Solution Structure of Heparin Pentasaccharide: NMR and DFT Analysis

The Journal of Physical Chemistry. B
M Hricovíni

Abstract

High-resolution NMR and density functional theory (DFT) calculations have been applied to analysis of heparin pentasaccharide 3D structure in aqueous solution. The fully optimized molecular geometry of two pentasaccharide conformations (differing from each other in the form, one (1)C4 and the other (2)S0, of the sulfated iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as explicit water molecules. The presented approach enabled insight into variations of the bond lengths, bond angles, and torsion angles, formations of intra- and intermolecular hydrogen bonds, and ionic interactions in the two pentasaccharide conformations. A rather complex hydrogen bond network is formed, including inter-residue and intraresidue bonds between the NH group in the GlcN,3,6S with oxygens linked to C-2 at the IdoA2S residue and the glycosidic O-1 and the neighboring OSO3(-) group linked to C-3 in the same residue. On the other hand, because the first hydration shell is strongly influenced by strong ion-ion and ion-dipole interactions between sodium ions, sulfates, carboxylates, and -OH groups, ionic interactions play an important role in the stabilization of the 3D str...Continue Reading

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Citations

Jun 7, 2016·International Journal of Cardiology·Edwin A Yates, Timothy R Rudd
Feb 12, 2019·Chemical Society Reviews·Hannah E CaputoMark W Grinstaff
Aug 6, 2019·The FEBS Journal·Mariana P StellingNicholas P Farrell
Nov 25, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Miloš Hricovíni, Michal Hricovíni
Aug 18, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·William de WildtEdwin Kellenbach
May 14, 2019·Wiley Interdisciplinary Reviews. Computational Molecular Science·Balaji NagarajanUmesh R Desai
Sep 29, 2019·Medicina·Anthony DevlinMark Skidmore
May 1, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Leonid B Krivdin
Aug 15, 2019·Journal of Chemical Theory and Computation·Poonam PandeySairam S Mallajosyula

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