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X-Ray Crystallography to Study Conformational Changes in a TPP Riboswitch

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RNA Structure and Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2568))

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Abstract

Conformational rearrangements are key to the function of riboswitches. These regulatory mRNA regions specifically bind to cellular metabolites using evolutionarily conserved sensing domains and modulate gene expression via adjacent downstream expression platforms, which carry gene expression signals. The regulation is achieved through the ligand-dependent formation of two alternative and mutually exclusive conformations involving the same RNA region. While X-ray crystallography cannot visualize dynamics of such dramatic conformational rearrangements, this method is pivotal to understand RNA–ligand interaction that stabilize the sensing domain and drive folding of the expression platform. X-ray crystallography can reveal local changes in RNA necessary for discriminating cognate and noncognate ligands. This chapter describes preparation of thiamine pyrophosphate riboswitch RNAs and its crystallization with different ligands, resulting in structures with local conformational changes in RNA. These structures can help to derive information on the dynamics of the RNA essential for specific binding to small molecules, with potential for using this information for developing designer riboswitch–ligand systems.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA

    Ashok Nuthanakanti, Ascensión Ariza-Mateos & Alexander Serganov

Authors
  1. Ashok Nuthanakanti
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  2. Ascensión Ariza-Mateos
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  3. Alexander Serganov
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Corresponding author

Correspondence to Alexander Serganov .

Editor information

Editors and Affiliations

  1. Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA

    Jienyu Ding

  2. Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA

    Jason R. Stagno

  3. Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA

    Yun-Xing Wang

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© 2023 This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply

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Nuthanakanti, A., Ariza-Mateos, A., Serganov, A. (2023). X-Ray Crystallography to Study Conformational Changes in a TPP Riboswitch. In: Ding, J., Stagno, J.R., Wang, YX. (eds) RNA Structure and Dynamics. Methods in Molecular Biology, vol 2568. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2687-0_14

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  • DOI: https://doi.org/10.1007/978-1-0716-2687-0_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2686-3

  • Online ISBN: 978-1-0716-2687-0

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