The knowledge about the conformation(s) that an oligosaccharide can access when it is either free or attached to a glycoprotein or glycolipid is important both in understanding their interactions with cellular lectins and receptors, as well with glycosidases and glycosyltransferases. During the biosynthesis and processing of these carbohydrates, the conformation of the oligosaccharide substrate plays an important role. In glycoprotein the conformation of the oligosaccharide may further depend on the protein sequence and the structure surrounding the glycosylation site. Thus it is essential to discern all the possible conformations that a particular oligosaccharide can access, the information that is relevant for understanding sugar induced protein-protein interactions and glycoprotein biosynthesis. We have investigated by molecular dynamics simulations the conformational preferences of N-linked oligosaccharides - high mannose, complex and hybrid type oligosaccharides which are also the sugar acceptor substrates for glycosyltransferases (1). Following conclusions were drawn from these MD simulations: (i) The preferred conformation of the oligosaccharide can not be derived from its disaccharide constituents. Addition/deletion of residues to the oligosaccharide can bring about significant differences in the conformational preferences of inter glycosidic torsion angles. (ii) The terminal sugars of the N-linked oligosaccharides can interact with the chitobiose core thus influencing their availability for the enzymatic reactions. (iii) The alpha-1,6- linkages access three distinct conformations for chi (180o, 60o, - 60o) which affect the overall shape of the oligosaccharide. (iv) Changes in the overall shape of the oligosaccharide need not be brought about only by changing chi of the alpha-1,6-linkage, but also by changing phi and psi while keeping c constant. (v) The conformational analysis of oligosaccharides, found in the protein-carbohydrate crystal structures, show that the less frequently accessed conformation of oligosaccharide at times may bind better to a protein molecule than the highly accessed conformation by providing better complementary surface and form additional hydrogen bonds with the protein. The information obtained from MD simulation have also been used to explain/rationalize some of the biochemical experimental observations. Utilizing the available experimental and computational data, a pathway for the possible processing of Man9GlcNAc2 to Man5GlcNAc2 during the biosynthesis of Asn- linked oligosaccharides has been proposed. Since glycosaminoglycans, the carbohydrate part of proteoglycans, play an important role in a wide range of biological functions, understanding their structure and conformation is of utmost importance. We carried out the conformational analysis of these molecules, specifically the conformation of iduronate ring in dermatan sulfate, since, its conformation in the literature is controversial. Our analysis showed that alpha-L-IdUA unit in dermatan sulfate solution exists predominantly in a 'slightly distorted' 1C4 conformation. This is consistent with the observed x-ray fiber repeat value for dermatan sulfate where 1C4 conformation for the alpha-L-IdUA unit has been taken into consideration. This information is vital and provides the bases for our current modeling studies on the binding of heparin or heparan sulfate proteoglycans to basic fibroblast growth factor and to its receptor.
| Schuyler, Adam D; Jernigan, Robert L; Qasba, Pradman K et al. (2009) Iterative cluster-NMA: A tool for generating conformational transitions in proteins. Proteins 74:760-76 |
