Molecular Dynamics Studies of Side Chain Effect on the β-1,3-d-Glucan Triple Helix in Aqueous Solution

• DOI: 10.1021/bm700511d
• Publication Date: 2008-02-08T06:01:22Z
• Authors: Tadashi Okobira; Kentaro Miyoshi; Kazuya Uezu; Kazuo Sakurai; Seiji Shinkai
• Keywords: Models, Molecular; 0301 basic medicine; beta-Glucans; Molecular Sequence Data; Molecular Conformation; Sizofiran; Water; Hydrogen Bonding; Solutions; 03 medical and health sciences; Carbohydrate Sequence; Thermodynamics; Proteoglycans

beta-1,3-D-glucans have been isolated from fungi as right-handed 6(1) triple helices. They are categorized by the side chains bound to the main triple helix through beta-(1-->6)-D-glycosyl linkage. Indeed, since a glucose-based side chain is water soluble, the presence and frequency of glucose-based side chains give rise to significant variation in the physical properties of the glucan family. Curdlan has no side chains and self-assembles to form an water-insoluble triple helical structure, while schizophyllan, which has a 1,6-D-glucose side chain on every third glucose unit along the main chain, is completely water soluble. A thermal fluctuation in the optical rotatory dispersion is observed for the side chain, indicating probable co-operative interaction between the side chains and water molecules. This paper documents molecular dynamics simulations in aqueous solution for three models of the beta-1,3-D-glucan series: curdlan (no side chain), schizophyllan (a beta-(1-->6)-D-glycosyl side-chain at every third position), and a hypothetical triple helix with a side chain at every sixth main-chain glucose unit. A decrease was observed in the helical pitch as the population of the side chain increased. Two types of hydrogen bonding via water molecules, the side chain/main chain and the side chain/side chain hydrogen bonding, play an important role in determination of the triple helix conformation. The formation of a one-dimensional cavity of diameter about 3.5 A was observed in the schizophyllan triple helix, while curdlan showed no such cavity. The side chain/side chain hydrogen bonding in schizophyllan and the hypothetical beta-1,3-D-glucan triple helix could cause the tilt of the main-chain glucose residues to the helix.