Deducing polymeric structure from aqueous molecular dynamics simulations of oligosaccharides: Predictions from simulations of hyaluronan tetrasaccharides compared with hydrodynamic and X-ray fibre diffraction data

Molecular dynamics simulations of the two hyaluronan tetrasaccharides in wa ter predict that over a period of 500 ps, their centrallinkages populate a single primary minima. Over the same period the peripheral linkages explore this minima, but also a secondary minima. Structures constructed using the primary minima were found to be extended left-handed helices of axial rise per disaccharide (h) 0.8 to 1.0 nm and 2.8 to 4.5 disaccharides per turn ( n), in good agreement with n = 3 and n = 4 helices found by X-ray fibre dif fraction studies. We have used the predicted average conformation from mole cular dynamics to calculate the translational diffusion coefficients of the oligosaccharide series up to decasaccharide, and compared these with exper imental measurements obtained using the method of capillary dispersion. Our calculated values are found to be in good agreement with experiment beyond the size of a tetrasaccharide. A partial digest of hyaluronan in the molec ular mass range 10 to 100 kDa was fractionated by gel chromatography. Molec ular weights were determined by in-line laser light-scattering measurements , and the translational diffusion coefficients of selected fractions were d etermined by dynamic laser light-scattering. A similar experiment was perfo rmed on hyaluronan with a molecular mass greater than 1 MDa. The data sugge st a change from rod-like to stiff coil behaviour beyond a molecular weight of 10 kDa. We have also examined the conformations available using the sec ondary minima, found at the peripheral linkages. Ln contrast to the extende d structures previously described we have found left and right-handed helic es with high values of n (5-10) and low values of h. Although there is no e xperimental evidence for these structures, they are of interest as, over sh ort stretches, they would introduce folds, loops, and turns into the hyalur onan molecule. Such shapes may play an important role in die hydrodynamics of hyaluronan and its interaction with Lipids and proteins. (C) 1998 Academ ic Press.