The authors present results of a comparatative MD simulation of both peptide-loaded and peptide-free MHCII molecules. Analyzing the first 10ns of simulation of the unloaded MHCII, they found that a part of the α-chain (residues 50-59) adopt similar position as the antigenic peptide in the loaded MHCII. Unfortunately, the authors do not present the behaviour of both, the loaded and unloaded MHCII molecules during the last 50 ns of simulation. Especially, the statement on p. 4 that after 15ns the „peptide-loaded simulation occasionally sampled conformations having some characteristics of the peptide-free form (not shown)“ is unclear. Does it mean that the models presented are not stable during the hole simulation ? What’s about the position of the α-chain residues 50-59 in the last 50ns ? Are they located in the antigen pocket stabilized by the described hydrogen bonds?
