The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study
Fig 8
Calculated free energy change (potential of mean force, PMF) obtained from umbrella sampling simulations along the distance between the alpha carbon of the Pω and the bottom of the F pocket.
Free energy changes were extracted from simulations of complexes with peptides derived from Kb/SIINFEKL (B) or Kb/FAPGNYPAL (C) structures. The start point and end point reaction coordinates are shown in the supporting material (S3 Fig).