comparison of epothilone and taxol binding in yeast tubulin using molecular modeling

microtubules are unique cytoskeletal structures that have structural subunits of αβ tubulin. taxol is a typical microtubule stabilizing drug. the epothilones are other natural products with similar mechanism of action totaxol. despite the highly conserved nature of β-tubulin, some organism like saccharomyces cerevesia is resistance to taxol, but sensitive to epothilones. in order to find differences in sensitivity of yeast tubulin to these molecules, we investigated binding mode of the taxol and epothilone a to yeast tubulin using molecular modeling. the multiple sequence alignment of β-tubulin of different species was performed using clustalw2. protein structure of yeast β-tubulin was constructed with swiss model 8.05 by using 1tvk. modeled tubulin was superimposed with pymol on1jff for comparison of three-dimensional structure of two proteins. our results showed that one of the most interesting differences in binding mode of these molecules is residue 227. the his227 in bovine makes a hydrogen bond by means of its δ-nitrogen with epothilone a and by means of its ε-nitrogen with taxol. the asn227 of yeast can play role of the δ-nitrogen of imidazole ring of h227, but not of ε-nitrogen of it. so yeast tubulin in contrast to taxol can interact with epothilone a. due to conservation of essential residues for binding (t274, r282 and q292), epothilone a in comparison with taxol can tolerate the interchange in the binding pocket (r276i). our findings may be of a great aid in the rational design of anti-tumor agents that bind to the taxol binding region of tubulin.