On the electrophoretic mobilities of partially charged oligosaccharides as a function of charge patterning and degree of polymerization

Abstract

Fully or partially charged oligosaccharide molecules play a key role in many areas of biology, where their fine structures are crucial in determining their functionality. However, the separation of specific charged oligosaccharides from similar moieties that typically coexist in extracted samples, even for those that are unbranched, and in cases where each saccharide moiety can only carry a single charge or not, is far from trivial. Typically such molecules are characterized by a degree of polymerization n and a number m (and distribution) of charged residues, and must be separated from a plethora of similar species possessing different combinations of n and m. Furthermore, the separation of the possible n!/m!(n-m)! isomers of each species of fixed n and m is a formidable challenge to analytical chemists. Herein, we report the results of molecular dynamics simulations that have been performed in order to calculate the free solution electrophoretic mobilities of galacturonides and charged oligosaccharides derived from digests of the important plant cell-wall polysaccharide pectin. The simulations are compared with an experiment and are found to correctly predict the loss of resolution of fully charged species above a critical degree of polymerization n and the ionic strength dependence of the electrophoretic mobilities of different partially charged oligosaccharides. It is expected that having a predictive tool for the calculation of the electrophoretic mobilities of differently charged oligosaccharide species in hand will allow experimental conditions that optimize the resolution of particular species to be ascertained and understood.

Differences in the structure of plant polygalacturonases specify enzymes’ dynamics and processivities to fine-tune cell wall pectins

“…The protonation states of each amino acid were assigned according to the pKa curves calculated at pH = 4 for PGLR and pH = 5 for ADPG2, using the PROPKA software (64). Atomic charges and radii for the protein atoms were assigned using the PDB2PQR software (65) according to the parameters of the AMBER14SB_parmbsc1 forcefield (54), while atomic charges and radii for the sugar atoms were obtained from our previous work (66). The surface electrostatic potentials for WT PGLR and ADPG2 were then calculated solving the non-linearized form of the Poisson-Boltzmann equation through the APBS (Adaptive Poisson–Boltzmann Solver) software on a cubic grid composed of 193 grid points across the x-, y-and z-directions (67).…”

“…The protonation states of each amino acid were assigned according to the pKa curves calculated at pH = 4 for PGLR and pH = 5 for ADPG2, using the PROPKA software (64). Atomic charges and radii for the protein atoms were assigned using the PDB2PQR software (65) according to the parameters of the AMBER14SB_parmbsc1 forcefield (54), while atomic charges and radii for the sugar atoms were obtained from our previous work (66). The surface electrostatic potentials for WT PGLR and ADPG2…”

Plant polygalacturonase structures specify enzyme dynamics and processivities to fine-tune cell wall pectins

“…The protonation states of each amino acid were assigned according to the pKa curves calculated at pH = 4 for PGLR and pH = 5 for ADPG2, using the PROPKA software (Søndergaard et al, 2011). Atomic charges and radii for the protein atoms were assigned using the PDB2PQR software (Dolinsky et al, 2004) according to the parameters of the AMBER14SB_parmbsc1 forcefield (Lindorff-Larsen et al, 2010), while atomic charges and radii for the sugar atoms were obtained from our previous work (Irani et al, 2018). The surface electrostatic potentials for WT PGLR and ADPG2…”