004, 86, 731.
17. (m) Fleming, P. J.; Fitzkee, N. C.; Mezei, M.; Srinivasan, R.; Rose, G. D. Protein Sci. 2005, 14, 111.
18. (n) Zagrovic, B.; Lipfert, J.; Sorin, E. J.; Millett, I. S.; van Gunsteren, W. F.; Doniach, S.; Pande, V. S. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 11698.
19. (o) Cubellis, M. V.; Caillez, F.; Blundell, T. L.; Lovell, S. C. Proteins: Struct., Funct., Bioinf. 2005, 58, 880.
20. (p) Whittington, S. J.; Chellgren, B. W.; Hermann, V. M.; Creamer, T. P. Biochemistry 2005, 44, 6269.
21. Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem. Rev. 2001, 101, 3893.
22. (a) Seebach, D.; Matthews, J. L. J. Chem. Soc., Chem. Commun. 1997, 2015.
23. (b) Hanessian, S.; Luo, X.; Schaum, R.; Michnick, S. J. Am. Chem. Soc. 1998, 120, 8569.
24. (c) Andrews, M. J. I.; Tabor, A. B. Tetrahedron 1999, 55, 11711.
25. (d) Baldauf, C.; Günther, R.; Hofmann, H.-J. J. Org. Chem. 2006, 71, 1200.
26. (a) Semetey, V.; Hemmerlin, C.; Didierjean, C.; Schaffner, A. P.; Gimenez-Giner, A.; Aubry, A.; Briand, J. P.; Marraud, M.; Guichard, G. Org. Lett. 2001, 3, 3843.
27. (b) Semetey, V.; Rognan, D.; Hemmerlin, C.; Graff, R.; Briand, J. P.; Marraud, M.; Guichard, G. Angew. Chem. 2002, 115, 1973;
28. Angew. Chem., Int. Ed. 2002, 41, 1893.
29. (c) Semetey, V.; Didierjean, C.; Briand, J. P.; Aubry, A.; Guichard, G. Angew. Chem. 2002, 115, 1975;
30. Angew. Chem., Int. Ed. 2002, 41, 1895.
31. (d) Hemmerlin, C.; Marraud, M.; Rognan, D.; Graff, R.; Semetey, V.; Briand, J. P.; Guichard, G. Helv. Chim. Acta 2002, 85, 3692.
32. (e) Violette, A.; Averlant-Petit, M. C.; Semetey, V.; Hemmerlin, C.; Casimir, R.; Graff, R.; Marraud, M.; Briand, J. P.; Rognan, D.; Guichard, G. J. Am. Chem. Soc. 2005, 127, 2156.
33. (f) Violette, A.; Fournel, S.; Lamour, K.; Chaloin, O.; Frisch, B.; Briand, J.-P.; Monteil, H.; Guichard, G. Chem. Biol. 2006, 13, 531.
34. (g) Oakley, M. T.; Guichard, G.; Hirst, J. D. J. Phys. Chem. B 2007, 111, 3274.
35. (a) Moehle, K.; Hofmann, H.-J. Biopolymers 1996, 38, 781.
36. (b) Armand, P.; Kirshenbaum, K.; Falicov, A.; Dunbrack, R. L., Jr.; Dill, K. A.; Zuckermann, R. N.; Cohen, F. E. Folding Des. 1997, 2, 369.
37. (c) Möhle, K.; Hofmann, H.-J. J. Pept. Res. 1998, 51, 19.
38. (d) Wu, C. W.; Sanborn, T. J.; Zuckermann, R. N.; Barron, A. E. J. Am. Chem. Soc. 2001, 123, 2958.
39. (e) Wu, C. W.; Sanborn, T. J.; Huang, K.; Zuckermann, R. N.; Barron, A. E. J. Am. Chem. Soc. 2001, 123, 6778.
40. (f) Sanborn, T. J.; Wu, C. W.; Zuckermann, R. N.; Barron, A. E. Biopolymers 2002, 63, 12.
41. (g) Burkoth, T. S.; Beausoleil, E.; Kaur, S.; Tang, D.; Cohen, F. E.; Zuckermann, R. N. Chem. Biol. 2002, 9, 647.
42. (h) Wu, C. W.; Kirshenbaum, K.; Sanborn, T. J.; Patch, J. A.; Huang, K.; Dill, K. A.; Zuckermann, R. N.; Barron, A. E. J. Am. Chem. Soc. 2003, 125, 13525.
43. (i) Lee, B. C.; Zuckermann, R. N.; Dill, K. A. J. Am. Chem.Soc. 2005, 127, 10999.
44. (j) Baldauf, C.; Günther, R.; Hofmann, H.-J. Phys. Biol. 2006, 3, S1.
45. Poteau, R.; Trinquier, G. J. Am. Chem. Soc. 2005, 127, 13875.
46. A comprehensive bibliography on non-proline cis peptide bonds in proteins and peptides is given in ref 10; see also: Bairaktari, E.; Mierke, D. F.; Mammi, S.; Peggion, E. J. Am. Chem. Soc. 1990, 112, 5383.
47. Scherer, G.; Kramer, M. L.; Schutkowski, M.; Reimer, U.; Fischer, G. J. Am. Chem. Soc. 1998, 120, 5568.
48. Forbes, C. C.; Beatty, A. M.; Smith, B. D. Org. Lett. 2001, 3, 3595.
49. Pauling, L.; Corey, R. B. Proc. Natl. Acad. Sci. U.S.A. 1952, 38, 86.
50. (a) Gong, B. Chem. Eur. J. 2001, 7, 4337.
51. (b) Haldar, D.; Jiang, H.; Léger, J.-M.; Huc, I. Tetrahedron 2007, 63, 6322.
52. (c) Hu, Z.-Q.; Hu, H.-Y.; Chen, C.-F. J. Org. Chem. 2006, 71, 1131.
53. (d) Appella, D. H.; Christianson, L. A.; Karle, I. L.; Powell, D. R.; Gellman, S. H. J. Am. Chem. Soc. 1999, 121, 6206.
54. (e) Delsuc, N.; Léger, J.-M.; Massip, S.; Huc, I. Angew. Chem., Int. Ed. 2007, 46, 214.
55. (f) Katayama, H.; de Greef, T. F. A.; Kooijman, H.; Spek, A. L.; Vekemans, J. A.; Meijer, E. W. Tetrahedron 2007, 63, 6642.
56. (g) Ohkita, M.; Lehn, J.-M.; Baum, G.; Fenske, D. Chem. Eur. J. 1999, 5, 3471.
57. (a) Krimm, S.; Venkatachalam, C. M. Proc. Natl. Acad. Sci. U.S.A. 1971, 68, 2468.
58. (b) Beausoleil, E.; Lubell, W. D. Biopolymers 2000, 53, 249.
59. (c) Sandvoss, L. M.; Carlson, H. A. J. Am. Chem. Soc. 2003, 125, 15855.
60. (d) Counterman, A. E.; Clemmer, D. E. J. Phys. Chem. B 2004, 108, 4885.
61. (e) Kakinoki, S.; Hirano, Y.; Oka, M. Polym. Bull. 2005, 53, 109.
62. (f) Kang, Y. K.; Park, H. S. Biophys. Chem. 2005, 113, 93.
63. (g) Horng, J. C.; Raines, R. T. Protein Sci. 2006, 15, 74.
64. (h) Zhong, H.; Carlson, H. A. J. Chem. Theory Comput. 2006, 2, 342.
65. Ho, B. K.; Thomas, A.; Brasseur, R. Protein Sci. 2003, 12, 2508.
66. Baldoni, H. A.; Zamarbide, G. N.; Enriz, R. D.; Jauregui, E. A.; Farkas, Ö.; Perczel, A.; Salpietro, S. J.; Csizmadia, I. G. J. Mol. Struct. (THEOCHEM) 2000, 500, 97.
67. For this preliminary exploration, the RHF/3-21G level is used, the reliability of which in such a context has been otherwise established (see: Perczel, A.; Farkas, Ö.; Jakli, I.; Topol, I.A.; Csizmadia, I. G. J. Comput. Chem. 2003, 24, 1026).
68. We use here a convenient labeling proposed for trans-peptide maps (see ref 17 and: Perczel, A.; Csizmadia, I. G. In The amide linkage; Greenberg A., Breneman, C. M., Liebman, J. F., Eds.; Wiley-Interscience: New York, 2003; Chapter 13).
69. R).
70. The main features of the Ramachandran map for the cis-dipeptide model formylglycinamide have been discussed in ref 16. In that model, both the lateral and the two end methyl groups are lacking, which account for some differences with the present model.
71. Mathieu, S.; Poteau, R.; Trinquier, G. Manuscript in preparation.
72. c, NH points onwards and CO points backwards, even if these bonds are here less parallel to the mean helical axis than in a the trans α-helix.
73. At the B3LYP/6-311G** level of calculation, a 25°-deviation of ω with respect to its ideal value (ω = 0°) in cis-NMA costs only +0.3 kcal/mol, while the same deviation from ideal value (ω = 180°) in trans-NMA costs +1.4 kcal/mol.
74. c mixed form. For further discussion on these themes, see: MacArthur, M. W.; Thornton, J. M. J. Mol. Biol. 1996, 264, 1180.
75. If peptidyl-prolyl cis/trans isomerases are well documented (for a review, see: Fischer, G.; Aumüller, T. Rev. Physiol. Biochem. Pharmacol. 2003, 148, 105), few occurrences are reported for the non-prolyl secondary-amide cases;
76. see for instance: Schiene-Fischer, C.; Habazettl, J.; Schmid, F. X.; Fischer, G. Nat. Struct. Biol. 2002, 9, 419.
77. Frisch, M. J.; et al. Gaussian 03, revision B.05; Gaussian, Inc.: Wallingford, CT, 2004.
78. Lynch, B. J.; Fast, P. L.; Harris, M.; Truhlar, D. G. J. Phys. Chem. A 2000, 104, 48.