A Bond-Anchored Network Structure Alignment (BANSA) Method for Graphical Analysis of Protein-Protein Interfacial Regions

We introduce a method to analyze and compare intermolecular bonds formed between protein-protein interactions. Utilizing the DiffBond software, we calculate potential intermolecular bonds, such as ionic bonds, hydrogen bonds, and salt bridges, based on amino acid structural and spatial parameters. This results in a graphical representation of bonds termed a bond network for each protein pair interaction. We then introduce an innovative strategy, the Bond-anchored Network Structural Alignment (BANSA), to align these networks using bond formation as anchor points. This alignment process uses the Root Mean Square Deviation (RMSD) to quantitatively assess the similarity between molecular structures. We validate the BANSA approach using several forms of analysis including a heatmap analysis, which provides a consolidated view of the entire bond network as well as a thorough comparison with existing literature. The results highlight the method’s potential to offer insights into molecular interactions across various protein pairs without a need for direct modelling of protein-protein interactions.