Construction of helix-bundle membrane proteins

Advances in Protein Chemistry

Volumn 63, Issue , 2003, Pages 19-46

  Chamberlain, Aaron K ^a   Faham, Salem ^a   Yohannan, Sarah ^a   Bowie, James U ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN; DIACYLGLYCEROL KINASE; HELIX LOOP HELIX PROTEIN; MEMBRANE PROTEIN; NITROGEN; OXYGEN; RHODOPSIN;

ESCHERICHIA COLI; HYDROGEN BOND; LIPID BILAYER; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN LIPID INTERACTION; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; THERMODYNAMICS;

ESCHERICHIA COLI;

EID: 0037287812     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3233(03)63002-0     Document Type: Review

References (135)

1. Abramovitch, D. A., Marsh, D., and Powell, G. L. (1990). Biochim. Biophys. Acta 1020, 34-42.
2. Adamian, L., and Liang, J. (2001). J. Mol. Biol. 311, 891-907.
3. Adamian, L., and Liang, J. (2002). Proteins 47, 209-218.
4. Allen, S. J., Kim, J. M., Khorana, H. G., Lu, H., and Booth, P. J. (2001). J. Mol. Biol. 308, 423-435.
5. Arkin, I. T., and Brunger, A. T. (1998). Biochim. Biophys. Acta 1429, 113-128.
6. Ben-Tal, N., and Honig, B. (1996). Biophys. J. 71, 3046-3050.
7. Bibi, E., and Kaback, H. R. (1990). Proc. Natl. Acad. Sci. USA 87, 4325-4329.
8. Blazquez, M., Thiele, C., Huttner, W. B., Docherty, K., and Shennan, K. I. J. (2000). Biochem. J. 349, 843-852.
9. Bogdanov, M., and Dowhan, W. (1999). J. Biol. Chem. 274, 36827-36830.
10. Booth, P. J. (2000). Biochim. Biophys. Acta 1460, 4-14.
11. Bowie, J. U. (1997a). J. Mol. Biol. 272, 780-789.
12. Bowie, J. U. (1997b). Nat. Struct. Biol. 4, 915-917.
13. Bowie, J. U. (2001). Curr. Opin. Struct. Biol. 11, 397-402.
14. Bowie, J. U., Reidhaar-Olson, J. F., Lim, W. A., and Sauer, R. T. (1990). Science 247, 1306-1310.
15. Bowie, J. U., Lüthy, R., and Eisenberg, D. (1991). Science 253, 164-170.
16. Brosig, B., and Langosch, D. (1998). Protein Sci. 7, 1052-1056.
17. Brouillette, C., McMichens, R., Stern, L., and Khorana, H. (1989). Proteins: Struct. Func. Genet. 5, 38.
18. Brown, D. A., and London, E. (1998). Annu. Rev. Cell Dev. Biol. 14, 111-136.
19. Brueckner, K., Labrador, J. P., Scheiffele, P., Herb, A., Seeburg, P. H., and Klein, R. (1999). Neuron 22, 511-524.
20. Chakrabarti, P., and Chakrabarti, S. (1998). J. Mol. Biol. 284, 867-873.
21. Chen, G. Q., and Gouaux, E. (1999). Biochemistry 38, 15380-15387.
22. Choma, C., Gratkowski, H., Lear, J. D., and DeGrado, W. E (2000). Nat. Struct. Biol. 7, 161-166.
23. Chothia, C., Levitt, M., and Richardson, D. (1981). J. Mol. Biol. 145, 215-250.
24. Cosson, P., Lankford, S., Bonifacino, J., and Klausner, R. (1991). Nature 351, 414.
25. Cotten, J. F., and Welsh, M. J. (1999). J. Biol. Chem. 274, 5429-5435.
26. Crick, F. (1953). Acta Crystallogr. 6, 689-697.
27. Curran, A. R., Templer, R. H., and Booth, P. J. (1999). Biochemistry 38, 9328-9336.
28. Deber, C. M., Wang, C., Liu, L. P., Prior, A. S., Agrawal, S., Muskat, B. L., and Cuticchia, A. J. (2001). Protein Sci. 10, 212-219.
29. Derewenda, Z. S., Derewenda, U., and Kobos, P. M. (1994). J. Mol. Biol. 241, 83-93.
30. Derewenda, Z. S., Lee, L., and Derewenda, U. (1995). J. Mol. Biol. 252, 248-262.
31. Desiraju, G. R., and Steiner, T. (1999). The Weak Hydrogen Bond in Structural Chemistry and Biology Oxford Univ. Press, Oxford.
32. Donohue, P. J., Sainz, E., Akeson, M., Kroog, G. S., Mantey, S. A., Battey, J. F.,Jensen, R. T., and Northup, J. K. (1999). Biochemistry 38, 9366-9372.
33. Dumas, F., Sperotto, M. M., Lebrun, C., Tocanne, J. F., and Mouritsen, O. G. (1997). Biophys. J. 73, 1940-1953.
34. Eilers, M., Shekar, S. C., Shieh, T., Smith, S. O., and Fleming, P. J. (2000). Proc. Natl. Acad. Sci. USA 97, 5796-5801.
35. Eisenberg, D., and McLachlan, A. D. (1986). Nature 319, 199-203.
36. Fisher, L. E., Engelman, D. M., and Sturgis, J. N. (1999). J. Mol. Biol. 293, 639-651.
37. Fleming, K. G., and Engelman, D. M. (2001). Proc. Natl. Acad. Sci. USA 98, 14340-14344.
38. Fleming, K. G., Ackerman, A. L., and Engelman, D. M. (1997). J. Mol. Biol. 272, 266-275.
39. Fu, D., Libson, A., Miercke, L. J., Weitzman, C., Nollert, P., Krucinski, J., and Stroud, R. M. (2000). Science 290, 481-486.
40. Galisteo, M., and Sanchez-Ruiz, J. (1993). Eur. Biophys. J. 22, 25-30.
41. Gilles-Gonzalez, M. A., Engelman, D. M., and Khorana, H. G. (1991). J. Biol. Chem. 266, 8545-8550.
42. Gratkowski, H., Lear, J. D., and DeGrado, W. F. (2001). Proc. Natl. Acad. Sci. USA 98, 880-885.
43. Green, R. D. (1974). Hydrogen Bonding by C-H Groups. Wiley, New York/Toronto.
44. Groves, J. D., Wang, L., and Tanner, M. J. (1998). FEBS Lett. 433, 223-227.
45. Guzman, L., Weiss, D., and Beckwith, J. (1997). J. Bacteriol. 179, 5094-5103.
46. Hall, J. A., and Maloney, P. C. (2001). J. Biol. Chem. 276, 25107-25113.
47. Haltia, T., and Freire, E. (1995). Biochim. Biophys. Acta 1228, 1-27.
48. Haltia, T., Semo, N., Arrondo, J. L., Goni, F. M., and Freire, E. (1994). Biochemistry 33, 9731-9740.
49. Harrenga, A., and Michel, H. (1999). J. Biol. Chem. 274, 33296-33299.
50. Hooper, N. M. (2001). Proteomics 1, 748-755.
51. Hunt, J. F., Earnest, T. N., Bousche, O., Kalghatgi, K., Reilly, K., Horvath, C., Rothschild, K. J., and Engelman, D. M. (1997). Biochemistry 36, 15156-15176.
52. Huschilt, J. C., Millman, B. M., and Davis, J. H. (1989). Biochim. Biophys. Acta 979, 139-141.
53. Huttner, W. B., and Zimmerberg, J. (2001). Curr. Opin. Cell Biol. 13, 478-484.
54. Ikonen, E. (2001). Curr. Opin. Cell Biol. 13, 470-477.
55. Ikonen, E., and Simons, K. (1998). Semin. Cell Devel. Biol. 9, 503-509.
56. Isenbarger, T. A., and Krebs, M. P. (2001). Biochemistry 40, 11923-11931.
57. Jacob, J., Duclohier, H., and Cafiso, D. S. (1999). Biophys. J. 76, 1367-1376.
58. Javadpour, M. M., Eilers, M., Groesbeek, M., and Smith, S. O. (1999). Biophys. J. 77, 1609-1618.
59. Jiang, S., and Vakser, I. A. (2000). Proteins 40, 429-435.
60. Kahn, T. W., Sturtevant, J. M., and Engelman, D. M. (1992). Biochemistry 31, 8829-8839.
61. Katragadda, M., Alderfer, J. L., and Yeagle, P. L. (2000). Biochim. Biophys. Acta 1466, 1-6.
62. Kim, J. M., Booth, P. J., Allen, S. J., and Khorana, H. G. (2001). J. Mol. Biol. 308, 409-422.
63. King, S. C., Hansen, C. L., and Wilson, T. H. (1991). Biochim. Biophys. Acta 1062, 177-186.
64. Klug, C. S., and Feix, J. B. (1998). Protein Sci. 7, 1469-1476.
65. Klug, C. S., Su, W., Liu, J., Klebba, P. E., and Feix, J. B. (1995). Biochemistry 34, 14230-14236.
66. Kralchevsky, P. A. (1997). Adv. Biophys. 34, 25-39.
67. Kralchevsky, P. A., and Nagayama, K. (2000). Adv. Colloid Interface Sci. 85, 145-192.
68. Kraulis, P. J. (1991). J. Appl. Crystallogr. 24, 946-950.
69. Kurzchalia, T. V., and Parton, R. G. (1999). Curr Opin. Cell Biol. 11, 424-431.
70. Langlet, C., Bernard, A.-M., Drevot, P., and He, H.-T. (2000). Curr. Opin. Immunol. 12, 250-255.
71. Langosch, D., and Heringa, J. (1998). Proteins 31, 150-159.
72. Lau, F., and Bowie, J. (1997). Biochemistry 36, 5884-5892.
73. Lehtonen, J. Y. A., Holopainen, J. M., and Kinnunen, P. K. J. (1996). Biophys. J. 70, 1753-1760.
74. Lemmon, M. A., Flanagan, J. M., Hunt, J. F., Adair, B. D., Bormann, B. J., Dempsey, C. E., and Engelman, D. M. (1992a). J. Biol. Chem. 267, 7683-7689.
75. Lemmon, M. A., Flanagan, J. M., Treutlein, H. R., Zhang, J., and Engelman, D. M. (1992b). Biochemistry 31, 12719-12725.
76. Liu, L. P., Li, S. C., Goto, N. K., and Deber, C. M. (1996). Biopolymers 39, 465-470.
77. Luecke, H., Schobert, B., Richter, H. T., Cartailler, J. P., and Lanyi, J. K. (1999). J. Mol. Biol. 291, 899-911.
78. Luneberg, J., Widmann, M., Dathe, M., and Marti, T. (1998). J. Biol. Chem. 273, 28822-28830.
79. MacKenzie, K. R., Prestegard, J. H., and Engelman, D. M. (1997). Science 276, 131-133.
80. Mall, S., Broadbridge, R., Sharma, R. P., East, J. M., and Lee, A. G. (2001). Biochemistry 40, 12379-12386.
81. Maneri, L. R., and Low, P. S. (1988). J. Biol. Chem. 263, 16170-16178.
82. Marti, T. (1998). J. Biol. Chem. 273, 9312-9322.
83. McAuley, K. E., Fyfe, P. K., Ridge, J. P., Isaacs, N. W., Cogdell, R. J., and Jones, M. R. (1999). Proc. Natl. Acad. Sci. USA 96, 14706-14711.
84. Meadows, E. S., De Wall, S. L., Barbour, L. J., Fronczek, F. R., Kim, M.-S., and Gokel, G. W. (2000). J. Am. Chem. Soc. 122, 3325-3335.
85. Nagle, J. F., and Tristram-Nagle, S. (2000). Biochim. Biophys. Acta 1469, 159-195.
86. O'Shea, E. K., Klemm, J. D., Kim, P. S., and Alber, T. (1991). Science 254, 539-544.
87. Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Le Trong, I., Teller, D. C., Okada, T., Stenkamp, R. E., Yamamoto, M., and Miyano, M. (2000). Science 289, 739-745.
88. Perutz, M. F., Kendrew, J. C., and Watson, H. C. (1965). J. Mol. Biol. 13, 669-678.
89. Pilot, J. D., East, J. M., and Lee, A. G. (2001). Biochemistry 40, 8188-8195.
90. Pohlschroder, M., Murphy, C., and Beckwith, J. (1996). J. Biol. Chem. 271, 19908-19914.
91. Popot, J. L., and Engelman, D. M. (1990). Biochemistry 29, 4031-4037.
92. Popot, J. L., Gerchman, S. E., and Engelman, D. M. (1987). J. Mol. Biol. 198, 655-676.
93. Porter, J. E., and Perez, D. M. (1999). J. Biol. Chem. 274, 34535-34538.
94. Ramachandran, G. N., and Sasisekharan, V. (1965). Biochim. Biophys. Acta 109, 314-316.
95. Ramachandran, G. N., Sasisekharan, V., and Ramakrishnan, C. (1966). Biochim. Biophys. Acta 112, 168-170.
96. Rees, D., DeAntonio, L., and Eisenberg, D. (1989a). Science 245, 510.
97. Rees, D. C., Komiya, H., Yeates, T. O., Allen, J. P., and Feher, G. (1989b). Annu. Rev. Biochem. 58, 607-633.
98. Richards, F. M. (1977). Annu. Rev. Biophys. Bioeng. 6, 151-176.
99. Riek, R. P., Rigoutsos, I., Novotny, J., and Graham, R. M. (2001). J. Mol. Biol. 306, 349-362.
100. Rietveld, A., Van Kemenade, T. J. J. M., Hak, T., Verkleij, A. J., and De Kruijff, B. (1987). Eur. J. Biochem. 164, 137-140.
101. Rost, B., Fariselli, P., and Casadio, R. (1996). Protein Sci. 5, 1704-1718.
102. Russ, W. P., and Engelman, D. M. (1999). Proc. Natl. Acad. Sci. USA 96, 863-868.
103. Russ, W. P., and Engelman, D. M. (2000). J. Mol. Biol. 296, 911-919.
104. Sahin-Toth, M. S., Dunten, R. L., Gonzalez, A., and Kaback, R. (1992). Proc. Natl. Acad. Sci. USA 89, 10547-10551.
105. Sansom, M. S., and Weinstein, H. (2000). Trends Pharmacol. Sci. 21, 445-451.
106. Schmidt-Rose, T., and Jentsch, T. J. (1997). J. Biol. Chem. 272, 20515-20521.
107. Senes, A., Gerstein, M., and Engelman, D. M. (2000). J. Mol. Biol. 296, 921-936.
108. Senes, A., Ubarretxena-Belandia, I., and Engelman, D. M. (2001). Proc. Natl. Acad. Sci. USA 98, 9056-9061.
109. Sheets, E. D., Holowka, D., and Baird, B. (1999). J. Cell Biol. 145, 877-887.
110. Shnyrov, V. L., Azuaga, A. I., and Mateo, P. L. (1994). Biochem. Soc. Trans. 22, 367S.
111. Simidjiev, I., Stoylova, S., Amenitsch, H., Javorfi, T., Mustardy, L., Laggner, P., Holzenburg, A., and Garab, G. (2000). Proc. Natl. Acad. Sci. USA 97, 1473-1476.
112. Simons, K., and Ikonen, E. (1997). Nature (London) 387, 569-572.
113. Smith, S., Smith, C., and Bormann, B. (1996). Nat. Struct. Biol. 3, 252-258.
114. Smith, S. O., Song, D., Shekar, S., Groesbeek, M., Ziliox, M., and Aimoto, S. (2001). Biochemistry 40, 6553-6558.
115. Surrey, T., and Jahnig, F. (1992). Proc. Natl. Acad. Sci. USA 89, 7457-7461.
116. Taylor, R., and Kennard, O. (1982). J. Am. Chem. Soc. 104, 5063-5070.
117. Therien, A. G., Grant, F. E., and Deber, C. M. (2001). Nat. Struct. Biol. 8, 597-601.
118. Ulmschneider, M. B., and Sansom, M. S. (2001). Biochim. Biophys. Acta 1512, 1-14.
119. Unemura, T., Tatsuno, I., Shibasaki, M., Homma, M., and Kagawishi, I. (1998). J. Biol. Chem. 273, 30110-30115.
120. van der Wel, P. C. A., Pott, T., Morein, S., Greathouse, D. V., Koeppe, R. E., II, and Killian, J. A. (2000). Biochemistry 39, 3124-3133.
121. Vargas, R., Garza, J., Dixon, D. A., and Hay, B. P. (2000). J. Am. Chem. Soc. 122, 4750-4755.
122. Walther, D., Eisenhaber, F., and Argos, P. (1996). J. Mol. Biol. 25, 536-553.
123. Waugh, M. G., Lawson, D., and Hsuan, J. J. (1999). Biochem. J. 337, 591-597.
124. Weiner, D., Liu, J., Cohen, J., Williams, W., and Greene, M. (1989). Nature 339, 230-231.
125. Wen, J., Chen, X., and Bowie, J. (1996). Nat. Struct. Biol. 3, 141-148.
126. White, S. H., and Wimley, W. C. (1998). Biochim. Biophys. Acta 1376, 339-352.
127. White, S. H., and Wimley, W. C. (1999). Annu. Rev. Biophys. Biomol. Struct. 28, 319-365.
128. White, S. H., Wimley, W. C., Ladokhin, A. S., and Hristova, K. (1998). Methods Enzymol. 295, 62-87.
129. Williamson, I. M., Alvis, S. J., East, J. M., and Lee, A. G. (2002). Biophys. J. 83, 2026-2038.
130. Wimley, W. C., and White, S. H. (1996). Nat. Struct. Biol. 3, 842-848.
131. Yau, W. M., Wimley, W. C., Gawrisch, K., and White, S. H. (1998). Biochemistry 37,14713-14718.
132. Zhou, F. X., Cocco, M. J., Russ, W. P., Brunger, A. T., and Engelman, D. M. (2000). Nat. Struct. Biol. 7, 154-160.
133. Zhou, F. X., Merianos, H. J., Brunger, A. T., and Engelman, D. M. (2001). Proc. Natl. Acad. Sci. USA 98, 2250-2255.
134. Zhou, Y., and Bowie, J. U. (2000). J. Biol. Chem. 275, 6975-6979.
135. Zhou, Y., Wen, J., and Bowie, J. U. (1997). Nat. Struct. Biol. 4, 986-990.