Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL

Zhou Gong; Zhu Liu; Xu Dong; Yue-He Ding; Meng-Qiu Dong; Chun Tang

doi:10.1007/s41048-017-0044-9

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Zhou Gong, Zhu Liu, Xu Dong, Yue-He Ding, Meng-Qiu Dong, Chun Tang. Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL. Biophysics Reports, 2017, 3(4-6): 100-108. doi: 10.1007/s41048-017-0044-9

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Zhou Gong, Zhu Liu, Xu Dong, Yue-He Ding, Meng-Qiu Dong, Chun Tang. Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL. Biophysics Reports, 2017, 3(4-6): 100-108. doi: 10.1007/s41048-017-0044-9

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Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL

doi: 10.1007/s41048-017-0044-9

Zhou Gong^{1,2
,
,},
Zhu Liu³,
Xu Dong^1,2,
Yue-He Ding⁴,
Meng-Qiu Dong^5
,,
Chun Tang^{1,2
,}

1 CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan 430071, China
2 National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan 430071, China
3 Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Zhejiang University School of Medicine, Hangzhou 310057, China
4 RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
5 National Institute of Biological Sciences, Beijing 102206, China

Funds: This work was supported by a Grant from the National Key R&D Program of China (2016YFA0501200), Chinese Ministry of Science and Technology (2013CB910200), and National Natural Science Foundation of China (31225007, 31400735 and 31500595).

More Information

Corresponding author: Zhou Gong, Chun Tang
Received Date: 19 July 2017
Rev Recd Date: 18 September 2017
Publish Date: 30 November 2017

Abstract

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 rigidbody 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.
- Chemical cross-linking,
- DynaXL,
- Ensemble refinement,
- Solvent accessible surface distance,
- Multi-domain protein,
- Protein-protein complex

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References(34)

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