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United States Department of Agriculture

Agricultural Research Service

Title: DFT Conformation and Energies of Amylose Fragments at Atomic Resolution Part 2: “Band-flip” and “Kink” Forms of Alpha-Maltotetraose)

item Schnupf, Udo
item Willett, Julious - J l
item Momany, Frank

Submitted to: Carbohydrate Research
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/19/2008
Publication Date: 2/11/2009
Citation: Schnupf, U., Willett, J.L., Momany, F.A. 2009. DFT Conformation and Energies of Amylose Fragments at Atomic Resolution Part 2: “Band-flip” and “Kink” Forms of Alpha-Maltotetraose. Carbohydrate Research. 344(1):374-383.

Interpretive Summary: The carbohydrate maltotetraose consists of four connected glucose fragments and its many uses include, for example, diagnostic testing material for enzymes and food additives in syrups. In the work reported here, we investigate the structure features allowing the carbohydrate to deform at the connection points giving us insight into how a carbohydrate would interact with enzymes/proteins or forming larger tightly packed biopolymers. Overall, the goal is to develop a model for larger starch based biopolymers. Our investigations, using cutting edge computational methods, have shown that there are two structural features that allow the carbohydrate to deform permitting it to pack into very tight spaces. Further, the structural and energetic features allow us to understand better how tightly packed biopolymers can be formed. This study will lead to more efficient design methods for chemical modifications of starch or polymer blends combined with starch that will result in new biodegradable polymers with physical and structural properties useful for pharmaceutical as well as carbohydrate food chemists in the design of new food products.

Technical Abstract: In Part 2 of this series of DFT optimization studies of '-maltotetraose, we present results at the B3LYP/6-311++G** level of theory for conformations denoted “band-flips” and “kinks”. Recent experimental X-ray studies have found examples of amylose fragments with conformations distorted from the usual syn forms, and it was of interest to examine these novel structural motifs by the same high level DFT methods used in Part 1. As in Part 1, we have examined numerous hydroxymethyl rotamers (gg, gt, tg) at different locations in the residue sequence, and include the two hydroxyl rotamers, the clockwise ‘c’ and counterclockwise ‘r’ forms. A total of fifty conformations were calculated and energy differences found to attempt to identify those source of electronic energy that dictate stressed amylose conformations. Most stressed conformations were found to have relative energies considerably greater (i.e. ~4-12 kcal/mol) than the lowest energy syn forms. Relative energy differences between ‘c’ and ‘r’ forms are somewhat mixed with some stressed conformations being ‘c’ favored and some ‘r’ favored, with the lowest energy “kink” form being an all-gg-r conformation with the “kink” in the bc glycosidic dihedral angles. Comparison of our calculated structures with experimental results shows very close correspondence in dihedral angles.

Last Modified: 8/24/2016
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