Disaccharides crystal structure

Model building in the computer is used to analyze the conformational effects of steric interactions between atoms of the polymer skeleton for x-carrageenan, t-carrageenan, A-carrageenan, agar, chondroltin, chondroitin sulfates, dermatan sulfate, keratan sulfate, hyaluronic acid, and related polysaccharides. Over 99% of the conformations are thus excluded and virtually all of the remainder for each polysaccharide lie close together. Predictions are also made from disaccharide crystal structures and checked against experimental results. 

Table 13.3. Summary of Hydrogen Bonding in Disaccharide Crystal Structures... 

The side chains in the latter are flexible disaccharides on account of poor-quality diffraction patterns, their tentative molecular structures are known only from computer modeling.1" On the other hand, well-defined crystal structures are available for gellan and welan, and they can be correlated with the physical properties of the polysaccharides the details are presented here. Their conformation angles are listed in Table VI. 

Fig. 2.5. Interactions of chemokines with heparin disaccharides. (A to C) Monomeric forms of chemokines are displayed as cartoons with residues found to interact with heparin colored red. (A) Monomer of crystal structure of CCL5 (RANTES) with heparin disaccharide I-S bound (red). (B) CXCL4 (PF4) with low-molecular-weight heparin (MW <9000d). (C) CXCL8 with heparin disaccharide I-S. (D) CXCL12 (SDF-la) with heparin disaccharide I-S. (E) CCL2, human IP-10, with conserved residues from murine IP-10 highlighted.

Aleshin and coworkers (49) have reported the X-ray crystal structure at 2.2-A resolution of a G2-type variant produced by Aspergillus awamori. Meanwhile, an attempt was made to determine the amino acid residues that participate in the substrate binding and catalysis provided by G2 of A. niger (52). The results of the chemical approach indicated that the Asp-176, Glu-179, and Glu-180 form an acidic cluster crucial to the functioning of the enzyme. This conclusion was then tested by site-specific mutagenesis of these amino acid residues, which were replaced, one at a time, with Asn, Gin, and Gin, respectively (53). The substitution at Glu-179 provided an inactive protein. The other two substitutions affected the kinetic parameters but were not of crucial importance to the maintenance of activity. The crystal structure (49) supports the conclusion that Glu-179 functions as the catalytic acid but Asp-17 6 does not appear to be a good candidate for provision of catalytic base. Thus, there still exists considerable uncertainty as to how the disaccharide is accepted into the combining site for hydrolysis. Nevertheless, the kind of scheme presented by Svensson and coworkers (52) almost surely prevails. 

With three linkage bonds as in the molecular mechanics study of the 1-6 disaccharide gentiobiose (12), the lowest 24 minima within 7 kcal mole which were reported did not include that observed in the crystal structure (20). Had the crystal structure conformation been one of the sets of starting parameters, it would have been included, but it is reasonable to assume that the conformational population in solution was also not fully represented. 

An aglyconic derivative of KDO, having 0-7 and 0-8 temporarily blocked, was required for the synthesis of the model disaccharide Koenigs-Knorr reaction of 3 with a suitable halide derivative of KDO would be expected to occur exclusively at the (equatorial) 0-4 while 0H-5, being axially-disposed and experiencing additional steric shielding by H-7, would be practically unreactive. X-ray crystal structure analysis of KDO derivatives (14, 15) has shown that H-7 is orient-... 

Catalytic hydrogenation of 1 9, over palladium catalyst gave a practically quantitative yield of the crystalline disaccharide derivative 2 2, the constitution, and configurations at all chiral centers, of which have been verified by x-ray crystal structure analysis ( 1 5). De- 0-silylation of the 5,8-diol 2 2. 

The crystal structure and solution conformation of the fully acetylated JVAcgal-a-(1 - 3)-AAcgaI disaccharide have been studied [188]. 

Wynn et al. have described a potential energy calculation which utilizes the non bonded interaction and a term for the electrostatic interaction with the inclusion of directed chargers , localized in certain atomic orbitals [192, 193]. With this potential, they obtained for the P-D-glucosyl-ceramide a conformation which is similar to the X-ray crystal structure of P-D-Gal-ceramide [194], The calculation of the a-D-NeuvVAc-(2-3)-P-o-Gal disaccharide shows a conformation with cp-ci = 120° (determined from the stereoplot presented in the publication) which is inconsistent with the data obtained by Sabesan et al. [191], who were able to show that their calculated conformation with (p = 165° is in agreement with NOE data. 

Temperini C, Messori L, Orioli P et al (2003) The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes. Nucleic Acids Res 31 1464—1469... 

---