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Does microsecond sugar ring flexing encode 3D-shape and bioactivity in the heparanome?

Benedict M Sattelle¹, Javad Shakeri, Andrew Almond

¹University of Manchester , Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, United Kingdom.

Biomacromolecules

|February 27, 2013

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Heparin and heparan sulfate (the heparanome) structure-function relationships are complex. Oligosaccharide sequence significantly impacts 3D-shape and biological activity, crucial for molecular design.

Area of Science:

Glycoscience
Biophysics
Computational Biology

Background:

Carbohydrate sequences encode vast biological information, surpassing proteins and nucleic acids.
Understanding heparin and heparan sulfate (heparanome) structure-function is challenging due to sequence diversity and computational demands.

Purpose of the Study:

Investigate how sequence affects the 3D-structure of heparanome oligosaccharides.
Develop a coarse-grained model for heparan sulfate consistent with atomic-level dynamics.
Explore the link between ring puckering, polymer shape, and bioactivity in the heparanome.

Main Methods:

Performed unbiased microsecond molecular dynamics simulations of 11 heparanome oligosaccharides (55 microseconds total).
Developed and validated a coarse-grained model against experimental data for long-time scale motions.

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Flexural Rigidity Measurements of Biopolymers Using Gliding Assays

Flexural Rigidity Measurements of Biopolymers Using Gliding Assays

Published on: November 9, 2012

Analyzed the effect of polymerization on pyranose ring flexing in 2-O-sulfo-α-l-iduronic acid.

Main Results:

Pyranose ring flexing in 2-O-sulfo-α-l-iduronic acid is modulated by polymerization (chain position, adjacent residues).
Inclusion of ring puckering in coarse-grained simulations is essential for predicting hydrodynamic properties of long heparan sulfate chains.
Structural findings reveal sequence-dependent 3D-structures and dynamics.

Conclusions:

Heparanome sequence diversity directly influences 3D-structure and dynamics.
A validated coarse-grained model incorporating ring puckering accurately predicts macroscopic properties.
Heparanome puckering, polymer 3D-shape, and bioactivity are intrinsically linked, enabling rational molecular design.