Compatibility of B-Sheets with Epitopes Predicted by Immunoinformatic in Human IgG

Background & Aims: Antibodies, well-known as immunoglobulins (Igs), are produced by B lymphocytes and specifically defend against pathogens. Igs are glycoproteins and have high diagnostic value in several diseases including infections (1). Igs are composed of light and heavy chains (2, 3). Each chain is comprised of about 110-120 amino acid residues which create immunoglobulin folds named domains (4, 5).  Domains play an important role in Igs biological functions. Every domain is included of two anti-parallel β-sheets. B-sheets play an important role in epitope formation because most of the epitopes are located in B-sheets (6, 7).  Epitope/ antigenic determinant is a part of antigen recognized by antibody (8).  For precise detections of Igs, diagnostic tools such as Igs- epitope specific monoclonal antibodies (MAbs) are needed (11). Therefore B-sheets are valuable tools in detection of proteins epitopes. IgG is the highest Ig in serum and has vital role in defense against infections (12). For optimizing current IgG diagnostic tests, accurate determination of IgG-specific epitopes is extremely important (18). Immunoinformatic is a branch of immunology uses a large amount of computer-generated biological information to solve immunological problems and diagnosis of diseases faster and more accurate (19-21). Immunoinformatic has spread to almost all areas of immunology and has exceedingly facilitated understanding of immune responses and their role in disease and health. Accordingly immunoinformatic has provided novel research opportunities to study the molecular mechanisms of immunological processes and related diseases and thus provide more effective diagnostic and treatment strategies (24-26). As B-sheets play an important role in epitope formation (6, 7) and immunogenic epitopes are very useful tools for production of specific monoclonal antibodies against a molecule (11), we conducted this research for recognition of human IgG B-sheets with immunoinformatic method and study their compatibility with IgG epitopes. Methods: The confirmed amino acid sequence of reference human IgG was determined with PDB data bank in http://www.rcsb.org/pdb/home/home.do web site. The second structure of human IgG was obtained with Phyre2 (Protein Homology/analogy Recognition Engine V 2.0) software available on the http://www.sbg.bio.ic.ac.uk/phyre website. The location of B-sheets and epitopes in IgG was determined by the IEDB (Immune Epitope Database) at www.immuneepitope.org. Website. Results: Figures 1 and 2 show the second structure of light and heavy chains of the human IgG molecule, respectively, obtained by phyre2 software. The IgG light and heavy chains second structure consists of alpha spirals and B-sheets. Figures 3 and 4 show the location of B-sheets in light and heavy chains of the human IgG molecule obtained by IEDB software. Most of  the  B-sheets in IgG molecules were located in 150 - 175 amino acid sequences of light chains and in 130-140, 160-170, 190-200, 220-245, 375-410 and 420-425 amino acid sequences of heavy chains respectively as was determined by IEDB software. Three epitopes sited to constant domain of IgG light chain (CL) were predicted. These epitopes were located at 150-175 and 180-205 amino acid sequences of light chain. Also three epitopes situated to second and third constant domains of IgG heavy chain (CH2 and CH3) were predicted. These epitopes were located at 200-270, 290-360 and 380-400 amino acid sequences of heavy chain. Based on the results of present study, 66% of human IgG light chain epitopes and 66% of human IgG heavy chain epitopes are situated at the IgG B-sheets locations. Also in present study, 91% of the amino acids forming B-sheets sited in the heavy chains of IgG molecule were located in the CH2 and CH3 domains and 100% of the human IgG heavy chain epitopes were located in the CH2 and CH3 domains Conclusion: According to the results of this study, most of human IgG epitopes are located in regions of the molecule where B-sheets are most likely situated, indicating a relatively high compatibility of B-sheets with IgG epitopes. Given that the B-sheets present in the second structure of proteins play an important role in epitope formation (6, 7), the occurrence of most human IgG epitopes (66%) at the location of B-sheets seems evident. Moreover, according to the findings of the present study, a total of 91% of the amino acids forming B-sheets sited in the heavy chains of IgG molecule were located in the CH2 and CH3 domains and 100% of the human IgG heavy chain epitopes were located in the CH2 and CH3 domains. This again indicates the high compatibility of B-sheets with epitopes located on the heavy chain of the human IgG molecule. The findings of our study are confirmed by Hajighasemi et al. study (31). In study of Hajighasemi et al. (31), about 91% of the linear epitopes located on the heavy chains of the IgG molecule, were situated in the CH2 and CH3 domains. Similarly, in our study 100%  of human IgG heavy chain  epitopes located on CH2 and CH3 domains. Also the results of present study are confirmed by another research (36) in which all (100% ) of spatial epitopes on fragment of crystallizable [Fc] component (part of heavy chains)  of the human IgG molecule were located in CH3 and CH2 domains as were  identified by DiscoTope and ElliPro  immunoinformatic softwares. Similarly in the present study, 100%  of IgG heavy chain  epitopes were located in the CH2 and CH3 domains. Moreover the results of another study performed by Rohani et al. (37) support the findings of current study. Rohani et al., reported that most of the areas with highest surface accessibility, hydrophilicity and flexibility, were situated in CH2 and CH3 domains of  human IgG heavy chains. (37). According to our results, most of  B-sheets are located in the CH2 and CH3 domains of  human IgG heavy chains. As B-sheets are regions with high accessibility, hydrophilicity and flexibility (6), presence of most B-sheets in the CH2 and CH3 domains  which are reported to be  highly accessible, hydrophilic and flexible ( 37), is reasonable. Furthermore, the high immunogenicity of B-sheets (39), once again confirms results of the present study. As immunogenicity plays an important role in epitope development, the high adaptation between the location of B-sheets and epitopes ( shown in our study) which both are highly immunogenic, seems logical. Besides since B-sheets play an important role in epitope formation(6, 7),  the high compatibility between location of B-sheets and IgG epitopes ( shown in present study) seems sensible. Overall, presence the most of B-sheets and IgG epitopes in CL, CH2 and CH3 domains of human IgG, shows the high compatibility between location of B-sheets and epitopes in human IgG. These findings are precious tools not only for prediction of IgG immunogenic epitopes in order to producing specific monoclonal anti IgG antibodies to optimize current human IgG diagnostic kits but also for more exact detection of IgG functions. Moreover our results are helpful in producing of similar proteins for diagnostic and therapeutic aims, structure- function relationships and phylogenic studies.