Ab initio calculations on various sialic acids provide valuable information about sialic acid-specific enzymes

Abstract

This study presents ab initio calculations on six sialic acid derivatives (N-acetylneuraminic acid, 2-deoxy-2,3-didehydro-Nacetylneuraminic acid, N-acetyl-4-O-acetylneuraminic acid, N-glycolylneuraminic acid, N-glycolyl-4-O-acetylneuraminic acid and N-acetyl-9-O-acetylneuraminic acid). The calculations were carried out using the GAMESS-UK-Program. Since the charge distribution of a ligand has an essential impact on the specific interaction with an enzyme or a receptor, the precise results of ab initio calculations lead to significant information concerning possible roles of the different functional groups occurring on sialic acids. In correlation to this, valuable conclusions about the activities of different sialic acid-specific enzymes, such as sialidases, trans-sialidases, lyases and O-acetyl-or O-methyltransferases can be drawn, since these activities strongly depend on the presence or absence of the various functional groups. q 2004 Published by Elsevier B.V.

Exploration of the Sialic Acid World

“…288 Finally, ab initio calculations (gas phase) were carried out on a series of neuraminic acid derivatives: α-Neu5Ac, α-Neu5Ac1,2Me 2 , β-Neu5Ac, β-Neu4,5Ac 2 , β-Neu5,9Ac 2 , β-Neu5Gc, β-Neu4Ac5Gc, and Neu2en5Ac. 307 The calculations for α-Neu5Ac1,2Me 2 were in close agreement with those of the crystal structure. 288 The calculated structure for α-Neu5Ac is depicted in Fig.…”

Molecular Basis of the Receptor Interactions of Polysialic Acid (polySia), polySia Mimetics, and Sulfated Polysaccharides

“…In this context, the strategic combination of methods led to new insight into molecular neurosciences, providing data that explained why bioactive compounds like cyclic and linear peptides or small organic molecules, especially polar molecules with partially equalized single and double bonds, can act as glycomimetics. [29,[35][36][37] The polySia mini-receptors used in this study were derived from structural modelso fS HL-1, [25] as wella s NMR and X-ray models from a-defensins HD5 and HNP 1, 2, and 3. [38][39][40][41][42] Ac ombination of molecular dynamics dockings imulations with ab initio calculations of the small organic glycomimeticm olecules provided detailed information about the fine-tuning of such binding processes.…”

<i>In silico</i> Study on Sulfated and Non-Sulfated Carbohydrate Chains from Proteoglycans in <i>Cnidaria</i> and Interaction with Collagen

“…The structural heterogeneity of these hexasaccharides reflects the polydiversity in the linkage region of the chondroitin sulfate chains: L-4-en-4-deoxy-thrHexpA(αl-3)GalNAc(4-O-or6-O-sulfate)(β1-4)GlcA and L-4-en-4-deoxy-thrHexpA (αl-3) GalNAc(4-O-or6-O-sulfate) (β1-4)GlcA(β1-3)Gal-NAc (4-O-sulfate), respectively. We have used the quantum chemical approach for a precise determination of energies and conformational angles [4][5][6][7][8].…”