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Using Chemical Shifts to Assess Transient Secondary Structure and Generate Ensemble Structures of Intrinsically Disordered Proteins

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Intrinsically Disordered Protein Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 895))

Abstract

The chemical shifts of backbone atoms in polypeptides are sensitive to the dihedral angles phi and psi and can be used to estimate transient secondary structure and to generate structural ensembles of intrinsically disordered proteins (IDPs). In this chapter, several of the random coil reference databases used to estimate transient secondary structure are described, and the procedure is outlined for using these databases to estimate transient secondary structure. A new protocol is also presented for generating a diverse ensemble of structures for an IDP and reweighting these structures to optimize the fit between simulated and experimental chemical shift values.

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Acknowledgments

GWD is supported by the American Cancer Society (RSG-07-289-01-GMC) and the National Science Foundation (MCB-0939014). FMY and GWD are supported by the National Institutes of Health (5R21GM083827).

Author information

Authors and Affiliations

  1. Department of Physics, University of Idaho, Moscow, ID, USA

    Stepan Kashtanov & F. Marty Ytreberg

  2. Department of Cell Biology, Microbiology, and Molecular Biology and the Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL, USA

    Wade Borcherds & Gary W. Daughdrill

  3. Department of Cell Biology, Microbiology, and Molecular Biology, the Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL, USA

    Hongwei Wu

Authors
  1. Stepan Kashtanov
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  2. Wade Borcherds
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  3. Hongwei Wu
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  4. Gary W. Daughdrill
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  5. F. Marty Ytreberg
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Corresponding author

Correspondence to F. Marty Ytreberg .

Editor information

Editors and Affiliations

  1. Department of Molecular Medicine, College of Medicine, University of South Florida, Bruce B. Downs Blvd 12901, Tampa, 33612, Florida, USA

    Vladimir N. Uversky

  2. Dept. Biochemistry & Molecular Biology, Center for Computational Biology &, Indiana University, West 10th Street 410, Indianapolis, 46202, Indiana, USA

    A. Keith Dunker

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Kashtanov, S., Borcherds, W., Wu, H., Daughdrill, G.W., Ytreberg, F.M. (2012). Using Chemical Shifts to Assess Transient Secondary Structure and Generate Ensemble Structures of Intrinsically Disordered Proteins. In: Uversky, V., Dunker, A. (eds) Intrinsically Disordered Protein Analysis. Methods in Molecular Biology, vol 895. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-927-3_11

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  • DOI: https://doi.org/10.1007/978-1-61779-927-3_11

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-926-6

  • Online ISBN: 978-1-61779-927-3

  • eBook Packages: Springer Protocols

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