Article | Published:

Molecular code for transmembrane-helix recognition by the Sec61 translocon

Nature volume 450, pages 10261030 (13 December 2007) | Download Citation

Abstract

Transmembrane α-helices in integral membrane proteins are recognized co-translationally and inserted into the membrane of the endoplasmic reticulum by the Sec61 translocon. A full quantitative description of this phenomenon, linking amino acid sequence to membrane insertion efficiency, is still lacking. Here, using in vitro translation of a model protein in the presence of dog pancreas rough microsomes to analyse a large number of systematically designed hydrophobic segments, we present a quantitative analysis of the position-dependent contribution of all 20 amino acids to membrane insertion efficiency, as well as of the effects of transmembrane segment length and flanking amino acids. The emerging picture of translocon-mediated transmembrane helix assembly is simple, with the critical sequence characteristics mirroring the physical properties of the lipid bilayer.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    , , & A limited universe of membrane protein families and folds. Protein Sci. 15, 1723–1734 (2006)

  2. 2.

    & Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. Biophys. J. 61, 437–447 (1992)

  3. 3.

    , & Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins 59, 252–265 (2005)

  4. 4.

    & Protein translocons: multifunctional mediators of protein translocation across membranes. Cell 112, 491–505 (2003)

  5. 5.

    et al. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433, 377–381 (2005)

  6. 6.

    , , & The Sec61p complex mediates the integration of a membrane protein by allowing lipid partitioning of the transmembrane domain. Cell 102, 233–244 (2000)

  7. 7.

    , & Membrane insertion of a potassium channel voltage sensor. Science 307, 1427 (2005)

  8. 8.

    , , , & Asn- and Asp-mediated interactions between transmembrane helices during translocon-mediated membrane protein assembly. EMBO Rep. 7, 1111–1116 (2006)

  9. 9.

    et al. Proline-induced disruption of a transmembrane α-helix in its natural environment. J. Mol. Biol. 284, 1165–1175 (1998)

  10. 10.

    , , , & Positively and negatively charged residues have different effects on the position in the membrane of a model transmembrane helix. J. Mol. Biol. 284, 1177–1183 (1998)

  11. 11.

    et al. Membrane insertion of the Shaker voltage sensor occurs both cotranslationally and posttranslationally. Proc. Natl Acad. Sci. USA 104, 8263–8268 (2007)

  12. 12.

    The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105, 1–12 (1976)

  13. 13.

    The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J. 5, 3021–3027 (1986)

  14. 14.

    et al. High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief. Bioinform. 3, 275–284 (2002)

  15. 15.

    et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000)

  16. 16.

    & Biogenesis of CFTR and other polytopic membrane proteins: new roles for the ribosome–translocon complex. J. Membr. Biol. 202, 115–126 (2004)

  17. 17.

    , , & A novel tripartite motif involved in aquaporin topogenesis, monomer folding and tetramerization. Nature Struct. Mol. Biol. 14, 762–769 (2007)

  18. 18.

    & How proteins adapt to a membrane–water interface. Trends Biochem. Sci. 25, 429–434 (2000)

  19. 19.

    & Protein–lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol. Membr. Biol. 20, 271–284 (2003)

  20. 20.

    , , & Transmembrane helices of membrane proteins may flex to satisfy hydrophobic mismatch. Biochim. Biophys. Acta 1768, 530–537 (2007)

  21. 21.

    & Effects of ‘hydrophobic mismatch’ on the location of transmembrane helices in the ER membrane. FEBS Lett. 496, 96–100 (2001)

  22. 22.

    & Cooperation of transmembrane segments during the integration of a double-spanning protein into the ER membrane. EMBO J. 22, 3654–3663 (2003)

  23. 23.

    et al. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433, 377–381 (2005)

  24. 24.

    , , & Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179, 125–142 (1984)

  25. 25.

    & An interior, trust region approach for nonlinear minimization subject to bounds. SIAM J. Optimiz. 6, 418–445 (1996)

  26. 26.

    et al. Ez, a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: Derivation and applications to determining the orientation of transmembrane and interfacial helices. J. Mol. Biol. 366, 436–448 (2007)

  27. 27.

    , , & OPM: orientations of proteins in membranes database. Bioinformatics 22, 623–625 (2006)

  28. 28.

    & Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006)

  29. 29.

    et al. High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief. Bioinform. 3, 275–284 (2002)

  30. 30.

    , & Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins 59, 252–265 (2005)

  31. 31.

    & An amino acid ‘transmembrane tendency’ scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: Relationship to biological hydrophobicity. Prot. Sci. 15, 1987–2001 (2006)

  32. 32.

    & A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105–132 (1982)

  33. 33.

    , & Solvation energies of amino acid sidechains and backbone in a family of host–guest pentapeptides. Biochemistry 35, 5109–5124 (1996)

Download references

Acknowledgements

We thank E. Missioux for technical assistance, and A. Elofsson and E. Lindahl for discussions. This work was supported by grants from the Swedish Foundation for Strategic Research, the Marianne and Marcus Wallenberg Foundation, the Swedish Cancer Foundation, the Swedish Research Council and the European Commission (BioSapiens) to G.v.H., the Magnus Bergvall Foundation to I.N., the National Institute of General Medical Sciences to S.H.W., the Swiss National Science Foundation to M.L.-B., and the Japan Society for the Promotion of Science to Y.S.

Author Contributions T.H. and N.M.M.-B. performed the experimental work together with H.K., Y.S., M.L.-B. and I.N. A.B. performed the computational work. T.H., N.M.M.-B., A.B., S.H.W. and G.v.H. prepared the manuscript. All authors discussed the results and commented on the manuscript.

Author information

Author notes

    • Tara Hessa
    • , Nadja M. Meindl-Beinker
    •  & Andreas Bernsel

    These authors contributed equally to this work.

Affiliations

  1. Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden

    • Tara Hessa
    • , Nadja M. Meindl-Beinker
    • , Hyun Kim
    • , Yoko Sato
    • , Mirjam Lerch-Bader
    • , IngMarie Nilsson
    •  & Gunnar von Heijne
  2. Stockholm Bioinformatics Center, AlbaNova, Stockholm University, SE-106 91 Stockholm, Sweden

    • Andreas Bernsel
    •  & Gunnar von Heijne
  3. Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California at Irvine, Irvine, California 92697-4560, USA

    • Stephen H. White

Authors

  1. Search for Tara Hessa in:

  2. Search for Nadja M. Meindl-Beinker in:

  3. Search for Andreas Bernsel in:

  4. Search for Hyun Kim in:

  5. Search for Yoko Sato in:

  6. Search for Mirjam Lerch-Bader in:

  7. Search for IngMarie Nilsson in:

  8. Search for Stephen H. White in:

  9. Search for Gunnar von Heijne in:

Corresponding author

Correspondence to Gunnar von Heijne.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    The file contains Supplementary Figures S1-S6 with Legends and Supplementary Tables S1-S2.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature06387

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.