Recognition of proline-rich motifs by protein-protein-interaction domains.

Protein-protein interactions are essential in every aspect of cellular activity. Multiprotein complexes form and dissociate constantly in a specifically tuned manner, often by conserved mechanisms. Protein domains that bind proline-rich motifs (PRMs) are frequently involved in signaling events. The unique properties of proline provide a mechanism for highly discriminatory recognition without requiring high affinities. We present herein a detailed, quantitative assessment of the structural features that define the interfaces between PRM-binding domains and their target PRMs, and investigate the specificity of PRM recognition. Together with the analysis of peptide-library screens, this approach has allowed the identification of several highly conserved key interactions found in all complexes of PRM-binding domains. The inhibition of protein-protein interactions by using small-molecule agents is very challenging. Therefore, it is important to first pinpoint the critical interactions that must be considered in the design of inhibitors of PRM-binding domains.

[1]  K. Constantine,et al.  Characterization of the three-dimensional solution structure of human profilin: proton, carbon-13, and nitrogen-15 NMR assignments and global folding pattern , 1993 .

[2]  Wesley I. Sundquist,et al.  Structure of the Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein , 2002, Nature Structural Biology.

[3]  G. Superti-Furga,et al.  An intramolecular SH3-domain interaction regulates c-Abl activity , 1998, Nature Genetics.

[4]  T. Pollard,et al.  Three-dimensional solution structure of Acanthamoeba profilin-I , 1993, The Journal of cell biology.

[5]  U. Walter,et al.  VASP interaction with vinculin: a recurring theme of interactions with proline‐rich motifs , 1996, FEBS letters.

[6]  H. Oschkinat,et al.  Synthese eines Arrays aus 837 Varianten der hYAP-WW-Proteindomäne , 2001 .

[7]  L. Butler,et al.  The specificity of proanthocyanidin-protein interactions. , 1981, The Journal of biological chemistry.

[8]  U. Walter,et al.  Molecular cloning, structural analysis and functional expression of the proline‐rich focal adhesion and microfilament‐associated protein VASP. , 1995, The EMBO journal.

[9]  C. Schutt,et al.  Mutagenesis of human profilin locates its poly(l‐prolme)‐bindmg site to a hydrophobic patch of aromatic amino acids , 1993, FEBS letters.

[10]  Steven C. Almo,et al.  Structure of the profilin-poly-L-proline complex involved in morphogenesis and cytoskeletal regulation , 1997, Nature Structural Biology.

[11]  P. Bucher,et al.  The rsp5‐domain is shared by proteins of diverse functions , 1995, FEBS letters.

[12]  U. Walter,et al.  The 46/50 kDa phosphoprotein VASP purified from human platelets is a novel protein associated with actin filaments and focal contacts. , 1992, The EMBO journal.

[13]  B. Mayer,et al.  A novel viral oncogene with structural similarity to phospholipase C , 1988, Nature.

[14]  R. Frank Spot-synthesis: an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support , 1992 .

[15]  U. Walter,et al.  Identification, purification, and characterization of a zyxin-related protein that binds the focal adhesion and microfilament protein VASP (vasodilator-stimulated phosphoprotein). , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[16]  L. Mueller,et al.  Identification of the poly-L-proline-binding site on human profilin. , 1994, The Journal of biological chemistry.

[17]  A. Sparks,et al.  Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[18]  P. Schmieder,et al.  Dual epitope recognition by the VASP EVH1 domain modulates polyproline ligand specificity and binding affinity , 2000, The EMBO journal.

[19]  Z. Dauter,et al.  Crystallization and structure determination of bovine profilin at 2.0 A resolution. , 1994, Journal of molecular biology.

[20]  T. Hunter,et al.  NeW Wrinkles for an Old Domain , 2000, Cell.

[21]  D. Baltimore,et al.  Modular binding domains in signal transduction proteins , 1995, Cell.

[22]  R. Frank,et al.  Epitope-targeted proteome analysis: towards a large-scale automated protein–protein-interaction mapping utilizing synthetic peptide arrays , 2003, Analytical and bioanalytical chemistry.

[23]  P. Worley,et al.  Structure of the Homer EVH1 Domain-Peptide Complex Reveals a New Twist in Polyproline Recognition , 2000, Neuron.

[24]  Patricia L. Widder,et al.  A Novel Adaptor Protein Orchestrates Receptor Patterning and Cytoskeletal Polarity in T-Cell Contacts , 1998, Cell.

[25]  U. Walter,et al.  EVH1 domains: structure, function and interactions , 2002, FEBS letters.

[26]  J. Wehland,et al.  A novel proline‐rich motif present in ActA of Listeria monocytogenes and cytoskeletal proteins is the ligand for the EVH1 domain, a protein module present in the Ena/VASP family , 1997, The EMBO journal.

[27]  L. Serrano,et al.  Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions. , 1998, Journal of molecular biology.

[28]  S. Schreiber,et al.  Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. , 1995, Science.

[29]  S. Schreiber,et al.  Molecular basis for the binding of SH3 ligands with non-peptide elements identified by combinatorial synthesis. , 1996, Chemistry & biology.

[30]  T. Pollard,et al.  X-ray structures of isoforms of the actin-binding protein profilin that differ in their affinity for phosphatidylinositol phosphates. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Steven C. Almo,et al.  Profilin binds proline-rich ligands in two distinct amide backbone orientations , 1999, Nature Structural Biology.

[32]  F E Cohen,et al.  Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. , 1998, Science.

[33]  Wendell A. Lim,et al.  Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains , 1995, Nature.

[34]  T. Pollard,et al.  Elucidation of the poly‐l‐proline binding site in Acanthamoeba profilin I by NMR spectroscopy , 1994, FEBS letters.

[35]  N. Pavletich,et al.  Structure of the p53 Tumor Suppressor Bound to the Ankyrin and SH3 Domains of 53BP2 , 1996, Science.

[36]  Alexander Shekhtman,et al.  A novel, specific interaction involving the Csk SH3 domain and its natural ligand , 2001, Nature Structural Biology.

[37]  M. Williamson,et al.  The structure and function of proline-rich regions in proteins. , 1994, The Biochemical journal.

[38]  D. Cussac,et al.  Molecular and cellular analysis of Grb2 SH3 domain mutants: interaction with Sos and dynamin. , 1999, Journal of molecular biology.

[39]  D. Baltimore,et al.  Crystal structure of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine-phosphorylated peptides , 1993, Nature.

[40]  I D Campbell,et al.  Structural and thermodynamic characterization of the interaction of the SH3 domain from Fyn with the proline-rich binding site on the p85 subunit of PI3-kinase. , 1996, Biochemistry.

[41]  M. Saraste,et al.  Pleckstrin homology domains: a fact file. , 1995, Current opinion in structural biology.

[42]  M. Sudol,et al.  Structure and function of the WW domain. , 1996, Progress in biophysics and molecular biology.

[43]  Hongtao Yu,et al.  Structural basis for the binding of proline-rich peptides to SH3 domains , 1994, Cell.

[44]  S. Shoelson,et al.  SH2 and PTB domain interactions in tyrosine kinase signal transduction. , 1997, Current opinion in chemical biology.

[45]  G. Wagner,et al.  SH3 domain recognition of a proline‐independent tyrosine‐based RKxxYxxY motif in immune cell adaptor SKAP55 , 2000, The EMBO journal.

[46]  Uchitel' IIa,et al.  [Study of the C14-leucine incorporation into microsomal fractions of rabbit spleen and liver after antigen injection]. , 1967 .

[47]  M. Sudol The WW module competes with the SH3 domain? , 1996, Trends in biochemical sciences.

[48]  D Cowburn,et al.  Modular peptide recognition domains in eukaryotic signaling. , 1997, Annual review of biophysics and biomolecular structure.

[49]  A. Kramer,et al.  Synthesis and screening of peptide libraries on continuous cellulose membrane supports. , 1998, Methods in molecular biology.

[50]  Wendell A. Lim,et al.  The Structure and Function of Proline Recognition Domains , 2003, Science's STKE.

[51]  Andrea Musacchio,et al.  A novel peptide–SH3 interaction , 1999, The EMBO journal.

[52]  P. Schmieder,et al.  WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains , 2003, Protein science : a publication of the Protein Society.

[53]  M. Volkenstein,et al.  Statistical mechanics of chain molecules , 1969 .

[54]  M. Sternberg,et al.  Left-handed polyproline II helices commonly occur in globular proteins. , 1993, Journal of molecular biology.

[55]  D. Linden,et al.  Homer Binds a Novel Proline-Rich Motif and Links Group 1 Metabotropic Glutamate Receptors with IP3 Receptors , 1998, Neuron.

[56]  M. Saraste,et al.  Insights into Src kinase functions: structural comparisons. , 1998, Trends in biochemical sciences.

[57]  M. Sudol,et al.  The importance of being proline: the interaction of proline‐rich motifs in signaling proteins with their cognate domains , 2000, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[58]  Gerhard Wagner,et al.  The GYF domain is a novel structural fold that is involved in lymphoid signaling through proline-rich sequences , 1999, Nature Structural Biology.

[59]  S. Schreiber,et al.  Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[60]  R. Frank The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports--principles and applications. , 2002, Journal of immunological methods.

[61]  H Oschkinat,et al.  Solution structures of the YAP65 WW domain and the variant L30 K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope. , 2001, Journal of molecular biology.

[62]  Tony Pawson,et al.  Structural basis for specific binding of the Gads SH3 domain to an RxxK motif-containing SLP-76 peptide: a novel mode of peptide recognition. , 2003, Molecular cell.

[63]  Andrea Musacchio,et al.  High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides , 1994, Nature Structural Biology.

[64]  M. Saraste,et al.  Transforming and membrane proteins , 1988, Nature.

[65]  T. Pawson,et al.  Signaling through scaffold, anchoring, and adaptor proteins. , 1997, Science.

[66]  J. Schneider-Mergener,et al.  Combining SPOT synthesis and native peptide ligation to create large arrays of WW protein domains. , 2003, Angewandte Chemie.

[67]  A. Sparks,et al.  Using Molecular Repertoires to Identify High-Affinity Peptide Ligands of the WW Domain of Human and Mouse YAP , 1997, Biological chemistry.

[68]  G. Stier,et al.  Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40. , 2002, Journal of molecular biology.

[69]  Xin Huang,et al.  Structure of a WW domain containing fragment of dystrophin in complex with β-dystroglycan , 2000, Nature Structural Biology.

[70]  A. Veis,et al.  Basicity differences among peptide bonds. , 1970, Journal of the American Chemical Society.

[71]  T. Pawson,et al.  SH2 domains recognize specific phosphopeptide sequences , 1993, Cell.

[72]  Xiao Zhen Zhou,et al.  Function of WW domains as phosphoserine- or phosphothreonine-binding modules. , 1999, Science.

[73]  G. Reuther,et al.  The roles of 14-3-3 proteins in signal transduction. , 1996, Vitamins and hormones.

[74]  J. Wehland,et al.  Mena, a Relative of VASP and Drosophila Enabled, Is Implicated in the Control of Microfilament Dynamics , 1996, Cell.

[75]  P. Worley,et al.  Shank, a Novel Family of Postsynaptic Density Proteins that Binds to the NMDA Receptor/PSD-95/GKAP Complex and Cortactin , 1999, Neuron.

[76]  W. Lim,et al.  Structure of the Enabled/VASP Homology 1 Domain–Peptide Complex A Key Component in the Spatial Control of Actin Assembly , 1999, Cell.

[77]  J. Jongstra,et al.  LSP1 Is the Major Substrate for Mitogen-activated Protein Kinase-activated Protein Kinase 2 in Human Neutrophils* , 1997, The Journal of Biological Chemistry.

[78]  M. Sudol,et al.  Yes-associated Protein and p53-binding Protein-2 Interact through Their WW and SH3 Domains* , 2001, The Journal of Biological Chemistry.

[79]  P. Bork,et al.  The WW domain: a signalling site in dystrophin? , 1994, Trends in biochemical sciences.

[80]  S. Schreiber,et al.  Regulatory intramolecular association in a tyrosine kinase of the Tec family , 1997, Nature.

[81]  Ronald Kühne,et al.  Dynamic interaction of CD2 with the GYF and the SH3 domain of compartmentalized effector molecules , 2002, The EMBO journal.

[82]  M. Tanaka,et al.  Poly(L-proline)-binding proteins from chick embryos are a profilin and a profilactin. , 1985, European journal of biochemistry.

[83]  W. Lim,et al.  Structure of the N-WASP EVH1 Domain-WIP Complex Insight into the Molecular Basis of Wiskott-Aldrich Syndrome , 2002, Cell.

[84]  Gianni Cesareni,et al.  Normalization of nomenclature for peptide motifs as ligands of modular protein domains , 2002, FEBS letters.

[85]  Tony Hunter,et al.  Structural basis for phosphoserine-proline recognition by group IV WW domains , 2000, Nature Structural Biology.

[86]  Rebecca L Rich,et al.  Structure and functional interactions of the Tsg101 UEV domain , 2002, The EMBO journal.

[87]  Michael J. Eck,et al.  Three-dimensional structure of the tyrosine kinase c-Src , 1997, Nature.

[88]  C. Schutt,et al.  The structure of crystalline profilin–β-actin , 1993, Nature.

[89]  G. Superti-Furga,et al.  The 2.35 A crystal structure of the inactivated form of chicken Src: a dynamic molecule with multiple regulatory interactions. , 1997, Journal of molecular biology.

[90]  Marius Sudol,et al.  WW and SH3 domains, two different scaffolds to recognize proline‐rich ligands , 2002, FEBS letters.

[91]  J. Forman-Kay,et al.  Solution structure of a Nedd4 WW domain–ENaC peptide complex , 2001, Nature Structural Biology.

[92]  R. Glockshuber Protein folding: Where do the electrons go? , 1999, Nature.

[93]  B. André,et al.  WWP, a new amino acid motif present in single or multiple copies in various proteins including dystrophin and the SH3-binding Yes-associated protein YAP65. , 1994, Biochemical and biophysical research communications.

[94]  S J Winder,et al.  The interaction of dystrophin with beta-dystroglycan is regulated by tyrosine phosphorylation. , 2001, Cellular signalling.

[95]  U. Walter,et al.  The EVH2 Domain of the Vasodilator-stimulated Phosphoprotein Mediates Tetramerization, F-actin Binding, and Actin Bundle Formation* , 1999, The Journal of Biological Chemistry.

[96]  M. Sudol,et al.  The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[97]  K. Inokuchi,et al.  vesl, a gene encoding VASP/Ena family related protein, is upregulated during seizure, long‐term potentiation and synaptogenesis 1 , 1997, FEBS letters.

[98]  Michael B. Yaffe,et al.  Signal transduction: Grabbing phosphoproteins , 1999, Nature.

[99]  E. Reinherz,et al.  Identification of a proline-binding motif regulating CD2-triggered T lymphocyte activation. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[100]  Dudley H. Williams,et al.  Toward an estimation of binding constants in aqueous solution: studies of associations of vancomycin group antibiotics. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[101]  T. Pollard,et al.  Structure of actin binding proteins: insights about function at atomic resolution. , 1994, Annual review of cell biology.

[102]  John Kuriyan,et al.  Crystal structure of the Src family tyrosine kinase Hck , 1997, Nature.

[103]  A. Sali,et al.  Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. , 1995, Structure.

[104]  K. Kishan,et al.  The SH3 domain of Eps8 exists as a novel intertwined dimer , 1997, Nature Structural Biology.

[105]  L. Blanchoin,et al.  Interaction of profilin with G-actin and poly(L-proline). , 1994, Biochemistry.

[106]  J. Kuriyan,et al.  Activation of the Sire-family tyrosine kinase Hck by SH3 domain displacement , 1997, Nature.

[107]  K. Thorn,et al.  The crystal structure of a major allergen from plants. , 1997, Structure.

[108]  R. Kriz,et al.  Sequence similarity of phospholipase C with the non-catalytic region of src , 1988, Nature.

[109]  P. Cowan,et al.  Structure of Poly-L-Proline , 1955, Nature.

[110]  Renu Malhotra,et al.  The origin of Pluto's peculiar orbit , 1995, Nature.

[111]  J. Schneider-Mergener,et al.  Synthesis of an Array Comprising 837 Variants of the hYAP WW Protein Domain. , 2001, Angewandte Chemie.

[112]  M. Saraste,et al.  Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide , 1996, Nature.

[113]  U. Walter,et al.  The proline‐rich focal adhesion and microfilament protein VASP is a ligand for profilins. , 1995, The EMBO journal.

[114]  M. Friedrichs,et al.  Solution structure of the Grb2 N-terminal SH3 domain complexed with a ten-residue peptide derived from SOS: direct refinement against NOEs, J-couplings and 1H and 13C chemical shifts. , 1997, Journal of molecular biology.