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NMR Explorations of Biomolecular Systems with Rapid Conformational Exchanges

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Molecular Science of Fluctuations Toward Biological Functions

Abstract

Biomolecules such as proteins and oligosaccharides undergo dynamic conformational exchanges, which are relevant to regulation of biologically functional processes as typified by molecular recognition. Nuclear magnetic resonance (NMR) spectroscopy provides useful approaches to characterize the conformational dynamics of biomolecules over a broad range of time scales. However, detailed characterizations of individual conformers are inherently challenging for those biomolecules that exhibit rapid conformational interconversions. Here we describe several NMR strategies to deal with dynamic conformational equilibria and ensembles using monomeric and dimeric ubiquitin (Ub) and the oligosaccharide moieties of gangliosides as model molecules. A specific Ub conformer could be enriched using high pressure combined with a single amino acid substitution. Introducing a covalent linkage constrained the conformational states of a Ub dimer. NMR spectroscopy was also useful for validating molecular dynamics simulations of highly flexible oligosaccharides. These methods provided for detailed determinations of dynamic conformational exchanges that involve minor conformational species.

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Acknowledgments

This work was partly supported by the JSPS/MEXT Grants in Aid for Scientific Research on Innovation Areas (23107729, 20107004, and 25102008), Young Scientists (B) (25840025 and 24750170), and Challenging Exploratory Research (26560451) and by the Okazaki ORION project. M. Y. U. is a recipient of the Naito Foundation Grant for Studying Overseas.

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Authors and Affiliations

  1. Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan

    Maho Yagi-Utsumi, Takumi Yamaguchi & Koichi Kato

  2. Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan

    Maho Yagi-Utsumi, Takumi Yamaguchi & Koichi Kato

  3. Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK

    Maho Yagi-Utsumi

  4. College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, 525-8577, Japan

    Ryo Kitahara

Authors
  1. Maho Yagi-Utsumi
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  2. Takumi Yamaguchi
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  3. Ryo Kitahara
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  4. Koichi Kato
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Corresponding author

Correspondence to Koichi Kato .

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Editors and Affiliations

  1. Kyoto University, Kyoto, Japan

    Masahide Terazima

  2. Nara Institute of Science and Tech, Ikoma, Japan

    Mikio Kataoka

  3. Sojo University, Kumamoto, Japan

    Ryuichi Ueoka

  4. Nagoya University, Nagoya, Japan

    Yuko Okamoto

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Yagi-Utsumi, M., Yamaguchi, T., Kitahara, R., Kato, K. (2016). NMR Explorations of Biomolecular Systems with Rapid Conformational Exchanges. In: Terazima, M., Kataoka, M., Ueoka, R., Okamoto, Y. (eds) Molecular Science of Fluctuations Toward Biological Functions . Springer, Tokyo. https://doi.org/10.1007/978-4-431-55840-8_4

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