Transfer entropy (TE) is a directional measure of uncertainty reduction one process has on another process. Transfer entropy has been used to model the intramolecular interactions of lac repressor peptides derived from the recognition helix in combination with specific and non-specific DNA. We calculate the pairwise transfer entropy across each peptide complex to examine the relationships between individual residues by taking the sum of the transfer entropy each residue sends to all other residues in the complex. We selected the most driving and most receiving residues for further analysis. Doing so allowed us to construct transfer entropy pathways to provide an analysis of how residues physically influence each other and contribute to the dynamics of the protein. We found that residues which have hydrogen bonding and/or hydrophobic interactions with the sequence specific DNA bases and/or the DNA backbone, play a large role in both the driving and receiving pathways, as do the sequence specific DNA bases. The information pathways eventually form continuous information “loops”. For each peptide complex, the most driving residue pathways eventually flow into a common information loop, as do the most receiving residue pathways. This implies that the majority of information flow within a protein is found in these loops.

Insights into protein-DNA binding specificity from transfer entropy calculations

ACS Spring Meeting 2021

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