Conformation of Amylose in Aqueous Solution:  Small-Angle X-ray Scattering Measurements and Simulations

Abstract

Small-angle X-ray scattering profiles for an amylose fragment (maltoheptaose) in aqueous solution were observed and compared with the theoretical profiles calculated for an ensemble of chain conformations generated by molecular dynamics simulations and Monte Carlo simulations. The Monte Carlo results based on the disaccharide conformation energy map obtained without explicitly considering surrounding water molecules were in satisfactory agreement with the experimental results, provided that the effective dielectric constant was set to four. In contrast, the results of the fully solvated molecular dynamics simulations performed using the Cff91, Cff, Gromos, Glycam93, and Glycam99 force-fields were unexpectedly different from each other. Among them, Cff91 gave most satisfactory agreement with experiment, but the other fields yielded conformations that were somewhat or highly extended. It was also shown that recently developed Glycam99 is a significant improvement over Glycam 93. The representative snapshots of the two successful simulations resembled the regular helical structure reported by Goldsmith et al. (J. Mol. Biol. 1982, 156, 411). The source of the large force-field dependence was investigated by examining the various Ramachandran-like plots for the glycosidic torsion angles. For comparison, similar plots of ab initio energy for maltose (i.e., a fragment with two glucose units) were also calculated at the Hartree-Fock level, although in a simplified manner. These plots suggest that the extended conformation arises from too strong a preference for a certain rotational isomeric state of the glycosidic linkage. A procedure to remedy this over-preference can be devised, although a need of further elaboration of the force-field is indicated. The significance of force-fields is also illustrated in modeling a cyclodextrin composed of 14 glucose units.

Solution Properties of Amylose Tris(Phenylcarbamate): Local Conformation and Chain Stiffness in 1,4-Dioxane and 2-Ethoxyethanol

“…It should be noted that the h values in the two solvents can be smaller by about 10% if the polydispersity correction is made for hS 2 i z with M z =M w $ 1:1. Conformational energy maps for both amylose 44,45 and amylose tris(3,5-dimethylphenylcarbamate) 46 have a shallow minimum which allows the left handed helices with various h values. This indicates that h of the amylosic chain may be influenced by a small perturbation, i.e., intramolecular hydrogen bonding, intermolecular hydrogen bonding with solvent molecules, and packing of substituents and solvent molecules, and thus must be susceptible to such effects.…”

Large-ring Cyclodextrins

“…In addition, it has been reported that the nucleation rate of sugars, which has to precede crystal growth, is generally very low, so sugars often form supersaturated solutions of syrup-like liquid (36,37). However, several LR-CD structures have been deduced from molecular dynamics simulations and small angle X-ray scattering analysis (38)(39)(40)(41). Recently, a conformation study on LR-CD was reported based on a conformational search with molecular dynamics simulations and principal component analysis (42).…”

Large-ring cyclodextrins. A molecular dynamics study of the conformational dynamics and energetics of CD10, CD14 and CD26

“…Several studies used molecular dynamics (MD) simulations (with lengths of 100-400 ps) to examine the macroring conformations of LR-CDs containing 10, 14, 18, 21, 24 and 48 glucose units either in vacuum or in water solution. 37,38,39,40 The circularized three-turn single helical structure proposed for CD21 from small-angle X-ray scattering was shown, with rather short MD simulations (100 ps), to persist in water at 300 K. 34 Recently we reported results from study on CDs with a degree of polymerization of 26,30,35,40,55,70, 85 and 100, using much longer molecular dynamics simulations (5.0 ns for all except for the one of 26 for which the MD was of 10.0 ns). 41,42 Although the results were later published, 43 53 Both, the monitoring of the structural variations during the simulations, as well as the analyses of energy balances were indicative for high flexibility of the macrorings.…”