Structural characterization of the short peptaibols trichobrachins by molecular-dynamics methods

Abstract

A structural characterization was carried out by molecular-dynamics methods for eight trichobrachin peptides, to identify the conformational features of these short peptaibols. For all peptides, the backbone and side-chain conformations were investigated, different secondary structures, such as type-I and -III β-turns as well as β-bend ribbon spirals, were determined in certain tetrapeptide units of the molecules, and the preferred rotamers of the side chains of amino acids were identified. Furthermore, the end-to-end and residueresidue distances were examined, as well as the fluctuations of backbone atoms were studied. Based on these results, the peptides were compared to one another. Our theoretical study indicated that trichobrachins could be characterized by typical structural properties, and both conformational similarities and dissimilarities were observed between these peptaibols. In summary, this structural investigation supplied a characterization of the various conformational features of eight trichobrachin peptides.