Simulation of Force Spectroscopy Experiments on Galacturonic Acid Oligomers

Abstract

Pectins, forming a matrix for cellulose and hemicellulose, determine the mechanics of plant cell walls. They undergo salient structural changes during their development. In the presence of divalent cations, usually calcium, pectins can form gel-like structures. Because of their importance they have been the subject of many force spectroscopy experiments, which have examined the conformational changes and molecular tensions due to external forces. The most abundant unit present in the pectin backbone is polygalacturonic acid. Unfortunately, experimental force spectroscopy on polygalacturonic acid molecules is still not a trivial task. The mechanism of the single-molecule response to external forces can be inferred by theoretical methods. Therefore, in this work we simulated such force spectroscopy experiments using the Enforced Geometry Optimization (EGO) method. We examined the oligomeric (up to hexamer) structures of α-D-galacturonic acid exposed to external stretching forces. The EGO simulation of the force spectroscopy appropriately reproduced the experimental course of the enforced conformational transition: chair →inverted chair via the twisted boat conformation(s) in the pyranose ring of α-D-galacturonic acid. Additionally, our theoretical approach also allowed to determine the minimum oligomer size adequate for the description of nano-mechanical properties of (poly)-α-D-galacturonic acid.

The primary, secondary, and structures of higher levels of pectin polysaccharides

“…One of the pioneering studies has produced evidence that for pectin (from citrus, purchased from Sigma) a two‐step transition of GalA units occurs from chair via boat to inverted chair (Marszalek et al., 2002). This finding was further confirmed by DFT simulations of galacturonic acid oligomers stretching (Cybulska et al., 2014). Force spectroscopy was also used to study the complexing mechanism of pectins, with other biomolecules, like the tumor signaling molecule Galectin‐3 (Gunning et al., 2009) and β‐lactoglobulin (Loveday & Gunning, 2018).…”

“…The overall conformation of the HG chain is determined by the relative orientation of the GalA monomers at the glycosidic linkage (Figure 2b). The linkage geometry, that is the torsion of the monomers along the chain allows for the formation of a number of regular helical conformations separated by a relatively low transition energy (Cybulska, Brzyska, Zdunek, & Woliński, 2014; Pérez, Mazeau, & Hervé du Penhoat, 2000). Molecular modeling showed that four conformations of chains are possible: right (3.1) and left (3.2) handed three‐fold helices, a two‐fold helix (2.1), and a right‐handed four‐fold helix (4.1) (Pérez et al., 2000), which may differ in their cross‐section dimensions as visualized in Figure 2b for 3.1 versus 2.1 conformations.…”

Simulation of the conformational flexibility of the mycodextran under external forces

“…This is confirmed by our earlier work on forced conformational transitions in various systems -not only for saccharides. [18,20,23] A typical EGOh for carbohydrate monomers usually displays a single energy maximum related to the structure being a good guess for the transition state (TS) searching procedure. Such TS can be treated as a specific linker between the starting and final EGO structures.…”

“…[18] Moreover, the type of the conformational conversion can also depend on the pyranose ring position in the oligosaccharide chain. [19,20] That is why the two types of monomeric: A (with the terminal glycosidic atoms in the position 1 and 3) and B (with the terminal glycosidic atoms in the position 1 and 4), dimeric: AB and BA (see Figure 1), trimeric: ABA and BAB etc. up to hexameric: ABABABA and BABABAB forms were considered here.…”

“…In order to simulate such enforced structural changes we used the Enforced Geometry Optimization (EGO) method. [21,22] The EGO method was so far effectively applied to the various problems in mechanochemistry, for example, the simulation of the AFM experiments for the selected oligosaccharides, [18][19][20]23] the generation of the new isomers of azobenzene and stilbene [22] and the prediction of the mechanical properties of the selected mechanophores, and so forth.…”