In silico determination of superficial clefts in antigen binding fragment of human IgG

Fatemeh Hajighasemi | Soheyla Rohani | Fatemeh Sefid

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URL :   http://research.shahed.ac.ir/WSR/WebPages/Report/PaperView.aspx?PaperID=85418
Date :  2018/04/26
Publish in :    14th Internatinal Congress of Immunology

Link :  http//icia.ir
Keywords : In silico, Human IgG, Clefts

Abstract :

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Background: Immunoglobulins (Igs) are a group of plasma proteins consist of heavy and light chains. Each chain contains variable and constant regions. Idiotypic determinants are epitopes sited on Igs variable region. Private idiotype is a marker exclusive to a singular clone of B cell. As epitopes are commonly positioned close to surface clefts of proteins, recognition of Igs clefts could be very helpful in Igs epitopes determination. In current study superficial clefts in antigen binding fragment of human IgG have been defined by computational immunology. Methods: Amino acid sequence and third structure of reference human IgG were found in PDB databank. The second IgG structure was determined by Phyre 2 software. Surface clefts in IgG antigen binding fragment have been distinguished by Isocleft finder software. Results: Three clefts were recognized by Isocleft finder software. These clefts were located in Fab region of human IgG. First two clefts were in variable and constant domains and third one was in constant domains of Fab region. First, second and third clefts contained 93, 60 and 32 amino acids respectly. The biggest and deepest cleft was in amino terminal (antigen binding site) of IgG molecule. Conclusion: In present study three clefts in human IgG Fab were identified by computational immunology. The first two clefts contained many amino acids of variable domains. Thus it is very probable that private idiotypes be located in these clefts. So these clefts are useful for private idiotypes determination and generating specific anti- idiotypic monoclonal antibodies to monitor/ target clonally expanded malignant B cells.

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