INVESTIGATION OF THE CONFORMATIONAL PROPERTIES OF A BETA-(1-]3) BRANCHED BETA-(1-]6) HEPTASACCHARIDE ELICITOR AND ITS ANALOGS BY INTERNAL COORDINATE STOCHASTIC DYNAMICS

A series of beta-(1-->3) branched beta-(1-->6) oligosaccharides that a re known to take part in switching immune reactions in plants was stud ied by a molecular dynamics approach. A novel technique was applied wh ich recently proved to be very efficient in polypeptide simulations. M olecular dynamics is simulated in internal rather than Cartesian coord inates with dramatically reduced numbers of degrees of freedom and a t ime step ten-fold larger than usual values. Comparison and classificat ion of most populated conformational states revealed a few conformatio nal motifs that are frequently adopted by highly active oligosaccharid es and are not populated in an inactive analogue. As a result a putati ve biologically active conformation of the oligosaccharides is propose d.