Conformational analysis of Infectious bursal disease virus

Aim: This study was designed to develop peptide analogs of Infectious Bursal Disease (IBD) virus VP5 protein segment having cell penetrating ability to improve their interaction with cargo molecule (Nucleic acid) without affecting the backbone conformation. Materials and Methods: IBDV VP5 protein segment designated as RATH peptide were synthesized using solid phase peptide synthesis and their solution conformation was elucidated using CD spectroscopy in polar (water) and apolar (TFE) solvents. Cell penetrating ability of RATH-CONH was observed using FITC labeled peptide internalization in to HeLa cells 2 under fluorescent microscopy. The efficacy of RATH analog interactions with nucleic acids was evaluated using FITC labeled oligonucleotides by fluorescence spectroscopy and plasmid constructs in gel retardation assay. Results: CD spectra of RATH analogs in water and apolar trifluroethanol (TFE) helped to compare their secondary structures which were almost similar with dominant beta conformations suggesting successful induction of positive charge in the analogs without affecting back bone conformation of CPP designed. Cell penetrating ability of RATH CONH in HeLa cell 2 was more than 90%. The fluorescence spectroscopy and plasmid constructs in gel retardation assay demonstrated successful interaction of amide analogs with nucleic acid. Conclusion: Intentional changes made in IBDV derived peptide RATH COOH to RATH CONH did not showed major 2 changes in backbone conformation and such modifications may help to improve the cationic charge in most CPPs to interact with nucleic acid.