Dec 17, 2015

Inferring protein-protein interaction networks from inter-protein sequence co-evolution

BioRxiv : the Preprint Server for Biology
Christoph FeinauerAndrea Pagnani

Abstract

Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on the Direct-Coupling Analysis of the co-evolution between inter-protein residue pairs. We use ribosomal and trp operon proteins as test cases: For the small resp. large ribosomal subunit our approach predicts protein-interaction partners at a true-positive rate of 70% resp. 90% within the first 10 predictions, with areas of 0.69 resp. 0.81 under the ROC curves for all predictions. In the trp operon, it assigns the two largest interaction scores to the only two interactions experimentally known. On the level of residue interactions we show that for both the small and the large ribosomal subunit our approach predicts interacting residues in the system with a true positive rate of 60% and 85% in the first 20 predictions. We...Continue Reading

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Mentioned in this Paper

Size
Ribosome Subunits, Large
Joints
Protein-Protein Interaction
Ribosomes
Respiratory, Thoracic and Mediastinal Disorders
Species
Analysis
Biological Evolution
Systems Biology

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