Conformational flexibility of the pentasaccharide LNF-2 deduced from NMR spectroscopy and molecular dynamics simulations

Organic & Biomolecular Chemistry
Elin SäwénG Widmalm

Abstract

Human milk oligosaccharides (HMOs) are important as prebiotics since they stimulate the growth of beneficial bacteria in the intestine and act as receptor analogues that can inhibit the binding of pathogens. The conformation and dynamics of the HMO Lacto-N-fucopentaose 2 (LNF-2), α-L-Fucp-(1 → 4)[β-D-Galp-(1 → 3)]-β-D-GlcpNAc-(1 → 3)-β-D-Galp-(1 → 4)-D-Glcp, having a Lewis A epitope, has been investigated employing NMR spectroscopy and molecular dynamics (MD) computer simulations. 1D (1)H,(1)H-NOESY experiments were used to obtain proton-proton cross-relaxation rates from which effective distances were deduced and 2D J-HMBC and 1D long-range experiments were utilized to measure trans-glycosidic (3)J(CH) coupling constants. The MD simulations using the PARM22/SU01 force field for carbohydrates were carried out for 600 ns with explicit water as solvent which resulted in excellent sampling for flexible glycosidic torsion angles. In addition, in vacuo MD simulations were performed using an MM3-2000 force field, but the agreement was less satisfactory based on an analysis of heteronuclear trans-glycosidic coupling constants. LNF-2 has a conformationally well-defined region consisting of the terminal branched part of the pentasacchar...Continue Reading

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Citations

Jun 28, 2017·Chemistry : a European Journal·Thomas AeschbacherMario Schubert
Sep 23, 2020·Vaccines·Sinthuja JegatheeswaranFrance-Isabelle Auzanneau
Oct 22, 2020·International Journal of Molecular Sciences·Sofya I Scherbinina, Philip V Toukach
Aug 13, 2021·Organic & Biomolecular Chemistry·Wojciech PlazinskiGöran Widmalm
Jan 17, 2014·Journal of Medicinal Chemistry·Trudy A JacksonFrance-Isabelle Auzanneau

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