Stiffness of poly(galacturonic acid) chains from Molecular Dynamics results under different solvent and charge states

SILVINA GUIDUGLI; CARMEN ESTEBAN; RODOLFO D. PORASSO; MYRIAM VILLEGAS; SERGIO PANTANO; ATILIO CESARO; JULIO C. BENEGAS

Montevideo

Congreso; 6th International Conference of Biological Physics, 5th Southern cone Biophysicl Congress, 34th annual meeting of the Argentinean Biophysical Society; 2007

The poly(galacturonic acid) is the most constituent of pectin, a natural polysaccharide with large industrial applications due to its ability to form gels under different physico-chemical conditions. Understanding the gelation mechanisms and how such processes are related to molecular structure and the solution conditions would allow controlling and manipulating the gel properties. The present work is a first step in building a computational model that can be compared with experimental results and recent theoretical developments, that will allow us to understand the initiation of the gelation mechanism. Preliminary experimental results show the existence of a conformational change of the poly(galacturonic acid) chain when it is ionized in aqueous solution, with a possible a change in the flexibility of the macromolecule upon ionization. Interestingly enough, preliminary results point to stiffer conformation at low ionization degree, as compared to the fully charge polymeric chain. This characteristic is opposed to the usual assumption of a less flexible charged polymer (electrostatic rigidity). In this work we report the results of study the stiffness properties of poly(galacturonic acid) chains generated using a Monte Carlo algorithm based on the results of Molecular Dynamics (MD) simulations of disaccharides molecules in explicit solvent molecules. Varying the solvent and the ionization state of the disaccharide allow us to study the effects of solvent and charge on the conformational properties of the polymeric chains. The methodology used consists in obtaining the probability contour map for the glycosidic torsional angles from the MD simulation of (1→4)--D-galacturonic dimers in two explicit solvent, water and DMSO, for neutral and fully charged molecules. An assembly of polymeric chains generated by this procedure allows us a full determination of polymeric properties and compare them for the different solvent and charged states used in the MD simulations.