Full Length Research Paper

Prediction of antigenic epitopes and MHC binders of neurotoxin alpha-KTx 3.8 from Mesobuthus tamulus sindicus

Gomase V. S.* and Shyamkumar K.

Department of Bioinformatics, Padmashree Dr. D.Y. Patil University, Plot No-50, Sector-15, CBD Belapur, Navi Mumbai, 400614, India.

*Corresponding author. E-mail: virusgene1@yahoo.co.in. Tel: +91-22-27563600. Fax: +91-39286176.

Accepted 16 October, 2008

   Abstract

The potassium channel inhibitor alpha-KTx 3.8, a 38-residue peptide was isolated from the venom of Mesobuthus tamulus sindicus. In this assay we have predicted the binding affinity of alpha-KTx 3.8 having 38 amino acids, which shows 30 nonamers. Peptide fragments of the neurotoxin can be used to select nonamers for use in rational vaccine design and to increase the understanding of roles of the immune system in neurotoxin studies. Small segment ‘4-INVKCRGSPQCIQPCR-19’of neurotoxin protein called the antigenic epitopes is sufficient for eliciting the desired immune response. We also found the SVM based MHCII-IAb peptide regions, 26- GKCMNGKCH, 20- DAGMRFGKC, 1- GVPINVKCR, 19- RDAGMRFGK, (optimal score is 0.388); MHCII-IAd peptide regions, 20- DAGMRFGKC, 14- CIQPCRDAG, 10- GSPQCIQPC, 25- FGKCMNGKC, (optimal score is 0.386); MHCII-IAg7 peptide regions, 18- CRDAGMRFG, 17- PCRDAGMRF, 14- CIQPCRDAG, 3- PINVKCRGS, (optimal score is 1.341); and MHCII- RT1.B peptide regions, 16- QPCRDAGMR, 29- MNGKCHCTP, 8- CRGSPQCIQ, 7- KCRGSPQCI,  (optimal score is -0.039)  which represented predicted binders from neurotoxin protein. CTL epitope with their (ANN/SVM) scores were predicted to be 1- GVPINVKCR (0.81/0.87220559). This theme is implemented in designing subunit and synthetic peptide vaccines. We have predicted a successful immunization.

Key words: Potassium channel inhibitor alpha-KTx 3.8 nonamers, subunit vaccine, antigenic epitope, CTL-prediction of alpha-KTx 3.8, MHC-binders.