Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: June 19, 2006
Publication Date: September 18, 2006
Citation: Momany, F.A., Schnupf, U., Willett, J.L., Bosma, W. 2006. Dft studies of dp-4 amylose fragments: comparison with the disaccharide maltose [abstract]. American Chemical Society. Paper No. 105. Technical Abstract: DFT optimization studies of over sixty DP-4 amylose fragments have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments studied include structures with V-helix, tightly compacted, and band-flip conformations. Different hydroxymethyl conformations (gg,gt,tg) were chosen on each of the four residue sites, as for example, gg-gg-gg-gt, gg-gg-gt-gg, gg-gt-gg-gg, and gt-gg-gg-gg. Calculation of this type of sequence of single residue conformational changes allows one to precisely determine the influence of hydroxymethyl variation on the bridge phi-psi values, as a function of position in the DP-4 sequence. Conformers where the only differences are as described above, show similar energies and bridge conformations, with energy trends of less than 1 kcal/mol being established as a result of the position of the modified residue in the fragment. The exocyclic hydroxyl groups were considered in either the all clockwise or "c" form, or the all reverse-clockwise or "r" form. Energy differences between conformations are examined in order to assess the stability of different hydroxyl/hydroxymethyl configurations and to identify the sources of energy that dictate amylose polymer formation. The calculated lowest energy conformations were similar to V-helix type "c" conformers', although a small nearly cyclic compact structure of low energy was also found. Band-flip conformations, similar to those found experimentally, are of modestly high energy (delta-E less than 5 kcal/mol and higher) relative to the lowest energy structures. For comparison, new maltose conformations have been calculated using the large DFT basis set and maltose conformations appear to be more similar to the bridge conformations at either end than to the central bridge. Significant geometry changes that appear with conformational differences are noted.