South African Journal of Chemistry
On-line version ISSN 1996-840X
Print version ISSN 0379-4350
SINGH, Parvesh. Conformational preferences of Amphibian peptides Brevinin-Ya and Brevinin-Yb explored using molecular dynamics. S.Afr.j.chem. (Online) [online]. 2013, vol.66, pp.00-00. ISSN 1996-840X.
The brevinin-1 family peptides obtained from different frog skins have great potency against bacterial and fungal infections. Their biological activities are significantly affected by mutations especially at positions 11 and 14. However, despite having great medicinal potential, the detailed information regarding their three-dimensional structures is still not fully known. In the present study, the conformational profiles of two brevinin peptides (Brevinin 1-Ya and Brevinin 1-Yb) were explored at molecular mechanics level using molecular dynamics (MD) method. Specifically, four MD simulations (Brev1_Ya(E), Brev1_Yb(E), Brev1_Ya(H), Brev1_Yb(H)) were performed starting from extended as well as helical conformations of both peptides under implicit solvent conditions. The analysis of the results indicated that both peptides have a strong tendency to attain α-helical character, preferably from their central residues extending towards their C-terminals12-23, whereas their N-terminal residues stay either in β-turn or extended forms. However, the extent of helicity was comparatively lower in Brevinin 1-Ya, irrespective of its starting structure in the simulations, and like other factors such as cationicity and hydrophobicity, could be related to the biological activity profiles of these peptides.
Keywords : Brevinin; cationicity; anti-microbial peptides; MD; AMBER.