Determination of Superficial Clefts on Fragment of Antigen Binding in Human Immunoglobulin G by Computational Immunology

Background: Immunoglobulins (Igs) are protective glycoproteins specifically identify and eradicate microbes. Fragment of antigen binding (Fab) is a portion of antibody which binds to antigen and consists of one variable and one constant domain of one heavy and one light chain. Idiotypes, epitopes situated on Igs variable region, could be exploited to monitor and target malignant B cells and are usually located near the surface clefts of the Igs. In present study the superficial clefts in human IgG Fab region have been determined by computational data analysis.  Methods: Amino acid sequences and third structure of reference human IgG were found in Protein Data Bank (PDB). Surface clefts in IgG-Fab have been defined by Profunc software in http://www.ebi.ac.uk/thornton-srv/databases/profunc data bank and Isocleft finder software on reference human IgG sequence. Results: Ten clefts on human IgG were recognized by Cleft analysis software. Two of the biggest clefts were located to variable region and third one was sited in constant region of the Fab. Also three clefts on human IgG were identified by Isocleft finder software in Fab region. First two clefts were in variable and constant domains and third one was in constant domains of the Fab. Conclusion: The surface clefts of human IgG identified in the present study could be useful in determination of IgG epitopes, specific idiotypes and generating specific anti- idiotypic monoclonal antibodies to monitor/ target clonally expanded malignant B cells, as well as designing and producing the similar proteins structures for diagnostic and therapeutic purposes.