3eg1 Citations

Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.

J. Biol. Chem. 285 2823-33 (2010)
Related entries: 3egu, 3eg0, 3eg3, 3eg2

Cited: 16 times
EuropePMC logo PMID: 19906645


The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.

Articles - 3eg1 mentioned but not cited (1)

  1. CARDIO-PRED: an in silico tool for predicting cardiovascular-disorder associated proteins. Jain P, Thukral N, Gahlot LK, Hasija Y. Syst Synth Biol 9 55-66 (2015)

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Articles citing this publication (13)

  1. Molecular origin of the binding of WWOX tumor suppressor to ErbB4 receptor tyrosine kinase. Schuchardt BJ, Bhat V, Mikles DC, McDonald CB, Sudol M, Farooq A. Biochemistry 52 9223-9236 (2013)
  2. Interfacial water molecules in SH3 interactions: a revised paradigm for polyproline recognition. Martin-Garcia JM, Ruiz-Sanz J, Luque I. Biochem. J. 442 443-451 (2012)
  3. Binding of the cSH3 domain of Grb2 adaptor to two distinct RXXK motifs within Gab1 docker employs differential mechanisms. McDonald CB, Seldeen KL, Deegan BJ, Bhat V, Farooq A. J. Mol. Recognit. 24 585-596 (2011)
  4. The promiscuous binding of the Fyn SH3 domain to a peptide from the NS5A protein. Martin-Garcia JM, Luque I, Ruiz-Sanz J, Camara-Artigas A. Acta Crystallogr. D Biol. Crystallogr. 68 1030-1040 (2012)
  5. Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II. Bacarizo J, Camara-Artigas A. Acta Crystallogr. D Biol. Crystallogr. 69 756-766 (2013)
  6. A thermodynamic characterization of the interaction of 8-anilino-1-naphthalenesulfonic acid with native globular proteins: the effect of the ligand dimerization in the analysis of the binding isotherms. Andujar-Sánchez M, Jara-Perez V, Cobos ES, Cámara-Artigas A. J. Mol. Recognit. 24 548-556 (2011)
  7. High-resolution crystal structure of spectrin SH3 domain fused with a proline-rich peptide. Gushchina LV, Gabdulkhakov AG, Nikonov SV, Filimonov VV. J. Biomol. Struct. Dyn. 29 485-495 (2011)
  8. Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations. Whalen KL, Spies MA. J Chem Inf Model 53 2349-2359 (2013)
  9. Fine-tuned broad binding capability of human lipocalin-type prostaglandin D synthase for various small lipophilic ligands. Kume S, Lee YH, Nakatsuji M, Teraoka Y, Yamaguchi K, Goto Y, Inui T. FEBS Lett. 588 962-969 (2014)
  10. Structure of the c-Src-SH3 domain in complex with a proline-rich motif of NS5A protein from the hepatitis C virus. Bacarizo J, Martínez-Rodríguez S, Cámara-Artigas A. J. Struct. Biol. 189 67-72 (2015)
  11. Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl. Bhatt VS, Zeng D, Krieger I, Sacchettini JC, Cho JH. Biophys. J. 110 2630-2641 (2016)
  12. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors. Zafra Ruano A, Cilia E, Couceiro JR, Ruiz Sanz J, Schymkowitz J, Rousseau F, Luque I, Lenaerts T. PLoS Comput. Biol. 12 e1004938 (2016)
  13. The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase. Camara-Artigas A, Ortiz-Salmeron E, Andujar-Sánchez M, Bacarizo J, Martin-Garcia JM. Acta Crystallogr F Struct Biol Commun 72 707-712 (2016)

Related citations provided by authors (1)

  1. Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand. Camara-Artigas A, Palencia A, Martinez JC, Luque I, Gavira JA, Garcia-Ruiz JM Acta Crystallogr. D Biol. Crystallogr. 63 646-652 (2007)