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Prediction of MHC Class Antigen Peptides from Echinococcus Multilocularis: Application of Computer Intelligence

Research Article Open Access
Gomase V.S* and Chitlange N.R
Department of Bioinformatics, JJT University, Jhunjhunu Rajasthan, 333001, India
*Corresponding authors: Virendra S Gomase
Department of Bioinformatics
JJT University, Jhunjhunu Rajasthan
333001, India
Tel: +91-9987770696
E-mail: gomase.viren@gmail.com
 
Received April 30, 2012; Published July 27, 2012
 
Citation: Gomase VS, Chitlange NR (2012) Prediction of MHC Class Antigen Peptides from Echinococcus Multilocularis: Application of Computer Intelligence. 1: 191. doi:10.4172/scientificreports.191
 
Copyright: © 2012 Gomase VS, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
 
Abstract
 
Echinococcus multilocularis is a cyclophyllid cestode that causes hydatid disease in many mammals, including rodents and humans and is becoming an increasing problem in urban areas. Peptide fragments of antigen protein can be used to select nonamers for use in rational vaccine design and to increase the understanding of roles of the immune system in infectious diseases. Analysis shows MHC class II binding peptides of antigen protein from Echinococcus multilocularis are important determinant for protection of host form parasitic infection. In this assay, we used PSSM and SVM algorithms for antigen design and predicted the binding affinity of antigen protein having 426 amino acids, which shows 417 nonamers. Binding ability prediction of antigen peptides to major histocompatibility complex (MHC) class I & II molecules is important in vaccine development from Echinococcus multilocularis.
 
Keywords
 
Antigen protein; Epitope; PSSM; SVM; MHC; Peptide vaccine
 
Abbreviations
 
GES: Goldman, Engelberg and Steitz; MHC: major histocompatibility complex; PSSMs: Position Specific Scoring Matrices; SVM: Support Vector Machine
 
Introduction
 
Echinococcus multilocularis is a cyclophyllid cestode that causes hydatid disease in many mammals, including rodents and humans and is becoming an increasing problem in urban areas [1,2]. Echinococcus multilocularis 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 a plant infected with a mild strain of virus is protected against a more severe strain of the same virus. The phenotype of the resistant transgenic hosts includes fewer centers of initial virus infection, a delay in symptom development, and low virus accumulation. Antigen protein from Echinococcus multilocularis is necessary for new paradigm of synthetic vaccine development and target validation [3-5].
 
Methodology
 
In this research work antigenic epitopes of antigen protein from Echinococcus multilocularis is determined using the Gomase in 2007, Bull & Breeze, Eisenberg, Rao & ArgosChou & 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].
 
Results and Interpretations
 
We found binding of peptides to a number of different alleles using Position Specific Scoring Matrix. An antigen protein sequence is 426 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 terminal regions of antigen protein is solvent accessible and unstructured, antibodies against those regions are also likely to recognize the native protein (Figure1, 2, 3). It was shown that a antigen protein is hydrophobic in nature and contains segments of low complexity and high-predicted flexibility (Figure 4, 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 ends are 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 Eisenberg, et al., scale.
 
Figure 2: Hydrophobicity plot of antigen protein by Bull & Breese scale.
 
Figure 3: Hydrophobicity plot of antigen protein by Hphob./ Rao &Argosscale.
 
Figure 4: Antigenicity plot of antigen protein by beta-sheet / Chou & Fasman, scale.
 
Figure 5: Antigenicity plot of antigen protein by Beta-Sheet / Levitt., scale.
 
Conclusion
 
An antigen protein from Echinococcus multilocularis 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 MHCII-ligands 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 bacterial antigen protein. These predicted of antigen protein antigenic peptides to MHC class molecules are important in vaccine development from Echinococcus multilocularis.
 
 
References