A simple physical model for scaling in protein-protein interaction networks. by Deeds, Ashenberg, Shakhnovich in Jan 2006 PNAS.

I've been sitting on this review for a few days because I wanted to really think about what the authors are saying in this paper and figure out the best way to convey it. What this paper posits is that the touted scale free property of protein-protein interaction networks may be misinformed. Scale free network theory says that the structure of the network is evolutionary favorable and allows for modularity, hierarchy, and redundancy on the molecular level. What Deeds et al. are saying is that this scale free topology can be achieved using a completely non evolutionary method.

As many in the field well know, protein-protein interaction networks are full of false positives, and there is little correlation between published studies. The authors shed light on the reason for this by using a hydrophobic model for protein interaction. Pretty much if you just take the proteins with the most hydrophobic exposed surface area and give them a higher probability to interact with each other (non-specifically and more importantly in a non-biological context) you can reconstruct the scale free nature of published yeast protein interaction networks.

So what does this mean? Well I think that to some extent this paper is getting at one of the true underlying sources of false positives in interaction networks. In fact, this model may lead to a good way to prune out non-specific interactions. What this paper does not say, and I agree with them, is that there is no biological information in these studies. It's true that alone the data may be noisy, but compiled with other sources of information including expression, function, and conservation, the data remain extremely useful.




tt: Biophysics, Networks, Scale Free