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Molecular recognition of a single sphingolipid species by a protein’s transmembrane domain

Nature volume 481, pages 525–529 (2012)Cite this article

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Abstract

Functioning and processing of membrane proteins critically depend on the way their transmembrane segments are embedded in the membrane1. Sphingolipids are structural components of membranes and can also act as intracellular second messengers. Not much is known of sphingolipids binding to transmembrane domains (TMDs) of proteins within the hydrophobic bilayer, and how this could affect protein function. Here we show a direct and highly specific interaction of exclusively one sphingomyelin species, SM 18, with the TMD of the COPI machinery protein p24 (ref. 2). Strikingly, the interaction depends on both the headgroup and the backbone of the sphingolipid, and on a signature sequence (VXXTLXXIY) within the TMD. Molecular dynamics simulations show a close interaction of SM 18 with the TMD. We suggest a role of SM 18 in regulating the equilibrium between an inactive monomeric and an active oligomeric state of the p24 protein3,4, which in turn regulates COPI-dependent transport. Bioinformatic analyses predict that the signature sequence represents a conserved sphingolipid-binding cavity in a variety of mammalian membrane proteins. Thus, in addition to a function as second messengers, sphingolipids can act as cofactors to regulate the function of transmembrane proteins. Our discovery of an unprecedented specificity of interaction of a TMD with an individual sphingolipid species adds to our understanding of why biological membranes are assembled from such a large variety of different lipids.

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Figure 1: p24 specifically interacts with SM 18.
Figure 2: Characterization of the sphingomyelin-binding pocket.
Figure 3: A conserved sphingolipid binding signature.
Figure 4: Binding of SM 18 to p24(TMD) affects protein transport and triggers p24 dimerization.

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Acknowledgements

The authors would like to thank T. Sachsenheimer for technical assistance, A. Brodde for help with lipid synthesis, D. Cassel for comments on the manuscript, and the members of the Wieland laboratory for discussion. This work was supported by a grant of the German research foundation (DFG, TRR83) to B.B. and F.W. and by ERC grants to E.L. (209825) and G.v.H. (AdG232648); F.-X.C. was supported by a FEBS fellowship and A.M.E. by the Peter and Traudl Engelhorn foundation.

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Author notes

  1. Per Haberkant

    Present address: Present address: Cell Biology and Biophysics Unit EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,

  2. F.-Xabier Contreras and Andreas M. Ernst: These authors contributed equally to this work.

Authors and Affiliations

  1. Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany ,

    F.-Xabier Contreras, Andreas M. Ernst, Per Haberkant, Başak Gönen, Felix Wieland & Britta Brügger

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

    Patrik Björkholm, Erik Lindahl, Arne Elofsson & Gunnar von Heijne

  3. Stockholm Bioinformatics Center, Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden ,

    Patrik Björkholm, Arne Elofsson & Gunnar von Heijne

  4. Theoretical & Computational Biophysics, Royal Institute of Technology, AlbaNova University Centre, SE-106 91 Stockholm, Sweden ,

    Erik Lindahl

  5. ALMF, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany ,

    Christian Tischer & Rainer Pepperkok

  6. LIMES Life and Medical Sciences Institute, Carl-Troll-Strasse 31, 53115 Bonn, Germany ,

    Christoph Thiele

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  1. F.-Xabier Contreras
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Contributions

F.-X.C., A.M.E. and P.H. designed and performed the experiments. P.B. performed the bioinformatics analyses under the supervision of A.E., G.v.H. and A.M.E.; E.L. designed, performed and interpreted molecular dynamics simulation experiments. B.G. performed in vivo crosslinking experiments. C.Th. provided reagents and helped to establish photolabelling and FRET experiments. C.Ti. and R.P. provided reagents and tools and supported A.M.E. concerning VSV-G experiments. F.W. and B.B. designed the experiments and wrote the manuscript.

Corresponding authors

Correspondence to Felix Wieland or Britta Brügger.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains a Supplementary Discussion, Supplementary Methods, Supplementary References, Supplementary Table 1, legends for Supplementary Movies 1-2 and Supplementary Figures 1-12 with legends. (PDF 24139 kb)

Supplementary Movie 1

The movie shows the dynamics of the SM 18:0-p24TMD interaction. A rigid interaction of the headgroup with Y21 is observed, while the chain packing to V13/T16/L17 appears to be dynamic in nature. The long chain wraps around the p24 backbone, with the end of the chain pointing to the centre of the bilayer (see Supplementary Information file for full legend). (MOV 3157 kb)

Supplementary Movie 2

The movie shows the dynamics of SM 14:0 close to the p24TMD. The headgroup interacts with Y21 from below, which rotates the chains out from the TMD (see Supplementary Information file for full legend). (MOV 2999 kb)

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Contreras, FX., Ernst, A., Haberkant, P. et al. Molecular recognition of a single sphingolipid species by a protein’s transmembrane domain. Nature 481, 525–529 (2012). https://doi.org/10.1038/nature10742

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