Conformation of Novel Cycloamylose:  Topological Aspects and Simulations

Abstract

It has recently been discovered that cycloamylose, cyclic α-1,4-glucan with a degree of polymerization ranging from 17 to several hundred, can be produced by the action of potato d-enzyme (EC 2.4.1.25) on amylose. To obtain structural insights into this new series of cycloamylose, the topological aspects of its circular structure were discussed in terms of a ribbon model properly introduced. A simple analysis of the chain-length dependence of the product population was performed on the basis of an elastic wire model. If the amylose chain is rather stiff, a double-helical structure with foldbacks is more reasonable than a circularized single-helical structure. This is because theoretical calculations for the latter predict a periodic population oscillation, which is caused by the need for the helix ends to meet, whereas such an oscillation was not experimentally observed. However, due to the unknown chain stiffness, it is difficult to draw a definite conclusion. To answer some questions that arose in the above analysis, atomistic models are necessary. Therefore, crude atomistic models were created in close analogy with the modeling of supercoiled DNA. The models were then refined by molecular dynamics simulation performed with a fast multipole method. Both structures formed a hollow tube with internal diameter of 5−6 Å. As far as the enthalpic contribution is concerned, the simulation results support the double-helical structure. The simulation results also indicated appreciable chain flexibility, which might play an important role in accommodating guest molecules.

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).…”

Translational diffusion coefficient of cycloamylose in aqueous sodium hydroxide

“…Normalized autocorrelation functions g (2) (t) at time t were determined for all cycloamylose samples and ␥-CD in 0.5 N aqueous NaOH at 25°C in the range of scattering angle between 40°and 90°, using an ALV/DLS/SLS-5000 light scattering photometer equipped with an ALV-5000E/ WIN correlator. A YAG laser of 0 ϭ 532 nm (DPSS model 532, Coherent) was used as the light source.…”

“…A YAG laser of 0 ϭ 532 nm (DPSS model 532, Coherent) was used as the light source. The experimental first cumulant ⌫ relative to the square of the scattering vector, i.e., ⌫/k 2 , was evaluated from the slope of a plot of ln[ g (2) (t) Ϫ 1] against k 2 t at a fixed for each solution according to the relation ln[ g (2) (t) Ϫ 1] ϭ Ϫ2⌫t ϩ constant, where the magnitude of the scattering vector is defined by k ϭ (4n 0 / 0 )sin(/2), with n 0 being the solvent refractive index. The zero-angle values of ⌫/k 2 , i.e., (⌫/k 2 ) kϭ0 , were then extrapolated to infinite dilution to obtain D. Table I, along with the molecular weight of ␥-CD.…”

“…It can be seen that our samples cover a range in molecular weight from 5 ϫ 10 3 to 1.8 ϫ 10 4 (i.e., from 33 to 110 in terms of x) and are narrow in molecular weight distribution. Typical DLS data are shown for sample Fr-3 in 0.5 N aqueous NaOH at 25°C in Figures 3 and 4, in which plots of ln[ g (2) (t) Ϫ 1] vs k 2 t at fixed scattering angles for a solution with c (the polymer mass concentration) ϭ 1.945 ϫ 10 Ϫ2 g cm Ϫ3 and the angleindependent behavior of ⌫/k 2 at different polymer concentrations are illustrated, respectively. Figure 5 shows the concentration dependence of (⌫/k 2 ) kϭ0 for all the samples including ␥-CD.…”

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.…”