The WW domain, (also known as the rsp5-domain or WWP repeating motif) is a modular protein domain that mediates specific interactions with protein ligands. This domain is found in a number of unrelated signaling and structural proteins and may be repeated up to four times in some proteins. Apart from binding preferentially to proteins that are proline-rich, with particular proline-motifs, [AP]-P-P-[AP]-Y, some WW domains bind to phosphoserine- phosphothreonine-containing motifs.
Structure and ligands
The WW domain is one of the smallest protein modules, composed of only 40 amino acids, which mediates specific protein-protein interactions with short proline-rich or proline-containing motifs. Named after the presence of two conserved tryptophans (W), which are spaced 20-22 amino acids apart within the sequence, the WW domain folds into a meandering triple-stranded beta sheet. The identification of the WW domain was facilitated by the analysis of two splice isoforms of YAP gene product, named YAP1-1 and YAP1-2, which differed by the presence of an extra 38 amino acids. These extra amino acids are encoded by a spliced-in exon and represent the second WW domain in YAP1-2 isoform.
The first structure of the WW domain was determined in solution by NMR approach. It represented the WW domain of human YAP in complex with peptide ligand containing Proline-Proline-x–Tyrosine (PPxY where x = any amino acid) consensus motif. Recently, the YAP WW domain structure in complex with SMAD-derived, PPxY motif-containing peptide was further refined. Apart from the PPxY motif, certain WW domains recognize LPxY motif (where L is Leucine), and several WW domains bind to phospho-Serine-Proline (p-SP) or phospho-Threonine-Proline (p-TP) motifs in a phospho-dependent manner. Structures of these WW domain complexes confirmed molecular details of phosphorylation-regulated interactions. There are also WW domains that interact with polyprolines that are flanked by arginine residues or interrupted by leucine residues, but they do not contain aromatic amino acids.
The WW domain is known to mediate regulatory protein complexes in various signaling networks, including the Hippo signaling pathway. The importance of WW domain-mediated complexes in signaling was underscored by the characterization of genetic syndromes that are caused by loss-of-function point mutations in the WW domain or its cognate ligand. These syndromes are Golabi-Ito-Hall syndrome of intellectual disability caused by missense mutation in a WW domain and Liddle syndrome of hypertension caused by point mutations within PPxY motif.
A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein; vertebrate YAP protein, substrate of LATS1 and LATS2 serine-theronine kinases of the Hippo tumor suppressor pathway; Mus musculus (Mouse) NEDD4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD4 in its molecular organization; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in brain; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.
In 2004, the first comprehensive protein-peptide interaction map for a human modular domain was reported using individually expressed WW domains and genome predicted, PPxY-containing synthetic peptides. At present in the human proteome, 98 WW domains and more than 2000 PPxY-containing peptides, have been identified from sequence analysis of the genome.
YAP is a WW domain-containing protein that functions as a potent oncogene. Its WW domains must be intact for YAP to act as a transcriptional co-activator that induces expression of proliferative genes. Recent study has shown that endohedral metallofullerenol, a compound that was originally developed as a contrasting agent for MRI (magnetic resonance imaging), has antineoplastic properties. Via molecular dynamic simulations, the ability of this compound to outcompete proline-rich peptides and bind effectively to the WW domain of YAP was documented. Endotheral metallofullerenol may represent a lead compound for the development of therapies for cancer patients who harbor amplified or overexpressed YAP.
In the study of protein folding
Because of its small size and well-defined structure, the WW domain became a favorite subject of protein folding studies. Among these studies, the work of Rama Ranganathan  and David E. Shaw are notable. Ranganathan’s team has shown that a simple statistical energy function, which identifies co-evolution between amino acid residues within the WW domain, is necessary and sufficient to specify sequence that folds into native structure. Using such an algorithm, he and his team synthesized libraries of artificial WW domains that functioned in a very similar manner to their natural counterparts, recognizing class-specific proline-rich ligand peptides, The Shaw laboratory developed a specialized machine that allowed elucidation of the atomic level behavior of the WW domain on a biologically relevant time scale. He and his team employed equilibrium simulations of a WW domain and identified seven unfolding and eight folding events that follow the same folding route.
Being a relatively short, 30 t0 35 amino acids long, WW domain is amenable to chemical synthesis. It is cooperatively folded and can host chemically introduced non-canonical amino acids. Based on these properties, WW domain has been shown to be a versatile platform for the chemical interrogation of intramolecular interactions and conformational propensities in folded proteins.
- doi:10.1016/S0092-8674(00)80273-1. PMID 9200606. ; Ranganathan R, Lu KP, Hunter T, Noel JP (June 1997). "Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent". Cell. 89 (6): 875–86.
- Bork P, Sudol M (December 1994). "The WW domain: a signalling site in dystrophin?". Trends in Biochemical Sciences. 19 (12): 531–3. doi:10.1016/0968-0004(94)90053-1. PMID 7846762.
- Hofmann K, Bucher P (January 1995). "The rsp5-domain is shared by proteins of diverse functions". FEBS Letters. 358 (2): 153–7. doi:10.1016/0014-5793(94)01415-W. PMID 7828727.
- André B, Springael JY (December 1994). "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". Biochemical and Biophysical Research Communications. 205 (2): 1201–5. doi:10.1006/bbrc.1994.2793. PMID 7802651.
- Sudol M, Chen HI, Bougeret C, Einbond A, Bork P (August 1995). "Characterization of a novel protein-binding module--the WW domain". FEBS Letters. 369 (1): 67–71. doi:10.1016/0014-5793(95)00550-S. PMID 7641887.
- Chen HI, Sudol M (August 1995). "The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules". Proceedings of the National Academy of Sciences of the United States of America. 92 (17): 7819–23. Bibcode:1995PNAS...92.7819C. doi:10.1073/pnas.92.17.7819. PMC 41237. PMID 7644498.
- Macias MJ, Hyvönen M, Baraldi E, Schultz J, Sudol M, Saraste M, Oschkinat H (August 1996). "Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide". Nature. 382 (6592): 646–9. Bibcode:1996Natur.382..646M. doi:10.1038/382646a0. PMID 8757138.
- Sudol M, Bork P, Einbond A, Kastury K, Druck T, Negrini M, Huebner K, Lehman D (June 1995). "Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain". The Journal of Biological Chemistry. 270 (24): 14733–41. doi:10.1074/jbc.270.24.14733. PMID 7782338.
- Aragón E, Goerner N, Xi Q, Gomes T, Gao S, Massagué J, Macias MJ (October 2012). "Structural basis for the versatile interactions of Smad7 with regulator WW domains in TGF-β Pathways". Structure. 20 (10): 1726–36. doi:10.1016/j.str.2012.07.014. PMC 3472128. PMID 22921829.
- Bruce MC, Kanelis V, Fouladkou F, Debonneville A, Staub O, Rotin D (October 2008). "Regulation of Nedd4-2 self-ubiquitination and stability by a PY motif located within its HECT-domain". The Biochemical Journal. 415 (1): 155–63. doi:10.1042/BJ20071708. PMID 18498246.
- Lu PJ, Zhou XZ, Shen M, Lu KP (February 1999). "Function of WW domains as phosphoserine- or phosphothreonine-binding modules". Science. 283 (5406): 1325–8. Bibcode:1999Sci...283.1325L. doi:10.1126/science.283.5406.1325. PMID 10037602.
- Verdecia MA, Bowman ME, Lu KP, Hunter T, Noel JP (August 2000). "Structural basis for phosphoserine-proline recognition by group IV WW domains". Nature Structural Biology. 7 (8): 639–43. doi:10.1038/77929. PMID 10932246.
- Bedford MT, Sarbassova D, Xu J, Leder P, Yaffe MB (April 2000). "A novel pro-Arg motif recognized by WW domains". The Journal of Biological Chemistry. 275 (14): 10359–69. doi:10.1074/jbc.275.14.10359. PMID 10744724.
- Ermekova KS, Zambrano N, Linn H, Minopoli G, Gertler F, Russo T, Sudol M (December 1997). "The WW domain of neural protein FE65 interacts with proline-rich motifs in Mena, the mammalian homolog of Drosophila enabled". The Journal of Biological Chemistry. 272 (52): 32869–77. doi:10.1074/jbc.272.52.32869. PMID 9407065.
- Sudol M, Harvey KF (November 2010). "Modularity in the Hippo signaling pathway". Trends in Biochemical Sciences. 35 (11): 627–33. doi:10.1016/j.tibs.2010.05.010. PMID 20598891.
- Lubs H, Abidi FE, Echeverri R, Holloway L, Meindl A, Stevenson RE, Schwartz CE (June 2006). "Golabi-Ito-Hall syndrome results from a missense mutation in the WW domain of the PQBP1 gene". Journal of Medical Genetics. 43 (6): e30. doi:10.1136/jmg.2005.037556. PMC 2564547. PMID 16740914.
- Tapia VE, Nicolaescu E, McDonald CB, Musi V, Oka T, Inayoshi Y, Satteson AC, Mazack V, Humbert J, Gaffney CJ, Beullens M, Schwartz CE, Landgraf C, Volkmer R, Pastore A, Farooq A, Bollen M, Sudol M (June 2010). "Y65C missense mutation in the WW domain of the Golabi-Ito-Hall syndrome protein PQBP1 affects its binding activity and deregulates pre-mRNA splicing". The Journal of Biological Chemistry. 285 (25): 19391–401. doi:10.1074/jbc.M109.084525. PMC 2885219. PMID 20410308.
- Schild L, Lu Y, Gautschi I, Schneeberger E, Lifton RP, Rossier BC (May 1996). "Identification of a PY motif in the epithelial Na channel subunits as a target sequence for mutations causing channel activation found in Liddle syndrome". The EMBO Journal. 15 (10): 2381–7. doi:10.1002/j.1460-2075.1996.tb00594.x. PMC 450168. PMID 8665845.
- Staub O, Gautschi I, Ishikawa T, Breitschopf K, Ciechanover A, Schild L, Rotin D (November 1997). "Regulation of stability and function of the epithelial Na+ channel (ENaC) by ubiquitination". The EMBO Journal. 16 (21): 6325–36. doi:10.1093/emboj/16.21.6325. PMC 1170239. PMID 9351815.
- InterPro: IPR001202
- Hu H, Columbus J, Zhang Y, Wu D, Lian L, Yang S, Goodwin J, Luczak C, Carter M, Chen L, James M, Davis R, Sudol M, Rodwell J, Herrero JJ (March 2004). "A map of WW domain family interactions". Proteomics. 4 (3): 643–55. doi:10.1002/pmic.200300632. PMID 14997488.
- Sudol M, McDonald CB, Farooq A (August 2012). "Molecular insights into the WW domain of the Golabi-Ito-Hall syndrome protein PQBP1". FEBS Letters. 586 (17): 2795–9. doi:10.1016/j.febslet.2012.03.041. PMC 3413755. PMID 22710169.
- Huang J, Wu S, Barrera J, Matthews K, Pan D (August 2005). "The Hippo signaling pathway coordinately regulates cell proliferation and apoptosis by inactivating Yorkie, the Drosophila Homolog of YAP". Cell. 122 (3): 421–34. doi:10.1016/j.cell.2005.06.007. PMID 16096061.
- Zhao B, Kim J, Ye X, Lai ZC, Guan KL (February 2009). "Both TEAD-binding and WW domains are required for the growth stimulation and oncogenic transformation activity of yes-associated protein". Cancer Research. 69 (3): 1089–98. doi:10.1158/0008-5472.CAN-08-2997. PMID 19141641.
- Kang SG, Zhou G, Yang P, Liu Y, Sun B, Huynh T, Meng H, Zhao L, Xing G, Chen C, Zhao Y, Zhou R (September 2012). "Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine". Proceedings of the National Academy of Sciences of the United States of America. 109 (38): 15431–6. Bibcode:2012PNAS..10915431K. doi:10.1073/pnas.1204600109. PMC 3458392. PMID 22949663.
- Kang SG, Huynh T, Zhou R (2012). "Non-destructive inhibition of metallofullerenol Gd@C(82)(OH)(22) on WW domain: implication on signal transduction pathway". Scientific Reports. 2: 957. Bibcode:2012NatSR...2E.957K. doi:10.1038/srep00957. PMC 3518810. PMID 23233876.
- Sudol M, Shields DC, Farooq A (September 2012). "Structures of YAP protein domains reveal promising targets for development of new cancer drugs". Seminars in Cell & Developmental Biology. 23 (7): 827–33. doi:10.1016/j.semcdb.2012.05.002. PMC 3427467. PMID 22609812.
- Fuller AA, Du D, Liu F, Davoren JE, Bhabha G, Kroon G, Case DA, Dyson HJ, Powers ET, Wipf P, Gruebele M, Kelly JW (July 2009). "Evaluating beta-turn mimics as beta-sheet folding nucleators". Proceedings of the National Academy of Sciences of the United States of America. 106 (27): 11067–72. Bibcode:2009PNAS..10611067F. doi:10.1073/pnas.0813012106. PMC 2708776. PMID 19541614.
- Jager M, Deechongkit S, Koepf EK, Nguyen H, Gao J, Powers ET, Gruebele M, Kelly JW (2008). "Understanding the mechanism of beta-sheet folding from a chemical and biological perspective". Biopolymers. 90 (6): 751–8. doi:10.1002/bip.21101. PMID 18844292.
- Jäger M, Zhang Y, Bieschke J, Nguyen H, Dendle M, Bowman ME, Noel JP, Gruebele M, Kelly JW (July 2006). "Structure-function-folding relationship in a WW domain". Proceedings of the National Academy of Sciences of the United States of America. 103 (28): 10648–53. Bibcode:2006PNAS..10310648J. doi:10.1073/pnas.0600511103. PMC 1502286. PMID 16807295.
- Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R (September 2005). "Natural-like function in artificial WW domains". Nature. 437 (7058): 579–83. Bibcode:2005Natur.437..579R. doi:10.1038/nature03990. PMID 16177795.
- Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R (September 2005). "Evolutionary information for specifying a protein fold". Nature. 437 (7058): 512–8. Bibcode:2005Natur.437..512S. doi:10.1038/nature03991. PMID 16177782.
- Piana S, Sarkar K, Lindorff-Larsen K, Guo M, Gruebele M, Shaw DE (January 2011). "Computational design and experimental testing of the fastest-folding β-sheet protein". Journal of Molecular Biology. 405 (1): 43–8. doi:10.1016/j.jmb.2010.10.023. PMID 20974152.
- Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W (October 2010). "Atomic-level characterization of the structural dynamics of proteins". Science. 330 (6002): 341–6. Bibcode:2010Sci...330..341S. doi:10.1126/science.1187409. PMID 20947758.
- Ardejani MS, Powers ET, Kelly JW (August 2017). "Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities". Accounts of Chemical Research. 50 (8): 1875–1882. doi:10.1021/acs.accounts.7b00195. PMC 5584629. PMID 28723063.