Hi All, I am trying to understand the mechanism of protein-peptide interaction in two complexes (protein-pepA and protein-pepB). While trying to perform some simulation experiments, I find that the* root mean square fluctuation (RMSF) by residues of protein in the complex is higher than that of the protein alone.* Please refer the figure attached to this email. pepA binds with higher affinity (in uM-range) than pepB according to invitro studies.
Does this happen normally?? Please advice. Thanks in advance Anita
<<attachment: RMSF.png>>
