Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions.

Area of Science:

• Computational Biology
• Biophysics
• Molecular Dynamics

Background:

• Accurate modeling of protein-DNA interactions is essential for understanding biological processes.
• Existing force fields may require refinement for coarse-grained simulations.

Purpose of the Study:

• To develop and validate physics-based potentials for protein-DNA interactions.
• To enable accurate coarse-grained simulations of protein-DNA complexes.

Main Methods:

• Developed UNRES + NARES-2P force field for protein-DNA interactions.
• Utilized umbrella-sampling molecular dynamics simulations in TIP3P water.
• Determined potentials of mean force (PMF) for 105 component pairs.
• Fitted approximate analytical expressions to PMF data.

Main Results:

• Established mean-field potentials for eight categories of protein-DNA interactions.
• Analytical expressions satisfactorily reproduced PMF curves across various orientations.
• Validated the accuracy of the developed potentials.

Conclusions:

• The developed physics-based mean-field potentials are suitable for coarse-grained simulations of protein-DNA interactions.
• These potentials provide a foundation for more detailed computational studies of DNA-binding proteins.