Protein‐protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis

Abstract

Protein‐protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein‐protein binding process and predicting the binding affinity. Our case study of designed ankyrin repeats proteins (DARPins)—AnkGAG1D4 and the single point mutated AnkGAG1D4‐Y56A for HIV‐1 capsid protein (CA) were investigated. As reported, AnkGAG1D4 bound with CA for inhibitory activity; however, it lost its inhibitory strength when tyrosine at residue 56 AnkGAG1D4, the most key residue was replaced by alanine (AnkGAG1D4‐Y56A). Through NTA, the binding of DARPins and CA was measured by monitoring the increment of the hydrodynamic radius of the AnkGAG1D4‐gold conjugated nanoparticles (AnkGAG1D4‐GNP) and AnkGAG1D4‐Y56A‐GNP upon interaction with CA in buffer solution. The size of the AnkGAG1D4‐GNP increased when it interacted with CA but not AnkGAG1D4‐Y56A‐GNP. In addition, a much higher binding free energy (∆GB) of AnkGAG1D4‐Y56A (−31 kcal/mol) obtained from MD further suggested affinity for CA completely reduced compared to AnkGAG1D4 (−60 kcal/mol). The possible mechanism of the protein‐protein binding was explored in detail by decomposing the binding free energy for crucial residues identification and hydrogen bond analysis.