Current Synthetic and Systems Biology
Open Access

Abstract

Can Proteins Use Electricity for Signaling One Another?

Fonseca SL and Nakaya HI

Base excision repair is of paramount importance in maintaining integrity of bacteria as well human genomes against chemical and oxidative damage. The enzymatic activity of the proteins involved in this process is well characterized. More obscure, though, is how DNA repair proteins effectively scan the genome in order to find these lesions. Scanning the genome by simply sliding through the double helix, or through random diffusion, takes up to 100 times longer than DNA repair proteins actually take to detect the lesions. For example, only 30 copies of DNA-repair protein MutY are usually found in an E. coli cell. If these 30 proteins slide through the 5 million base pairs of E. coli genome at 200 bps-1, it would take more than 13 min to scan the genome entirely. This is not compatible to an organism that can replicate every 30 minutes. Similarly, transcriptional regulators are able to find its binding site much faster than the theoretical limit of diffusion within the cell. This faster-than-diffusion paradox was originally described for transcriptional repressors, but it could be applied to most, if not all target-specific DNA-binding proteins. Several mathematical models were created to explain this paradox, but still numbers do not seem to match up.