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

Area of Science:

• Biochemistry
• Molecular Biology
• Biophysics

Background:

• Protein-protein interactions are crucial for cellular functions.
• Accurate prediction of binding affinity is essential for understanding biological processes and drug development.

Purpose of the Study:

• To investigate the binding affinity between Designed Ankyrin Repeat Proteins (DARPins) and HIV-1 capsid protein (CA).
• To evaluate the impact of a specific mutation (Y56A) on the binding affinity.
• To demonstrate a combined approach using molecular dynamics (MD) and nanoparticle tracking analysis (NTA) for studying protein-protein interactions.

Main Methods:

• Nanoparticle Tracking Analysis (NTA) was used to measure changes in hydrodynamic radius upon protein binding.
• Molecular Dynamics (MD) simulations were employed to calculate binding free energy (∆GB).
• Detailed analysis of binding free energy decomposition and hydrogen bonds was performed to understand the binding mechanism.

Main Results:

• AnkGAG1D4-conjugated gold nanoparticles showed increased hydrodynamic radius upon interaction with HIV-1 CA, indicating binding.
• AnkGAG1D4-Y56A-conjugated gold nanoparticles did not show significant size changes with CA, suggesting reduced binding.
• MD simulations revealed a significantly lower binding free energy for AnkGAG1D4-Y56A (-31 kcal/mol) compared to AnkGAG1D4 (-60 kcal/mol) with CA.

Conclusions:

• The combined MD and NTA approach provides a robust method for monitoring protein-protein binding and predicting affinity.
• The mutation at residue 56 (Y56A) in AnkGAG1D4 critically diminishes its binding affinity to HIV-1 CA.
• Understanding these interactions is vital for developing targeted inhibitors for viral proteins.