Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Innovation
  • Published:

The systematic analysis of protein–lipid interactions comes of age

Nature Reviews Molecular Cell Biology volume 16, pages 753–761 (2015)Cite this article

Subjects

Abstract

Lipids tailor membrane identities and function as molecular hubs in all cellular processes. However, the ways in which lipids modulate protein function and structure are poorly understood and still require systematic investigation. In this Innovation article, we summarize pioneering technologies, including lipid-overlay assays, lipid pull-down assays, affinity-purification lipidomics and the liposome microarray-based assay (LiMA), that will enable protein–lipid interactions to be deciphered on a systems level. We discuss how these technologies can be applied to the charting of system-wide networks and to the development of new pharmaceutical strategies.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: System-wide methods for capturing protein–lipid interactions.
Figure 2: Timeline of key events in protein–lipid interaction research.
Figure 3: Future scientific and technological challenges for liposome microarray-based assays (LiMA).

Similar content being viewed by others

References

  1. van Meer, G., Voelker, D. R. & Feigenson, G. W. Membrane lipids: where they are and how they behave. Nat. Rev. Mol. Cell. Biol. 9, 112–124 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Holthuis, J. C. & Menon, A. K. Lipid landscapes and pipelines in membrane homeostasis. Nature 510, 48–57 (2014).

    CAS  PubMed  Google Scholar 

  3. Fahy, E. et al. Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res. 50, S9–S14 (2009).

    PubMed  PubMed Central  Google Scholar 

  4. Overington, J. P., Al-Lazikani, B. & Hopkins, A. L. How many drug targets are there? Nat. Rev. Drug Discov. 5, 993–996 (2006).

    CAS  PubMed  Google Scholar 

  5. Wymann, M. P. & Schneiter, R. Lipid signalling in disease. Nat. Rev. Mol. Cell. Biol. 9, 162–176 (2008).

    CAS  PubMed  Google Scholar 

  6. Babu, M. et al. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature 489, 585–589 (2012).

    CAS  PubMed  Google Scholar 

  7. Capelluto, D. G. Lipid-mediated Protein Signaling (Springer, 2013).

    Google Scholar 

  8. Sharpe, H. J., Stevens, T. J. & Munro, S. A comprehensive comparison of transmembrane domains reveals organelle-specific properties. Cell 142, 158–169 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Nury, H. et al. Structural basis for lipid-mediated interactions between mitochondrial ADP/ATP carrier monomers. FEBS Lett. 579, 6031–6036 (2005).

    CAS  PubMed  Google Scholar 

  10. Whorton, M. R. & MacKinnon, R. Crystal structure of the mammalian GIRK2 K+ channel and gating regulation by G proteins, PIP2, and sodium. Cell 147, 199–208 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Contreras, F. X. et al. Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature 481, 525–529 (2012).

    CAS  PubMed  Google Scholar 

  12. Lemmon, M. A. Membrane recognition by phospholipid-binding domains. Nat. Rev. Mol. Cell. Biol. 9, 99–111 (2008).

    CAS  PubMed  Google Scholar 

  13. Antonny, B. Mechanisms of membrane curvature sensing. Annu. Rev. Biochem. 80, 101–123 (2011).

    CAS  PubMed  Google Scholar 

  14. Scott, J. D. & Pawson, T. Cell signaling in space and time: where proteins come together and when they're apart. Science 326, 1220–1224 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Yu, J. W. et al. Genome-wide analysis of membrane targeting by S. cerevisiae pleckstrin homology domains. Mol. Cell 13, 677–688 (2004).

    CAS  PubMed  Google Scholar 

  16. Gallego, O. et al. A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae. Mol. Syst. Biol. 6, 430 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Moravcevic, K., Oxley, C. L. & Lemmon, M. A. Conditional peripheral membrane proteins: facing up to limited specificity. Structure 20, 15–27 (2012).

    CAS  PubMed  Google Scholar 

  18. Lev, S. Non-vesicular lipid transport by lipid-transfer proteins and beyond. Nat. Rev. Mol. Cell. Biol. 11, 739–750 (2010).

    CAS  PubMed  Google Scholar 

  19. Forman, B. M., Chen, J. & Evans, R. M. Hypolipidemic drugs, polyunsaturated fatty acids, and eicosanoids are ligands for peroxisome proliferator-activated receptors α and δ. Proc. Natl Acad. Sci. USA 94, 4312–4317 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Grabon, A., Khan, D. & Bankaitis, V. A. Phosphatidylinositol transfer proteins and instructive regulation of lipid kinase biology. Biochim. Biophys. Acta 1851, 724–735 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Musille, P. M., Kohn, J. A. & Ortlund, E. A. Phospholipid-driven gene regulation. FEBS Lett. 587, 1238–1246 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Li, X., Gianoulis, T. A., Yip, K. Y., Gerstein, M. & Snyder, M. Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses. Cell 143, 639–650 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Maeda, K. et al. Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins. Nature 501, 257–261 (2013).

    CAS  PubMed  Google Scholar 

  24. Charbonnier, S., Gallego, O. & Gavin, A. C. The social network of a cell: recent advances in interactome mapping. Biotechnol. Annu. Rev. 14, 1–28 (2008).

    CAS  PubMed  Google Scholar 

  25. Barrera, N. P., Zhou, M. & Robinson, C. V. The role of lipids in defining membrane protein interactions: insights from mass spectrometry. Trends Cell Biol. 23, 1–8 (2013).

    CAS  PubMed  Google Scholar 

  26. Narayan, K. & Lemmon, M. A. Determining selectivity of phosphoinositide-binding domains. Methods 39, 122–133 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Zhao, H. & Lappalainen, P. A simple guide to biochemical approaches for analyzing protein-lipid interactions. Mol. Biol. Cell 23, 2823–2830 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Besenicar, M., Macek, P., Lakey, J. H. & Anderluh, G. Surface plasmon resonance in protein-membrane interactions. Chem. Phys. Lipids 141, 169–178 (2006).

    CAS  PubMed  Google Scholar 

  29. Zhang, Z., Wu, S., Stenoien, D. L. & Pasa-Tolic, L. High-throughput proteomics. Annu. Rev. Anal. Chem. 7, 427–454 (2014).

    CAS  Google Scholar 

  30. Barrera, N. P. et al. Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions. Nat. Methods 6, 585–587 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Laganowsky, A. et al. Membrane proteins bind lipids selectively to modulate their structure and function. Nature 510, 172–175 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Hopper, J. T. et al. Detergent-free mass spectrometry of membrane protein complexes. Nat. Methods 10, 1206–1208 (2013).

    CAS  PubMed  Google Scholar 

  33. Bechara, C. et al. A subset of annular lipids is linked to the flippase activity of an ABC transporter. Nat. Chem. 7, 255–262 (2015).

    CAS  PubMed  Google Scholar 

  34. Zhou, M. et al. Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding. Science 334, 380–385 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Zhang, P., Wang, Y., Sesaki, H. & Iijima, M. Proteomic identification of phosphatidylinositol (3,4,5) triphosphate-binding proteins in Dictyostelium discoideum. Proc. Natl Acad. Sci. USA 107, 11829–11834 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Dowler, S., Kular, G. & Alessi, D. R. Protein lipid overlay assay. Sci. STKE 2002, pl6 (2002).

    PubMed  Google Scholar 

  37. Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 293, 2101–2105 (2001).

    CAS  PubMed  Google Scholar 

  38. Lu, K. Y. et al. Profiling lipid–protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays. Mol. Cell. Proteomics 11, 1177–1190 (2012).

    PubMed  PubMed Central  Google Scholar 

  39. Saliba, A. E. et al. A quantitative liposome microarray to systematically characterize protein-lipid interactions. Nat. Methods 11, 47–50 (2014).

    CAS  PubMed  Google Scholar 

  40. Pepperkok, R. & Ellenberg, J. High-throughput fluorescence microscopy for systems biology. Nat. Rev. Mol. Cell. Biol. 7, 690–696 (2006).

    CAS  PubMed  Google Scholar 

  41. Vonkova, I. et al. Lipid cooperativity as a general membrane-recruitment principle for PH domains. Cell Rep. 12, 1519–1530 (2015).

    CAS  PubMed  Google Scholar 

  42. Hansen, J. S., Thompson, J. R., Helix-Nielsen, C. & Malmstadt, N. Lipid directed intrinsic membrane protein segregation. J. Am. Chem. Soc. 135, 17294–17297 (2013).

    CAS  PubMed  Google Scholar 

  43. Costanzo, M. et al. The genetic landscape of a cell. Science 327, 425–431 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Laufer, C., Fischer, B., Huber, W. & Boutros, M. Measuring genetic interactions in human cells by RNAi and imaging. Nat. Protoc. 9, 2341–2353 (2014).

    CAS  PubMed  Google Scholar 

  45. Aguilar, P. S. et al. A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Nat. Struct. Mol. Biol. 17, 901–908 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Surma, M. A. et al. A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress. Mol. Cell 51, 519–530 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Isakoff, S. J. et al. Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast. EMBO J. 17, 5374–5387 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Moravcevic, K. et al. Kinase associated-1 domains drive MARK/PAR1 kinases to membrane targets by binding acidic phospholipids. Cell 143, 966–977 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Park, W. S. et al. Comprehensive identification of PIP3-regulated PH domains from C. elegans to H. sapiens by model prediction and live imaging. Mol. Cell 30, 381–392 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Cowart, L. A. et al. Revealing a signaling role of phytosphingosine-1-phosphate in yeast. Mol. Syst. Biol. 6, 349 (2010).

    PubMed  PubMed Central  Google Scholar 

  51. Gavin, A. C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006).

    CAS  PubMed  Google Scholar 

  52. Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003).

    CAS  PubMed  Google Scholar 

  53. Thiele, C., Hannah, M. J., Fahrenholz, F. & Huttner, W. B. Cholesterol binds to synaptophysin and is required for biogenesis of synaptic vesicles. Nat. Cell Biol. 2, 42–49 (2000).

    CAS  PubMed  Google Scholar 

  54. Haberkant, P. & Holthuis, J. C. Fat and fabulous: bifunctional lipids in the spotlight. Biochim. Biophys. Acta 1841, 1022–1030 (2014).

    CAS  PubMed  Google Scholar 

  55. Hulce, J. J., Cognetta, A. B., Niphakis, M. J., Tully, S. E. & Cravatt, B. F. Proteome-wide mapping of cholesterol-interacting proteins in mammalian cells. Nat. Methods 10, 259–264 (2013).

    PubMed  PubMed Central  Google Scholar 

  56. Gubbens, J. et al. Photocrosslinking and click chemistry enable the specific detection of proteins interacting with phospholipids at the membrane interface. Chem. Biol. 16, 3–14 (2009).

    CAS  PubMed  Google Scholar 

  57. Peng, T. & Hang, H. C. Bifunctional fatty acid chemical reporter for analyzing S-palmitoylated membrane protein–protein interactions in mammalian cells. J. Am. Chem. Soc. 137, 556–559 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Subramanian, D. et al. Activation of membrane-permeant caged PtdIns(3)P induces endosomal fusion in cells. Nat. Chem. Biol. 6, 324–326 (2010).

    CAS  PubMed  Google Scholar 

  59. Hoglinger, D., Nadler, A. & Schultz, C. Caged lipids as tools for investigating cellular signaling. Biochim. Biophys. Acta 1841, 1085–1096 (2014).

    PubMed  Google Scholar 

  60. Niphakis, M. J. et al. A global map of lipid-binding proteins and their ligandability in cells. Cell 161, 1668–1680 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Wei, L. et al. Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering. Nat. Methods 11, 410–412 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Folick, A., Min, W. & Wang, M. C. Label-free imaging of lipid dynamics using coherent anti-stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) microscopy. Curr. Opin. Genet. Dev. 21, 585–590 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. McLaughlin, S. & Murray, D. Plasma membrane phosphoinositide organization by protein electrostatics. Nature 438, 605–611 (2005).

    CAS  PubMed  Google Scholar 

  64. Mouchlis, V. D., Bucher, D., McCammon, J. A. & Dennis, E. A. Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates. Proc. Natl Acad. Sci. USA 112, E516–E525 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Leonard, T. A., Rozycki, B., Saidi, L. F., Hummer, G. & Hurley, J. H. Crystal structure and allosteric activation of protein kinase C βII. Cell 144, 55–66 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Groves, J. T. & Kuriyan, J. Molecular mechanisms in signal transduction at the membrane. Nat. Struct. Mol. Biol. 17, 659–665 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. van den Bogaart, G. et al. Membrane protein sequestering by ionic protein-lipid interactions. Nature 479, 552–555 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Yang, S. T., Kiessling, V., Simmons, J. A., White, J. M. & Tamm, L. K. HIV gp41-mediated membrane fusion occurs at edges of cholesterol-rich lipid domains. Nat. Chem. Biol. 11, 424–431 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Koberlin, M. S. et al. A conserved circular network of coregulated lipids modulates innate immune responses. Cell 162, 170–183 (2015).

    PubMed  PubMed Central  Google Scholar 

  70. Carpten, J. D. et al. A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature 448, 439–444 (2007).

    CAS  PubMed  Google Scholar 

  71. Lindhurst, M. J. et al. A mosaic activating mutation in AKT1 associated with the Proteus syndrome. N. Engl. J. Med. 365, 611–619 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Arya, V. B. et al. Activating AKT2 mutation: hypoinsulinemic hypoketotic hypoglycemia. J. Clin. Endocrinol. Metab. 99, 391–394 (2014).

    CAS  PubMed  Google Scholar 

  73. Yadav, K. K. & Bar-Sagi, D. Allosteric gating of Son of sevenless activity by the histone domain. Proc. Natl Acad. Sci. USA 107, 3436–3440 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Matute, J. D. et al. A new genetic subgroup of chronic granulomatous disease with autosomal recessive mutations in p40 phox and selective defects in neutrophil NADPH oxidase activity. Blood 114, 3309–3315 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Ling, L. L. et al. A new antibiotic kills pathogens without detectable resistance. Nature 517, 455–459 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Anderson, T. M. et al. Amphotericin forms an extramembranous and fungicidal sterol sponge. Nat. Chem. Biol. 10, 400–406 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Salomon, D. et al. Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides. Nat. Commun. 4, 2973 (2013).

    PubMed  Google Scholar 

  78. Hsu, N. Y. et al. Viral reorganization of the secretory pathway generates distinct organelles for RNA replication. Cell 141, 799–811 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Bhattacharjee, S., Stahelin, R. V. & Haldar, K. Host targeting of virulence determinants and phosphoinositides in blood stage malaria parasites. Trends Parasitol. 28, 555–562 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Miao, B. et al. Small molecule inhibition of phosphatidylinositol-3,4,5-triphosphate (PIP3) binding to pleckstrin homology domains. Proc. Natl Acad. Sci. USA 107, 20126–20131 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Jo, H. et al. Deactivation of Akt by a small molecule inhibitor targeting pleckstrin homology domain and facilitating Akt ubiquitination. Proc. Natl Acad. Sci. USA 108, 6486–6491 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Jesorka, A. & Orwar, O. Liposomes: technologies and analytical applications. Annu. Rev. Anal. Chem. 1, 801–832 (2008).

    CAS  Google Scholar 

  83. Walde, P., Cosentino, K., Engel, H. & Stano, P. Giant vesicles: preparations and applications. ChemBioChem 11, 848–865 (2010).

    CAS  PubMed  Google Scholar 

  84. Horger, K. S., Estes, D. J., Capone, R. & Mayer, M. Films of agarose enable rapid formation of giant liposomes in solutions of physiologic ionic strength. J. Am. Chem. Soc. 131, 1810–1819 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Stachowiak, J. C. et al. Unilamellar vesicle formation and encapsulation by microfluidic jetting. Proc. Natl Acad. Sci. USA 105, 4697–4702 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Lemmon, M. A., Ferguson, K. M., O'Brien, R., Sigler, P. B. & Schlessinger, J. Specific and high-affinity binding of inositol phosphates to an isolated pleckstrin homology domain. Proc. Natl Acad. Sci. USA 92, 10472–10476 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Jerabek-Willemsen, M., Wienken, C. J., Braun, D., Baaske, P. & Duhr, S. Molecular interaction studies using microscale thermophoresis. Assay Drug Dev. Technol. 9, 342–353 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank all members of A.-C.G.'s groups for continuous discussions and support. This work was partially funded by the German Federal Ministry of Education and Research (BMBF; 01GS0865) in the framework of the IG-Cellular System Genomics project and the CellNetworks (Excellence Initiative of the University of Heidelberg) community to A.-C.G. A.-E.S. was supported by the European Molecular Biology Laboratory and the EU Marie Curie Actions Interdisciplinary Postdoctoral cofund Programme.

Author information

Authors and Affiliations

  1. Institute for Molecular Infection Biology and Core Unit Systems Medicine, University of Würzburg, Josef-Schneider-Strasse 2, Würzburg, D-97080, Germany

    Antoine-Emmanuel Saliba

  2. European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg, D-69117, Germany

    Ivana Vonkova

  3. European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit and Molecular Medicine Partnership Unit, Meyerhofstrasse 1, Heidelberg, D-69117, Germany

    Anne-Claude Gavin

Authors
  1. Antoine-Emmanuel Saliba
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ivana Vonkova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Anne-Claude Gavin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Anne-Claude Gavin.

Ethics declarations

Competing interests

The authors declare competing financial interests in the form of a patent application based on the method liposome microarray-based assay (LiMA).

PowerPoint slides

Supplementary information

Supplementary information S1 (table)

List of lipid suppliers (PDF 59 kb)

Related links

Related links

FURTHER INFORMATION

LIPID MAPS Structure Database

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Saliba, AE., Vonkova, I. & Gavin, AC. The systematic analysis of protein–lipid interactions comes of age. Nat Rev Mol Cell Biol 16, 753–761 (2015). https://doi.org/10.1038/nrm4080

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm4080

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing