Molecular modelling of the specific interactions involved in the amylose complexation by fatty acids

Comprehensive modelling of a fatty acid molecule inside a VH amylose helix is described. In a first step, the docking of an acetic acid molecule near the helix entry was performed. The low energy solutions were propagated by an iterative procedure involving the sequential addition of single CH2 groups up to a C12 fatty acid followed by energy minimizations. The main result is the superposition of the aliphatic and the helix axes. For the low-energy complexes, the mean plane of the aliphatic carbons has three potential orientations. In each, the aliphatic hydrogens point towards the less crowded regions near the glycosidic oxygens of the amylose. The close packing is due to the related symmetries of both the helix and aliphatic chain. In a second step, the relative roles of the aliphatic part and the polar group were studied separately. For the aliphatic chain, a map based on the two major internal parameters (translation and rotation) along the helix axis shows that the isolated docking solutions are related by a combination of a 60 degrees (360 degrees/6) rotation and a translation of p/6 (p = 0.804 nm corresponds to the pitch of Vhydrate amylose). The H5 glucopyranose atoms participate in close contacts and are responsible for steric conflicts in structures intermediate to the stable docking solutions. The four possible low-energy arrangements of the carboxylic group were added to the calculated amylose/aliphatic structures. Two stable conformations of the total fatty acid molecule were determined. For both stable solutions, the polar group is located near the entrance of the helix cavity.(ABSTRACT TRUNCATED AT 250 WORDS)