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).
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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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