Conformational features of galacturonans. I. Structure and energy minimization of charged and uncharged galacturonan dimeric units.
Structural parameters (e.g. the geometry, partial charges and dipole moment) of the alpha-D-galacturonic residue have been calculated by using semi-empirical quantum mechanical methods on several combinations of either the uncharged or charged forms, GalAH and GalA-, respectively. Three residue types have been explored: (i) the isolated residue, termed GEO1 and GEO1C for GalAH and GalA-, respectively; (ii) the residue with a methyl group attached to the O4 and O1 positions (GEO2 and GEO2C); and (iii) the internal residue in a trimer, e.g. GalAH-GalAH-GalAH or the corresponding fully charged version (GEO3 and GEO3C). The presence of a charged group in the galacturonate residue and the distribution of the excess negative charge on the molecule lead to significant differences in the structural parameters in comparison with those of the uncharged galacturonic residue. These perceptible differences in internal coordinates of GalAH and GalA- residues appear to play a major role in the delimitation of the conformational space that is accessible to the dimers, as clearly seen by inspection of the conformational maps. Although the overall features seem alike, the maps show that the position of the minimum and the shape of the lower energy region significantly change if one or both residues in the dimer are charged. The relevance of these results for the conformational properties of polygalacturonate chains is discussed elsewhere (Ruggiero et al. Int. J. Biol. Macromol. 1995, 17, 213-218).
Ruggiero
J R
JR
Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy.
Urbani
R
R
Cesàro
A
A
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D004187:Disaccharides / Q000737:chemistry; D006603:Hexuronic Acids / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010368:Pectins / Q000737:chemistry*; D014312:Trisaccharides / Q000737:chemistry
D004187:Disaccharides; D006603:Hexuronic Acids; D014312:Trisaccharides; C007819:galacturonic acid; D010368:Pectins; C003181:polygalacturonic acid