Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigid-body refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein-protein complexes, and is freely available at www.tanglab.org/resources.
CITATION STYLE
Gong, Z., Liu, Z., Dong, X., Ding, Y.-H., Dong, M.-Q., & Tang, C. (2017). Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL. Biophysics Reports, 3(4–6), 100–108. https://doi.org/10.1007/s41048-017-0044-9
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