Role of charges and solvent on the conformational properties of poly(galacturonic acid) chains: a molecular dynamics study.
Pectin shares with many other polysaccharides an intrinsic chemical and physical complexity. The widespread industrial applications have made it one of the most studied polysaccharides. This work presents a theoretical model of poly(galacturonic acid), the major constituent of pectin, suitable to study its structural and dynamical properties. In particular, the effects of solvent and charge status are studied. The dynamics is shown to be severely affected by the presence of charged groups on each residue, making the charged chain much more rigid than the uncharged one. A key structural property for a semirigid polymer, the asymptotic persistence length, is calculated for relatively short charged and uncharged chains in molecular water solvent using a new method. The influence of charge on structural properties of poly(galacturonic acid) is shown to be strong and solvent-dependent. In fact, a large difference is found between continuum solvent adiabatic map calculations and molecular dynamics with explicit solvent, with the latter showing a much larger persistence length.
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CNR, Instituto di BioFisica, Section of Palermo, Via Ugo La Malfa 153, I-90147 Palermo, Italy.
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Bulone
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San Biagio
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D004058:Diffusion; D019281:Dimerization; D006603:Hexuronic Acids / Q000737:chemistry; D006860:Hydrogen Bonding; D046911:Macromolecular Substances / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D009010:Monte Carlo Method; D010368:Pectins / Q000737:chemistry; D011108:Polymers / Q000737:chemistry; D011134:Polysaccharides / Q000737:chemistry*; D012984:Software; D012997:Solvents; D013997:Time Factors
D006603:Hexuronic Acids; D046911:Macromolecular Substances; D011108:Polymers; D011134:Polysaccharides; D012997:Solvents; C007819:galacturonic acid; D010368:Pectins; C003181:polygalacturonic acid