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  • Perspective
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Future opportunities in solute carrier structural biology

Abstract

Solute carriers (SLCs) control the flow of small molecules and ions across biological membranes. Over the last 20 years, the pace of research in SLC biology has accelerated markedly, opening new opportunities to treat metabolic diseases, cancer and neurological disorders. Recently, new families of atypical SLCs, with roles in organelle biology, metabolite signaling and trafficking, have expanded their roles in the cell. This Perspective discusses work leading to current advances and the emerging opportunities to target and modulate SLCs to uncover new biology and treat human disease.

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Fig. 1: The many roles of SLCs in the cell.

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References

  1. Nicholls, D. G. & Ferguson, S. J. Bioenergetics 4th edn (Elsevier, 2013).

  2. Drew, D. & Boudker, O. Ion and lipid orchestration of secondary active transport. Nature 626, 963–974 (2024).

    CAS  PubMed  Google Scholar 

  3. Drew, D. & Boudker, O. Shared molecular mechanisms of membrane transporters. Annu. Rev. Biochem. 85, 543–572 (2016).

    CAS  PubMed  Google Scholar 

  4. Abramson, J. et al. Structure and mechanism of the lactose permease of Escherichia coli. Science 301, 610–615 (2003).

    CAS  PubMed  Google Scholar 

  5. Huang, Y., Lemieux, M. J., Song, J., Auer, M. & Wang, D.-N. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 301, 616–620 (2003).

    CAS  PubMed  Google Scholar 

  6. White, S. H. mpstruc: Membrane Proteins of Known 3D Structure. Stephen White laboratory at UC Irvine https://blanco.biomol.uci.edu/mpstruc/ (2024).

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

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Bill, R. M. et al. Overcoming barriers to membrane protein structure determination. Nat. Biotechnol. 29, 335–340 (2011).

    CAS  PubMed  Google Scholar 

  9. Kawate, T. & Gouaux, E. Fluorescence-detection size-exclusion chromatography for precrystallization screening of integral membrane proteins. Structure 14, 673–681 (2006).

    CAS  PubMed  Google Scholar 

  10. Newstead, S., Kim, H., Von Heijne, G., Iwata, S. & Drew, D. High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 104, 13936–13941 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Sonoda, Y. et al. Benchmarking membrane protein detergent stability for improving throughput of high-resolution X-ray structures. Structure 19, 17–25 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Newstead, S., Ferrandon, S. & Iwata, S. Rationalizing α-helical membrane protein crystallization. Protein Sci. 17, 466–472 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Caffrey, M. & Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nat. Protoc. 4, 706–731 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Cherezov, V. et al. Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 µm size X-ray synchrotron beam. J. R. Soc. Interface 6, S587–S597 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Kuhlbrandt, W. Biochemistry. The resolution revolution. Science 343, 1443–1444 (2014).

    PubMed  Google Scholar 

  16. Vallese, F. et al. Architecture of the human erythrocyte ankyrin-1 complex. Nat. Struct. Mol. Biol. 29, 706–718 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Hediger, M. A. et al. The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteins. Pflugers Arch. 447, 465–468 (2004).

    CAS  Google Scholar 

  18. Schlessinger, A., Zatorski, N., Hutchinson, K. & Colas, C. Targeting SLC transporters: small molecules as modulators and therapeutic opportunities. Trends Biochem. Sci. 48, 801–814 (2023).

    CAS  PubMed  Google Scholar 

  19. Dvorak, V. & Superti-Furga, G. Structural and functional annotation of solute carrier transporters: implication for drug discovery. Expert Opin. Drug Discov. 18, 1099–1115 (2023).

    CAS  PubMed  Google Scholar 

  20. Wang, N. et al. Structural basis of human monocarboxylate transporter 1 inhibition by anti-cancer drug candidates. Cell 184, 370–383 (2021).

    CAS  PubMed  Google Scholar 

  21. Han, L. et al. Structure and mechanism of the SGLT family of glucose transporters. Nature 601, 274–279 (2022).

    CAS  PubMed  Google Scholar 

  22. Niu, Y. et al. Structural basis of inhibition of the human SGLT2–MAP17 glucose transporter. Nature 601, 280–284 (2022).

    CAS  PubMed  Google Scholar 

  23. Lin, L., Yee, S. W., Kim, R. B. & Giacomini, K. M. SLC transporters as therapeutic targets: emerging opportunities. Nat. Rev. Drug Discov. 14, 543–560 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Giacomini, K. M. et al. Membrane transporters in drug development. Nat. Rev. Drug Discov. 9, 215–236 (2010).

    CAS  PubMed  Google Scholar 

  25. Parker, J. L. et al. Structural basis of antifolate recognition and transport by PCFT. Nature 595, 130–134 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Laursen, L. et al. Cholesterol binding to a conserved site modulates the conformation, pharmacology, and transport kinetics of the human serotonin transporter. J. Biol. Chem. 293, 3510–3523 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Zeppelin, T., Ladefoged, L. K., Sinning, S., Periole, X. & Schiott, B. A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition. PLoS Comput. Biol. 14, e1005907 (2018).

    PubMed  PubMed Central  Google Scholar 

  28. Mostyn, S. N. et al. Identification of an allosteric binding site on the human glycine transporter, GlyT2, for bioactive lipid analgesics. eLife 8, e47150 (2019).

    PubMed  PubMed Central  Google Scholar 

  29. Yan, R., Zhao, X., Lei, J. & Zhou, Q. Structure of the human LAT1–4F2hc heteromeric amino acid transporter complex. Nature 568, 127–130 (2019).

    CAS  PubMed  Google Scholar 

  30. Pardon, E. et al. A general protocol for the generation of nanobodies for structural biology. Nat. Protoc. 9, 674–693 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Zimmermann, I. et al. Generation of synthetic nanobodies against delicate proteins. Nat. Protoc. 15, 1707–1741 (2020).

    CAS  PubMed  Google Scholar 

  32. Pleiner, T. et al. Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation. eLife 4, e11349 (2015).

    PubMed  PubMed Central  Google Scholar 

  33. Kriel, J., Haesendonckx, S., Rubio-Texeira, M., Van Zeebroeck, G. & Thevelein, J. M. From transporter to transceptor: signaling from transporters provokes re-evaluation of complex trafficking and regulatory controls: endocytic internalization and intracellular trafficking of nutrient transceptors may, at least in part, be governed by their signaling function. BioEssays 33, 870–879 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Schothorst, J. et al. Yeast nutrient transceptors provide novel insight in the functionality of membrane transporters. Curr. Genet. 59, 197–206 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Fan, S. J. & Goberdhan, D. C. I. PATs and SNATs: amino acid sensors in disguise. Front. Pharmacol. 9, 640 (2018).

    PubMed  PubMed Central  Google Scholar 

  36. Wang, S. et al. Metabolism. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1. Science 347, 188–194 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Goberdhan, D. C., Wilson, C. & Harris, A. L. Amino acid sensing by mTORC1: intracellular transporters mark the spot. Cell Metab. 23, 580–589 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Newstead, S. & Barr, F. Molecular basis for KDEL-mediated retrieval of escaped ER-resident proteins — SWEET talking the COPs. J. Cell Sci. 133, jcs250100 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Ishida, H. et al. Cryo-EM structures of Toll-like receptors in complex with UNC93B1. Nat. Struct. Mol. Biol. 28, 173–180 (2021).

    CAS  PubMed  Google Scholar 

  40. Heinz, L. X. et al. TASL is the SLC15A4-associated adaptor for IRF5 activation by TLR7–9. Nature 581, 316–322 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Wiedmer, T. et al. Accelerating SLC transporter research: streamlining knowledge and validated tools. Clin. Pharmacol. Ther. 112, 439–442 (2022).

    PubMed  PubMed Central  Google Scholar 

  42. Necelis, M., McDermott, C., Belcher Dufrisne, M., Baryiames, C. & Columbus, L. Solution NMR investigations of integral membrane proteins: challenges and innovations. Curr. Opin. Struct. Biol. 82, 102654 (2023).

    CAS  PubMed  Google Scholar 

  43. Heath, G. R. & Scheuring, S. Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters. Curr. Opin. Struct. Biol. 57, 93–102 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Bolla, J. R., Agasid, M. T., Mehmood, S. & Robinson, C. V. Membrane protein–lipid interactions probed using mass spectrometry. Annu. Rev. Biochem. 88, 85–111 (2019).

    CAS  PubMed  Google Scholar 

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Acknowledgements

S.N. receives support from Wellcome through grants 215519 and 219531.

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Newstead, S. Future opportunities in solute carrier structural biology. Nat Struct Mol Biol 31, 587–590 (2024). https://doi.org/10.1038/s41594-024-01271-0

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