GES: Goldman; Engelberg and Steitz; MHC: Major Histocompatibility Complex; PSSMs: Position Specific Scoring Matrices; SVM: Support Vector Machine

Trichinella species are the smallest nematode parasite of humans; have an unusual life cycle and are one of the most widespread and clinically important parasites in the world [1]. The small adult worms mature in the intestines of an intermediate host such as a pig [1,2]. Taenia crassiceps antigen peptides are most suitable for subunit vaccine development because with single epitope; the immune response can be generated in large population. This approach is based on the phenomenon of cross-protection; whereby infected with a mild strain and is protected against a more severe strain of the same. The phenotype of the resistant transgenic hosts includes fewer centers of initial infection; a delay in symptom development; and low accumulation. Antigen protein from Taenia crassiceps is necessary for new paradigm of synthetic vaccine development and target validation [3-5].

In this research work antigenic epitopes of antigen protein from Taenia crassiceps is determined using the Gomase in 2007; Welling; Eisenberg; Parker and Chou & Fasman and Levitt antigenicity [6- 8]. The major histocompatibility complex (MHC) peptide binding of antigen protein is predicted using neural networks trained on C terminals of known epitopes. In analysis predicted MHC/peptide binding of antigen protein is a log-transformed value related to the IC50 values in nM units. MHC2Pred predicts peptide binders to MHCI and MHCII molecules from protein sequences or sequence alignments using Position Specific Scoring Matrices (PSSMs). Support Vector Machine (SVM) based method for prediction of promiscuous MHC class II binding peptides. SVM has been trained on the binary input of single amino acid sequence [9-14]. In addition; we predict those MHC ligands from whose C-terminal end is likely to be the result of proteosomal cleavage [15-18].

We found binding of peptides to a number of different alleles using Position Specific Scoring Matrix. An antigen protein sequence is 44 residues long; having antigenic MHC binding peptides. MHC molecules are cell surface glycoproteins; which take active part in host immune reactions and involvement of MHC class-I and MHC II in response to almost all antigens. PSSM based server predict the peptide binders to MHCI molecules of antigen protein sequence are as 11mer_H2_Db; 10mer_H2_Db; 9mer_H2_Db; 8mer_H2_Db and also peptide binders to MHCII molecules of antigen protein sequence as I_Ab.p;I_Ad.p; analysis found antigenic epitopes region in putative antigen protein (Table 1). We also found the SVM based MHCII-IAb peptide regions; MHCII-IAd peptide regions; MHCII-IAg7 peptide regions and MHCII- RT1.B peptide regions; which represented predicted binders from bacterial antigen protein (Table 2). The predicted binding affinity is normalized by the 1% fractil. We describe an improved method for predicting linear epitopes (Table 2). The region of maximal hydrophilicity is likely to be an antigenic site; having hydrophobic characteristics; because a terminal region of antigen protein is solvent accessible and unstructured; antibodies against those regions are also likely to recognize the native protein (Figure 1, 2 and 3). It was shown that an antigen protein is hydrophobic in nature and contains segments of low complexity and high-predicted flexibility (Figure 4 and 5). Predicted antigenic fragments can bind to MHC molecule is the first bottlenecks in vaccine design.

Table 1: PSSM based prediction of MHC ligands, from whose C-terminal end is proteosomal cleavage sites.

Table 2: SVM based prediction of promiscuous MHC class II binding peptides from antigen protein.

Figure 1: Hydrophobicity plot of antigen protein by Hphob / Welling & al., scale.

Figure 2: Hydrophobicity plot of antigen protein by Hphob/ Eisenberg, et al., scale.

Figure 3: Hydrophobicity plot of antigen protein by Hphob. HPLC /Parker & et al., scale.

Figure 4: Antigenicity plot of antigen protein by Hphob. / Rao & Argos, scale.

Figure 5: Antigenicity plot of antigen protein by Hphob. / Manavalan et al., scale.

An antigen protein from Taenia crassiceps peptide nonamers are from a set of aligned peptides known to bind to a given MHC molecule as the predictor of MHC-peptide binding. MHCII molecules bind peptides in similar yet different modes and alignments of MHCIIligands were obtained to be consistent with the binding mode of the peptides to their MHC class; this means the increase in affinity of MHC binding peptides may result in enhancement of immunogenicity of antigen protein. These predicted of antigen protein antigenic peptides to MHC class molecules are important in vaccine development from Taenia crassiceps.