Paper Citing NAMD - Abstract
Zhang, Q.M.; Lee, G.R.; Marszalek, P.E.
Atomic cranks and levers control sugar ring conformations
JOURNAL OF PHYSICS-CONDENSED MATTER, 17:S1427-S1442, MAY 11 2005
In this paper we review the conformational analysis of sugar rings placed under tension during mechanical manipulations of single polysaccharide molecules with the atomic force microscope and during steered molecular dynamics simulations. We examine the role of various chemical bonds and linkages between sugar rings in inhibiting or promoting their conformational transitions by means of external forces. Small differences in the orientation of one chemical bond on the sugar ring can produce significantly different mechanical properties at the polymer level as exemplified by two polysaccharides: cellulose, composed of beta-1 -> 4-linked D-glucose, and amylose, composed of alpha-1 -> 4-linked D-glucose. In contrast to beta-glucose rings, which are mechanically stable and produce simple entropic elasticity of the chain, a-glucose rings flip under tension from their chair to a boat-like structure and these transitions produce deviations of amylose elasticity from the freely jointed chain model. We also examine the deformation of two mechanically complementary 1 -> 6-linked polysaccharides: pustulan, a beta-1 -> 6-linked glucan, and dextran, a alpha-1 -> 6-linked glucan. Forced rotations about the C-5-C-6 bonds govern the elasticity of pustulan, and complex conformational transitions that involve simultaneous C-5-C-6 rotations and chair-boat transitions govern the elasticity of dextran. Finally, we discuss the likelihood of various conformational transitions in sugar rings in biological settings and speculate on their significance.
