Structural Analysis of Protein Conformations

All trajectories were aligned to their crystal structure conformation using Moleculekit implemented in HTMD tools (Doerr et al., 2016 (link)). To visualize the structures representing each state, the structures collected from the PCCA distributions were loaded and superimposed in Pymol-mdanalysis (https://github.com/bieniekmateusz/pymol-mdanalysis; Bieniek, 2022 ). The structural analysis was performed using mdtraj (McGibbon et al., 2015 (link)) and MDAnalysis (Michaud-Agrawal et al., 2011 (link)). Figures capturing major conformational changes were generated using the Protein Imager (Tomasello et al., 2020 (link)). All plots were made using the matplotlib libraries (Hunter, 2007 (link)).