Energy Network Analysis to Quantify Effects of Nanotubes on DNA/Peptide Strength of Interaction

We have developed an energy-based network analysis method, which allows for the characterization of communication pathways in a protein. The method describes protein aminoacids as network nodes, which are connected (or not) based on the average strength of interaction obtained from an equilibrium molecular dynamics simulation. We have shown that this method can accurately describe the ability of a protein to propagate a signal throughout its structure to communicate two domains that are distant from each other. Here, we show that this type of analysis can also be used to quantify the strength of interaction between two molecules, potentially providing a computationally inexpensive alternative to free-energy methods to predict strength of binding. We used our method to measure the effects of nanotube-DNA interaction on the strength of interaction between the same DNA segment and a DNA-binding zinc finger domain peptide. Successful binding of a zinc-finger domain to a DNA segment that is already attached to a carbon nanotube could enable assembly of a system that could function as a biomimetic metabolon for the production of energy in biofuels.