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NMR Studies of Protein-Nucleic Acid Interactions

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Protein NMR Techniques

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 278))

Abstract

Protein–DNA and protein–RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein–protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

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Author information

Authors and Affiliations

  1. Department of Biochemistry and Department of Chemistry, University of Washington, Seattle, WA

    Gabriele Varani & Thomas C. Leeper

  2. Departments of Biochemistry and Chemistry, University of Washington, Seattle, WA

    Yu Chen

Authors
  1. Gabriele Varani
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  2. Yu Chen
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  3. Thomas C. Leeper
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Editors and Affiliations

  1. Department of Biochemistry, University of Oxford, Oxford, UK

    A. Kristina Downing

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© 2004 Humana Press Inc., Totowa, NJ

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Varani, G., Chen, Y., Leeper, T.C. (2004). NMR Studies of Protein-Nucleic Acid Interactions. In: Downing, A.K. (eds) Protein NMR Techniques. Methods in Molecular Biology™, vol 278. Humana Press. https://doi.org/10.1385/1-59259-809-9:289

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  • DOI: https://doi.org/10.1385/1-59259-809-9:289

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-246-9

  • Online ISBN: 978-1-59259-809-0

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