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A sequence and structural study of transmembrane helices

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Abstract

A comparison is made between the distribution of residue preferences, three dimensional nearest neighbour contacts, preferred rotamers, helix-helix crossover angles and peptide bond angles in three sets of proteins: a non-redundant set of accurately determined globular protein structures, a set of four-helix bundle structures and a set of membrane protein structures. Residue preferences for the latter two sets may reflect overall helix stabilising propensities but may also highlight differences arising out of the contrasting nature of the solvent environments in these two cases. The results bear out the expectation that there may be differences between residue type preferences in membrane proteins and in water soluble globular proteins. For example, the β-branched residue types valine and isoleucine are considerably more frequently encountered in membrane helices. Likewise, glycine and proline, residue types normally associated with `helix-breaking' propensity are found to be relatively more common in membrane helices. Three dimensional nearest neighbour contacts along the helix, preferred rotamers, and peptide bond angles are very similar in the three sets of proteins as far as can be ascertained within the limits of the relatively low resolution of the membrane proteins dataset. Crossing angles for helices in the membrane protein set resemble the four helix bundle set more than the general non-redundant set, but in contrast to both sets they have smaller crossing angles consistent with the dual requirements for the helices to form a compact structure while having to span the membrane. In addition to the pairwise packing of helices we investigate their global packing and consider the question of helix supercoiling in helix bundle proteins.

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References

  1. Murzin, A.G., Brenner, S. E., Hubbard, T. and Chothia, C. J. Mol. Biol., 247 (1995) 536.

    Google Scholar 

  2. Palczewski, K., Kumasaka, T., Hori, T., Behnke, C.A., Motoshima, H., Fox, B.A., Le Tromg, I., Teller, D.C., Okada, T., Stenkamp, R.E., Yamamoto, M. and Miyano, M., Science, 289 (2000) 739-745.

    Google Scholar 

  3. Arkin, I.T., Brünger, A.T. and Engelman, D.M., Proteins, 28 (1997) 465-466.

    Google Scholar 

  4. Frishman, D. and Mewes, H.W., Nat. Struct. Biol., 4 (1997) 626-628.

    Google Scholar 

  5. Jones, D.T., FEBS Lett., 423 (1998) 281-285.

    Google Scholar 

  6. Findlay, J.B.C. and Eliopoulos, E., TIPS, 11 (1990) 492-499.

    Google Scholar 

  7. Dahl, S.G., Edvardsen, Ø. and Sylte, I., Proc. Natl. Acad. Sci. USA, 88 (1991) 8111-8115.

    Google Scholar 

  8. Hibert, M.F., Trumpp-Kallmeyer, S., Bruinvels, A. and Hoflack, J., Mol. Pharmacol., 40 (1991) 8-15.

    Google Scholar 

  9. Lewell, X.G., Drug Design Discovery, 9 (1992) 29-48.

    Google Scholar 

  10. MaloneyHuss, K. and Lybrand, T.P., J. Mol. Biol., 225 (1992) 859-871.

    Google Scholar 

  11. Kontoyanni, M. and Lybrand, T.P., Med. Chem. Res., 3 (1993) 407-418.

    Google Scholar 

  12. Cronet, P., Sander, C. and Vriend, G., Prot. Eng., 6 (1993) 59-64.

    Google Scholar 

  13. Taylor, W.R., Jones, D.T. and Green, N.M., Proteins, 18 (1994) 281-294.

    Google Scholar 

  14. Donnelly, D., Findlay, J.B.C. and Blundell, L.T., Receptors and Channels, 2 (1994) 61-78.

    Google Scholar 

  15. Lin, S.W., Biochemistry, 33 (1994) 2151-2160.

    Google Scholar 

  16. Herzyk, P. and Hubbard, R.E., Biophys. J., 69 (1995) 2419-2442.

    Google Scholar 

  17. Shieh, T., Han, M., Sakmar, T.P. and Smith, S.O., J. Mol. Biol., 269 (1997) 373-384.

    Google Scholar 

  18. Perez, J.J., Filizola, M. and Cariteni-Farina, M., J. Math. Chem., 23 (1998) 229-238.

    Google Scholar 

  19. Frimurer, T.M. and Bywater, R.P., Proteins, 35 (1999) 375-386.

    Google Scholar 

  20. Kristiansen, K., Dahl, S. G. and Edvardsen, Ø., Proteins, 26 (1996) 81-94.

    Google Scholar 

  21. Edvardsen, Ø. and Kristiansen, K., 7TM J., 6 (1997) 1.

    Google Scholar 

  22. Seeman, P., Receptor Tables, Vol. 2, SZ Research, Toronto, 1993.

  23. Kuipers, W., Oliveira, L., Vriend, G. and Ijzerman, A.P., Receptors Channels, 3 (1997) 159.

    Google Scholar 

  24. Horn, F., Bywater, R., Krause, G., Kuipers, W., Oliveira, L., Paiva, A.C.M., Sander, C. and Vriend, G., Receptors Channels, 5 (1998) 305.

    Google Scholar 

  25. Farahbakhsh, Z.T., Ridge, K.D., Khorana, H.G. and Hubbell, W.L., Biochemistry, 34 (1995) 8812.

    Google Scholar 

  26. Yang, K., Farrens, D.L., Altenbach, C., Farahbahksh, Z.T., Hubbell, W.L. and Khorana, H.G., Biochemistry, 35 (1996) 14040.

    Google Scholar 

  27. Yang, K., Farrens, D.L., Hubbell, W.L. and Khorana, H.G., Biochemistry, 35 (1996) 12464.

    Google Scholar 

  28. Farrens, D.L., Altenbach, C., Yang, K., Hubbell, W.L. and Khorana, H.G., Science, 274 (1996) 768.

    Google Scholar 

  29. Baldwin, J.M., Schertler, G.F.X. and Unger, V.M., J. Mol. Biol., 272 (1997) 144.

    Google Scholar 

  30. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., Arch. Biochem. Biophys., 185 (1978) 584.

    Google Scholar 

  31. Hooft, R.W., Sander, C. and Vriend, G. J., Appl. Cryst., 29 (1996) 714.

    Google Scholar 

  32. Holm, L. and Sander, C., Nucl. Acids Res., 26 (1998) 316.

    Google Scholar 

  33. Banner, B.W., Kokkinidis, M. and Tsernoglou, D. J., Mol. Biol., 196 (1987) 657.

    Google Scholar 

  34. Li, S.C. and Deber, C.M., Nat. Struct. Biol., 1 (1994) 368.

    Google Scholar 

  35. Deber, C.M. and Li, S.C., Bioploymers, 37 (1995) 295.

    Google Scholar 

  36. Chou, P.Y. and Fasman, G.D., Biochemistry, 13 (1974) 211

    Google Scholar 

  37. Chakrabarti, P., Bernard, M. and Rees, D.C., Biopolymers, 25 (1986) 1087.

    Google Scholar 

  38. Karplus, P.A., Prot. Sci., 5 (1996) 1406.

    Google Scholar 

  39. Mingarro, I., Elofsson, A. and Von Heijne, G.J., Mol. Biol., 272 (1997) 633.

    Google Scholar 

  40. Lemmon, M.A., MacKenzie K.R., Arkin I.T. and Engelman, D., in von Heijne, G. (Ed.), "Membrane Protein Assembly'. Springer-Verlag, New York/Landes Austin TX, 1997, pp. 3-23.

    Google Scholar 

  41. Chothia, C., Levitt, M. and Richardson, D. J., Mol. Biol., 145 (1981) 215.

    Google Scholar 

  42. Walther, D., Eisenhaber, F. and Argos, P. J., Mol. Biol., 255 (1996) 536.

    Google Scholar 

  43. Crick, F.H.C., Acta Crystallogr., 6 (1953) 689.

    Google Scholar 

  44. Bowie, J.U., J. Mol. Biol., 272 (1997) 780.

    Google Scholar 

  45. Bragg, L., in Phillips, D.C. and Lipson, H. (eds), "The Development of X-ray Analysis', Bell, London, 1975.

    Google Scholar 

  46. Zerger, M.J., Mathematical Intelligencer, 20 (1998) 5.

    Google Scholar 

  47. Seo J. and Cohen, C., Proteins, 15 (1993) 223.

    Google Scholar 

  48. Langosch, D. and Heringa, J., Proteins, 31 (1998) 150.

    Google Scholar 

  49. Sansom, M.S., Son, H.S., Sankararamakrishnan, R., Kerr, I.D. and Breed, J., Biophys. J., 68 (1995) 1295.

    Google Scholar 

  50. Vriend, G., J. Mol. Graph., 8 (1990) 52.

    Google Scholar 

  51. Jones, T.A. and Thirup, S., EMBO J., 5 (1986) 819.

    Google Scholar 

  52. De Filippis, V., Sander, C. and Vriend, G., Prot. Eng., 7 (1994) 1203.

    Google Scholar 

  53. Chinea, G., Padron, G., Hooft, R.W.W., Sander, C. and Vriend, G., Proteins, 23 (1995) 415.

    Google Scholar 

  54. Thomas, D.J., J. Mol. Biol., 222 (1991) 805.

    Google Scholar 

  55. Luecke, H., Schobert, B., Richter, H.T., Cartailler, J.P. and Lanyi, J.K. Structure of bacteriorhodopsin at 1.55 A resolution. J. Mol. Biol., 291 (1999) 899.

    Google Scholar 

  56. Thorgeirsson, T.E., Russell, C.R., King, D.S. and Shin, Y.K.

  57. Wallace, B.A., Cascio, M. and Miele, D.L., Proc. Natl. Acad. Sci. USA, 83 (1986) 9423.

    Google Scholar 

  58. Oliveira, L., Paiva, A.C.M., Sander, C. and Vriend, G., TIPS, 15 (1994) 170.

    Google Scholar 

  59. Peters, G.H. and Bywater, R.P., Prot. Eng., 12 (1999) 747.

    Google Scholar 

  60. Serrano, L., Neira, J.L., Sancho, J. and Fersht, A.R., Nature, 356 (1992) 453.

    Google Scholar 

  61. Piela, L., Némethy, G. and Scheraga H.A., Bioploymers, 26 (1987) 1587.

    Google Scholar 

  62. Barlow, D.J. and Thornton, J.M., J. Mol. Biol., 201 (1988) 601.

    Google Scholar 

  63. Deber, C.M., Glibowicka, M. and Woolley G.A., Bioploymers, 29 (1990) 149.

    Google Scholar 

  64. MacArthur, M. W. and Thornton, J. M., J. Mol. Biol., 218 (1991) 397.

    Google Scholar 

  65. Von Heijne, G., J. Mol. Biol.,218 (1991) 499.

    Google Scholar 

  66. Ballesteros, J.A. and Weinstein H., Biophys. J., 2 (1992) 07.

    Google Scholar 

  67. Kabsch, W. and Sander, C., Biopolymers, 22 (1983) 577.

    Google Scholar 

  68. Yuan, H.S., Wang, S.S., Yang, W.Z., Finkel, S.E., and Johnson, R.C., J. Biol. Chem., 269 (1994) 28947.

    Google Scholar 

  69. Jacob, J., Duclohier, H. and Cafiso, D.S., Biophys. J., 76 (1999) 1367.

    Google Scholar 

  70. Bak, M., Bywater, R.P., Hohwy, M., Thomsen, J.K., Adelhorst, K., Jakobsen, H.J., SØrensen, O.W. and Nielsen, N.C., Biophys. J. (2000) (submitted).

  71. Han M., Smith S.O. and Shakmar T.P. Biochemistry, 37 (1998) 8253.

    Google Scholar 

  72. William, K.A. and Deber, C.M., Biochemistry, 30 (1991) 8919.

    Google Scholar 

  73. Lomize, A.L., Pogozheva, I.D. and Mosberg, H.I., J. Comput. Aid. Mol. Des., 13 (1999) 325.

    Google Scholar 

  74. Borhan, B., Souto, M.L., Imai, H., Schichida, Y. and Nakanishi, K., Science, 288 (2000) 2209.

    Google Scholar 

  75. Isralewitz, B., Izrailev, S. and Schulten, K., Biophys. J., 73 (1997) 2972.

    Google Scholar 

  76. Kandori, H., Kinoshita, N., Yamazaki, Y., Maeda, A., Shichida, Y., Needleman, R., Lanyi, J.K., Bizounok, M., Herzfeld, J., Raap, J. and Lugtenburg, J., Proc. Natl. Acad. Sci. USA., 97 (2000) 4643.

    Google Scholar 

  77. Pogozheva, I.D., Lomize, A.L. and Mosberg, H.I., Biophys. J., 72 (1997) 1963.

    Google Scholar 

  78. Cooper, A., Biophys. Chem (2000) 25.

  79. Zhou, F.X., Cocco, M.J., Russ, W.P., Brunger, A.T. and Engelman, D.M., Nat. Struct. Biol., 7 (2000) 154.

    Google Scholar 

  80. Senes, A., Gerstein, M. and Engelman, D.M., J. Mol. Biol., 296 (2000) 921.

    Google Scholar 

  81. Aubry, A., Ghermani, N. and Marraud, M., Int. J. Peptide Protein Res. 23, (1984) 113.

    Google Scholar 

  82. Dey, S., Kaur, P. and Singh, T.P., Int. J. Peptide Protein Res., 48 (1996) 299.

    Google Scholar 

  83. Vijayakumar, M., Qian, H. and Zhou, H.X., Proteins, 34 (1999) 497.

    Google Scholar 

  84. Lew, S., Ren, J. and London, E., Biochemistry, 39 (2000) 9632.

    Google Scholar 

  85. Von Heijne, G., J. Mol. Biol., 225 (1992) 487.

    Google Scholar 

  86. Rippmann, F., 7TM J., 4 (1994) 1.

    Google Scholar 

  87. Morris, A.L., MacArthur, M.W., Hutchinson, E.G. and Thornton J.M., Proteins, 12 (1992) 345.

    Google Scholar 

  88. Brunet, A.P., Huang, E.S., Huffine, M.E., Loeb, J.E., Weltman, R.J. and Hecht, M.H., Nature, 364 (1993) 355.

    Google Scholar 

  89. Rost, B. and Sander, C., Proc. Natl. Acad. Sci. USA, 90 (1993) 7558.

    Google Scholar 

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Authors and Affiliations

  1. Biostructure Group, Novo Nordisk A/S, Novo Nordisk Park, DK-2760, MÅLØV, Denmark

    Robert P. Bywater

  2. Biocomputing Group, EMBL, Meyerhofstrasse 1, D-69117, Heidelberg, Germany

    David Thomas & Gerrit Vriend

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  1. Robert P. Bywater
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  2. David Thomas
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Bywater, R.P., Thomas, D. & Vriend, G. A sequence and structural study of transmembrane helices. J Comput Aided Mol Des 15, 533–552 (2001). https://doi.org/10.1023/A:1011197908960

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