title: Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases.
abstract: Mitogen-activated protein kinases (MAPK) are broadly used regulators of cellular signaling. However, how these enzymes can be involved in such a broad spectrum of physiological functions is not understood. Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less-characterized disordered regions. We used a structurally consistent model on kinase-docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under-explored part of the human proteome and applied experimental tools specifically tailored to detect low-affinity protein-protein interactions for their validation in vitro and in cell-based assays. The combined computational and experimental approach enabled the identification of many novel MAPK-docking motifs that were elusive for other large-scale protein-protein interaction screens. The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase-mediated partnerships evolved over time. The analysis suggests that most human MAPK-binding motifs are surprisingly new evolutionarily inventions and newly found links highlight (previously hidden) roles of MAPKs. We propose that short MAPK-binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles.
authors.affiliation: Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: András
authors.initials: A
authors.lastname: Zeke
authors.affiliation: Max Planck Institute for Informatics, Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Saarbrücken, Germany.
authors.forename: Tomas
authors.initials: T
authors.lastname: Bastys
authors.affiliation: Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: Anita
authors.initials: A
authors.lastname: Alexa
authors.affiliation: Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: Ágnes
authors.initials: Á
authors.lastname: Garai
authors.affiliation: Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: Bálint
authors.initials: B
authors.lastname: Mészáros
authors.affiliation: Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: Klára
authors.initials: K
authors.lastname: Kirsch
authors.affiliation: MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.
authors.forename: Zsuzsanna
authors.initials: Z
authors.lastname: Dosztányi
authors.affiliation: Max Planck Institute for Informatics, Saarbrücken, Germany.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Kalinina
authors.affiliation: Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary remenyi.attila@ttk.mta.hu.
authors.forename: Attila
authors.initials: A
authors.lastname: Reményi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D006801:Humans; D020928:Mitogen-Activated Protein Kinases / Q000737:chemistry* / Q000648:ultrastructure*; D062105:Molecular Docking Simulation; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D015398:Signal Transduction; D013499:Surface Properties
chemical_list: D020928:Mitogen-Activated Protein Kinases
keywords: MAP kinase; cellular signaling; linear motif; protein–protein interaction