Tamap Journal of Physical Science, cilt.2019, ss.1-7, 2019 (Hakemli Üniversite Dergisi)
Selection and binding of peptides to MHC-I molecules play an important role in the adaptive immune
system. Some molecular dynamic (MD) simulations methods have been developed to understand the MHC class Ipeptide
binding mechanism. Behçet’s disease (BD) is a chronic multisystem inflammatory disorder of unknown
etiology. In this study, we use steered molecular dynamics (SMD) simulations to unravel the binding mechanism of
different peptides to human leukocyte antigens (HLA-B*51:01), an antigen associated with Behcet's disease (BD).
We approached this problem by employing 195 ns simulations. The maximum force as a function of time was
determined to 2.16 ns for NPYD peptide. The Jarzynski’s equation was used to obtain the binding free energy. This
result showed that the experimental IC50 values with calculated IC50 values are not compatible. Then, the present
study showed that SMD simulation is an important approach in the MHC I-peptide binding mechanism for
autoimmune diseases and methodology to drug design and peptide immunogenicity.