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J Phys Chem B. 2018 Jan 25;122(3):1169-1175. doi: 10.1021/acs.jpcb.7b11085. Epub 2018 Jan 9.

Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study.

Author information

1
Leadership Computing Facility, Argonne National Laboratory , 9700 Cass Avenue, Argonne 60439, Illinois, United States.
2
ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory , Harwell, Oxfordshire OX11 OQX, U.K.
3
College of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.
4
Department of Biological Sciences and Bioengineering, Lehigh University , Bethlehem 18015, Pennsylvania, United States.
5
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden.

Abstract

The inherent flexibility of carbohydrates is dependent on stereochemical arrangements, and characterization of their influence and importance will give insight into the three-dimensional structure and dynamics. In this study, a β-(1→4)/β-(1→3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (Rg) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated Rg values from the MD simulation reveal that in addition to syn-conformers the presence of anti-ψ conformational states is required to reproduce experimental scattering data, unveiling inherent glycosidic linkage flexibility. The CHARMM36 force field for carbohydrates thus describes the conformational flexibility of the decasaccharide very well and captures the conceptual importance that anti-conformers are to be anticipated at glycosidic linkages of carbohydrates.

PMID:
29268602
DOI:
10.1021/acs.jpcb.7b11085
[Indexed for MEDLINE]

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