title: Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design.
abstract: Characterization of lysine methylation has proven challenging despite its importance in biological processes such as gene transcription, protein turnover, and cytoskeletal organization. In contrast to other key posttranslational modifications, current proteomics techniques have thus far shown limited success at characterizing methyl-lysine residues across the cellular landscape. To complement current biochemical characterization methods, we developed a multistate computational protein design procedure to probe the substrate specificity of the protein lysine methyltransferase SMYD2. Modeling of substrate-bound SMYD2 identified residues important for substrate recognition and predicted amino acids necessary for methylation. Peptide- and protein- based substrate libraries confirmed that SMYD2 activity is dictated by the motif [LFM]-1-K(∗)-[AFYMSHRK]+1-[LYK]+2 around the target lysine K(∗). Comprehensive motif-based searches and mutational analysis further established four additional substrates of SMYD2. Our methodology paves the way to systematically predict and validate posttranslational modification sites while simultaneously pairing them with their associated enzymes.
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Lanouette
authors.affiliation: Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
authors.forename: James A
authors.initials: JA
authors.lastname: Davey
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
authors.forename: Fred
authors.initials: F
authors.lastname: Elisma
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Ning
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
authors.forename: Daniel
authors.initials: D
authors.lastname: Figeys
authors.affiliation: Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada. Electronic address: rchica@uottawa.ca.
authors.forename: Roberto A
authors.initials: RA
authors.lastname: Chica
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada. Electronic address: jean-francois.couture@uottawa.ca.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Couture
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D057809:HEK293 Cells; D011495:Histone-Lysine N-Methyltransferase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D015202:Protein Engineering / Q000379:methods; D054730:Protein Interaction Domains and Motifs / Q000235:genetics; D060066:Protein Interaction Maps; D017434:Protein Structure, Tertiary / Q000235:genetics; D013379:Substrate Specificity
chemical_list: D011495:Histone-Lysine N-Methyltransferase; C512569:SMYD2 protein, human