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

Authors

Stepan Kashtanov, University of Idaho
Wade M. Borcherds, University of South FloridaFollow
Hongwei Wu, University of South Florida
Gary W. Daughdrill, University of South FloridaFollow
F. Marty Ytreberg, University of Idaho

Document Type

Article

Publication Date

2020

Keywords

Ensemble Structure, Random Coil, Secondary Chemical Shift, Intrinsically Disordered Proteins, Nuclear Magnetic Resonance Spectroscopy

Digital Object Identifier (DOI)

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

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.

Was this content written or created while at USF?

Yes

Citation / Publisher Attribution

Using Chemical Shifts to Assess Transient Secondary Structure and Generate Ensemble Structures of Intrinsically Disordered Proteins, in V. Uversky & A. Dunker (Eds.), Intrinsically Disordered Protein Analysis, Humana Press, p. 139-152

Scholar Commons Citation

Kashtanov, Stepan; Borcherds, Wade M.; Wu, Hongwei; Daughdrill, Gary W.; and Ytreberg, F. Marty, "Using Chemical Shifts to Assess Transient Secondary Structure and Generate Ensemble Structures of Intrinsically Disordered Proteins" (2020). Molecular Biosciences Faculty Publications. 162.
https://digitalcommons.usf.edu/bcm_facpub/162