Quantifying the two-state facilitated diffusion model of protein-DNA interactions.

ABSTRACT: The current report extends the facilitated diffusion model to account for conflict between the search and recognition binding modes adopted by DNA-binding proteins (DBPs) as they search DNA and subsequently recognize and bind to their specific binding site. The speed of the search dynamics is governed by the energetic ruggedness of the protein-DNA landscape, whereas the rate for the recognition process is mostly dictated by the free energy barrier for the transition between the DBP's search and recognition binding modes. We show that these two modes are negatively coupled, such that fast 1D sliding and rapid target site recognition probabilities are unlikely to coexist. Thus, a tradeoff occurs between optimizing the timescales for finding and binding the target site. We find that these two

SUBMITTER: Leven I 

PROVIDER: S-EPMC6582340 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature