Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1986 Dec;83(24):9423–9427. doi: 10.1073/pnas.83.24.9423

Evaluation of methods for the prediction of membrane protein secondary structures.

B A Wallace, M Cascio, D L Mielke
PMCID: PMC387150  PMID: 3467313

Abstract

With the advent of molecular cloning methods, the amino acid sequences for a number of membrane proteins have been determined. The relative paucity of detailed three-dimensional structural information available for these molecules has led to attempts to predict the secondary structures of membrane proteins based on folding motifs found in soluble proteins of known three-dimensional structure and sequence. In this study, we evaluated the accuracy of several of these methods in predicting the conformation of 15 integral membrane proteins and membrane-spanning polypeptides for which both primary and secondary structural information are available. chi 2 analyses indicated a less than 0.5% correlation between the net predicted secondary structures and the experimental results. A more stringent test of the accuracy of the methods, the index of prediction, was calculated for individual residues in four of the polypeptides for which the crystal structures were known; this criterion also indicated that the predicted assignments for the secondary structures of the residues were inaccurate. Thus, prediction schemes using soluble protein bases appear to be inappropriate for the prediction of membrane protein folding.

Full text

PDF
9423

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. ANFINSEN C. B., HABER E., SELA M., WHITE F. H., Jr The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci U S A. 1961 Sep 15;47:1309–1314. doi: 10.1073/pnas.47.9.1309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brunden K. R., Uratani Y., Cramer W. A. Dependence of the conformation of a colicin E1 channel-forming peptide on acidic pH and solvent polarity. J Biol Chem. 1984 Jun 25;259(12):7682–7687. [PubMed] [Google Scholar]
  3. Chang C. T., Wu C. S., Yang J. T. Circular dichroic analysis of protein conformation: inclusion of the beta-turns. Anal Biochem. 1978 Nov;91(1):13–31. doi: 10.1016/0003-2697(78)90812-6. [DOI] [PubMed] [Google Scholar]
  4. Chang C. T., Wu C. S., Yang J. T. Circular dichroic analysis of protein conformation: inclusion of the beta-turns. Anal Biochem. 1978 Nov;91(1):13–31. doi: 10.1016/0003-2697(78)90812-6. [DOI] [PubMed] [Google Scholar]
  5. Chetverin A. B., Brazhnikov E. V. Do sodium and potassium forms of Na,K-ATPase differ in their secondary structure? J Biol Chem. 1985 Jul 5;260(13):7817–7819. [PubMed] [Google Scholar]
  6. Chou P. Y., Fasman G. D. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry. 1974 Jan 15;13(2):211–222. doi: 10.1021/bi00699a001. [DOI] [PubMed] [Google Scholar]
  7. Chou P. Y., Fasman G. D. Prediction of beta-turns. Biophys J. 1979 Jun;26(3):367–383. doi: 10.1016/S0006-3495(79)85259-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chou P. Y., Fasman G. D. Prediction of protein conformation. Biochemistry. 1974 Jan 15;13(2):222–245. doi: 10.1021/bi00699a002. [DOI] [PubMed] [Google Scholar]
  9. Claudio T., Ballivet M., Patrick J., Heinemann S. Nucleotide and deduced amino acid sequences of Torpedo californica acetylcholine receptor gamma subunit. Proc Natl Acad Sci U S A. 1983 Feb;80(4):1111–1115. doi: 10.1073/pnas.80.4.1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dailey H. A., Strittmatter P. Structural and functional properties of the membrane binding segment of cytochrome b5. J Biol Chem. 1978 Nov 25;253(22):8203–8209. [PubMed] [Google Scholar]
  11. Dailey H. A., Strittmatter P. Structural and functional properties of the membrane binding segment of cytochrome b5. J Biol Chem. 1978 Nov 25;253(22):8203–8209. [PubMed] [Google Scholar]
  12. Engelman D. M., Steitz T. A., Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem. 1986;15:321–353. doi: 10.1146/annurev.bb.15.060186.001541. [DOI] [PubMed] [Google Scholar]
  13. Finer-Moore J., Stroud R. M. Amphipathic analysis and possible formation of the ion channel in an acetylcholine receptor. Proc Natl Acad Sci U S A. 1984 Jan;81(1):155–159. doi: 10.1073/pnas.81.1.155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Finer-Moore J., Stroud R. M., Prescott B., Thomas G. J., Jr Subunit secondary structure in filamentous viruses: predictions and observations. J Biomol Struct Dyn. 1984 Aug;2(1):93–100. doi: 10.1080/07391102.1984.10507549. [DOI] [PubMed] [Google Scholar]
  15. Finer-Moore J., Stroud R. M., Prescott B., Thomas G. J., Jr Subunit secondary structure in filamentous viruses: predictions and observations. J Biomol Struct Dyn. 1984 Aug;2(1):93–100. doi: 10.1080/07391102.1984.10507549. [DOI] [PubMed] [Google Scholar]
  16. Fleming P. J., Dailey H. A., Corcoran D., Strittmatter P. The primary structure of the nonpolar segment of bovine cytochrome b5. J Biol Chem. 1978 Aug 10;253(15):5369–5372. [PubMed] [Google Scholar]
  17. Foster D. L., Boublik M., Kaback H. R. Structure of the lac carrier protein of Escherichia coli. J Biol Chem. 1983 Jan 10;258(1):31–34. [PubMed] [Google Scholar]
  18. Foster D. L., Boublik M., Kaback H. R. Structure of the lac carrier protein of Escherichia coli. J Biol Chem. 1983 Jan 10;258(1):31–34. [PubMed] [Google Scholar]
  19. Furthmayr H., Galardy R. E., Tomita M., Marchesi V. T. The intramembranous segment of human erythrocyte glycophorin A. Arch Biochem Biophys. 1978 Jan 15;185(1):21–29. doi: 10.1016/0003-9861(78)90139-x. [DOI] [PubMed] [Google Scholar]
  20. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
  21. Gray G. S., Kehoe M. Primary sequence of the alpha-toxin gene from Staphylococcus aureus wood 46. Infect Immun. 1984 Nov;46(2):615–618. doi: 10.1128/iai.46.2.615-618.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Gresalfi T. J., Wallace B. A. Secondary structural composition of the Na/K-ATPase E1 and E2 conformers. J Biol Chem. 1984 Feb 25;259(4):2622–2628. [PubMed] [Google Scholar]
  23. Henderson R. The structure of the purple membrane from Halobacterium hallobium: analysis of the X-ray diffraction pattern. J Mol Biol. 1975 Apr 5;93(2):123–138. doi: 10.1016/0022-2836(75)90123-0. [DOI] [PubMed] [Google Scholar]
  24. Henderson R., Unwin P. N. Three-dimensional model of purple membrane obtained by electron microscopy. Nature. 1975 Sep 4;257(5521):28–32. doi: 10.1038/257028a0. [DOI] [PubMed] [Google Scholar]
  25. Honig B. H., Hubbell W. L. Stability of "salt bridges" in membrane proteins. Proc Natl Acad Sci U S A. 1984 Sep;81(17):5412–5416. doi: 10.1073/pnas.81.17.5412. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Huang K. S., Bayley H., Liao M. J., London E., Khorana H. G. Refolding of an integral membrane protein. Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments. J Biol Chem. 1981 Apr 25;256(8):3802–3809. [PubMed] [Google Scholar]
  27. Huang K. S., Bayley H., Liao M. J., London E., Khorana H. G. Refolding of an integral membrane protein. Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments. J Biol Chem. 1981 Apr 25;256(8):3802–3809. [PubMed] [Google Scholar]
  28. Kaback H. R. The lac carrier protein in Escherichia coli. J Membr Biol. 1983;76(2):95–112. doi: 10.1007/BF02000610. [DOI] [PubMed] [Google Scholar]
  29. Khorana H. G., Gerber G. E., Herlihy W. C., Gray C. P., Anderegg R. J., Nihei K., Biemann K. Amino acid sequence of bacteriorhodopsin. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5046–5050. doi: 10.1073/pnas.76.10.5046. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Khorana H. G., Gerber G. E., Herlihy W. C., Gray C. P., Anderegg R. J., Nihei K., Biemann K. Amino acid sequence of bacteriorhodopsin. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5046–5050. doi: 10.1073/pnas.76.10.5046. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Kleffel B., Garavito R. M., Baumeister W., Rosenbusch J. P. Secondary structure of a channel-forming protein: porin from E. coli outer membranes. EMBO J. 1985 Jun;4(6):1589–1592. doi: 10.1002/j.1460-2075.1985.tb03821.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Kleffel B., Garavito R. M., Baumeister W., Rosenbusch J. P. Secondary structure of a channel-forming protein: porin from E. coli outer membranes. EMBO J. 1985 Jun;4(6):1589–1592. doi: 10.1002/j.1460-2075.1985.tb03821.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Kopito R. R., Lodish H. F. Primary structure and transmembrane orientation of the murine anion exchange protein. Nature. 1985 Jul 18;316(6025):234–238. doi: 10.1038/316234a0. [DOI] [PubMed] [Google Scholar]
  34. Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. doi: 10.1016/0022-2836(82)90515-0. [DOI] [PubMed] [Google Scholar]
  35. Lim V. I. Algorithms for prediction of alpha-helical and beta-structural regions in globular proteins. J Mol Biol. 1974 Oct 5;88(4):873–894. doi: 10.1016/0022-2836(74)90405-7. [DOI] [PubMed] [Google Scholar]
  36. Mao D., Wachter E., Wallace B. A. Folding of the mitochondrial proton adenosinetriphosphatase proteolipid channel in phospholipid vesicles. Biochemistry. 1982 Sep 28;21(20):4960–4968. doi: 10.1021/bi00263a020. [DOI] [PubMed] [Google Scholar]
  37. Mao D., Wachter E., Wallace B. A. Folding of the mitochondrial proton adenosinetriphosphatase proteolipid channel in phospholipid vesicles. Biochemistry. 1982 Sep 28;21(20):4960–4968. doi: 10.1021/bi00263a020. [DOI] [PubMed] [Google Scholar]
  38. Mao D., Wallace B. A. Differential light scattering and absorption flattening optical effects are minimal in the circular dichroism spectra of small unilamellar vesicles. Biochemistry. 1984 Jun 5;23(12):2667–2673. doi: 10.1021/bi00307a020. [DOI] [PubMed] [Google Scholar]
  39. Michel H., Weyer K. A., Gruenberg H., Dunger I., Oesterhelt D., Lottspeich F. The 'light' and 'medium' subunits of the photosynthetic reaction centre from Rhodopseudomonas viridis: isolation of the genes, nucleotide and amino acid sequence. EMBO J. 1986 Jun;5(6):1149–1158. doi: 10.1002/j.1460-2075.1986.tb04340.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Michel H., Weyer K. A., Gruenberg H., Lottspeich F. The ;heavy' subunit of the photosynthetic reaction centre from Rhodopseudomonas viridis: isolation of the gene, nucleotide and amino acid sequence. EMBO J. 1985 Jul;4(7):1667–1672. doi: 10.1002/j.1460-2075.1985.tb03835.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Nabedryk E., Bardin A. M., Breton J. Further characterization of protein secondary structures in purple membrane by circular dichroism and polarized infrared spectroscopies. Biophys J. 1985 Dec;48(6):873–876. doi: 10.1016/S0006-3495(85)83848-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Noda M., Takahashi H., Tanabe T., Toyosato M., Kikyotani S., Furutani Y., Hirose T., Takashima H., Inayama S., Miyata T. Structural homology of Torpedo californica acetylcholine receptor subunits. Nature. 1983 Apr 7;302(5908):528–532. doi: 10.1038/302528a0. [DOI] [PubMed] [Google Scholar]
  43. Noda M., Takahashi H., Tanabe T., Toyosato M., Kikyotani S., Furutani Y., Hirose T., Takashima H., Inayama S., Miyata T. Structural homology of Torpedo californica acetylcholine receptor subunits. Nature. 1983 Apr 7;302(5908):528–532. doi: 10.1038/302528a0. [DOI] [PubMed] [Google Scholar]
  44. Ovchinnikov YuA Rhodopsin and bacteriorhodopsin: structure-function relationships. FEBS Lett. 1982 Nov 8;148(2):179–191. doi: 10.1016/0014-5793(82)80805-3. [DOI] [PubMed] [Google Scholar]
  45. Ovchinnikov Y. A., Abdulaev N. G., Feigina M. Y., Kiselev A. V., Lobanov N. A. Recent findings in the structure-functional characteristics of bacteriorhodopsin. FEBS Lett. 1977 Dec 1;84(1):1–4. doi: 10.1016/0014-5793(77)81046-6. [DOI] [PubMed] [Google Scholar]
  46. Ovchinnikov Y. A., Abdulaev N. G., Feigina M. Y., Kiselev A. V., Lobanov N. A. Recent findings in the structure-functional characteristics of bacteriorhodopsin. FEBS Lett. 1977 Dec 1;84(1):1–4. doi: 10.1016/0014-5793(77)81046-6. [DOI] [PubMed] [Google Scholar]
  47. Ovchinnikov Y. A., Abdulaev N. G., Feigina M. Y., Kiselev A. V., Lobanov N. A. The structural basis of the functioning of bacteriorhodopsin: an overview. FEBS Lett. 1979 Apr 15;100(2):219–224. doi: 10.1016/0014-5793(79)80338-5. [DOI] [PubMed] [Google Scholar]
  48. Ovchinnikov Y. A., Abdulaev N. G., Feigina M. Y., Kiselev A. V., Lobanov N. A. The structural basis of the functioning of bacteriorhodopsin: an overview. FEBS Lett. 1979 Apr 15;100(2):219–224. doi: 10.1016/0014-5793(79)80338-5. [DOI] [PubMed] [Google Scholar]
  49. Overbeeke N., Bergmans H., van Mansfeld F., Lugtenberg B. Complete nucleotide sequence of phoE, the structural gene for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12. J Mol Biol. 1983 Feb 5;163(4):513–532. doi: 10.1016/0022-2836(83)90110-9. [DOI] [PubMed] [Google Scholar]
  50. Paul C., Rosenbusch J. P. Folding patterns of porin and bacteriorhodopsin. EMBO J. 1985 Jun;4(6):1593–1597. doi: 10.1002/j.1460-2075.1985.tb03822.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Rosenbusch J. P. Characterization of the major envelope protein from Escherichia coli. Regular arrangement on the peptidoglycan and unusual dodecyl sulfate binding. J Biol Chem. 1974 Dec 25;249(24):8019–8029. [PubMed] [Google Scholar]
  52. Rothman J. E., Lodish H. F. Synchronised transmembrane insertion and glycosylation of a nascent membrane protein. Nature. 1977 Oct 27;269(5631):775–780. doi: 10.1038/269775a0. [DOI] [PubMed] [Google Scholar]
  53. Rothschild K. J., Sanches R., Hsiao T. L., Clark N. A. A spectroscopic study of rhodopsin alpha-helix orientation. Biophys J. 1980 Jul;31(1):53–64. doi: 10.1016/S0006-3495(80)85040-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Rothschild K. J., Sanches R., Hsiao T. L., Clark N. A. A spectroscopic study of rhodopsin alpha-helix orientation. Biophys J. 1980 Jul;31(1):53–64. doi: 10.1016/S0006-3495(80)85040-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Schulte T. H., Marchesi V. T. Conformation of human erythrocyte glycophorin A and its constituent peptides. Biochemistry. 1979 Jan 23;18(2):275–280. doi: 10.1021/bi00569a006. [DOI] [PubMed] [Google Scholar]
  56. Schulte T. H., Marchesi V. T. Conformation of human erythrocyte glycophorin A and its constituent peptides. Biochemistry. 1979 Jan 23;18(2):275–280. doi: 10.1021/bi00569a006. [DOI] [PubMed] [Google Scholar]
  57. Sebald W., Machleidt W., Wachter E. N,N'-dicyclohexylcarbodiimide binds specifically to a single glutamyl residue of the proteolipid subunit of the mitochondrial adenosinetriphosphatases from Neurospora crassa and Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1980 Feb;77(2):785–789. doi: 10.1073/pnas.77.2.785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Shull G. E., Schwartz A., Lingrel J. B. Amino-acid sequence of the catalytic subunit of the (Na+ + K+)ATPase deduced from a complementary DNA. Nature. 1985 Aug 22;316(6030):691–695. doi: 10.1038/316691a0. [DOI] [PubMed] [Google Scholar]
  59. Stubbs G. W., Smith H. G., Jr, Litman B. J. Alkyl glucosides as effective solubilizing agents for bovine rhodopsin. A comparison with several commonly used detergents. Biochim Biophys Acta. 1976 Feb 19;426(1):46–56. doi: 10.1016/0005-2736(76)90428-4. [DOI] [PubMed] [Google Scholar]
  60. Stubbs G. W., Smith H. G., Jr, Litman B. J. Alkyl glucosides as effective solubilizing agents for bovine rhodopsin. A comparison with several commonly used detergents. Biochim Biophys Acta. 1976 Feb 19;426(1):46–56. doi: 10.1016/0005-2736(76)90428-4. [DOI] [PubMed] [Google Scholar]
  61. Teeter M. M., Mazer J. A., L'Italien J. J. Primary structure of the hydrophobic plant protein crambin. Biochemistry. 1981 Sep 15;20(19):5437–5443. doi: 10.1021/bi00522a013. [DOI] [PubMed] [Google Scholar]
  62. Tobkes N., Wallace B. A., Bayley H. Secondary structure and assembly mechanism of an oligomeric channel protein. Biochemistry. 1985 Apr 9;24(8):1915–1920. doi: 10.1021/bi00329a017. [DOI] [PubMed] [Google Scholar]
  63. Tobkes N., Wallace B. A., Bayley H. Secondary structure and assembly mechanism of an oligomeric channel protein. Biochemistry. 1985 Apr 9;24(8):1915–1920. doi: 10.1021/bi00329a017. [DOI] [PubMed] [Google Scholar]
  64. Vogel H., Wright J. K., Jähnig F. The structure of the lactose permease derived from Raman spectroscopy and prediction methods. EMBO J. 1985 Dec 16;4(13A):3625–3631. doi: 10.1002/j.1460-2075.1985.tb04126.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Wallace B. A., Kohl N., Teeter M. M. Crambin in phospholipid vesicles: Circular dichroism analysis of crystal structure relevance. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1406–1410. doi: 10.1073/pnas.81.5.1406. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Wallace B. A., Kohl N., Teeter M. M. Crambin in phospholipid vesicles: Circular dichroism analysis of crystal structure relevance. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1406–1410. doi: 10.1073/pnas.81.5.1406. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Williams R. W., Teeter M. M. Raman spectroscopy of homologous plant toxins: crambin and alpha 1- and beta-purothionin secondary structures, disulfide conformation, and tyrosine environment. Biochemistry. 1984 Dec 18;23(26):6796–6802. doi: 10.1021/bi00321a080. [DOI] [PubMed] [Google Scholar]
  68. Williams R. W., Teeter M. M. Raman spectroscopy of homologous plant toxins: crambin and alpha 1- and beta-purothionin secondary structures, disulfide conformation, and tyrosine environment. Biochemistry. 1984 Dec 18;23(26):6796–6802. doi: 10.1021/bi00321a080. [DOI] [PubMed] [Google Scholar]
  69. Yager P., Chang E. L., Williams R. W., Dalziel A. W. The secondary structure of acetylcholine receptor reconstituted in a single lipid component as determined by Raman spectroscopy. Biophys J. 1984 Jan;45(1):26–28. doi: 10.1016/S0006-3495(84)84095-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Yamada M., Ebina Y., Miyata T., Nakazawa T., Nakazawa A. Nucleotide sequence of the structural gene for colicin E1 and predicted structure of the protein. Proc Natl Acad Sci U S A. 1982 May;79(9):2827–2831. doi: 10.1073/pnas.79.9.2827. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES