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
Open Access articles citing this article.
Nature Communications Open Access 20 March 2023
Communications Biology Open Access 26 May 2022
Communications Biology Open Access 30 April 2021
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Rent or buy this article
Prices vary by article type
Prices may be subject to local taxes which are calculated during checkout
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).
Holthuis, J. C. & Menon, A. K. Lipid landscapes and pipelines in membrane homeostasis. Nature 510, 48–57 (2014).
Fahy, E. et al. Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res. 50, S9–S14 (2009).
Overington, J. P., Al-Lazikani, B. & Hopkins, A. L. How many drug targets are there? Nat. Rev. Drug Discov. 5, 993–996 (2006).
Wymann, M. P. & Schneiter, R. Lipid signalling in disease. Nat. Rev. Mol. Cell. Biol. 9, 162–176 (2008).
Babu, M. et al. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature 489, 585–589 (2012).
Capelluto, D. G. Lipid-mediated Protein Signaling (Springer, 2013).
Sharpe, H. J., Stevens, T. J. & Munro, S. A comprehensive comparison of transmembrane domains reveals organelle-specific properties. Cell 142, 158–169 (2010).
Nury, H. et al. Structural basis for lipid-mediated interactions between mitochondrial ADP/ATP carrier monomers. FEBS Lett. 579, 6031–6036 (2005).
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).
Contreras, F. X. et al. Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature 481, 525–529 (2012).
Lemmon, M. A. Membrane recognition by phospholipid-binding domains. Nat. Rev. Mol. Cell. Biol. 9, 99–111 (2008).
Antonny, B. Mechanisms of membrane curvature sensing. Annu. Rev. Biochem. 80, 101–123 (2011).
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).
Yu, J. W. et al. Genome-wide analysis of membrane targeting by S. cerevisiae pleckstrin homology domains. Mol. Cell 13, 677–688 (2004).
Gallego, O. et al. A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae. Mol. Syst. Biol. 6, 430 (2010).
Moravcevic, K., Oxley, C. L. & Lemmon, M. A. Conditional peripheral membrane proteins: facing up to limited specificity. Structure 20, 15–27 (2012).
Lev, S. Non-vesicular lipid transport by lipid-transfer proteins and beyond. Nat. Rev. Mol. Cell. Biol. 11, 739–750 (2010).
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).
Grabon, A., Khan, D. & Bankaitis, V. A. Phosphatidylinositol transfer proteins and instructive regulation of lipid kinase biology. Biochim. Biophys. Acta 1851, 724–735 (2015).
Musille, P. M., Kohn, J. A. & Ortlund, E. A. Phospholipid-driven gene regulation. FEBS Lett. 587, 1238–1246 (2013).
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).
Maeda, K. et al. Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins. Nature 501, 257–261 (2013).
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).
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).
Narayan, K. & Lemmon, M. A. Determining selectivity of phosphoinositide-binding domains. Methods 39, 122–133 (2006).
Zhao, H. & Lappalainen, P. A simple guide to biochemical approaches for analyzing protein-lipid interactions. Mol. Biol. Cell 23, 2823–2830 (2012).
Besenicar, M., Macek, P., Lakey, J. H. & Anderluh, G. Surface plasmon resonance in protein-membrane interactions. Chem. Phys. Lipids 141, 169–178 (2006).
Zhang, Z., Wu, S., Stenoien, D. L. & Pasa-Tolic, L. High-throughput proteomics. Annu. Rev. Anal. Chem. 7, 427–454 (2014).
Barrera, N. P. et al. Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions. Nat. Methods 6, 585–587 (2009).
Laganowsky, A. et al. Membrane proteins bind lipids selectively to modulate their structure and function. Nature 510, 172–175 (2014).
Hopper, J. T. et al. Detergent-free mass spectrometry of membrane protein complexes. Nat. Methods 10, 1206–1208 (2013).
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).
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).
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).
Dowler, S., Kular, G. & Alessi, D. R. Protein lipid overlay assay. Sci. STKE 2002, pl6 (2002).
Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 293, 2101–2105 (2001).
Lu, K. Y. et al. Profiling lipid–protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays. Mol. Cell. Proteomics 11, 1177–1190 (2012).
Saliba, A. E. et al. A quantitative liposome microarray to systematically characterize protein-lipid interactions. Nat. Methods 11, 47–50 (2014).
Pepperkok, R. & Ellenberg, J. High-throughput fluorescence microscopy for systems biology. Nat. Rev. Mol. Cell. Biol. 7, 690–696 (2006).
Vonkova, I. et al. Lipid cooperativity as a general membrane-recruitment principle for PH domains. Cell Rep. 12, 1519–1530 (2015).
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).
Costanzo, M. et al. The genetic landscape of a cell. Science 327, 425–431 (2010).
Laufer, C., Fischer, B., Huber, W. & Boutros, M. Measuring genetic interactions in human cells by RNAi and imaging. Nat. Protoc. 9, 2341–2353 (2014).
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).
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).
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).
Moravcevic, K. et al. Kinase associated-1 domains drive MARK/PAR1 kinases to membrane targets by binding acidic phospholipids. Cell 143, 966–977 (2010).
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).
Cowart, L. A. et al. Revealing a signaling role of phytosphingosine-1-phosphate in yeast. Mol. Syst. Biol. 6, 349 (2010).
Gavin, A. C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006).
Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003).
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).
Haberkant, P. & Holthuis, J. C. Fat and fabulous: bifunctional lipids in the spotlight. Biochim. Biophys. Acta 1841, 1022–1030 (2014).
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).
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).
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).
Subramanian, D. et al. Activation of membrane-permeant caged PtdIns(3)P induces endosomal fusion in cells. Nat. Chem. Biol. 6, 324–326 (2010).
Hoglinger, D., Nadler, A. & Schultz, C. Caged lipids as tools for investigating cellular signaling. Biochim. Biophys. Acta 1841, 1085–1096 (2014).
Niphakis, M. J. et al. A global map of lipid-binding proteins and their ligandability in cells. Cell 161, 1668–1680 (2015).
Wei, L. et al. Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering. Nat. Methods 11, 410–412 (2014).
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).
McLaughlin, S. & Murray, D. Plasma membrane phosphoinositide organization by protein electrostatics. Nature 438, 605–611 (2005).
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).
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).
Groves, J. T. & Kuriyan, J. Molecular mechanisms in signal transduction at the membrane. Nat. Struct. Mol. Biol. 17, 659–665 (2010).
van den Bogaart, G. et al. Membrane protein sequestering by ionic protein-lipid interactions. Nature 479, 552–555 (2011).
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).
Koberlin, M. S. et al. A conserved circular network of coregulated lipids modulates innate immune responses. Cell 162, 170–183 (2015).
Carpten, J. D. et al. A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature 448, 439–444 (2007).
Lindhurst, M. J. et al. A mosaic activating mutation in AKT1 associated with the Proteus syndrome. N. Engl. J. Med. 365, 611–619 (2011).
Arya, V. B. et al. Activating AKT2 mutation: hypoinsulinemic hypoketotic hypoglycemia. J. Clin. Endocrinol. Metab. 99, 391–394 (2014).
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).
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).
Ling, L. L. et al. A new antibiotic kills pathogens without detectable resistance. Nature 517, 455–459 (2015).
Anderson, T. M. et al. Amphotericin forms an extramembranous and fungicidal sterol sponge. Nat. Chem. Biol. 10, 400–406 (2014).
Salomon, D. et al. Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides. Nat. Commun. 4, 2973 (2013).
Hsu, N. Y. et al. Viral reorganization of the secretory pathway generates distinct organelles for RNA replication. Cell 141, 799–811 (2010).
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).
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).
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).
Jesorka, A. & Orwar, O. Liposomes: technologies and analytical applications. Annu. Rev. Anal. Chem. 1, 801–832 (2008).
Walde, P., Cosentino, K., Engel, H. & Stano, P. Giant vesicles: preparations and applications. ChemBioChem 11, 848–865 (2010).
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).
Stachowiak, J. C. et al. Unilamellar vesicle formation and encapsulation by microfluidic jetting. Proc. Natl Acad. Sci. USA 105, 4697–4702 (2008).
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).
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).
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.
The authors declare competing financial interests in the form of a patent application based on the method liposome microarray-based assay (LiMA).
About this article
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
This article is cited by
Nature Chemical Biology (2023)
Nature Communications (2023)
Communications Biology (2022)
Journal of Cardiovascular Translational Research (2022)
Communications Biology (2021)