Protein Interactions Extrapolated from Feline Protein Complexes

The determination of protein-protein interaction networks is a difficult and important problem in biology. Present day approaches to this problem are usually based on two hybrid experimental measurements coupled with refinement and extrapolation using computational techniques. Here we consider a computational method for similar refinement and extrapolation using experimental data from which protein interactions can not be directly inferred. Our dataset was derived from an experiment designed to examine cell growth, tumorigenesis, and differentiation in a highly malignant cat melanoma cell line using 2-D gel electrophoresis and MALDI-TOF mass spectrometry. Instead of direct information about protein-protein interactions, this experiment yields protein complexes. We analyze and interpret these complexes to provide predictions of protein-protein interactions. We find that we are able to predict when a protein pair belongs to a complex with ~96% accuracy, suggesting that these protein pairs interact. We extrapolate the experimentally identified interaction pairs to the entire cat proteome in order to obtain a cat protein interaction network. This network has a scale free degree distribution, in agreement with previous observations about protein interaction networks.