Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models

Area of Science:

• Biophysics
• Molecular Biology
• Computational Biology

Background:

• Transcription factors (TFs) are crucial for gene regulation.
• TFs locate specific DNA sequences through a combination of 3D diffusion and 1D sliding.
• The microscopic details of TF-DNA sliding have been difficult to observe experimentally.

Purpose of the Study:

• To investigate the free-energy landscape governing the sliding dynamics and dissociation kinetics of the LacI dimer on DNA.
• To connect microscopic molecular dynamics to macroscopic search kinetics observed in vitro and in vivo.

Main Methods:

• Developed an analytical formulation of umbrella sampling along a helical coordinate.
• Performed extensive, fully atomistic molecular dynamics simulations.
• Combined molecular dynamics with Brownian simulations, including rotational diffusion.
• Used single-molecule imaging to validate predictions in living cells.

Main Results:

• Quantified the free-energy landscape for LacI dimer sliding and dissociation.
• Identified a fine structure in potential of mean force distributions with specific energy amplitudes for sliding and dissociation.
• Determined that LacI slides approximately 8 base pairs (bp) in close contact before microscopic dissociation.
• Estimated a macroscopic residence time of 48 ms and an in vitro sliding distance of 240 bp.
• Validated in vitro predictions with in vivo single-molecule imaging data.

Conclusions:

• The study provides unprecedented detail on the microscopic mechanisms of transcription factor search kinetics.
• Established a quantitative link between microscopic dynamics and macroscopic rate constants.
• The findings enhance understanding of how transcription factors efficiently locate their target DNA sequences.