Molecular Dynamics Simulation Reveals the Selective Binding of Human Leukocyte Antigen Alleles Associated with Behçet's Disease

PloS One
Sirilak KongkaewSupot Hannongbua

Abstract

Behçet's disease (BD), a multi-organ inflammatory disorder, is associated with the presence of the human leukocyte antigen (HLA) HLA-B*51 allele in many ethnic groups. The possible antigen involvement of the major histocompatibility complex class I chain related gene A transmembrane (MICA-TM) nonapeptide (AAAAAIFVI) has been reported in BD symptomatic patients. This peptide has also been detected in HLA-A*26:01 positive patients. To investigate the link of BD with these two specific HLA alleles, molecular dynamics (MD) simulations were applied on the MICA-TM nonapeptide binding to the two BD-associated HLA alleles in comparison with the two non-BD-associated HLA alleles (B*35:01 and A*11:01). The MD simulations were applied on the four HLA/MICA-TM peptide complexes in aqueous solution. As a result, stabilization for the incoming MICA-TM was found to be predominantly contributed from van der Waals interactions. The P2/P3 residue close to the N-terminal and the P9 residue at the C-terminal of the MICA-TM nonapeptide served as the anchor for the peptide accommodated at the binding groove of the BD associated HLAs. The MM/PBSA free energy calculation predicted a stronger binding of the HLA/peptide complexes for the BD-associated HL...Continue Reading

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Citations

Jan 26, 2018·Frontiers in Molecular Biosciences·Changhao WangRay Luo
Oct 13, 2016·Molecular BioSystems·Arthitaya MeeprasertThanyada Rungrotmongkol
Jun 27, 2019·Physical Chemistry Chemical Physics : PCCP·Bodee NuthoThanyada Rungrotmongkol
Jan 27, 2019·Scientific Reports·Sirilak KongkaewSupot Hannongbua
Nov 19, 2019·Current Topics in Medicinal Chemistry·Panupong MahalapbutrThanyada Rungrotmongkol
Jan 21, 2020·ACS Omega·Kamonpan SanachaiThanyada Rungrotmongkol
Jul 20, 2020·Current Drug Targets·Jermilia CharlesVictoria A Ploplis

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Methods Mentioned

BETA
X-ray

Software Mentioned

Discovery studio
AMBER10
MICA
TM
AMBER
PROPKA
SHAKE

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