Extended Data Fig. 4: Markov State Model (MSM) kinetic maps of all simulated DRB1 allotypes (twelve allotypes).
From: MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange
Black discs represent metastable states (MSs) with areas proportional to their relative stationary weights (maximum likelihood values). Black arrows indicate transitions between MSs, where the width of each arrow increases with the corresponding transition rate. Relative free energies and transition rates for the MSs are each shown with a with a superscript and subscript 1σ confidence interval (from bootstrapping trajectory MSMs). Each MS is illustrated by ribbon representations of MHCII (white) and CLIP (magenta) of eight simulated conformations (one opaque, seven transparent, viewed from the top into the binding groove). The α-helices of α55–66 and β74-93 are highlighted in green and orange, respectively, with corresponding arrows indicating conformational changes with respect to the ground state MS3.
