Conformational properties of l-fucose and the tetrasaccharide building block of the sulfated l-fucan from Lytechinus variegatus

Francisco F Bezerra; William P Vignovich; AyoOluwa O Aderibigbe; Hao Liu; Joshua S Sharp; Robert J Doerksen; Vitor H Pomin

doi:10.1016/j.jsb.2019.107407

Conformational properties of l-fucose and the tetrasaccharide building block of the sulfated l-fucan from Lytechinus variegatus

J Struct Biol. 2020 Jan 1;209(1):107407. doi: 10.1016/j.jsb.2019.107407. Epub 2019 Nov 4.

Authors

Francisco F Bezerra¹, William P Vignovich², AyoOluwa O Aderibigbe², Hao Liu², Joshua S Sharp³, Robert J Doerksen³, Vitor H Pomin⁴

Affiliations

¹ Institute of Medical Biochemistry Leopoldo de Meis, University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941, RJ, Brazil.
² BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA.
³ BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, 38677 MS, USA.
⁴ Institute of Medical Biochemistry Leopoldo de Meis, University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941, RJ, Brazil; BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, 38677 MS, USA. Electronic address: vpomin@olemiss.edu.

Abstract

Although the 3D structure of carbohydrates is known to contribute to their biological roles, conformational studies of sugars are challenging because their chains are flexible in solution and consequently the number of 3D structural restraints is limited. Here, we investigate the conformational properties of the tetrasaccharide building block of the Lytechinus variegatus sulfated fucan composed of the following structure [l-Fucp4(SO₃^-)-α(1-3)-l-Fucp2,4(SO₃^-)-α(1-3)-l-Fucp2(SO₃^-)-α(1-3)-l-Fucp2(SO₃^-)] and the composing monosaccharide unit Fucp, primarily by nuclear magnetic resonance (NMR) experiments performed at very low temperatures and using H₂O as the solvent for the sugars rather than using the conventional deuterium oxide. By slowing down the fast chemical exchange rates and forcing the protonation of labile sites, we increased the number of through-space ¹H-¹H distances that could be measured by NMR spectroscopy. Following this strategy, additional conformational details of the tetrasaccharide and l-Fucp in solution were obtained. Computational molecular dynamics was performed to complement and validate the NMR-based measurements. A model of the NMR-restrained 3D structure is offered for the tetrasaccharide.

Keywords: Conformation; Fucose; NMR spectroscopy; Structural glycobiology; Sulfated fucan.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Carbohydrates / chemistry
Fucose / chemistry*
Lytechinus / chemistry
Magnetic Resonance Spectroscopy
Molecular Conformation*
Molecular Dynamics Simulation
Oligosaccharides / chemistry
Oligosaccharides / ultrastructure*
Polysaccharides / chemistry
Polysaccharides / ultrastructure*

Substances

Carbohydrates
Oligosaccharides
Polysaccharides
Fucose

Abstract

Publication types

MeSH terms

Substances

Grants and funding