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Molecules ; 26(18)2021 Sep 20.
Article in English | MEDLINE | ID: mdl-34577167

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.


Subject(s)
Capsid Proteins/metabolism , Metal Nanoparticles/chemistry , Recombinant Proteins/metabolism , Amino Acids/chemistry , Amino Acids/metabolism , Ankyrin Repeat , Binding Sites , Capsid Proteins/chemistry , Dielectric Spectroscopy , Gold/chemistry , HIV-1/chemistry , Hydrogen Bonding , Metal Nanoparticles/analysis , Molecular Dynamics Simulation , Mutagenesis, Site-Directed , Point Mutation , Protein Binding , Recombinant Proteins/chemistry , Thermodynamics
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