Biomodeling: DNA-binding proteins (PCNA)
There are several well known DNA-binding motif proteins.
In those DNA-binding proteins, basic residues bind to
Backbone phosphates: non-specific (e.g., RNA polymerase).
Major grooves: motif-level, specific and relatively weaker (e.g., zinc finger, helix-turn-helix etc.).
Minor grooves: single residue-level, specific and relatively stronger (e.g., histone, exonuclease etc.).
DNA-binding proteins diffuse along DNA to find the target sites!!!
Diffusion of PCNA in MD simulations
PCNA in MD simulations
Mean-Squared Displacement (MSD) and Diffusion Coefficient
For a 1D diffusion case, the diffusion coefficient is defined as MSD(∆ t)= 2D∆.t
A Python example.