In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2.
Phys Chem Chem Phys
; 24(27): 16876-16883, 2022 Jul 13.
Article
in English
| MEDLINE | ID: covidwho-1921736
ABSTRACT
The COVID-19 epidemic, caused by virus SARS-CoV-2, has turned into a pandemic and threatened everyone's health for the past two years. In SARS-CoV-2, ORF8 is one of the most important accessory proteins with a role in immune modulation. There are multiple disulfide bonds in the wild type (WT) ORF8. Here, we present an in silico study on the effects of the disulfide bonds in ORF8 on the aspects of the structural properties and binding properties with the human leukocyte antigen (HLA-A). We first define five possible states for ORF8 with different disulfide bond reduction schemes. For each state, we collect the conformational ensemble using molecular dynamics (MD) simulations in an explicit solvent. From the analysis of the structural properties, we find that the reduction of the disulfide bonds has small effects on the global properties but much larger effects on the ORF8-specific region that is located on the surface of the ORF8 dimer. Interestingly, we find that the dimer does not break into two monomers at room temperature even if all the disulfide bonds get reduced. Further, we investigate the role of the disulfide bonds in the interactions with the human leukocyte antigen (HLA) by performing docking between HLA-A and the conformational ensembles of ORF8 in different states. We give predictions on the preferred binding sites for each state and validate the predictions for the WT dimer with the experimental data on epitopes. In the end, we evaluate the stability of the complexes formed between HLA-A and ORF8 in each state using MD simulations. Our observations can provide inspiration for inhibitor/drug design against ORF8 based on the binding pathway with HLA-A.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Viral Proteins
/
SARS-CoV-2
/
COVID-19
Type of study:
Experimental Studies
/
Observational study
/
Prognostic study
Limits:
Humans
Language:
English
Journal:
Phys Chem Chem Phys
Journal subject:
Biophysics
/
Chemistry
Year:
2022
Document Type:
Article
Affiliation country:
D2cp01724e
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