This Article Full Text Full Text (PDF) Supplement All Versions of this Article: biophysj.106.098236v1 93/7/2562    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Stibius, K. B. Articles by Sneppen, K. Search for Related Content PubMed PubMed Citation Articles by Stibius, K. B. Articles by Sneppen, K.

Modeling the Two-Hybrid Detector: Experimental Bias on Protein Interaction Networks

Karin B. Stibius ^*  and Kim Sneppen ^*

^* Niels Bohr Institute, Copenhagen, Denmark; and Risø National Laboratory, Roskilde, Denmark

Correspondence: Address reprint requests to Karin B. Stibius, E-mail: karin_stibius{at}hotmail.com.

This work was done to investigate the two-hybrid experiment for finding protein-protein interactions to explain the asymmetry found in the experimental data, and to help screen the data for high confidence interactions. By looking at the bait-prey experimental setup the resulting protein interaction network can be examined as a directed network (bait prey). We have investigated two possible scenarios for the asymmetry in the directed network by developing a biochemical model for the protein-DNA and protein-protein bindings inside the living yeast. One scenario assumes a background activity of bait proteins acting even without the prey, the other scenario explores the asymmetry in the chemistry associated with the bait being automatically located in the right position on the DNA. We conclude that the latter model gives the best description of the observed asymmetry.

This article has been cited by other articles:

				I. Feldman, A. Rzhetsky, and D. Vitkup Network properties of genes harboring inherited disease mutations PNAS, March 18, 2008; 105(11): 4323 - 4328. [Abstract] [Full Text] [PDF]