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Recognition of transmembrane helices by the endoplasmic reticulum translocon

Abstract

Membrane proteins depend on complex translocation machineries for insertion into target membranes. Although it has long been known that an abundance of nonpolar residues in transmembrane helices is the principal criterion for membrane insertion, the specific sequence-coding for transmembrane helices has not been identified. By challenging the endoplasmic reticulum Sec61 translocon with an extensive set of designed polypeptide segments, we have determined the basic features of this code, including a ‘biological’ hydrophobicity scale. We find that membrane insertion depends strongly on the position of polar residues within transmembrane segments, adding a new dimension to the problem of predicting transmembrane helices from amino acid sequences. Our results indicate that direct protein–lipid interactions are critical during translocon-mediated membrane insertion.

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Figure 1: Integration of H-segments into the microsomal membrane.
Figure 2: Biological and biophysical ΔGaa scales.
Figure 3: Positional dependencies in ΔGapp.

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References

  1. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. Predicting transmembrane protein topology with a hidden Markov model. Application to complete genomes. J. Mol. Biol. 305, 567–580 (2001)

    Article  CAS  Google Scholar 

  2. von Heijne, G. Recent advances in the understanding of membrane protein assembly and structure. Q. Rev. Biophys. 32, 285–307 (2000)

    Article  Google Scholar 

  3. von Heijne, G. Membrane protein assembly in vivo. Adv. Protein Chem. 63, 1–18 (2003)

    Article  CAS  Google Scholar 

  4. Snapp, E., Reinhart, G., Bogert, B., Lippincott-Schwartz, J. & Hegde, R. The organization of engaged and quiescent translocons in the endoplasmic reticulum of mammalian cells. J. Cell Biol. 164, 997–1007 (2004)

    Article  CAS  Google Scholar 

  5. Rapoport, T. A., Goder, V., Heinrich, S. U. & Matlack, K. E. Membrane-protein integration and the role of the translocation channel. Trends Cell Biol. 14, 568–575 (2004)

    Article  CAS  Google Scholar 

  6. Alder, N. N. & Johnson, A. E. Cotranslational membrane protein biogenesis at the endoplasmic reticulum. J. Biol. Chem. 279, 22787–22790 (2004)

    Article  CAS  Google Scholar 

  7. van den Berg, B. et al. X-ray structure of a protein-conducting channel. Nature 427, 36–44 (2004)

    Article  CAS  Google Scholar 

  8. Woolhead, C. A., McCormick, P. J. & Johnson, A. E. Nascent membrane and secretory proteins differ in FRET-detected folding. Cell 116, 725–736 (2004)

    Article  CAS  Google Scholar 

  9. de Planque, M. R. R. & Killian, J. A. Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol. Membr. Biol. 20, 271–284 (2003)

    Article  CAS  Google Scholar 

  10. White, S. H. & Wimley, W. C. Membrane protein folding and stability: Physical principles. Annu. Rev. Biophys. Biomol. Struct. 28, 319–365 (1999)

    Article  CAS  Google Scholar 

  11. Ulmschneider, M. B. & Sansom, M. S. P. Amino acid distributions in integral membrane protein structures. Biochim. Biophys. Acta 1512, 1–14 (2001)

    Article  CAS  Google Scholar 

  12. Beuming, T. & Weinstein, H. A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. Bioinformatics 20, 1822–1835 (2004)

    Article  CAS  Google Scholar 

  13. Sääf, A., Wallin, E. & von Heijne, G. Stop-transfer function of pseudo-random amino acid segments during translocation across prokaryotic and eukaryotic membranes. Eur. J. Biochem. 251, 821–829 (1998)

    Article  Google Scholar 

  14. Wimley, W. C., Creamer, T. P. & White, S. H. Solvation energies of amino acid sidechains and backbone in a family of host-guest pentapeptides. Biochemistry 35, 5109–5124 (1996)

    Article  CAS  Google Scholar 

  15. Jayasinghe, S., Hristova, K. & White, S. H. Energetics, stability, and prediction of transmembrane helices. J. Mol. Biol. 312, 927–934 (2001)

    Article  CAS  Google Scholar 

  16. Cornette, J. L. et al. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol. 195, 659–685 (1987)

    Article  CAS  Google Scholar 

  17. Degli Esposti, M., Crimi, M. & Venturoli, G. A critical evaluation of the hydropathy profile of membrane proteins. Eur. J. Biochem. 190, 207–219 (1990)

    Article  CAS  Google Scholar 

  18. Heinrich, S., Mothes, W., Brunner, J. & Rapoport, T. The Sec61p complex mediates the integration of a membrane protein by allowing lipid partitioning of the transmembrane domain. Cell 102, 233–244 (2000)

    Article  CAS  Google Scholar 

  19. Lu, L. P. & Deber, C. M. Guidelines for membrane protein engineering derived from de novo designed model peptides. Biopolymers 47, 41–62 (1998)

    Article  Google Scholar 

  20. Bechinger, B. Membrane insertion and orientation of polyalanine peptides: A N-15 solid-state NMR spectroscopy investigation. Biophys. J. 81, 2251–2256 (2001)

    Article  ADS  CAS  Google Scholar 

  21. Lewis, R. N. et al. A polyalanine-based peptide cannot form a stable transmembrane alpha-helix in fully hydrated phospholipid bilayers. Biochemistry 40, 12103–12111 (2001)

    Article  MathSciNet  CAS  Google Scholar 

  22. Wallin, E., Tsukihara, T., Yoshikawa, S., von Heijne, G. & Elofsson, A. Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci. 6, 808–815 (1997)

    Article  CAS  Google Scholar 

  23. Killian, J. A. & von Heijne, G. How proteins adapt to a membrane-water interface. Trends Biochem. Sci. 25, 429–434 (2000)

    Article  CAS  Google Scholar 

  24. Yau, W. M., Wimley, W. C., Gawrisch, K. & White, S. H. The preference of tryptophan for membrane interfaces. Biochemistry 37, 14713–14718 (1998)

    Article  CAS  Google Scholar 

  25. Wimley, W. C. & White, S. H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Struct. Biol. 3, 842–848 (1996)

    Article  CAS  Google Scholar 

  26. Eisenberg, D., Schwarz, E., Komaromy, M. & Wall, R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179, 125–142 (1984)

    Article  CAS  Google Scholar 

  27. Plath, K., Mothes, W., Wilkinson, B. M., Stirling, C. J. & Rapoport, T. A. Signal sequence recognition in posttranslational protein transport across the yeast ER membrane. Cell 94, 795–807 (1998)

    Article  CAS  Google Scholar 

  28. McCormick, P. J., Miao, Y., Shao, Y., Lin, J. & Johnson, A. E. Cotranslational protein integration into the ER membrane is mediated by the binding of nascent chains to translocon proteins. Mol. Cell 12, 329–341 (2003)

    Article  CAS  Google Scholar 

  29. Presta, L. G. & Rose, G. D. Helix signals in proteins. Science 240, 1632–1641 (1988)

    Article  ADS  CAS  Google Scholar 

  30. Richardson, J. S. & Richardson, D. C. Amino acid preferences for specific locations at the ends of α-helices. Science 240, 1648–1652 (1988)

    Article  ADS  CAS  Google Scholar 

  31. Yohannan, S. et al. Proline substitutions are not easily accommodated in a membrane protein. J. Mol. Biol. 341, 1–6 (2004)

    Article  CAS  Google Scholar 

  32. Kuroiwa, T., Sakaguchi, M., Mihara, K. & Omura, T. Systematic analysis of stop-transfer sequence for microsomal membrane. J. Biol. Chem. 266, 9251–9255 (1991)

    CAS  PubMed  Google Scholar 

  33. Anthony, V. & Skach, W. R. Molecular mechanism of P-glycoprotein assembly into cellular membranes. Curr. Protein Pept. Sci. 3, 485–501 (2002)

    Article  CAS  Google Scholar 

  34. Kozak, M. Initiation of translation in prokaryotes and eukaryotes. Gene 234, 187–208 (1999)

    Article  CAS  Google Scholar 

  35. Liljeström, P. & Garoff, H. A new generation of animal cell expression vectors based on the Semliki Forest virus replicon. Biotechnology 9, 1356–1361 (1991)

    Article  Google Scholar 

  36. Liljeström, P., Lusa, S., Huylebroeck, D. & Garoff, H. In vitro mutagenesis of a full-length cDNA clone of Semliki Forest virus: the small 6,000-molecular-weight membrane protein modulates virus release. J. Virol. 65, 4107–4113 (1991)

    PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We wish to thank E. Missioux for technical assistance and R. MacKinnon, D. Rees, and T. Rapoport for comments. This work was supported by grants from the Swedish Cancer Foundation to G.v.H. and I.M.N., the Marianne and Marcus Wallenberg Foundation and the Swedish Research Council to G.v.H., the Magnus Bergvall Foundation to I.M.N., and the National Institute of General Medical Sciences to S.H.W.

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Correspondence to Gunnar von Heijne.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Data S1

Derivation of the δGaaapp scale. (PDF 60 kb)

Supplementary Data S2

Additivity of δGaaapp values (PDF 58 kb)

Supplementary Data S3

H-segment constructs expressed in vivo. (PDF 73 kb)

Supplementary Data S4

H-segments used to analyse the role of flanking residues. (PDF 58 kb)

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Hessa, T., Kim, H., Bihlmaier, K. et al. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433, 377–381 (2005). https://doi.org/10.1038/nature03216

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