Gong, ZhouLiu, ZhuDong, XuDing, Yue-HeDong, Meng-QiuTang, Chun2022-08-232022-08-232017-11-202018-03-27<p>Biophys Rep. 2017;3(4):100-108. doi: 10.1007/s41048-017-0044-9. Epub 2017 Nov 20. <a href="https://doi.org/10.1007/s41048-017-0044-9">Link to article on publisher's site</a></p>2364-3439 (Linking)10.1007/s41048-017-0044-929238747https://hdl.handle.net/20.500.14038/40515Chemical 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.en-USCopyright © The Author(s) 2017. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.http://creativecommons.org/licenses/by/4.0/Chemical cross-linkingDynaXLEnsemble refinementMulti-domain proteinProtein–protein complexSolvent accessible surface distanceAmino Acids, Peptides, and ProteinsBiophysicsInvestigative TechniquesResearch Methods in Life SciencesStructural BiologyJournal Articlehttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=4329&amp;context=oapubs&amp;unstamped=1https://escholarship.umassmed.edu/oapubs/331811856469oapubs/3318