Abstract
To gain insight into the molecular details and hydration of amylopectin, the five constituting trisaccharides have been chemically synthesized as their methyl α‐glycosides. All five trisaccharides were subjected to 950 MHz NMR spectroscopy for complete assignment and nanosecond molecular dynamics trajectories were calculated to study the structure and dynamics of the trisaccharides in aqueous solution. Systematic analysis of the simulation data revealed several examples of bridging water molecules playing an important role in the stabilization of specific amylopectin conformations, which was also supported by the experimental NMR data such as interresidue NOE's and heteronuclear scalar couplings between nuclei from neighboring residues. Although α‐maltotriose, α‐iso‐maltotriose, α‐panose and α‐isopanose are relatively well characterized structures, the study also includes one less characterized trisaccharide with the structure αGlcp(1→4)αGlcp(1→6)αGlcp. This trisaccharide, tentatively labelled α‐forkose, is located at the branch point of amylopectin, forking the amylopectin into two strands that align into double‐helical segments. The results show that the conformation of α‐forkose takes a natural bend form which fits well into the structure of the double‐helical segment of amylopectin. As the only trisaccharide in this study the structure of α‐forkose is not significantly influenced by the hydration. In contrast, α‐isopanose takes a restricted, but rather extended form due to an exceptionally strong localized water density. The two homo‐linkage oligomers, α‐maltotriose and α‐iso‐maltotriose, showed to be the most extended and the most flexible trimers, respectively, providing regular structure for crystalline domains and maximum linker flexibility for amorphous domains. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 1179–1193, 2008.
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