Theoretical analysis of a high performance protein imprint on a nanosensor

• The formation of a high performance protein imprint was computationally analyzed.
• The binding interface for protein recognition was found in the imprint.
• 189 compounds were virtually screened by docking analysis.
• A novel parameter was used to screen functional monomers for protein imprint.

The structural details and flexibilities of protein impose significant challenges to develop protein imprint, especially for the selection of functional monomer. Using NAMD, AutoDock 4 and AutoDock Vina, we investigated the formation of a high performance protein imprint on a nanosensor that detected human papillomavirus (HPV) biomarker protein E7 with high sensitivity. According to molecular dynamics, the phenolic oligomers were shown to assemble with the E7 protein and form a complex at specific targeting areas on the protein. Docking analysis efficiently screened chemical compounds by evaluating the binding affinity. A new parameter, i.e., average binding energy (ΔG/contact), was used together with binding energy (ΔG) to screen compounds. The screening went through 189 compounds and identified a subpopulation of 22 compounds showing unique characteristics of binding, and could potentially be used to develop the specific and robust imprint. Accordingly, the study implicated a novel approach to screen functional compounds for rational design of the protein imprint.