Free Energy Landscape (FEL) analysis
Folding funnel is a fundamental concept in the free energy landscape of ordered proteins. It helps in understanding the different conformational ensembles explored by the protein throughout the simulations and how they fold into an ensemble having a global energy minimum. Each funnel in the free energy landscape diagram represents a reaction path in the folding process, and ideally, a protein folds into its native structure, having the lowest energy, with a single narrow funnel, where the intermediate structures are represented within the funnel at higher energy levels [47, 48]. But the folding scenario in IDP is different, as they do not have proper tertiary structure and tend to fold once bound to a binding partner. This indicates that the free energy landscape of IDPs is rugged and contains multiple funnels [49-51]. But they can provide insights into the folding pattern and minimum energy conformations occupied by the protein. A FEL diagram was generated for each of the simulated systems, with Radius of gyration and End to end distance as the two reaction coordinates using the gmx sham module [52] and and 2D contour plots and 3D projections of the free energy are plotted in figure 4 and supporting informationFigure S4 respectively.