Exploration of Conformational Spaces of Oligosaccharides byCombining Molecular Dynamics Simulation and NMR Spectroscopy

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  • YAMAGUCHI Takumi
    School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292 Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University,3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603
  • WATANABE Tokio
    Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University,3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603
  • YAGI Hirokazu
    Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University,3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603
  • KATO Koichi
    Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University,3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603 Okazaki Institute for Integrative Bioscience and Institute for Molecular Science,National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787

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  • 分子動力学計算とNMR計測を用いた糖鎖の配座空間探査

Abstract

<p>Oligosaccharides are highly flexible molecules having branched structures and significant degrees of freedom in internal motion. To gain insights into the molecular basis of their biological functions, it is essential to describe the conformational dynamics of oligosaccharides. By combining NMR spectroscopy and molecular simulation, we developed a method giving the quantitative interpretation of dynamic behaviors of oligosaccharides. Paramagnetism-assisted NMR approaches with replica-exchange molecular dynamics simulations revealed the conformations of a series of oligosaccharides involved in the glycoprotein quality control system in cells. Exploration of the conformational spaces of the oligosaccharides also provided dynamical views of the interaction mechanisms of carbohydrate recognition proteins, complementing the static crystallographic analyses.</p>

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