Investigation of the conformational properties of a β-(1 → 3) branched β-(1 → 6) heptasaccharide elicitor and its analogues by internal coordinate stochastic dynamics

A series of β-(1 → 3) branched β-(1 → 6) oligosaccharides that are known to take part in switching immune reactions in plants was studied by a molecular dynamics approach. A novel technique was applied which recently proved to be very efficient in polypeptide simulations. Molecular dynamics is simulated in internal rather than Cartesian coordinates with dramatically reduced numbers of degrees of freedom and a time step ten-fold larger than usual values. Comparison and classification of most populated conformational states revealed a few conformational motifs that are frequently adopted by highly active oligosaccharides and are not populated in an inactive analogue. As a result a putative biologically active conformation of the oligosaccharides is proposed.