Research News
Dr. Meng-Qiu Dong's lab in collaboration with the pFind team developed a high-throughput mass spectrometry method for analyzing protein disulfide bonds
On Feb. 9, 2015, Meng-Qiu Dong's lab of National Institute of Biological Sciences (NIBS), Beijing, published a research article titled "Mapping Native Disulfide Bonds at a Proteome Scale" on Nature Methods. In collaboration with the pFind team of Institute of Computing Technology (ICT), Chinese Academy of Sciences (CAS), we developed two mass spectrometry (MS)-based workflows for accurate and high-through identification of protein disulfide bonds from low- and high-complexity samples, respectively. Both workflows feature a sample preparation method that can maintain the native disulfide structures in proteins and a software tool pLink-SS for automated data analysis and false discovery rate control.
Disulfide bonds are indispensable for numerous secreted proteins including hormones, growth factors and cell surface receptors, but mapping disulfide bonds has long been a challenge. In this paper, we report a high-throughput MS method for precise identification of native protein disulfide bonds. We successfully identified all the disulfide bonds in a monoclonal antibody and those in a ten-protein mixture, as well as 199, 334 and 568 disulfide bonds in E. coli, human epithelial and endothelial cells, respectively. Previously unrecognized substrates of DsbA, a thiol-disulfide oxidoreductase, were also found. These proteome-scale analyses revealed a large number of regulatory disulfide bonds involving catalytic or metal-binding cysteine residues. We verified nine newly identified disulfide bonds in eight E. coli proteins, including an inter-subunit disulfide bond of LuxS, which inactivates LuxS in a redox-sensitive and reversible manner.
Shan Lu (NIBS), Sheng-Bo Fan (ICT) and Bing Yang (NIBS) are co-first authors of this paper. Other authors are: from NIBS, Yu-Xin Li, Mei-Jun Zhang and Meng-Qiu Dong; from ICT, Jia-Ming Meng, Long Wu, Kun Zhang, Rui-Xiang Sun and Si-Min He; from Peking University, Pin Li and Jincai Luo; from NCMIS, CAS, Yan Fu. Meng-Qiu Dong and Si-Min He are corresponding authors. The research was supported by grants from the Ministry of Science and Technology of China, National Natural Science Foundation of China, and the Municipal Government of Beijing.
