Investigation of Molecular Dynamics of Peptides Bound with HLA * B51: 01 Protein

Denkdaş C., Cantürk Rodop M.

Tamap Journal of Physical Sciences, no.2021, pp.1-11, 2021 (Peer-Reviewed Journal)

  • Publication Type: Article / Article
  • Publication Date: 2021
  • Journal Name: Tamap Journal of Physical Sciences
  • Page Numbers: pp.1-11
  • Yıldız Technical University Affiliated: Yes


In the human body, there is the human leukocyte antigen (hereafter HLA) gene system, which recognizes whether the gene belongs to that body or not. This system encodes HLA antigens proteins to function. HLA antigens are classified as Class I, Class II and Class III according to their structural and functional properties. Class I and Class II HLA proteins form stable complex structures by binding with various peptides. However, some mutations on these proteins affect the binding process by causing lack of binding or poor binding of peptides and causes the development of many important diseases such as ankylosing spondalitis, systemic lupus, type 1 diabetes, Behçet's disease and autoimmune chronic hepatitis-B. The statistical thermodynamic properties of peptides (experimentally shown to be associated with HLA-B * 51: 01 Class I protein) that causes Behçet's disease (a very common disease in Turkey), has been investigated. Within the scope of the research, molecular dynamics (MD) method was used to determine the common aspects of peptides’ behavior. In the MD method, peptides were carried out in solvent medium using the TIP3 water model.

Keywords: Molecular Dynamics Simulation (MD), protein, peptide, statistical thermodynamic properties