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Crystallographic Studies of PDZ Domain–Peptide Interactions of the Scribble Polarity Module

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PDZ Mediated Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2256))

Abstract

The determination of high-resolution crystal structures of cell polarity regulatory proteins bound to their functional interactors has proven to be invaluable for deciphering the underlying molecular mechanisms. Here we describe methods to identify suitable complexes of cell polarity protein domains bound to interacting ligands with subsequent preparation of such complexes for X-ray crystallographic analysis.

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References

  1. Nelson WJ (2003) Adaptation of core mechanisms to generate cell polarity. Nature 422:766–774

    Article  CAS  Google Scholar 

  2. Halaoui R, McCaffrey L (2015) Rewiring cell polarity signaling in cancer. Oncogene 34:939–950

    Article  CAS  Google Scholar 

  3. Stephens R, Lim K, Portela M, Kvansakul M, Humbert PO, Richardson HE (2018) The scribble cell polarity module in the regulation of cell signaling in tissue development and tumorigenesis. J Mol Biol 430:3585–3612

    Article  CAS  Google Scholar 

  4. Subbaiah VK, Kranjec C, Thomas M, Banks L (2011) PDZ domains: the building blocks regulating tumorigenesis. Biochem J 439:195–205

    Article  CAS  Google Scholar 

  5. Ye F, Zhang M (2013) Structures and target recognition modes of PDZ domains: recurring themes and emerging pictures. Biochem J 455:1–14

    Article  CAS  Google Scholar 

  6. Alié A, Manuel M (2010) The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans. BMC Evol Biol 10:34

    Article  Google Scholar 

  7. Belahbib H, Renard E, Santini S, Jourda C, Claverie JM, Borchiellini C, Le Bivic A (2018) New genomic data and analyses challenge the traditional vision of animal epithelium evolution. BMC Genomics 19:393

    Article  Google Scholar 

  8. Daulat AM, Puvirajesinghe TM, Camoin L, Borg JP (2018) Mapping cellular polarity networks using mass spectrometry-based strategies. J Mol Biol 430:3545–3564

    Article  CAS  Google Scholar 

  9. Pires HR, Boxem M (2018) Mapping the polarity interactome. J Mol Biol 430:3521–3544

    Article  CAS  Google Scholar 

  10. Wen W, Zhang M (2018) Protein complex assemblies in epithelial cell polarity and asymmetric cell division. J Mol Biol 430:3504–3520

    Article  CAS  Google Scholar 

  11. Songyang Z, Fanning AS, Fu C, Xu J, Marfatia SM, Chishti AH, Crompton A, Chan AC, Anderson JM, Cantley LC (1997) Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science 275:73–77

    Article  CAS  Google Scholar 

  12. Hillier BJ, Christopherson KS, Prehoda KE, Bredt DS, Lim WA (1999) Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science 284:812–815

    Article  CAS  Google Scholar 

  13. Awadia S, Huq F, Arnold TR, Goicoechea SM, Sun YJ, Hou T, Kreider-Letterman G, Massimi P, Banks L, Fuentes EJ, Miller AL, Garcia-Mata R (2019) SGEF forms a complex with scribble and Dlg1 and regulates epithelial junctions and contractility. J Cell Biol 218:2699–2525

    Article  CAS  Google Scholar 

  14. Penkert RR, DiVittorio HM, Prehoda KE (2004) Internal recognition through PDZ domain plasticity in the Par-6-Pals1 complex. Nat Struct Mol Biol 11:1122–1127

    Article  CAS  Google Scholar 

  15. Chetkovich DM, Chen L, Stocker TJ, Nicoll RA, Bredt DS (2002) Phosphorylation of the postsynaptic density-95 (PSD-95)/discs large/zona occludens-1 binding site of stargazin regulates binding to PSD-95 and synaptic targeting of AMPA receptors. J Neurosci 22:5791–5796

    Article  CAS  Google Scholar 

  16. Clairfeuille T, Mas C, Chan AS, Yang Z, Tello-Lafoz M, Chandra M, Widagdo J, Kerr MC, Paul B, Mérida I, Teasdale RD, Pavlos NJ, Anggono V, Collins BM (2016) A molecular code for endosomal recycling of phosphorylated cargos by the SNX27-retromer complex. Nat Struct Mol Biol 23:921–932

    Article  CAS  Google Scholar 

  17. Sundell GN, Arnold R, Ali M, Naksukpaiboon P, Orts J, Güntert P, Chi CN, Ivarsson Y (2018) Proteome-wide analysis of phospho-regulated PDZ domain interactions. Mol Syst Biol 14:e8129

    Article  Google Scholar 

  18. Grant SGN (2019) Synapse diversity and synaptome architecture in human genetic disorders. Hum Mol Genet 21:219–225

    Article  Google Scholar 

  19. Thomas M, Banks L (2018) Upsetting the balance: when viruses manipulate cell polarity control. J Mol Biol 430:3481–3503

    Article  CAS  Google Scholar 

  20. Franck B (1965) Optical circular dichroism. Principles, measurements, and applications. Von L. Velluz, M. Legrand und M. Grosjean. Angew Chem 77:875–875

    Article  Google Scholar 

  21. Greenfield NJ (2006) Using circular dichroism spectra to estimate protein secondary structure. Nat Protoc 1:2876–2890

    Article  CAS  Google Scholar 

  22. Aviv Biomedical, Inc. Circular dichroism spectrophotometer. Instrument manual, 2009

    Google Scholar 

  23. Saponaro A (2018) Isothermal titration calorimetry: a biophysical method to characterize the interaction between label-free biomolecules in solution. Bio-protocol 8:e2957

    Article  CAS  Google Scholar 

  24. Zhang Y, Yeh S, Appleton BA, Held HA, Kausalya PJ, Phua DC, Wong WL, Lasky LA, Wiesmann C, Hunziker W, Sidhu SS (2006) Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families. J Biol Chem 281:22299–22311

    Article  CAS  Google Scholar 

  25. Lim KYB, Gödde NJ, Humbert PO, Kvansakul M (2017) Structural basis for the differential interaction of scribble PDZ domains with the guanine nucleotide exchange factor beta-PIX. J Biol Chem 292:20425–20436

    Article  CAS  Google Scholar 

  26. Caria S, Stewart BZ, Jin R, Smith BJ, Humbert PO, Kvansakul M (2019) Structural analysis of phosphorylation-associated interactions of human MCC with scribble PDZ domains. FEBS J 286:4910–4925

    Article  CAS  Google Scholar 

  27. Feng W, Zhang M (2009) Organization and dynamics of PDZ-domain-related supramodules in the postsynaptic density. Nat Rev Neurosci 10:87–99

    Article  CAS  Google Scholar 

  28. Ren J, Feng L, Bai Y, Pei H, Yuan Z, Feng W (2015) Interdomain interface-mediated target recognition by the scribble PDZ34 supramodule. Biochem J 468:133–144

    Article  CAS  Google Scholar 

  29. Caria S, Magtoto CM, Samiei T, Portela M, Lim KYB, How JY, Stewart BZ, Humbert PO, Richardson HE, Kvansakul M (2018) Drosophila melanogaster Guk-holder interacts with the scribbled PDZ1 domain and regulates epithelial development with scribbled and discs large. J Biol Chem 293(12):4519–4531

    Article  CAS  Google Scholar 

  30. How JY, Caria S, Humbert PO, Kvansakul M (2019) Crystal structure of the human scribble PDZ1 domain bound to the PDZ-binding motif of APC. FEBS Lett 593:533–542

    Article  CAS  Google Scholar 

  31. Zhang Z, Li H, Chen L, Lu X, Zhang J, Xu P, Lin K, Wu G (2011) Molecular basis for the recognition of adenomatous polyposis coli by the discs large 1 protein. PLoS One 6:e23507

    Article  CAS  Google Scholar 

  32. Slep KC (2012) Structure of the human discs large 1 PDZ2- adenomatous polyposis coli cytoskeletal polarity complex: insight into peptide engagement and PDZ clustering. PLoS One 7:e50097

    Article  CAS  Google Scholar 

  33. Mischo A, Ohlenschläger O, Hortschansky P, Ramachandran R, Görlach M (2013) Structural insights into a wildtype domain of the oncoprotein E6 and its interaction with a PDZ domain. PLoS One 8:e62584

    Article  CAS  Google Scholar 

  34. Liu Y, Henry GD, Hegde RS, Baleja JD (2007) Solution structure of the hDlg/SAP97 PDZ2 domain and its mechanism of interaction with HPV-18 papillomavirus E6 protein. Biochemistry 46:10864–10874

    Article  CAS  Google Scholar 

  35. Zhang Y, Dasgupta J, Ma RZ, Banks L, Thomas M, Chen XS (2007) Structures of a human papillomavirus (HPV) E6 polypeptide bound to MAGUK proteins: mechanisms of targeting tumor suppressors by a high-risk HPV oncoprotein. J Virol 81:3618–3626

    Article  CAS  Google Scholar 

  36. Sainlos M, Iskenderian-Epps WS, Olivier NB, Choquet D, Imperiali B (2013) Caged mono- and divalent ligands for light-assisted disruption of PDZ domain-mediated interactions. J Am Chem Soc 135:4580–4583

    Article  CAS  Google Scholar 

  37. Wang W, Weng J, Zhang X, Liu M, Zhang M (2009) Creating conformational entropy by increasing interdomain mobility in ligand binding regulation: a revisit to N-terminal tandem PDZ domains of PSD-95. J Am Chem Soc 131:787–796

    Article  CAS  Google Scholar 

  38. Zeng M, Shang Y, Araki Y, Guo T, Huganir RL, Zhang M (2016) Phase transition in postsynaptic densities underlies formation of synaptic complexes and synaptic plasticity. Cell 166:1163–1175

    Article  CAS  Google Scholar 

  39. Raman AS, White KI, Ranganathan R (2016) Origins of allostery and evolvability in proteins: a case study. Cell 166:468–480

    Article  CAS  Google Scholar 

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Author notes

  1. Janesha C. Maddumage and Bryce Z. Stewart contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Genetics, La Trobe University, Bundoora, VIC, Australia

    Janesha C. Maddumage, Bryce Z. Stewart, Patrick O. Humbert & Marc Kvansakul

  2. La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia

    Janesha C. Maddumage, Bryce Z. Stewart, Patrick O. Humbert & Marc Kvansakul

Authors
  1. Janesha C. Maddumage
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  2. Bryce Z. Stewart
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  3. Patrick O. Humbert
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  4. Marc Kvansakul
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Corresponding authors

Correspondence to Patrick O. Humbert or Marc Kvansakul .

Editor information

Editors and Affiliations

  1. Centre de Recherche en CancÕrologie de Marseille, Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France

    Jean-Paul Borg

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Maddumage, J.C., Stewart, B.Z., Humbert, P.O., Kvansakul, M. (2021). Crystallographic Studies of PDZ Domain–Peptide Interactions of the Scribble Polarity Module. In: Borg, JP. (eds) PDZ Mediated Interactions. Methods in Molecular Biology, vol 2256. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1166-1_7

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  • DOI: https://doi.org/10.1007/978-1-0716-1166-1_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1165-4

  • Online ISBN: 978-1-0716-1166-1

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