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Force Fields for Carbohydrate-Divalent Cation Interactions.

Hsieh Chen¹, Jason R Cox¹, Athanassios Z Panagiotopoulos²

¹Aramco Services Company: Aramco Research Center - Boston, Cambridge, Massachusetts 02139, United States.

The Journal of Physical Chemistry. B

|May 24, 2016

Summary

This summary is machine-generated.

Standard molecular dynamics simulations struggle with carbohydrate-divalent cation interactions. A modified approach accurately predicts stability constants and reveals specific binding structures for these essential complexes.

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Area of Science:

Computational Chemistry
Biophysical Chemistry
Molecular Modeling

Background:

Accurate modeling of carbohydrate-divalent cation interactions is crucial for understanding biological processes.
Existing molecular dynamics force fields often fail to reproduce experimental stability constants for these complexes.

Purpose of the Study:

To investigate intermolecular interactions between carbohydrates and divalent cations using molecular dynamics simulations.
To develop and validate a modified computational approach for improved accuracy in predicting carbohydrate-divalent cation complex stability.

Main Methods:

Employed molecular dynamics simulations to study complexes of α-d-Allopyranose with alkali earth metal cations (Mg2+, Ca2+, Sr2+, Ba2+).
Introduced a modified combining rule with a rescaled effective cross-interaction radius between cations and carbohydrate hydroxyl oxygens.
Validated the modified approach by comparing simulation results with experimental stability constants.

Main Results:

Standard force fields with Lorentz-Berthelot rules failed to reproduce experimental stability constants.
The modified combining rule successfully reproduced experimental stability constants.
Observed preferential complexation structures, highlighting the ax-eq-ax sequence of O-1, O-2, and O-3 on α-d-Allopyranose.
Demonstrated transferability of the scaling factor to similar six-membered ring carbohydrates (α-d-Ribopyranose) but noted potential need for reparameterization for five-membered rings (α-d-Ribofuranose).

Conclusions:

A modified force field approach is necessary for accurate molecular dynamics simulations of carbohydrate-divalent cation interactions.
The developed method provides a more reliable prediction of complex stability and binding preferences.
The findings offer insights into cation-carbohydrate recognition mechanisms and guide future computational studies in glycobiology and materials science.