Submitted to: Carbohydrate Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 17, 1999
Publication Date: N/A
Interpretive Summary: Starch is one of the most important biological molecules known, in addition to being one of the largest renewable crops on the planet. For these reasons, very detailed scientific investigations into its nature have been carried out. In this paper, we present results using powerful computer simulation methods available in our laboratory. With these computational tools, we can relate previous information from solution observations obtained by other researchers to details on the basic flexibility and structure. Further, we can now study the preferred solution structures of different molecules to examine how observed kinks and bends occur in structures. This work has allowed us to better understand the flexibility and structural organization of these components, as well as to more accurately define their roles in making up the starch granule. This work will lead to more efficient design methods for chemical modifications of starch that will result in biodegradable polymer with physical and structural properties useful for numerous commercial applications.
Technical Abstract: The empirical force field, denoted AMBER99C, has been used to study molecular properties of alpha-(1 >4)-linked carbohydrates in solution. AMBER99C was parameterized using structural and energetic parameters from density functional ab initio methodology. In this work, we examine the solution behavior of maltose, alpha-, beta-, and gamma-cyclodextrin, as well as CA10 and CA21. Experimental data used for comparison purposes includes X-ray structures, small angle scattering radius of gyration values, NMR nuclear Overhauser enhancements (n O e's), and proton coupling constants. Molecular dynamics simulations were carried out using explicit water molecules (TIP3P) to establish equilibrium populations of conformations in solution and these results are compared to other calculated values and a variety of experimental parameters such as average H1 H4' distances between the rings in beta-maltose, and the primary hydroxyl groups conformational populations. Medium to large cycloamylose molecules were studied to test glucose-ring puckering and for appearance of observed conformational kinks and "flipped" transitions.