Cavitands are effective templates for inducing stability and nativelike structure in de novo four-helix bundles

Journal of the American Chemical Society

Volumn 121, Issue 39, 1999, Pages 8983-8994

  Mezo, Adam R ^a   Sherman, John C ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DEUTERIUM; GUANIDINE; HYDROGEN; SYNTHETIC PEPTIDE;

ARTICLE; CIRCULAR DICHROISM; HYDROGEN BOND; OLIGOMERIZATION; PEPTIDE SYNTHESIS; PH; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTON NUCLEAR MAGNETIC RESONANCE;

EID: 0032878568     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja990487f     Document Type: Article

References (106)

1. (a) Bryson, J. W.; Betz, S. F.; Lu, H. S.; Suich, D. J.; Zhou, H. X.; O'Neil, K. T.; DeGrado, W. F. Science 1995, 270, 935-94.
2. (b) Harbury, P. B.; Plecs, J. J.; Tidor, B.; Alber, T.; Kim, P. S. Science 1998, 282, 1462-1467.
3. (c) Struthers, M. D.; Cheng, R. P.; Imperiali, B. Science 1996, 271, 342-345.
4. (d) Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82-87.
5. (e) Kortemme, T.; Ramirez-Alvarado, M.; Serrano, L. Science 1998, 281, 253-256.
6. (a) Eisenberg, D.; Wilcox, W.; Eshita, S. M.; Pryciak, P. M.; Ho, S. P.; DeGrado, W. F. Proteins: Struct., Funct., Genet. 1986, 1, 16-22.
7. (b) Ho, S. P.; DeGrado, W. F. J. Am. Chem. Soc. 1987, 109, 6751-6758.
8. (c) Hill, C. P.; Anderson, D. H.; Wesson, L.; DeGrado, W. F.; Eisenberg, D. Science 1990, 249, 543-546.
9. (d) Osterhout, J. J.; Handel, T.; Na, G.; Toumadje, A.; Long, R. C.; Connolly, P. J.; Hoch, J. C.; Johnson, W. C., Jr.; Live, D.; DeGrado, W. F. J. Am. Chem. Soc. 1992, 114, 331-337.
10. (e) Betz, S.; Fairman, R.; O'Neil, K.; Lear, J.; DeGrado. W. Philos. Trans. R. Soc. London B 1995, 348, 81-88.
11. (f) Regan, L.; DeGrado, W. F. Science 1988, 241, 976-978.
12. (g) Handel, T. M.; Williams, S. A.; Menyhard, D.; DeGrado, W. F. J. Am. Chem. Soc. 1993, 115, 4457-4460.
13. (h) Handel, T. M.; Williams, S. A.; DeGrado, W. F. Science 1993, 261, 879-885.
14. (a) Kamtekar, S.; Schiffer, J. M.; Xiong, H.; Babik, J. M.; Hecht, M. H. Science 1993, 262, 1680-1685.
15. (b) Hecht, M. H.; Richardson, J. S.; Richardson, D. C.; Ogden, R. C. Science 1990, 249, 884-891.
16. (c) Fezoui, Y.; Connolly, P. J.; Osterhout, J. J. Protein Sci. 1997, 6, 1869-1877.
17. (d) Chmielewski, J.; Lipton, M. Int. J. Pept. Protein Res. 1994, 44, 152-157.
18. (e) Ciesla, D. J.; Gilbert, D. E.; Feignon, J. J. Am. Chem. Soc. 1991, 113, 3957-3961.
19. (f) Olofsson, S.; Johansson, G.; Baltzer, L. J. Chem. Soc., Perkin Trans. 2 1995, 2047-2056.
20. (g) Kaumaya, P. T. P.; Berndt, K. D.; Heidorn, D. B.; Trewhella, J.; Kezdy, F. J.; Goldberg, E. Biochemistry 1990, 29, 13-23.
21. (a) Betz, S. F.; Raleigh, D. P.; DeGrado, W. F. Curr. Opin. Struct. Biol. 1993, 3, 601-610.
22. (b) Betz, S. F.; Bryson, J. W.; DeGrado, W. F. Curr. Opin. Struct. Biol. 1995, 5, 457-463.
23. (a) Raleigh, D. P.; Betz, S. F.; DeGrado, W. F. J. Am. Chem. Soc. 1995, 117, 7558-7559.
24. (b) Betz, S. F.; Liebman, P. A.; DeGrado, W. F. Biochemistry 1997, 36, 2450-2458.
25. (c) Hill, R. B., DeGrado, W. F. J. Am. Chem. Soc. 1998, 120, 1138-1145.
26. (d) Jiang, X.; Bishop, E. J.; Farid, R. S. J. Am. Chem. Soc. 1997, 119, 838-839.
27. (e) Roy, S.; Ratnaswamy, G.; Boice, J. A.; Fairman, R.; McLendon, G.; Hecht, M. H. J. Am. Chem. Soc. 1997, 119, 5302-5306.
28. (f) Brive, L.; Dolphin, G. T.; Baltzer, L. J. Am. Chem. Soc. 1997, 119, 8598-8607.
29. (g) Gibney, B. R.; Rabanal, F.; Skalicky, J. J.; Wand, A. J.; Dutton, P. L. J. Am. Chem. Soc. 1997, 119, 2323-2324.
30. (a) Broo, K. S.; Nilsson, H.; Nilsson, J.; Baltzer, L. J. Am. Chem. Soc. 1998, 120, 10287-10295.
31. (b) Broo, K. S.; Nilsson, H.; Nilsson, J.; Flodberg, A.; Baltzer, L. J. Am. Chem. Soc. 1998, 120, 4063-4068.
32. (c) Broo, K. S.; Brive, L.; Ahlberg, P.; Baltzer, L. J. Am. Chem. Soc. 1997, 119, 11362-11372.
33. (a) Robertson, D. E.; Farid, R. S.; Moser, C. C.; Urbauer, J. L.; Mulholland, S. E.; Pidikiti, R.; Lear, J. D.; Wand, A. J.; DeGrado, W. F.; Dutton, P. L. Nature 1994, 368, 425-432.
34. (b) Sharp, R. E.; Diers, J. R.; Bocian, D. F.; Dutton, P. L. J. Am. Chem. Soc. 1998, 120, 7103-7104.
35. (c) Shifman, J. M.; Moser, C. C.; Kalsbeck, W. A.; Bocian, D. F.; Dutton, P. L. Biochemistry 1998, 37, 16815-16827.
36. (d) Gibney, B. R.; Rabanal, F.; Reddy, K. S.; Dutton, P. L. Biochemistry 1998, 37, 4635-4643.
37. (e) Rau, H. K.; Haehnel, W. J. Am. Chem. Soc. 1998, 120, 468-476.
38. (a) Mutter, M.; Altmann, E.; Altmann, K.-H.; Hersperger, R.; Koziej, P.; Nebel, K.; Tuchscherer, G.; Vuilleumier, S. Helv. Chim. Acta 1988, 71, 835-847; Mutter, M.;
39. (b) Mutter, M.; Vuilleumier, S. Angew. Chem., Int. Ed. Engl. 1989, 28, 535-554.
40. (a) Schneider, J. P.; Kelly, J. W. Chem. Rev. 1995, 95, 2169-2187.
41. (b) Tuchscherer, G.; Mutter, M. J. Biotechnol. 1995, 41, 197-210.
42. (a) Mutter, M.; Tuchscherer, G. G.; Miller C.; Altmann, K.-H.; Carey, R. I.; Wyss, D. F.; Labhardt, A. M.; Rivier, J. E. J. Am. Chem. Soc. 1992, 114, 1463-1470.
43. (b) Tuchscherer, G.; Dömer, B.; Sila, U.; Kamber, B.; Mutter, M. Tetrahedron 1993, 49, 3559-3575.
44. (a) Sasaki, T.; Kaiser, E. J. Am. Chem. Soc. 1989, 111, 380-381.
45. (b) Sasaki, T.; Kaiser, E. T. Biopolymers 1990, 29, 79-88.
46. (c) Akerfeldt, K. S.; Kim, R. M.; Camac, D.; Groves, J. T.; Lear, J. D.; DeGrado, W. F. J. Am. Chem. Soc. 1992, 114, 9656-9657.
47. (d) Arai, T.; Kobata, K.; Mihara, H.; Fujimoto, T.; Nishino, N. Bull. Chem. Soc. Jpn. 1995, 68, 1989-1998.
48. (e) Mihara, H.; Nishino, N.; Hasegawa, R.; Fujimoto, T. Chem. Lett. 1992, 1805-1808.
49. (a) Ghadiri, M. R.; Case, M. A. Angew. Chem., Int. Ed. Engl. 1993, 32, 1594-1597.
50. (b) Ghadiri, M. R.; Soares, C.; Choi, C.; J. Am. Chem. Soc. 1992, 114, 825-831.
51. (c) Ghadiri, M. R.; Soares, C.; Choi, C. J. Am. Chem. Soc. 1992, 114, 4000-4002.
52. (d) Lieberman, M.; Sasaki, T. J. Am. Chem. Soc. 1991, 113, 1470-1471.
53. Wong, A. K.; Jacobsen, M. P.; Winzor, D. J.; Fairlie, D. P. J. Am. Chem. Soc. 1998, 120, 3836-3841.
54. (a) Gibb, B. C.; Mezo, A. R.; Sherman, J. C. Tetrahedron Lett. 1995, 36, 7587-7590.
55. (b) Causton, A. S.; Sherman, J. C. Bioorg. Med. Chem. 1999, 7, 23-27.
56. Cavitands are defined as rigid organic macrocycles with an enforced cavity. See: Cram, D. J.; Cram, J. M. Container Molecules and Their Guests, Monographs in Supramolecular Chemistry; Stoddart, J. F., Ed.; Royal Society of Chemistry:Cambridge, 1994; Vol. 4.
57. Gibb, B. C.; Mezo, A. R.; Causton, A. S.; Fraser, J. R.; Tsai, F. C. S.; Sherman, J. C. Tetrahedron 1995, 51, 8719-8732.
58. Aurora, R.; Rose, G. D. Protein Sci. 1998, 7, 21-38.
59. One particularly exciting aspect of using cavitands as templates is their enforced cavity which has been shown to bind neutral guest molecules. See: (a) Tucker, J. A.; Knobler, C. B.; Trueblood, K. N.; Cram, D. J. J. Am. Chem. Soc. 1989, 111, 3688-3699.
60. (b) Rudkevich, D. M.; Hilmersson, G.; Rebek, J. J. Am. Chem. Soc. 1997, 119, 9911-9912. In the future, this enforced cavity may prove useful in the design of caviteins with catalytic properties.
61. The crystal structure of a tetrabromo analogue of tetrathiol 1 shows that the distance between adjacent bromines is 6.8 Å and that of opposing bromines is 9.6 Å. See: Cram, D. J.; Karbach, S.; Kim, H.-E.; Knobler, C. B.; Maverick, E. F.; Ericson, J. L.; Helgeson, R. C. J. Am. Chem. Soc. 1988, 110, 2229-2237.
62. Reddy, B. V. B.; Blundell, T. L. J. Mol. Biol. 1993, 233, 464-479.
63. Mezo, A. R.; Sherman, J. C. J. Org. Chem. 1998, 63, 6824-6829.
64. Cram, D. J.; Karbach, S.; Kim, Y. H.; Baczynskyj, L.; Marti, K.; Sampson, R. M.; Kalleymeyn, G. W. J. Am. Chem. Soc. 1988, 110, 2554-2560.
65. Sorrell, T. N.; Pigge, F. C. J. Org. Chem. 1993, 58, 784-785.
66. Chen, Y.; Yang, J.; Chau, K. Biochemistry 1974, 13, 3350.
67. Nelson, J. W.; Kallenbach, N. R. Proteins 1986, 1, 211-217.
68. See Supporting Information.
69. Kohn, W. D.; Kay, C. M.; Hodges, R. S. Protein Sci. 1995, 4, 237-250.
70. Woody, R. W. Biopolymers 1978, 17, 1451-1467.
71. Chakrabartty, A.; Kortemme, T.; Padmanabhan, S.; Baldwin, R. L. Biochemistry 1993, 32, 5560-5565.
72. Oligomerization of single peptides (similar to that of 8) into helical bundles has been studied extensively by others (refs 2a-e, 3c-e) and thus is not emphasized here. Nevertheless, some elements of the structure and stability of 8 (e.g., GuHCl melts) are reported for comparative purposes.
73. Analytical Ultracentrifugation in Biochemistry and Polymer Science; Harding, S. E., Rowe, A. J., Horton, J. C., Eds.; Royal Society of Chemisty: Oxford, 1992.
74. We also conducted gel filtration experiments using a Waters Protein Pak 125 column in an attempt to assess the oligomeric state of each cavitein. Unfortunately, we deemed these experiments unreliable as some of the caviteins appeared to interact with the stationary phase.
75. Due to the errors associated with this experiment, calculation of the association constant for dimerization is not reported.
76. The largest error arises in estimating v, the partial specific volume of each cavitein, as the large cavitand component of each cavitein is not considered in estimating v. In addition, small errors in v can manifest themselves into large errors in the estimated molecular weight. We therefore conducted a sedimentation equilibrium experiment on N1GG/Ar/Me in the presence of 7.2 M guanidine hydrochloride (GuHCl). At this concentration of denaturant, N1GG/Ar/Me is fully unfolded and therefore is expected to be monomeric in solution. We find that the estimated molecular weight for this experiment is near 11 kDa, suggesting that this may be considered a "baseline" value for this monomeric cavitein. Of course, the presence of a small amount of higher-order aggregates (<10%) may go undetected when analyzed by single-species analysis despite giving rise to the best fit. See: Condino, J. Determination of Molecular Weights by Sedimentation Equilibrium. In Technical Information DS820; Beckman Coulter Inc.:Palo Alto, California,1992.
77. Pace, C. N. Methods Enzymol. 1986, 131, 266-280.
78. Santoro, M. M.; Bolen, D. W. Biochemistry 1988, 27, 8063-8068.
79. Myers, J. K.; Pace, C. N.; Scholtz, J. M. Protein Sci. 1995, 4, 2138-2148.
80. It has been found that the salt GuHCl is able to screen electrostatic interactions at low [GuHCl], while urea, in general, does not: Monera, O. D.; Kay, C. M.; Hodges, R. S. Protein Sci. 1994, 3, 1984-1991; Zou, Q.; Habermann-Rottinghaus, S. M.; Murphy, K. P. Proteins 1998, 31, 107- 115.
81. It has been found that the salt GuHCl is able to screen electrostatic interactions at low [GuHCl], while urea, in general, does not: Monera, O. D.; Kay, C. M.; Hodges, R. S. Protein Sci. 1994, 3, 1984-1991; Zou, Q.; Habermann-Rottinghaus, S. M.; Murphy, K. P. Proteins 1998, 31, 107-115.
82. Possible aggregation via the hydrophobic cavitand foot is unlikely since several monomeric caviteins possessing methyl feet are reported here (see Discussion).
83. Ptitsyn, O. B. Adv. Protein. Chem. 1995, 47, 83-229.
84. Kuwajima, K. Proteins 1989, 6, 87-103.
85. Semisotnov, G.; Rodionova, N. A.; Razjulyaev, O. I.; Uversky, V. N. Biopolymers 1991, 31, 119-128.
86. (a) Cavanagh, J.; Fairbrother, W. J.; Palmer, A. G., III; Skelton, N. J. Protein NMR Spectroscopy: Principles and Practice; Academic Press: San Diego, 1996.
87. (b) Roy, S.; Helmer, K. J.; Hecht, M. H. Folding Des. 1997, 2, 89-92.
88. In the NMR spectrum of N1G/Ar/Me, the cavitand peak near 6.0 ppm is split into two peaks, which suggests asymmetry in the cavitand template, likely a result of the observed dimerization.
89. The effect of dimerization of N1/Bzl/Me cannot be ruled out completely as a possible cause of the broadening; however, the NMR spectra of both N1/Ar/Me (monomer-dimer mixture) and N1G/Ar/Me (dimer) possess significantly sharper and more disperse peaks.
90. (a) Englander, S. W.; Downer, N. W.; Teitelbaum, H. Annu. Rev. Biochem. 1972, 41, 903-924.
91. (b) Englander, S. W.; Kallenbach, N. Q. Rev. Biophys. 1984, 16, 521-655.
92. (c) Raschke, T. M.; Marqusee, S. Curr. Opin. Biotechnol. 1998, 9, 80-86.
93. (a) Hughson, F. M.; Wright, P. E.; Baldwin, R. L. Science 1990, 249, 1544-1548.
94. (b) Jeng, M.-F.; Englander, S. W.; Elove, G. A.; Wand, A. J.; Roder, H. Biochemistry 1990, 29, 10433-10437.
95. (c) Chamberlain, A. K.; Marqusee, S. Biochemistry 1998, 37, 1736-1742.
96. pH was corrected for isotope effects by using the equation: pD = pH (apparent) +0.4. See: Glasoe, P. K.; Long, F. A. J. Phys. Chem. 1960, 64, 188-190.
97. Assignments of individual amide protons was not performed, and therefore the listed protection factors are not sequence-corrected as described in: Bai, Y.; Milne, J. S.; Mayne, L.; Englander, S. W. Proteins 1993, 17, 75-86. Instead, a context-independent equation was used as described in ref 46a.
98. Note that in natural proteins molten globules are often meta-stable intermediates on the path toward native proteins. In de novo proteins, molten globules are often the most stable state, as nativelike structures are rarely present at all on the folding-energy landscape.
99. MM2 calculations were performed with the computer program CS Chem3D Pro, version 3.2; CambridgeSoft Corporation: Cambridge, MA, 1995.
100. Two less plausible explanations for elimination of dimerization by incoproration of phosphates are: (1) the caviteins are self-associating via the hydrophobic methyl feet of the cavitand. This is unlikely since several monomeric caviteins presented herein possess methyl feet. (2) The helices are interacting significantly with the cavitand foot such that altering the foot can alter the overall structure and result in monomers or dimers. This cannot be ruled out entirely; however, it is unlikely that the peptides could be in such dissimilar conformations and possess the observed near-identical GuHCl denaturation curves and stabilities.
101. Rink, H. Tetrahedron Lett. 1987, 28, 3787-3788.
102. Regan, L.; Rockwell, A.; Wasserman, Z.; DeGrado, W. F. Protein Sci. 1994, 3, 2419-2427.
103. (a) Neet, K. E.; Timm, D. E. Protein Sci. 1994, 3, 2167-2174.
104. (b) Mok, Y.-K.; Gay, G. D.; Butler, P. J.; Bycroft, M. Protein Sci. 1996, 5, 310-319.
105. (c) De Francesco, R. D.; Pastore, A.; Vecchio, G.; Cortese, R. Biochemistry 1991, 30, 143-147.
106. (d) Bowie, J. U.; Sauer, R. T. Biochemistry 1989, 28, 7140-7143.