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Mining proteomes for short motifs (possible potential as bioactive peptides) Proteomes – Man – pathogens – food organisms Computation – Evolutionary conservation.

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Presentation on theme: "Mining proteomes for short motifs (possible potential as bioactive peptides) Proteomes – Man – pathogens – food organisms Computation – Evolutionary conservation."— Presentation transcript:

1 Mining proteomes for short motifs (possible potential as bioactive peptides) Proteomes – Man – pathogens – food organisms Computation – Evolutionary conservation – Evolutionary convergence – Predicting SLiM-like properties

2 Short linear motifs SLiMPRED predictor α-Helixβ-SheetPolyproline II LIG_EH1_1 LIG_Dynein_DLC8_1 LIG_CAP-Gly_1 LIG_GLEBS_BUB3_1 LIG_PDZ_1LIG_SH3_1 LIG_IQLIG_PP1LIG_SH3_2 LIG_MDM2LIG_PP2B_1LIG_SH3_3 LIG_NRBOXLIG_SH2_GRB2LIG_SH3_5 LIG_Sin3_1LIG_SH2_SRCLIG_TRAF2_1 LIG_Sin3_3LIG_SH2_STAT3LIG_TRAF6 LIG_SH2_STAT5LIG_WW_1 LIG_SIAH_1 LIG_TRFH_1 LIG_WRPW_1 Restricted training set to protein-binding motifs including:

3 Training a short linear motif predictor (SLiMPred) α-Helixβ-SheetPolyproline IIOther sequences304930141 Unique ELMs711831 SLiM residues3873242181239 197,410 Non-SLiM residues Most motifs lie in disordered regions of proteins Existing predictor ANCHOR predicts protein-binding within disordered regions

4 SLiMPred (blue) v ANCHOR (red) Alpha-helix Beta-sheet Polyproline-II helix Other

5 SLIMPred has some predictive ability in ordered regions too Disordered regions Ordered regions

6 SLiMPred: predicting motif-like regions along a protein Disorder SLIMPred Relative Local Conservation http://bioware.ucd.iehttp://bioware.ucd.ie Mooney et al J Mol Biol (2012) 415:193-204

7 Which kinds of interactions should we use in searching for novel motifs? ALLYeast 2 hybrid complex

8 http://bioinfo- casl.ucd.ie/empa/programberlin/2- uncategorised/52

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16 Potential workflows to identify novel peptides from proteins Conservation analysis SLiMPrints Convergent evolution analysis SLiMFinder Extracellular peptides PeptideRanker Intracellular peptides SLiMPred ANCHOR Known structure of protein ligand, candidate peptide sequence Pepsite (Trabuco et al Nucleic Acids Res. 2012) Known structure with linear peptide in complex Predict cyclised peptide mimetic (CYCLOPS virtual library; Duffy et al 2012).

17 SLiMFinder human known versus the new Known true positive motifs are discovered With variations in many protein interaction sets Novel motifs are much sparser, often only discovered once

18 All the human motif discovery results are available in an online searchable database (search on genes or motifs) bioware.soton.ac.uk/slimdb

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