Predicting PDZ Domain Mediated Protein Interactions from Structure

Shirley Hui, Xiang Xing, and Gary D. Bader

Website: http://webservice.baderlab.org/domains/POW/

Background

PDZ domains are structural protein domains that recognize ligands containing simple linear amino acid motifs and mediate protein-protein interactions (PPIs) in important biological processes, such as ion channel regulation, cell polarity determination and neural development. PDZ domain-peptide interaction predictors have recently been developed and can predict peptide ligands using primary amino acid sequence information, however they are limited to PDZ sequences that are similar in sequence to the training domains. Since domain structure is known to influence binding specificity, we hypothesized that the use of structural information should result in the prediction of new interactions and should be less dependent on sequence similarity than the sequence-based predictors.

Results

We developed a novel support vector machine-based predictor of PDZ domain and C-terminal peptide interactions using PDZ domain structure and peptide sequence information. Different cross validation strategies and blind tests show that the predictor can correctly predict interactions in multiple organisms. We used the structure-based predictor to scan the human proteome for ligands of 218 PDZ domains and show that predictions correspond to known PDZ domain-peptide interactions and PPIs in curated databases. The structure-based predictor is complementary to the sequence-based predictor, finding unique known and novel PPIs. We used a functional enrichment analysis of our hits to create a predicted map of PDZ domain biology. This map highlights PDZ domain involvement in diverse biological processes, some only found by the structure-based predictor. Based on this analysis, we predict novel PDZ domain involvement in xenobiotic metabolism and innate immune signalling and suggest new PDZ interactions for other processes including wound healing and Wnt signalling.

SVM Predictions

SVM predictions were validated using known interactions from PDZBase, a domain peptide interaction database and known protein-protein interactions (PPIs) from iRefIndex. iRefIndex is a PPI database which consolidates PPIs from different databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT.

The following are SVM proteome scanning structure-based and sequence-based predictions for human, fly and worm PDZ domains. Only domains with predicted interactions are included. For example: The structure-based predictor returned predictions for 215 out of 218 human domains scanned.

The format of the output files is:

• <indicator> <predicted binder sequence> <decision value> <source> <transcript ids>

• <indicator> is one of the following symbols:

  • * = validated by PDZBase, corresponds to an iRefIndex PPI (human only), or validated by protein microarray experiments (fly and worm only)
  • X = false positive as determined by protein microarray experiments (fly and worm only)
  • empty = no experiment or other evidence to validate or support this prediction

• <predicted binder sequence> is the sequence of length five of the predicted binder

• <decision value> is a real number computed by the SVM to evaluate if a given sequence should be predicted as a binder or not. All values will be greater than zero since the files only contain predicted binders.

• <source> is non empty if only indicator is non empty and is one of the following codes:

  • PB = found in PDZBase
  • IR = corresponds to a PPI in iRefIndex (transcript index1, ..., transcript index n)
  • PM = found in protein microarray experiment
  • - = not found in any of the above sources

• <protein ids>

  • Ensembl protein ids corresponding to the predicted binder

Supplementary Information

• Cytoscape BiNGO

  • BiNGO Enrichment Files (zip)

    • BiNGO enrichment files created by the Cytoscape BiNGO Plugin from sequence-based and structure-based hits. Cytoscape v2.8.1 and the BiNGO Plugin v1.44 were used. Only terms with greater than 5 and less than 300 genes (based on the GMT file below) were used from the GO ontology v1.2 (Dec 7, 2011).
• Cytoscape Enrichment Map

  • Sequence vs. Structure Enrichment Map (cys)

  • Structure vs. iRefIndex Enrichment Map (cys)

  • Sequence vs. iRefIndex Enrichment Map (cys)

  • Gene-set File (GMT)

    • Cytoscape session file for the summary enrichment map comparing sequence-based and structure-based predictions for human PDZ domains. Cytoscape v2.8.1 and the Enrichment Map Plugin v1.2 were used.

• Data Files (zip)

  • Domain Structures
    • PDB files for experimentally determined and homology modelled structures for human, mouse, worm and fly
  • Proteomes
    • Ensembl proteome files for Human, Worm and Fly
  • Experiment Interaction files (in peptide file format)
    • Fly files from Chen
    • Human files from Tonikian
    • Mouse files from Stiffler
    • Worm files from Chen
  • Negative Interaction files (in raw format)
    • Human files generated by SVM
    • Mouse files generated by SVM
  • Curated Interaction files (flat files)
    • PDZBase for Human (Mouse, Worm and Fly included, but not used)
    • iRefIndex interactions for Human
  • Phage codon bias files

  • ProteomeScan Files

    • Files required to run the proteome scanning software

Source Code

• GNU LGP License (txt)

• Java Code + Dependency Jars (zip)

  • jfreechart 1.0.12 (and dependencies)
  • weka 3.9.1

  • auc calculator (Davis & Goadrich, 2006)

  • BioJava 1.5

  • iText 2.1.3
  • jmatio
  • Bingo 2.3
  • Cytoscape 2.6.3
  • Cytoscape-task 2.6.3
  • BRAIN 1.0.5 (pdzsvm)
  • libSVM 2.8.9 (pdzsvmstruct)

Team

• Shirley Hui
• Xiang Xing
• Gary Bader

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