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Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p.

Stollar EJ, Garcia B, Chong PA, Rath A, Lin H, Forman-Kay JD, Davidson AR
J Biol Chem 284 26918-27 (2009)
Cited: 24 times
EuropePMC logo PMID: 19590096

Abstract

SH3 domains, which are among the most frequently occurring protein interaction modules in nature, bind to peptide targets ranging in length from 7 to more than 25 residues. Although the bulk of studies on the peptide binding properties of SH3 domains have focused on interactions with relatively short peptides (less than 10 residues), a number of domains have been recently shown to require much longer sequences for optimal binding affinity. To gain greater insight into the binding mechanism and biological importance of interactions between an SH3 domain and extended peptide sequences, we have investigated interactions of the yeast Abp1p SH3 domain (AbpSH3) with several physiologically relevant 17-residue target peptide sequences. To obtain a molecular model for AbpSH3 interactions, we solved the structure of the AbpSH3 bound to a target peptide from the yeast actin patch kinase, Ark1p. Peptide target complexes from binding partners Scp1p and Sjl2p were also characterized, revealing that the AbpSH3 uses a common extended interface for interaction with these peptides, despite K(d) values for these peptides ranging from 0.3 to 6 mum. Mutagenesis studies demonstrated that residues across the whole 17-residue binding site are important both for maximal in vitro binding affinity and for in vivo function. Sequence conservation analysis revealed that both the AbpSH3 and its extended target sequences are highly conserved across diverse fungal species as well as higher eukaryotes. Our data imply that the AbpSH3 must bind extended target sites to function efficiently inside the cell.

Articles - 2rpn mentioned but not cited (8)

  1. Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p. Stollar EJ, Garcia B, Chong PA, Rath A, Lin H, Forman-Kay JD, Davidson AR. J Biol Chem 284 26918-26927 (2009)
  2. A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway. Gerlach GJ, Carrock R, Stix R, Stollar EJ, Ball KA. PLoS Comput Biol 16 e1007815 (2020)
  3. Most yeast SH3 domains bind peptide targets with high intrinsic specificity. Brown T, Brown N, Stollar EJ. PLoS One 13 e0193128 (2018)
  4. Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks. Holland DO, Shapiro BH, Xue P, Johnson ME. Sci Rep 7 5631 (2017)
  5. How a highly acidic SH3 domain folds in the absence of its charged peptide target. Jaramillo-Martinez V, Dominguez MJ, Bell GM, Souness ME, Carhart AH, Cuibus MA, Masoumzadeh E, Lantz BJ, Adkins AJ, Latham MP, Ball KA, Stollar EJ. Protein Sci 32 e4635 (2023)
  6. An Unbound Proline-Rich Signaling Peptide Frequently Samples Cis Conformations in Gaussian Accelerated Molecular Dynamics Simulations. Alcantara J, Stix R, Huang K, Connor A, East R, Jaramillo-Martinez V, Stollar EJ, Ball KA. Front Mol Biosci 8 734169 (2021)
  7. Development and Application of a High Throughput Protein Unfolding Kinetic Assay. Wang Q, Waterhouse N, Feyijinmi O, Dominguez MJ, Martinez LM, Sharp Z, Service R, Bothe JR, Stollar EJ. PLoS One 11 e0146232 (2016)
  8. Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. Dionne U, Bourgault É, Dubé AK, Bradley D, Chartier FJM, Dandage R, Dibyachintan S, Després PC, Gish GD, Pham NTH, Létourneau M, Lambert JP, Doucet N, Bisson N, Landry CR. Nat Commun 12 1597 (2021)


Reviews citing this publication (1)

  1. The mammalian actin-binding protein 1 (mAbp1): a novel molecular player in leukocyte biology. Schymeinsky J, Sperandio M, Walzog B. Trends Cell Biol 21 247-255 (2011)

Articles citing this publication (15)

  1. Tunable growth factor delivery from injectable hydrogels for tissue engineering. Vulic K, Shoichet MS. J Am Chem Soc 134 882-885 (2012)
  2. Affinity-based release of chondroitinase ABC from a modified methylcellulose hydrogel. Pakulska MM, Vulic K, Shoichet MS. J Control Release 171 11-16 (2013)
  3. Differential dynamic engagement within 24 SH3 domain: peptide complexes revealed by co-linear chemical shift perturbation analysis. Stollar EJ, Lin H, Davidson AR, Forman-Kay JD. PLoS One 7 e51282 (2012)
  4. Proline substitutions and threonine pseudophosphorylation of the SH3 ligand of 18.5-kDa myelin basic protein decrease its affinity for the Fyn-SH3 domain and alter process development and protein localization in oligodendrocytes. Smith GS, De Avila M, Paez PM, Spreuer V, Wills MK, Jones N, Boggs JM, Harauz G. J Neurosci Res 90 28-47 (2012)
  5. Distinct peptide binding specificities of Src homology 3 (SH3) protein domains can be determined by modulation of local energetics across the binding interface. Gorelik M, Davidson AR. J Biol Chem 287 9168-9177 (2012)
  6. Fast and accurate discovery of degenerate linear motifs in protein sequences. Kelil A, Dubreuil B, Levy ED, Michnick SW. PLoS One 9 e106081 (2014)
  7. The importance of conserved features of yeast actin-binding protein 1 (Abp1p): the conditional nature of essentiality. Garcia B, Stollar EJ, Davidson AR. Genetics 191 1199-1211 (2012)
  8. A semi-automated method for purification of milligram quantities of proteins on the QIAcube. McGraw J, Tatipelli VK, Feyijinmi O, Traore MC, Eangoor P, Lane S, Stollar EJ. Protein Expr Purif 96 48-53 (2014)
  9. Exhaustive search of linear information encoding protein-peptide recognition. Kelil A, Kelil A, Dubreuil B, Levy ED, Michnick SW. PLoS Comput Biol 13 e1005499 (2017)
  10. PakB binds to the SH3 domain of Dictyostelium Abp1 and regulates its effects on cell polarity and early development. Yang Y, de la Roche M, Crawley SW, Li Z, Furmaniak-Kazmierczak E, Côté GP. Mol Biol Cell 24 2216-2227 (2013)
  11. Structural basis for recognition of the third SH3 domain of full-length R85 (R85FL)/ponsin by ataxin-7. Jiang YJ, Zhou CJ, Zhou ZR, Wu M, Hu HY. FEBS Lett 587 2905-2911 (2013)
  12. A multi-column plate adapter provides an economical and versatile high-throughput protein purification system. Dominguez MJ, Lantz BJ, Rhode RJ, Sharp ZL, Finney KC, Martinez VJ, Stollar EJ. Protein Expr Purif 152 84-91 (2018)
  13. Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning. Lu AX, Lu AX, Pritišanac I, Zarin T, Forman-Kay JD, Moses AM. PLoS Comput Biol 18 e1010238 (2022)
  14. Activation of caspase-9 on the apoptosome as studied by methyl-TROSY NMR. Sever AIM, Alderson TR, Rennella E, Aramini JM, Liu ZH, Harkness RW, Kay LE. Proc Natl Acad Sci U S A 120 e2310944120 (2023)
  15. Exploiting conformational dynamics to modulate the function of designed proteins. Rennella E, Sahtoe DD, Baker D, Kay LE. Proc Natl Acad Sci U S A 120 e2303149120 (2023)


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