The 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 A 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 A, 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 A). 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. © 1993 John Wiley & Sons, Inc.