Journal
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Volume 40, Issue 4, Pages 1586-1596Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/07391102.2020.1830852
Keywords
Hepatitis B virus; stability; affinity; immune escape; molecular dynamics
Categories
Funding
- National Natural Science Foundation of China [31900473, 31430035, 31171041, 31871322]
- Jiangsu innovative and entrepreneurial talent program [KY216R201805]
- Natural Science Foundation of the Jiangsu Higher Education Institutions of China [18KJB180015]
- Nanjing Medical University Science and Technology Development Fund [2016NJMUZD003]
- Fundamental Research Funds for the Central Universities [2242017K3DN23, 2242017K41041]
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This study identified important mutation sites in HBV and evaluated their impact using molecular dynamics simulation. The findings provide insights for immunotherapy.
Hepatitis B virus (HBV) infection is an important problem threatening human health. After HBV virus invades human body, it may assemble a complete virus particle in the cytoplasm to trigger the immune reaction, especially the interaction between the HBV virus and the host that mediated by CD8(+)T cell. We collected the sequences of HBV from the HBVdb database, then screened candidate mutation sites in Chinese, European and American populations based on conservation and physicochemical properties. After that we constructed the three-dimensional structure of Major histocompatibility complex class I (MHC I) -peptide complexes, performed molecular docking, run molecular dynamics to compare the binding free energy, stability, and affinity of MHC I-peptide complexes with the aim to estimate the effect of peptide mutation. The specific HBV virus subtypes of the Chinese, European and American population were studied and the candidate mutation sites were used to predict the mutant peptide antigen. Finally, based on physical and chemical properties and peptide antigen prediction scores, 21 HBV mutation sites were selected. Then combined with specific Human lymphocyte antigen (HLA) subtypes, 11 mutations were found to have a significant negative impact on affinity, stability and binding free energy. Overall, our work found important potential mutations, which provide an evaluation of HBV mutations and a clue of it in immunotherapy. Communicated by Ramaswamy H. Sarma
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