jp075330l_si_001.pdf (106.91 kB)
Conformational Structure of Some Trimeric and Pentameric Structural Units of Heparin
journal contribution
posted on 2007-12-27, 00:00 authored by Milan Remko, Claus-Wilhelm von der LiethThe molecular structure of trimeric units (D−E−F and F−G−H) and the pentamer D−E−F−G−H of
heparin (sodium salts and their anionic forms) was studied using the B3LYP/6-31G(d) method. The equilibrium
structure of the sodium salts of the trimers and pentamer investigated in the isolated state was determined
by multidentate coordination of the sodium cations with oxygen atoms of the sulfate, carboxyl, and hydroxyl
(hydroxymethyl) groups, respectively. The displacement of Na+ ions from the binding sites in the sodium
salt of oligosaccharides studied resulted in the appreciable change of the overall conformation of the
corresponding anion. Upon dissociation, a large change in both the position of the sulfate groups and
the conformation across the glycosidic bonds was observed. The stable energy conformations around the
glysosidic bonds found for the pentamer investigated are compared and discussed with the available
experimental X-ray structural data for the structurally related heparin-derived pentasaccharides in cocrystals
with proteins.