Bioinformatic protein sequence and 3D structure similarity between retinal and endothelial cell proteins and antigens. A mathematical in-silico model of molecular mimickry and AI response using SARS-COV2 as example.
Purpose
Sequence and 3D similarities of viral and human proteins may trigger AI reactions afterinfections due to similarities between viral and human structures.
Methods
Using SARS-COV2 as a model, we investigate the protein sequence similarity between retinal proteins, retinal pigment epithelium (RPE) surface proteins and 158 retinal vascular endothelial cell proteins and the virus proteins(Protein S, N, M, E and ORF1ab). Protein similarity comparison, 3D protein structure prediction, T cell epitopes-MHC binding prediction, B cell epitopes-MHC binding prediction and the evaluation of antigenicity were assessed.
Results
We found meaningful similarities between 6 RPE surface transport proteins (MRP-4, MRP-5, RFC1, SNAT7, TAUT and MATE) and the SARS CoV-2 E-protein. Immunoreactive epitopic sites of these proteins which are similar to protein E epitope can create an immune stimulation on T-cytotoxic and T-helper cells. There was also a high structural similarity between E protein and ACE, ACE-2, LAT-1 and TM9SF4 endothelial proteins. PECAM1 was structurally similar to ORF1ab- and S protein. TLR-2 and TLR-3, which are highly susceptible to SARS-CoV2, showed a potential receptor-protein interaction with retinal vascular endothelial proteins.
Conclusion
These results imply that AI cross-reaction is likely between retinal cell proteins and SARS-CoV-2 proteins. The potential of molecular mimicry may be assessed using mathematical in-silico models and may help to predict autoimmune response.
Conflict of interest
No
Authors 1
Last name
MUNK
Initials of first name(s)
MRM
Department
Gutblick
City
Bern
Country
Switzerland
Authors 2
Last name
Karabaş
Initials of first name(s)
L
Department
University of Health Science, Derince Training and Research Hospital, Ophthalmology Department
City
Istanbul
Country
Turkey
Authors 3
Last name
Kaya
Initials of first name(s)
M
Department
Diagen Biotechnology, Ankara, Turkey
City
Istanbul
Country
Turkey
Authors 4
Last name
Rückert
Initials of first name(s)
R
Department
Eyegnos Consulting
City
Bern
Country
Switzerland
Authors 5
Last name
Kutluturk Karagöz
Initials of first name(s)
I
Department
Ümraniye Trn. And Rch. Hospital, Division of Ophthalmology
City
Istanbul
Country
Turkey
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