ArticleMolecules (Basel, Switzerland)2021
Protein-Protein Interactions: Insight from Molecular Dynamics Simulations and Nanoparticle Tracking Analysis.
Article in Molecules (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Positional scanning and computational modeling reveal determinants of legumain transpeptidase activity.Protein science : a publication of the Protein Society · 2026Article
- Protective effect of Carica papaya leaf extract against dental pulp damage induced by gamma irradiation.Journal of molecular histology · 2025Article
- Exploring Placental Protein-Target Protein Interactions:Current protein & peptide science · 2025Article
- Solid CaCOCurrent cancer drug targets · 2025Article
- In Silico Modeling of Myelin Oligodendrocyte Glycoprotein Disulfide Bond Reduction by Phosphine-Borane Complexes.Pharmaceuticals (Basel, Switzerland) · 2024Article
- Proteomic Characterization of Human Placenta: Insights into Potential Therapeutic Applications for Osteoarthritis.AAPS PharmSciTech · 2024Article
- Genetic architecture of hippocampus subfields volumes in Alzheimer's disease.CNS neuroscience & therapeutics · 2024Article
- Specific Interaction of DARPin with HIV-1 CAViruses · 2022Article
- The effect of mutation on neurotoxicity reduction of new chimeric reteplase, a computational study.Research in pharmaceutical sciencesArticle
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Authors and funding
9 authors.
Funding
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.
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