Investigation of Binding Free Energy of Different Peptides by Jarzynski’s Equation

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Denkdaş C., Cantürk Rodop M.

Tamap Journal of Physical Science, no.2019, pp.1-7, 2019 (Peer-Reviewed Journal)

  • Publication Type: Article / Article
  • Publication Date: 2019
  • Journal Name: Tamap Journal of Physical Science
  • Journal Indexes: Other Indexes
  • Page Numbers: pp.1-7
  • Yıldız Technical University Affiliated: Yes


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.