Protein-Protein Interactions: Insight from Molecular Dynamics Simulations and Nanoparticle Tracking Analysis

• Published in: Molecules (Basel, Switzerland) Vol. 26; no. 18; p. 5696
• Main Authors: Chong, Wei Lim, Chupradit, Koollawat, Chin, Sek Peng, Khoo, Mai Mai, Khor, Sook Mei, Tayapiwatana, Chatchai, Nimmanpipug, Piyarat, Thongkum, Weeraya, Lee, Vannajan Sanghiran
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 20.09.2021; MDPI
• Subjects: Affinity; Alanine; Amino acids; Binding; Binding energy; Biological activity; Buffer solutions; Capsid protein; Case studies; DARPins; Energy; Free energy; HIV-1; Hydrogen bonds; Molecular dynamics; molecular dynamics simulations; Monitoring; Mutagenesis; Mutation; nanoparticle tracking analysis; Nanoparticles; Protein interaction; protein-protein binding; Proteins; Residues; Simulation; Tyrosine
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules26185696

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.