Resolving the nanostructure of sodium carbonate extracted pectins (DASP) from apple cell walls with atomic force microscopy and molecular dynamics

Abstract The diluted alkali-soluble fraction of the cell wall pectic matrix extracted with sodium carbonate (DASP) from apple fruit (M. domestica cv. Golden Delicious) was subjected to extensive analysis aimed at refining the current view concerning its molecular structure. Pectins were examined by means of atomic force microscopy (AFM) and HPLC chemical analysis. In addition to this, computational chemistry was employed to characterize the structural features of the basic plant cell wall polysaccharides and their possible assemblies. The AFM imaging revealed that DASP molecules deposited on mica structurally resembled rod-like objects, consisting of relatively long linear sections separated by bend points or branches. Locally molecules also formed aggregates, which were visible as an amorphous phase, concentrated around linear sections. Based on chemical analysis combined with molecular dynamics (MD) the linear chains were identified as sections of unbranched homogalacturonan, while the second most abundant polysaccharide present in DASP – arabinose – was considered to constitute the amorphous aggregates. The study showed that despite being present in small amounts, rhamnose is an important factor affecting the formation of the characteristic shape of DASP molecules on mica. The structural characterization of the bend points showed that linear molecules oriented at specific angles are most likely to be formed by two sections of homogalacturonan separated by a single rhamnose unit. AFM images confirmed that this is a common feature of the molecular structure of the DASP fraction, suggesting a possible role in the networking of pectic polysaccharides. Rhamnose interspersions within the homogalacturonan chains lead to the formation of spatial structures, which resemble kinked rods with segments having the ability to change their relative positions. The higher mobility of the linear sections as well as the higher number of segments increases the number of possible interactions with surrounding molecules and thus increases its ability to form gels. Therefore, it is expected that the number of rhamnose units and the length of the linear homogalacturonan sections will be one of the factors that influence the gelling abilities of pectin. Furthermore, it was proposed that branch points are created, similar to bend points, by single interspersions of rhamnose, which connect three homogalacturonan chains or short sections (two or three dimers) of rhamnogalacturonan-I with a homogalacturonan side branch. The third proposed alternative was a complex of two adjacent homogalacturonan chains, one of them having a single rhamnose insertion causing a bend in the structure.