Structure of the left-handed antiparallel amylose double helix: theoretical studies
The atomic coordinates from the crystal structure of a hexasaccharide complex accommodating a zigzag polyiodide [W. Hinrichs, G. Buttner, M. Steifa, Ch. Betzel, V. Zabel, B. Pfannemuller, and W. Saenger (1987) Science Vol. 238, pp. 205-208; W. Hinrichs and W. Saenger (1990) Journal of the American Chemical Society, Vol. 112, pp. 2789-2796] served to construct an antiparallel-stranded amylose double helix with a 5 angstrom wide central cavity. Using our methodology for the energetic optimization of polymer structures in the internal/helical variable space [H. Sklenar, R. Lavery, and B. Pullman (1986) Journal of Biomolecular Structure Dynamics, Vol. 3, pp. 967-987, 989-1014; 1015-1031], we have calculated a theoretical counterpart of this idealized double helix by constraining the helical twist and rise to their experimental values (-45° and 2.33 angstrom, respectively). Applying the same constraints to the parallel-stranded duplex, this also leads to a low-energy structure with wide central cavity. It is considered as an alternative model to accommodate iodine as observed in the starch-iodine complex. Release of the helical constraints leads to left-handed antiparallel- and parallel-stranded double helices, respectively, with narrow central cavities. Both structures have very similar helix parameters and correspond, in their main characteristics, to the experimentally derived parallel-stranded structure of amylose in starch (6 residues per turn and a pitch height of about 21 angstrom). The intramolecular energy calculated for the optimized antiparallel-stranded amylose double helix is comparable to that of the parallel-stranded structure. This result raises the question why parallel-stranded amylose seems to be favored in nature.(Author abstract)
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