Simulation of Force Spectroscopy Experiments on Galacturonic Acid Oligomers

• Published in: PloS one Vol. 9; no. 9; p. e107896
• Main Authors: Cybulska, Justyna, Brzyska, Agnieszka, Zdunek, Artur, Woliński, Krzysztof
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17.09.2014; Public Library of Science (PLoS)
• Subjects: Acids; Biology; Biology and Life Sciences; Calcium; Carbohydrate Conformation; Cations; Cell walls; Cellulose; Chemistry; Conformation; D-Galacturonic acid; Dimerization; Divalent cations; Experiments; Food; Geometry; Hemicellulose; Hexuronic Acids - chemistry; Mechanical Phenomena; Mechanical properties; Microscopy, Atomic Force; Models, Molecular; Molecular physics; Oligomers; Optimization; Pectin; Physical Sciences; Polygalacturonic acid; Polymers - chemistry; Research and Analysis Methods; Simulation; Spectroscopy; Thermodynamics; Poland
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0107896

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.