Abstract
A Ramachandran map of the conformational potential of mean force (pmf) for neocarrabiose in water was obtained using molecular dynamics (MD) simulations with umbrella sampling. The potential energy map calculated in a previous study for this molecule in vacuum exhibited a global minimum located at ( φ=81°, ψ=−141°). However, the global minimum on the new pmf map in aqueous solution is located in an area centered around ( φ=175°, ψ=180°), indicating a considerable solvent shift. This new global minimum-energy solution conformation was found to correspond to the experimental value obtained from NMR–NOE measurements, and is also consistent with the experimental crystal structure for neocarrabiose and the fiber diffraction conformation for ι-carrageenan. The global minimum of the solution pmf and its local topology were found to be approximately reproduced by quick vacuum conformational energy mapping using several approximations that mimic solvation effects by de-emphasizing intramolecular hydrogen bonding.
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