Abstract
BackgroundLevan and levan-type fructo-oligosaccharides (LFOs) have various potential applications in pharmaceutical and food industries due to their beneficial properties such as their low intrinsic viscosity and high water solubility. Previous studies showed that they exhibited prebiotic effects, anti-inflammatory and anti-tumor activities against Sarcoma-180 tumor cells of human. Despite their various potential applications, the structural and molecular properties of LFOs of various chain lengths are not well understood.ResultsWe employed the replica-exchange molecular dynamics simulations method (REMD) in AMBER14 to elucidate structural and molecular properties of LFOs with chain lengths of 5 (LFO5), 10 (LFO10) and 15 (LFO15) residues in two models of generalized Born implicit solvent (GBHCT and GBOBC1). For LFO10 and LFO15, four distinct conformations (helix-like, partial helix, zig-zag and random structures) were characterized by their upper-middle and lower-middle torsions. For LFO5, two distinct conformations (partial helix and random structures) were characterized by their middle torsion and molecular angle of residues 1, 3 and 5. To determine hydrogen bonds important for the formation of helix-like structures of LFO10 and LFO15, occurrence frequencies of hydrogen bonds were analyzed, and the O6(i)--H3O(i+1) hydrogen bond was found with the highest frequency, suggesting its importance in helix formation. Among three dihedral angles between two fructosyl units [ϕ (O5’-C2’-O6-C6), ψ (C2’-O6-C6-C5) and ω (O6-C6-C5-C4)], dihedral angle distributions showed that ω was the most flexible dihedral angle and probably responsible for conformational differences of LFOs.ConclusionsOur study provides important insights into the structural and molecular properties of LFOs, which tend to form helical structures as the chain length increases from 5 to 15 residues. This information could be beneficial for the selection of LFOs with appropriate lengths and properties for pharmaceutical and biological applications.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1182-7) contains supplementary material, which is available to authorized users.
Highlights
Levan and levan-type fructo-oligosaccharides (LFOs) have various potential applications in pharmaceutical and food industries due to their beneficial properties such as their low intrinsic viscosity and high water solubility
For the systems simulated in the GBOBC1 model, the results of replica-exchange molecular dynamics simulations method (REMD) simulations were similar to those simulated in the GBHCT model, and their average acceptance ratios were almost constant around 28, 36 and 50 % for LFO15, LFO10 and LFO5, respectively
To elucidate the structural and molecular properties of LFOs as well as the relationship between these properties and their chain lengths, REMD were performed on systems of LFO5, LFO10 and LFO15 in GBHCT and GBOBC1 solvent models
Summary
Levan and levan-type fructo-oligosaccharides (LFOs) have various potential applications in pharmaceutical and food industries due to their beneficial properties such as their low intrinsic viscosity and high water solubility. Previous studies showed that they exhibited prebiotic effects, anti-inflammatory and anti-tumor activities against Sarcoma-180 tumor cells of human Despite their various potential applications, the structural and molecular properties of LFOs of various chain lengths are not well understood. The properties of levan and LFOs depend on their chain lengths and branching degrees [6], and they have various desirable properties such as their unusually low intrinsic viscosity [7] and high water solubility [8] These properties are very beneficial for various industrial applications, especially in food and pharmaceutical industries. Levan and LFOs showed prebiotic effects, stimulating the growth of beneficial intestinal bacteria, and could potentially act as cholesterol lowering agents (MW 2000 kDa) [9, 10] They could be served as carbon sources for probiotics such as four strains of Bifidobacterium sp. Despite their various potential applications, the knowledge on the structural and molecular properties of levan and LFOs of various chain lengths is still limited
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