Abstract
We carried out the structural analysis of /β-1, 3-D-glucan/Polynucleotide complexes by molecular mechanics, semiempirical molecular orbital, and molecular dynamics methods.
The calculation results of semi-empirical molecular orbital method exhibited that two types of hydrogen bonds are formed between the curdlan and the Poly (C) ; the 3rd nitrogen (N3) in cytosine forms a hydrogen bond with the 2nd OH of one curdlan chain and the proton of N4 is interacting with the O2 of another curdlan chain. In our model, the helix diameter of Poly (C) is expanded from 11.0 to 15.3Å upon complexation. Despite of such large conformational changes, the 61 helix structure of Poly (C) was maintained even after the complexation. The chain length dependence of the reaction enthalpy indicated that the complexation becomes thermodynamically more favorable with the chain length increasing. These features are consistent with the experimental data.
The calculation results of molecular dynamics simulation exhibited that the pitch of, 8-1, 3-D-glucan/Poly (C) complex is almost the same as that of the, β-1, 3-D-glucan crystal structure, while β-1, 3-D-glucan by itself is significantly stretched in aqueous solution. The β-1, 3-D-glucan/Poly (C) complexes maintained triple helices throughout the simulation period, and the dynamic behavior of the complex such as the pitch fluctuation was much different depending on a structural difference of β-1, 3-D-glucan.
