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Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides.

Publication ,  Journal Article
Lee, G; Nowak, W; Jaroniec, J; Zhang, Q; Marszalek, PE
Published in: Biophysical journal
September 2004

Recent atomic force microscopy stretching measurements of single polysaccharide molecules suggest that their elasticity is governed by force-induced conformational transitions of the pyranose ring. However, the mechanism of these transitions and the mechanics of the pyranose ring are not fully understood. Here we use steered molecular dynamics simulations of the stretching process to unravel the mechanism of forced conformational transitions in 1,6 linked polysaccharides. In contrast to most sugars, 1,6 linked polysaccharides have an extra bond in their inter-residue linkage, C5-C6, around which restricted rotations occur and this additional degree of freedom increases the mechanical complexity of these polymers. By comparing the computational results with the atomic force microscopy data we determine that forced rotations around the C5-C6 bond have a significant and different impact on the elasticity of alpha- and beta-linked polysaccharides. Beta-linkages of a polysaccharide pustulan force the rotation around the C5-C6 bonds and produce a Hookean-like elasticity but do not affect the conformation of the pyranose rings. However, alpha-linkages of dextran induce compound conformational transitions that include simultaneous rotations around the C5-C6 bonds and chair-boat transitions of the pyranose rings. These previously not-recognized transitions are responsible for the characteristic plateau in the force-extension relationship of dextran.

Duke Scholars

Published In

Biophysical journal

DOI

EISSN

1542-0086

ISSN

0006-3495

Publication Date

September 2004

Volume

87

Issue

3

Start / End Page

1456 / 1465

Related Subject Headings

  • Time Factors
  • Polysaccharides
  • Molecular Sequence Data
  • Microscopy, Atomic Force
  • Lichens
  • Glucose
  • Dextrans
  • Computer Simulation
  • Carbon
  • Carbohydrates
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Lee, G., Nowak, W., Jaroniec, J., Zhang, Q., & Marszalek, P. E. (2004). Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides. Biophysical Journal, 87(3), 1456–1465. https://doi.org/10.1529/biophysj.104.042879
Lee, Gwangrog, Wiesław Nowak, Justyna Jaroniec, Qingmin Zhang, and Piotr E. Marszalek. “Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides.Biophysical Journal 87, no. 3 (September 2004): 1456–65. https://doi.org/10.1529/biophysj.104.042879.
Lee G, Nowak W, Jaroniec J, Zhang Q, Marszalek PE. Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides. Biophysical journal. 2004 Sep;87(3):1456–65.
Lee, Gwangrog, et al. “Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides.Biophysical Journal, vol. 87, no. 3, Sept. 2004, pp. 1456–65. Epmc, doi:10.1529/biophysj.104.042879.
Lee G, Nowak W, Jaroniec J, Zhang Q, Marszalek PE. Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides. Biophysical journal. 2004 Sep;87(3):1456–1465.
Journal cover image

Published In

Biophysical journal

DOI

EISSN

1542-0086

ISSN

0006-3495

Publication Date

September 2004

Volume

87

Issue

3

Start / End Page

1456 / 1465

Related Subject Headings

  • Time Factors
  • Polysaccharides
  • Molecular Sequence Data
  • Microscopy, Atomic Force
  • Lichens
  • Glucose
  • Dextrans
  • Computer Simulation
  • Carbon
  • Carbohydrates