Molecular Dynamics Simulation of Glycans

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  • Re Suyong
    Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research
  • Yamaguchi Yoshiki
    Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster Synthetic Cellular Chemistry Laboratory, RIKEN Cluster for Pioneering Research Laboratory of Pharmaceutical Physical Chemistry, Tohoku Medical and Pharmaceutical University
  • Sugita Yuji
    Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research Computational Biophysics Research Team, RIKEN Center for Computational Science Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research

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  • 糖鎖の分子動力学シミュレーション
  • トウサ ノ ブンシ ドウリキガク シミュレーション

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Abstract

<p>Three-dimensional structural diversity (conformational diversity) of glycans is essential for their biological functions. Molecular dynamics (MD) simulations provide insight into the three-dimensional (3D-) structures of biomolecules in atomic resolution which are difficult to obtain by experiment. However, their highly complex and flexible structures make glycans difficult to simulate. This minireview summarizes recent challenges in MD simulations of glycans using enhanced sampling techniques. Using MD simulations, various 3D-structures are revealed at atomic resolution, not only for isolated glycans but also for glycoconjugates and glycan-bound complexes. The role of MD simulations is not limited for interpretation of experimental results. The simulations are used to predict experiments, leading the integrated computational and experimental studies on the structure-function relationship of glycans. We hope that this article will help prompt various integrated studies of glycans in the future.</p>

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