Ramachandran-type Plots for Glycosidic Linkages: Examples from Molecular Dynamics Simulations using the Glycam06 Force Field

The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these carbohydrate Ramachandran-type (carb-Rama) plots reveal the coupling between the glycosidic angles by displaying the allowed and disallowed conformational space. Considering two-bond glycosidic linkages, there are 18 possible conformational regions that can be defined by (α, ϕ, ψ) and (β, ϕ, ψ), whereas for three-bond linkages, there are 54 possible regions that can be defined by (α, ϕ, ψ, ω) and (β, ϕ, ψ, ω). Illustrating these ideas are molecular dynamic simulations on an implicitly hydrated oligosaccharide (700 ns) and its eight constituent disaccharides (50 ns/disaccharide). For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, and discuss the general trends observed in the plots.

(Table 1) Species richness and diversity of tundra plants in herbivore exclosure and control plots near Barrow, Alaska

To determine the role lemmings play in structuring plant communities and their contribution to the 'greening of the Arctic', we measured plant cover and biomass in 50 + year old lemming exclosures and control plots in the coastal tundra near Barrow, Alaska. The response of plant functional types to herbivore exclusion varied among land cover types. In general, the abundance of lichens and bryophytes increased with the exclusion of lemmings, whereas graminoids decreased, although the magnitude of these responses varied among land cover types. These results suggest that sustained lemming activity promotes a higher biomass of vascular plant functional types than would be expected without their presence and highlights the importance of considering herbivory when interpreting patterns of greening in the Arctic. In light of the rapid environmental change ongoing in the Arctic and the potential regional to global implications of this change, further exploration regarding the long-term influence of arvicoline rodents on ecosystem function (e.g. carbon and energy balance) should be considered a research priority.