UMMS Affiliation
RNA Therapeutics Institute
Publication Date
2017-11-20
Document Type
Article
Disciplines
Amino Acids, Peptides, and Proteins | Biophysics | Investigative Techniques | Research Methods in Life Sciences | Structural Biology
Abstract
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.
Keywords
Chemical cross-linking, DynaXL, Ensemble refinement, Multi-domain protein, Protein–protein complex, Solvent accessible surface distance
Rights and Permissions
Copyright © 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.
DOI of Published Version
10.1007/s41048-017-0044-9
Source
Biophys Rep. 2017;3(4):100-108. doi: 10.1007/s41048-017-0044-9. Epub 2017 Nov 20. Link to article on publisher's site
Journal/Book/Conference Title
Biophysics reports
Related Resources
PubMed ID
29238747
Repository Citation
Gong, Zhou; Liu, Zhu; Dong, Xu; Ding, Yue-He; Dong, Meng-Qiu; and Tang, Chun, "Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL" (2017). Open Access Articles. 3318.
https://escholarship.umassmed.edu/oapubs/3318
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Amino Acids, Peptides, and Proteins Commons, Biophysics Commons, Investigative Techniques Commons, Research Methods in Life Sciences Commons, Structural Biology Commons