Guidelines for membrane protein engineering derived from de novo designed model peptides

Biopolymers

Volumn 47, Issue 1, 1998, Pages 41-62

  Liu, Li Ping ^a   Deber, Charles M ^a  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

De novo designed model peptides; Helix propensity; Membrane protein engineering

Indexed keywords

ALCOHOLS; BIOLOGICAL MEMBRANES; BIOSYNTHESIS; CONFORMATIONS; MOLECULAR STRUCTURE; SOLUBILITY;

BUTANOL; HYDROPHOBICITY;

PROTEINS;

AMINO ACID; BUTANOL; GLOBULAR PROTEIN; MEMBRANE PROTEIN; PEPTIDE; SOLVENT;

BIOENGINEERING; HYDROPHOBICITY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SYNTHESIS; REVIEW;

AMINO ACID SEQUENCE; BIOPOLYMERS; CIRCULAR DICHROISM; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN CONFORMATION; PROTEIN ENGINEERING; SOLVENTS;

EID: 0031926765     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(1998)47:1<41::AID-BIP6>3.0.CO;2-X     Document Type: Article

References (125)

1. Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckman, E. & Downing, K. H. (1990) J. Mol Biol. 213, 899-929.
2. Deisenhofer, J. & Michel, H. (1989) Science 245, 1463-1473.
3. Savage, H., Cyrklaff, M., Montoya, G., Kuhlbrandt, W. & Sinning, I. (1996) Structure 4, 243-252.
4. Montoya, G., Cyrklaff, M. & Sinning, I. (1995) J. Mol. Biol. 250, 1-10.
5. Cowan, S. W., Garavito, R. M., Jansonius, J. N., Jenkins, J. A., Karlsson, R., Konig, N., Pai, E. F., Pauptit, R. A., Rizkallah, P. J., Rosenbusch, J. P., Rummel, G. & Schirmer, T. (1995) Structure 3, 1041-1050.
6. Pebay-Peyroula, E., Garavito, R. M., Rosenbusch, J. P., Zulauf, M. &Timmins, P. A. ( 1995) Structure 3, 1051-1059.
7. Przybylski, M., Glocker, M. O., Nestel, U., Schnaible, V., Bluggel, M., Diederichs, K., Weckesser, J., Schad, M., Schmid, A., Weite, W. & Benz, R. (1996) Protein Sei. 5, 1477-1489.
8. Schmid, B., Kromer, M. & Schulz, G. E. (1996) FEES Lett. 381, 111-114.
9. Song, L., Hobaugh, M. R., Shustak, C., Cheley, S., Bayley, H. & Gouaux, J. E. ( 1996) Science 274, 1859-1866.
10. MacKenzie, K. R., Prestegard, J. H. & Engelman, D. M. (1997) Science 276, 131-133.
11. Popot, J.-L. & Saraste, M. (1995) Curr. Opin. Biotech. 6, 394-402.
12. Whitley, P., Nilsson, I. & von Heijne, G. (1994) Nature Struct. Biol. 1, 858-862.
13. Murphy, J. R. (1996) Curr. Opin. Struct. Biol. 6, 541-545.
14. Shao, Z. & Arnold, F. H. ( 1996) Curr. Opin. Struct. Biol. 6,513-518.
15. Buckel, P. ( 1996) Trends Pharm. Sei. 17,450-456.
16. Ulmer, K. M. (1983) Science 219, 666-671.
17. Brinkmann, U. (1996) Mol. Med. Today 2, 439446.
18. Schwanz, T. W. (1994) Curr. Opin. Biotech. 5, 434-444.
19. Girotti, M. & Banting, G. (1996) J. Cell Sei. 109, 2915-2926.
20. Husain, S. R., Gill, P., Kreitman, R. J., Pastan, I. & Puri, R. K. (1997) Mol. Med. 3, 327-338.
21. Ye, F., Melcher, U. & Fletcher, J. ( 1997) Gene 189, 95-100.
22. Brandi, C. J., Deber, R. B., Hsu, L. C., Woolley, G. A., Young, X. K. & Deber, C. M. (1988) Biopolymers27, 1171-1182.
23. Deber, C. M., Glibowicka, M. & Woolley, G. A. (1990) Biopolymers 29, 149-157.
24. Deber, C. M., Sorrell, B. J. & Xu, G. Y. (1990) Biochem. Biophys. Res. Commun. 172, 862-869.
25. Li, S. C., Goto, N. K., Williams, K. A. & Deber, C. M. (1996) Proc. Nail. Acad. Sei. USA 93, 6676-6681.
26. Li, S. C. & Deber, C. M. (1992) FEBS Lett. 311, 217-220.
27. Williams, K. A. & Deber, C. M. ( 1991 ) Biochemistry 30, 8919-8923.
28. Li, S. C. & Deber, C. M. (1994) Nature Struct. Biol. 1, 368-373.
29. Wallace, B. A. (1996) Adv. Exp. Med. Biol. 398, 607-614.
30. Sychev, S. V., Sukhanov, S. V., Barsukov, L. I. & Ivanov, V. T. (1996) J. Peptide Sei. 2, 141-156.
31. Sagnella, D. E. & Voth, G. A. (1996) Biophys. J. 70, 2043-2051.
32. You, S., Peng, S., Lien, L., Breed, J., Sansom, M. S. & Woolley, G. A. (1996) Biochemistry 35, 6225-6232.
33. Bechinger, B. (1997) J. Membrane Biol. 156,197211.
34. Biggin, P. C., Breed, J., Son, H. S. & Sansom, M. S. (1997) Biophys. J. 72, 627-636.
35. Kothekar, V., Mahajan, K., Raha, K. & Gupta, D. (1996) J. Biomol. Struct. Dynam. 14, 303-316.
36. Ben-Efraim, I. & Shai, Y. (1997) Biophys. J. 72, 85-96.
37. Shi, Y. L., Edwards, C. & Lazarovici, P. (1995) Natural Toxins 3, 151-155.
38. Shai, Y. (1994) Toxicology 87, 109-129.
39. Thennarasu, S. & Nagaraj, R. (1997) Biopolymers 41, 635-645.
40. Oblatt-Montal, M., Buhler, L. K., Iwamoto, T., Tomich, J. M. & Montai, M. (1993) J. Biol. Chem. 268, 14601-14607.
41. Oblatt-Montal, M., Reddy, G. L., Iwamoto, T., Tomich, J. M. & Montai, M. (1994) Proc. Natl. Acad. Sei. USA 91, 1495-1499.
42. Oblatt-Montal, M., Yamazaki, M., Nelson, R. & Montai, M. (1995) Protein Sei. 4, 1490-1497.
43. Arkin, I. T., Adams, P. D., Brunger, A. T., Smith, S.O. & Engelman, D. M. (1997) Ann. Rev. Biophys. Biomol. Struct. 26, 157-179.
44. Dieckmann, G. R. & DeGrado, W. F. (1997) Curr. Opin. Struct. Biol. 7, 486-494.
45. Ben-Efraim, L, Bach, D. & Shai, Y. (1993) Biochemistry 32,2371-2377.
46. Mercer, E. A., Abbott, G. W., Brazier, S. P., Ramesh, B., Haris, P. I. & Srai, S. K. (1997) Biochein. J. 325, 475-479.
47. Deber, C. M. & Li, S. C. (1995) Biopolymers 37, 295-318.
48. Liu, L. P., Li, S. C., Goto, N. K. & Deber, C. M. (1996) Biopolymers 39, 465-470.
49. Liu, L.-P. & Deber, C. M. ( 1997) Biochemistry 36, 5476-5482.
50. Reithmeier, R. A. F. (1995) Curr. Opin. Struct. Biol. 5,491-500.
51. Chou, P. Y. & Fasman, G. D. (1974) Biochemistry 13,211-222.
52. Chou, P. Y. & Fasman, G. D. (1974) Biochemistry 13, 222-245.
53. Williams, R. W., Chang, A., Juretic, D. & Loughran, S. (1987) Biochim. Biophys. Acta 916, 200204.
54. Altmann, K. H., Wojcik, J., Vasquez, M. & Scheraga, H. A. (1990) Biopolymers 30, 107-120.
55. Anderson, A. G. & Hermans, J. ( 1988) Proteins 3, 262-265.
56. Lyu, P. C., Liff, M. I., Marky, L. A. & Kallenbach, N. R. (1990) Science 250, 669-673.
57. Merutka, G., Lipton, W., Shalongo, \V., Park, S. H. & Stellwagen, E. (1990) Biochemistry 29, 7511-7515.
58. O'Neil, K. T. & DeGrado, W. F. (1990) Science 250, 646-651.
59. Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M. & Baldwin, R. L. (1990) Nature 344, 268-270.
60. Padmanabhan, S. & Baldwin, R. L. (1991) J. Mol. Biol. 219, 135-137.
61. Stellwagen, E., Park, S. H., Shalongo, W. & Jain, A. (1992) Biopolymers 32, 1193-1200.
62. Vila, J., Williams, R. L., Grant, J. A., Wojcik, J. & Scheraga, H. A. (1992) Proc. Natl. Acad. Sei. USA 89,7821-7825.
63. Blaber, M., Zhang, X.-J. & Matthews, B. W. (1993) Science 260, 1637-1640.
64. Blaber, M., Zhang, X. J., Lindstrom, J. D., Pepiot, S. D., Baase, W. A. & Matthews, B. W. (1994) J. Mol. Biol. 235, 600-624.
65. Horovitz, A., Matthews, J. M. & Fersht, A. R. ( 1992) J. Mol. Biol. 227, 560-568:
66. Creamer, T. P. & Rosé, G. D. (1992) Proc. Natl. Acad. Sei. USA 89, 5937-5941.
67. Hermans, J., Anderson, A. G. & Yun, R. H. ( 1992) Biochemistry 31, 5646-5653.
68. Engelman, D. M., Steitz, T. A. & Goldman, A. (1986) Ann. Rev. Biophys. Biophys. Chem. 15, 321-353.
69. Kyte, J. & Doolittle, R. F. (1982) J. Mol. Biol. 157, 105-132.
70. Chakrabartty, A., Kortemme, T. & Baldwin, R. L. (1994) Protein Sei. 3, 843-852.
71. Munoz, V. & Serrano, L. (1994) Proleins 20,301311.
72. Munoz, V. & Serrano, L. (1995) J. Mol. Biol. 245, 275-296.
73. Janin, J. & Wodak, S. (1978) J. Mol. Biol. 125, 357-386.
74. McGregor, M. J., Islam, S. A. & Stemberg, M. J. (1987) J. Mol. Biol. 198, 295-310.
75. Chung, L. A. ( 1997) Anal. Biochem. 248,195-201.
76. Morein, S., Trouard, T. P., Hauksson, J. B., Rilfors, L., Arvidson, G. & Lindblom, G. (1996) Eur. J. Biochem. 241, 489-497.
77. Vinogradova, O., Badola, P., Czerski, L., Sonnich-sen, F. D. & Sanders, C. R. (1997) Biophys. J. 72, 2688-2701.
78. Xu, G. Y. & Deber, C. M. (1991) Int. J. Peptide Protein Res. 37, 528-535.
79. Berlose, J. P., Convert, O., Brunissen, A., Chassaing, G. & Lavielle, S. ( 1994) Eur. J. Biochem. 225, 827-843.
80. Li, S. C., Kim, P. K. & Deber, C. M. (1995) Biopolymers 35, 667-675.
81. Maslennikov, I. V., Sobol, A. G., Anagli, J., James, P., Vorherr, T., Arseniev, A. S. & Carafoli, E. (1995) Biochem. Biophys. Res. Commun. 217, 1200-1207.
82. Blankenfeldt, W., Nokihara, K., Naruse, S., Lessei, U., Schomburg, D. & Wray, V. (1996) Biochemistry 35, 5955-5962.
83. Chuang, W. J., Abeygunawardana, C., Gittis, A. G., Pedersen, P. L. & Mildvan, A. S. (1995) Arch. Biochem. Biophys. 319, 110-122.
84. Waterhous, D. V. & Johnson, W. C., Jr. (1994) Biochemistry 33, 2121-2128.
85. Mitaku, S., Ikuta, K., Itoh, H., Kataoka, R., Naka, M., Yamada, M. & Suwa, M. (1988) Biophys. Cliem. 30, 69-79.
86. Stein, \V. D. (1986) Transport and Diffusion Across Cell Membranes, Academic Press, Orlando, FL.
87. Landolt-Marticorena, C., Williams, K. A., Deber, C. M. & Reithmeier, R. A. (1993) J. Mol. Biol. 229, 602-608.
88. Taylor, W. R., Jones, D. T. & Green, N. M. ( 1994) Proteins 18, 281-294.
89. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1994) Biochemistry 33, 3038-3049.
90. Samatey, F. A., Xu, C. & Popot, J. L. (1995) Proc. Natl. Acad. Sei. USA 92, 4577-4581.
91. Rao, J. K. M. & Argos, P. (1986) Biochim. Biophys. Acta 869, 197-214.
92. Engelman, D. M. & Steitz, T. A. (1981) Cell 23, 411-422.
93. Ohlendorf, D. H., Anderson, W. F. & Matthews, B. W. (1983) J. Mol. Evol. 19, 109-114.
94. Gary, T. M. & Matthews, B. W. (1984) J. Mol. Biol. 175, 75-81.
95. Sternberg, M. J. & Gullick, W. J. (1990) Protein Eng. 3, 245-248.
96. Sternberg, M. J. & Gullick, W. J. (1989) Nature 339, 587.
97. Gullick, W. J., Bottomley, A. C., Lofts, F. J., Doak, D. G., Mulvey, D., Newman, R., Crumpton, M. J., Stemberg, M. J. & Campbell, I. D. (1992) EMBO J. 11, 43-48.
98. Weiss, M. S. & Schulz, G. E. (1992) J. Mol. Biol. 227, 493-509.
99. Kreusch, A. & Schulz, G. E. (1994) J. Mol. Biol. 243,891-905.
100. Klebba, P. E., Hofnung, M. & Charbit, A. (1994) EMBO J. 13, 4670-4675.
101. Cowan, S. W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R. A., Jansonius, J. N. & Rosenbusch, J. P. (1992) Nature 358, 727-733.
102. Kaiser, E. T. & Kezdy, F. J. (1983) Proc. Natl Acad. Sei. USA 80, 1137-1143.
103. Papavoine, C. H., Remerowski, M. L., Horstink, L. M., Konings, R. N., Hilbers, C. W. & van de Yen, F. J. (1997) Biochemistry 36, 4015-4026.
104. Tanford, C. (1980) The Hydrophobie Effect: Formation of Micelles and Biological Membranes, John Wiley & Sons, New York.
105. Li, S. C. & Deber, C. M. (1993) J. Biol. Cliem. 268, 22975-22978.
106. Li, Z., Glibowicka, M., Joensson, C. & Deber, C. M. (1993) J. Biol. Chem. 268, 4584-4587.
107. Furtos-Matei, A., Li, J. & Waldron, K. C. (1997) J. Chromatog. B Biomed. Applicat. 695, 39-47.
108. Thorsteinsdottir, M., Beijersten, I. & Westerlund, D. (1995) Electrophorcsis 16, 564-573.
109. Patemostre, M., Viard, M., Meyer, O., Ghanam, M., Ollivon, M. & Blumenthal, R. (1997) Biophys. J. 72, 1683-1694.
110. Worman, H. J., Brasitus, T. A., Dudeja, P. K., Fozzard, H. A. & Field, M. (1986) Biochemistry 25, 1549-1555.
111. Franks, F., Mathias, S. F. & Hatley, R. H. (1990) Phil. Trans. Roy. Soc. London Ser. B Biol. Sei. 326, 517-531; discussion 531-533.
112. Waneck, G. L., Stein, M. E. & Flavell, R. A. ( 1988) Science 241, 697-699.
113. Hoyt, D. W. & Gierasch, L. M. (1991) J. Biol Chem. 266, 14406-14412.
114. Lee, E. & Manoil, C. (1994) J. Biol Chem. 269, 28822-28828.
115. Kuroiwa, T., Sakaguchi, M., Mihara, K. & Omura, T. (1991) J. Biol. Chem. 266, 9251-9255.
116. Chen, H. & Kendall, D. A. (1995) J. Biol Chem. 270, 14115-14122.
117. Nakai, K., Kidera, A. & Kanehisa, M. ( 1988) Protein Eng. 2,93-100.
118. Dill, K. A. (1990) Science 250, 297.
119. Porath, J. ( 1976) in Analysis and Control of Immobilized Enzyme Systems, Amsterdam, North Holland, pp. 71-80.
120. Parker, J. M. R., Guo, R. & Hodges, R. S. (1986) Biochemistry 25, 5425-5432.
121. Sereda, T. J., Mant, C. T., Sonnichsen, F. D. & Hodges, R. S. (1994) J. Chromatog. A 676, 139153.
122. Hofmann, K. & Stoffel, W. (1993) Biol. Chem. Hoppe-Seyler 374, 166.
123. Chakrabartty, A. & Baldwin, R. L. (1995) Adv. Protein Chem. 46, 141-176.
124. Liu, L.-P., Wang, C., Goto, N. K., Reithmeier, R. A. F. & Deber, C. M. (1998), submitted.
125. Liu, L.-P. & Deber, C. M. (1998), submitted.