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Structure. 2014 Dec 2;22(12):1862-1874. doi: 10.1016/j.str.2014.09.013. Epub 2014 Nov 6.

Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.

Author information

1
Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
2
Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
3
Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA.
4
Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada. Electronic address: carrow@uhnresearch.ca.

Abstract

Multidomain proteins in which individual domains are connected by linkers often possess inherent interdomain flexibility that significantly complicates their structural characterization in solution using either nuclear magnetic resonance (NMR) spectroscopy or small-angle X-ray scattering (SAXS) alone. Here, we report a protocol for joint refinement of flexible multidomain protein structures against NMR distance and angular restraints, residual dipolar couplings, and SAXS data. The protocol is based on the ensemble optimization method principle (Bernadó et al., 2007) and is compared with different refinement strategies for the structural characterization of the flexible two-domain protein sf3636 from Shigella flexneri 2a. The results of our refinement suggest the existence of a dominant population of configurational states in solution possessing an overall elongated shape and restricted relative twisting of the two domains.

PMID:
25456817
PMCID:
PMC5046226
DOI:
10.1016/j.str.2014.09.013
[Indexed for MEDLINE]
Free PMC Article

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