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

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 beta-(1 -> 4)/beta-(1 -> 3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (R-g) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated R-g values from the MD simulation reveal that in addition to syn-conformers the presence of anti-psi 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.

Authors:
 [1];  [2];  [3];  [2];  [2];  [4]; ORCiD logo [5]
  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
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
Swedish Research Council (SRC)
OSTI Identifier:
1483622
DOE Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Volume: 122; Journal Issue: 3; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English

Citation Formats

Jo, Sunhwan, Myatt, Daniel, Qi, Yifei, Doutch, James, Clifton, Luke A., Im, Wonpil, and Widmalm, Göran. Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study. United States: N. p., 2018. Web. doi:10.1021/acs.jpcb.7b11085.
Jo, Sunhwan, Myatt, Daniel, Qi, Yifei, Doutch, James, Clifton, Luke A., Im, Wonpil, & Widmalm, Göran. Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study. United States. doi:10.1021/acs.jpcb.7b11085.
Jo, Sunhwan, Myatt, Daniel, Qi, Yifei, Doutch, James, Clifton, Luke A., Im, Wonpil, and Widmalm, Göran. Fri . "Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study". United States. doi:10.1021/acs.jpcb.7b11085.
@article{osti_1483622,
title = {Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study},
author = {Jo, Sunhwan and Myatt, Daniel and Qi, Yifei and Doutch, James and Clifton, Luke A. and Im, Wonpil and Widmalm, Göran},
abstractNote = {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 beta-(1 -> 4)/beta-(1 -> 3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (R-g) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated R-g values from the MD simulation reveal that in addition to syn-conformers the presence of anti-psi 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.},
doi = {10.1021/acs.jpcb.7b11085},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
issn = {1520-6106},
number = 3,
volume = 122,
place = {United States},
year = {2018},
month = {1}
}