Accurate Description of Protein-Protein Recognition and Protein Aggregation with the Implicit-Solvent-Based PACSAB Protein Model

We used the PACSAB protein model, based on the implicit solvation approach, to simulate protein-protein recognition and study the effect of helical structure on the association of aggregating peptides. After optimization, the PACSAB force field was able to reproduce correctly both the correct binding interface in ubiquitin dimerization and the conformational ensemble of the disordered protein activator for hormone and retinoid receptor (ACTR). The PACSAB model allowed us to predict the native binding of ACTR with its binding partner, reproducing the refolding upon binding mechanism of the disordered protein.

Automated summary

Using the PACSAB protein model, researchers simulated protein-protein recognition and studied the impact of helical structure on the association of aggregating peptides. The optimized PACSAB force field accurately reproduced the correct binding interface in ubiquitin dimerization and the conformational ensemble of the disordered protein activator for hormone and retinoid receptor (ACTR). The PACSAB model allowed for the prediction of the native binding of ACTR with its binding partner, reproducing the refolding mechanism of the disordered protein upon binding.