Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers

Alexander X. Jones, Yong Cao, Yu-Liang Tang, Jian-Hua Wang, Yue-He Ding, Hui Tan, Zhen-Lin Chen, Run-Qian Fang, Jili Yin, Rong-Chang Chen, Xing Zhu, Yang She, Niu Huang, Feng Shao, Keqiong Ye, Rui-Xiang Sun, Si-Min He, Xiaoguang Lei () and Meng-Qiu Dong ()
Additional contact information
Alexander X. Jones: Peking University
Yong Cao: Peking University
Yu-Liang Tang: Peking University
Jian-Hua Wang: National Institute of Biological Sciences (NIBS)
Yue-He Ding: National Institute of Biological Sciences (NIBS)
Hui Tan: Peking University
Zhen-Lin Chen: Institute of Computing Technology, CAS
Run-Qian Fang: Institute of Computing Technology, CAS
Jili Yin: Institute of Computing Technology, CAS
Rong-Chang Chen: University of Chinese Academy of Sciences
Xing Zhu: University of Chinese Academy of Sciences
Yang She: National Institute of Biological Sciences (NIBS)
Niu Huang: National Institute of Biological Sciences (NIBS)
Feng Shao: National Institute of Biological Sciences (NIBS)
Keqiong Ye: University of Chinese Academy of Sciences
Rui-Xiang Sun: National Institute of Biological Sciences (NIBS)
Si-Min He: Institute of Computing Technology, CAS
Xiaoguang Lei: Peking University
Meng-Qiu Dong: National Institute of Biological Sciences (NIBS)

Nature Communications, 2019, vol. 10, issue 1, 1-11

Abstract: Abstract Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially.

Date: 2019
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DOI: 10.1038/s41467-019-11917-z

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