Systematic profiling and identification of the peptide‐mediated interactions between human Yes‐associated protein and its partners in esophageal cancer

• Published in: Journal of molecular recognition Vol. 35; no. 3; pp. e2947 - n/a
• Main Authors: Chen, Fei, Wang, Qifei, Mu, Yushu, Sun, Shibin, Yuan, Xulong, Shang, Pan, Ji, Bo
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.03.2022
• Subjects: Affinity; Amino Acid Motifs; Binding; Bonding strength; Cancer; Chemical compounds; Dishevelled protein; Esophageal cancer; Esophageal Neoplasms; Esophagus; Fluorescence; Fluorescence spectroscopy; Gastric cancer; Gene expression; Humans; Hydrogen bonding; Hydrogen bonds; peptide; Peptides; Peptides - chemistry; peptide‐mediated interaction; Pharmacology; Proline; proline‐rich motif; Protein Binding; Protein Structure, Tertiary; Proteins; Recognition; recognition site; Segments; Selectivity; Signal transduction; Transcription factors; Transcription Factors - metabolism; WW domain; YAP-Signaling Proteins - metabolism; Yes-associated protein; Yes-associated protein; proline-rich motif; selectivity; peptide; esophageal cancer; peptide-mediated interaction; WW domain; recognition site; affinity
• ISSN: 0952-3499; 1099-1352; 1099-1352
• DOI: 10.1002/jmr.2947

Human Yes‐associated protein (YAP) is involved in the Hippo signaling pathway and serves as a coactivator to modulate gene expression, which contains a transactivation domain (TD) responsible for binding to the downstream TEA domain family (TEAD) of transcription factors and two WW1/2 domains that recognize the proline‐rich motifs (PRMs) present in a variety of upstream protein partners through peptide‐mediated interactions (PMIs). The downstream YAP TD‐TEAD interactions are closely associated with gastric cancer, and a number of therapeutic agents have been developed to target the interactions. In contrast, the upstream YAP WW1/2‐partner interactions are thought to be involved in esophageal cancer but still remain largely unexplored. Here, we attempted to elucidate the complicated PMIs between the YAP WW1/2 domains and various PRMs of YAP‐interacting proteins. A total of 106 peptide segments carrying the class I WW‐binding motif [P/L]Px[Y/P] were extracted from 22 partner candidates, which are potential recognition sites of YAP WW1/2 domains. Structural and energetic analyses of the intermolecular interactions between the domains and peptides created a systematic domain‐peptide binding profile, from which a number of biologically functional PMIs were identified and then substantiated in vitro using fluorescence spectroscopy assays. It is revealed that: (a) The sequence requirement for the partner recognition site binding to YAP WW1/2 domains is a decapeptide segment that contains a core PRM motif as well as two three‐residue extensions from each side of the motif; the core motif and extended sections are responsible for the binding stability and recognition specificity of domain‐peptide interaction, respectively. (b) There is an exquisite difference in the recognition specificity of the two domains; the LPxP and PPxP appear to more prefer WW1 than WW2, whereas the WW2 can bind more effectively to LPxY and PPxY than WW1. (c) WW2 generally exhibits a higher affinity to the panel of recognition site candidates than WW1. In addition, a number of partner peptides were found as promising recognition sites of the two domains and/or to have a good selectivity between the two domains. For example, the DVL1 peptide was determined to have moderate affinity to WW2 and strong selectivity for WW2 over WW1. Hydrogen bonds play a central role in selectivity. The peptide‐mediated interactions of YAP WW1 and WW2 domains with various proline‐rich motifs of YAP‐interacting partners in esophageal cancer are systematically investigated at molecular level, from which a variety of peptide segments are identified from the partner candidates as potential recognition sites. They exhibit a good selectivity between the two domains, confirming an exquisite difference in the domain recognition specificity.