Investigation of Binding Free Energy of Different Peptides by Jarzynski’s Equation
Tamap Journal of Physical Science, sa.2019, ss.1-7, 2019 (Hakemli Dergi)
- Yayın Türü: Makale / Tam Makale
- Basım Tarihi: 2019
- Dergi Adı: Tamap Journal of Physical Science
- Derginin Tarandığı İndeksler: Other Indexes
- Sayfa Sayıları: ss.1-7
- Açık Arşiv Koleksiyonu: AVESİS Açık Erişim Koleksiyonu
- Yıldız Teknik Üniversitesi Adresli: Evet
Özet
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.