Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening

Leili Zhang; David R. Bell; Binquan Luan; Ruhong Zhou

Umbrella sampling was adopted here to estimate the binding free energies of the 11 binding modes for the purpose of finding a practical approach of ranking binding modes from PPI docking programs and to explore the associated binding mechanism. The most rigorous way of calculating binding free energies has been discussed in multiple previous papers and is not the main focus in this study. 36, 38 Here, we used a simplified way of finding the relative binding free energy to ensure specifically that the calculated PMF differences directly correlate with the binding mode stability, by setting the two end points to be the final binding modes (shown in Figure 1 ) and their respective unbound states (defined when the minimal distance between the All rights reserved. No reuse allowed without permission.