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Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions.

Kozlov G, Banville D, Gehring K, Ekiel I
J Mol Biol 320 813-20 (2002)
Cited: 56 times
EuropePMC logo PMID: 12095257

Abstract

The solution structure of the second PDZ domain from human phosphatase hPTP1E in complex with a C-terminal peptide from the guanine nucleotide exchange factor RA-GEF-2 has been determined using 2D and 3D heteronuclear NMR experiments. Compared to previously solved structures, the hPTP1E complex shows an enlarged interaction surface with the C terminus of the bound peptide. Novel contacts were found between the long structured beta2/beta3 loop of the PDZ domain and the sixth amino acid residue from the C terminus of the peptide. This work underlines the importance of the beta2/beta3 loop for ligand selection by PDZ domains.

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  1. The origin of allosteric functional modulation: multiple pre-existing pathways. del Sol A, Tsai CJ, Ma B, Nussinov R. Structure 17 1042-1050 (2009)
  2. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Igumenova TI, Frederick KK, Wand AJ. Chem Rev 106 1672-1699 (2006)
  3. Frameworks for understanding long-range intra-protein communication. Whitley MJ, Lee AL. Curr Protein Pept Sci 10 116-127 (2009)
  4. Emerging Themes in PDZ Domain Signaling: Structure, Function, and Inhibition. Liu X, Fuentes EJ. Int Rev Cell Mol Biol 343 129-218 (2019)

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  1. Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Kong Y, Karplus M. Proteins 74 145-154 (2009)
  2. Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions. Elkins JM, Papagrigoriou E, Berridge G, Yang X, Phillips C, Gileadi C, Savitsky P, Doyle DA. Protein Sci 16 683-694 (2007)
  3. Functional dynamics of PDZ binding domains: a normal-mode analysis. De Los Rios P, Cecconi F, Pretre A, Dietler G, Michielin O, Piazza F, Juanico B. Biophys J 89 14-21 (2005)
  4. Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E. Zhang J, Sapienza PJ, Ke H, Chang A, Hengel SR, Wang H, Phillips GN, Lee AL. Biochemistry 49 9280-9291 (2010)
  5. Kinetic response of a photoperturbed allosteric protein. Buchli B, Waldauer SA, Walser R, Donten ML, Pfister R, Blöchliger N, Steiner S, Caflisch A, Zerbe O, Hamm P. Proc Natl Acad Sci U S A 110 11725-11730 (2013)
  6. Putting into practice domain-linear motif interaction predictions for exploration of protein networks. Luck K, Fournane S, Kieffer B, Masson M, Nominé Y, Travé G. PLoS One 6 e25376 (2011)
  7. MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues. Kaya C, Armutlulu A, Ekesan S, Haliloglu T. Nucleic Acids Res 41 W249-55 (2013)
  8. Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility. Ho BK, Agard DA. Protein Sci 19 398-411 (2010)
  9. Accurate prediction of the dynamical changes within the second PDZ domain of PTP1e. Cilia E, Vuister GW, Lenaerts T. PLoS Comput Biol 8 e1002794 (2012)
  10. Effects of NMR spectral resolution on protein structure calculation. Tikole S, Jaravine V, Orekhov VY, Güntert P. PLoS One 8 e68567 (2013)
  11. Multi-Dimensional Structure and Dynamics Landscape of Proteins in Mammalian Cells Revealed by In-Cell NMR. Kadavath H, Cecilia Prymaczok N, Eichmann C, Riek R, Gerez JA. Angew Chem Int Ed Engl 62 e202213976 (2023)
  12. SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations. Schneider M, Antes I. PLoS One 17 e0265194 (2022)


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  3. Allosterism in the PDZ Family. Stevens AO, He Y. Int J Mol Sci 23 1454 (2022)

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  3. Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families. Zhang Y, Yeh S, Appleton BA, Held HA, Kausalya PJ, Phua DCY, Lee Wong W, Lasky LA, Wiesmann C, Hunziker W, Sidhu SS. J Biol Chem 281 22299-22311 (2006)
  4. Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. Fuentes EJ, Gilmore SA, Mauldin RV, Lee AL. J Mol Biol 364 337-351 (2006)
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  24. Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex. Chen Q, Niu X, Xu Y, Wu J, Shi Y. Protein Sci 16 1053-1062 (2007)
  25. Recognition of protein allosteric states and residues: Machine learning approaches. Zhou H, Dong Z, Tao P. J Comput Chem 39 1481-1490 (2018)
  26. Peptide binding to the PDZ3 domain by conformational selection. Steiner S, Caflisch A. Proteins 80 2562-2572 (2012)
  27. Targeting the PDZ domains of molecular scaffolds of transmembrane ion channels. Piserchio A, Spaller M, Mierke DF. AAPS J 8 E396-401 (2006)
  28. Characterization of PDZ domain-peptide interaction interface based on energetic patterns. Li N, Hou T, Ding B, Wang W. Proteins 79 3208-3220 (2011)
  29. Inhibition of Fas associated phosphatase 1 (Fap1) facilitates apoptosis of colon cancer stem cells and enhances the effects of oxaliplatin. Huang W, Bei L, Eklund EA. Oncotarget 9 25891-25902 (2018)
  30. Spotting the difference in molecular dynamics simulations of biomolecules. Sakuraba S, Kono H. J Chem Phys 145 074116 (2016)
  31. Redox-regulated affinity of the third PDZ domain in the phosphotyrosine phosphatase PTP-BL for cysteine-containing target peptides. van den Berk LC, Landi E, Harmsen E, Dente L, Hendriks WJ. FEBS J 272 3306-3316 (2005)
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  33. Real-time observation of ligand-induced allosteric transitions in a PDZ domain. Bozovic O, Zanobini C, Gulzar A, Jankovic B, Buhrke D, Post M, Wolf S, Stock G, Hamm P. Proc Natl Acad Sci U S A 117 26031-26039 (2020)
  34. Understanding the effect of alternative splicing in the folding and function of the second PDZ from protein tyrosine phosphatase-BL. Di Silvio E, Toto A, Bonetti D, Morrone A, Gianni S. Sci Rep 5 9299 (2015)
  35. Atomic resolution protein allostery from the multi-state structure of a PDZ domain. Ashkinadze D, Kadavath H, Pokharna A, Chi CN, Friedmann M, Strotz D, Kumari P, Minges M, Cadalbert R, Königl S, Güntert P, Vögeli B, Riek R. Nat Commun 13 6232 (2022)
  36. ESI-MS and FTIR studies of the interaction between the second PDZ domain of hPTP1E and target peptides. Papp R, Ekiel I, English AM. Biochem Cell Biol 81 71-80 (2003)
  37. Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Jurásek M, Kumar J, Paclíková P, Kumari A, Tripsianes K, Bryja V, Vácha R. Sci Rep 11 1484 (2021)


Related citations provided by authors (1)

  1. Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor.. Kozlov G, Gehring K, Ekiel I Biochemistry 39 2572-80 (2000)

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