How the Barrierless Folding Helps DNA Recognition: Theoretical Investigation on Ultrafast Folding Protein Engrailed Homeodomain

Engrailed homeodomain (EngHD), a 3-helix bundle fast-folding protein, has been found to play a critical role in transcription regulation during its binding to DNA. Evidence shows that protein efficiently recognizes the short target DNA sequence from the enormous pool of binding sites via the process of “facilitated diffusion”, including sliding and hopping. During the facilitated diffusion, protein is supposed to go through “speed” mode, where protein nonspecifically interacts with DNA in fast diffusion, and “stability” mode, where protein strongly and specifically scans the base pairs in DNA with slow displacement.