Mapping disulfide bonds from sub-micrograms of purified proteins or micrograms of complex protein mixtures

Shan Lu; Yong Cao; Sheng-Bo Fan; Zhen-Lin Chen; Run-Qian Fang; Si-Min He; Meng-Qiu Dong

doi:10.1007/s41048-018-0050-6

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Article Navigation > Biophysics Reports > 2018 > 4(2): 68-81

Shan Lu, Yong Cao, Sheng-Bo Fan, Zhen-Lin Chen, Run-Qian Fang, Si-Min He, Meng-Qiu Dong. Mapping disulfide bonds from sub-micrograms of purified proteins or micrograms of complex protein mixtures. Biophysics Reports, 2018, 4(2): 68-81. doi: 10.1007/s41048-018-0050-6

Citation:

Shan Lu, Yong Cao, Sheng-Bo Fan, Zhen-Lin Chen, Run-Qian Fang, Si-Min He, Meng-Qiu Dong. Mapping disulfide bonds from sub-micrograms of purified proteins or micrograms of complex protein mixtures. Biophysics Reports, 2018, 4(2): 68-81. doi: 10.1007/s41048-018-0050-6

Citation:

Shan Lu, Yong Cao, Sheng-Bo Fan, Zhen-Lin Chen, Run-Qian Fang, Si-Min He, Meng-Qiu Dong. Mapping disulfide bonds from sub-micrograms of purified proteins or micrograms of complex protein mixtures. Biophysics Reports, 2018, 4(2): 68-81. doi: 10.1007/s41048-018-0050-6

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Mapping disulfide bonds from sub-micrograms of purified proteins or micrograms of complex protein mixtures

doi: 10.1007/s41048-018-0050-6

1 National Institute of Biological Sciences, Beijing, Beijing 102206, China
2 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences(CAS), University of CAS, Institute of Computing Technology, CAS, Beijing 100190, China
3 University of Chinese Academy of Sciences, Beijing 100049, China

Funds: The authors would like to thank the Beijing Municipal Science and Technology Commission,the Ministry of Science and Technology of China,and the Natural Science Foundation of China (21475141) for research funding.

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Corresponding author: Si-Min He, Meng-Qiu Dong
Received Date: 16 February 2018
Rev Recd Date: 08 March 2018
Publish Date: 30 April 2018

Abstract

Abstract

Disulfide bonds are vital for protein functions, but locating the linkage sites has been a challenge in protein chemistry, especially when the quantity of a sample is small or the complexity is high. In 2015, our laboratory developed a sensitive and efficient method for mapping protein disulfide bonds from simple or complex samples (Lu et al. in Nat Methods 12:329, 2015). This method is based on liquid chromatography-mass spectrometry (LC-MS) and a powerful data analysis software tool named pLink. To facilitate application of this method, we present step-by-step disulfide mapping protocols for three types of samples-purified proteins in solution, proteins in SDS-PAGE gels, and complex protein mixtures in solution. The minimum amount of protein required for this method can be as low as several hundred nanograms for purified proteins, or tens of micrograms for a mixture of hundreds of proteins. The entire workflow-from sample preparation to LC-MS and data analysis-is described in great detail. We believe that this protocol can be easily implemented in any laboratory with access to a fastscanning, high-resolution, and accurate-mass LC-MS system.
- Disulfide,
- Identification of disulfide bonds,
- Cross-linking,
- Mass spectrometry,
- PLink,
- PLink-SS

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References(24)

References

Choi S, Jeong J, Na S, Lee HS, Kim H-Y, Lee K-J, Paek E (2009) New algorithm for the identification of intact disulfide linkages based on fragmentation characteristics in tandem mass spectra. J Proteome Res 9:626-635

Götze M, Pettelkau J, Schaks S, Bosse K, Ihling CH, Krauth F, Fritzsche R, Kühn U, Sinz A (2012) StavroX—a software for analyzing crosslinked products in protein interaction studies. J Am Soc Mass Spectrom 23:76-87

Haniu M, Acklin C, Kenney WC, Rohde MF (1994) Direct assignment of disulfide bonds by Edman degradation of selected peptide fragments. Chem Biol Drug Des 43:81-86

Hartman MD, Figueroa CM, Arias DG, Iglesias AA (2016) Inhibition of recombinant aldose-6-phosphate reductase from peach leaves by hexose-phosphates, inorganic phosphate and oxidants. Plant Cell Physiol 58:145-155

Hogg PJ (2003) Disulfide bonds as switches for protein function. Trends Biochem Sci 28:210-214

Huang SY, Chen SF, Chen CH, Huang HW, Wu WG, Sung WC (2014) Global disulfide bond profiling for crude snake venom using dimethyl labeling coupled with mass spectrometry and RADAR algorithm. Anal Chem 86:8742-8750

Hung C-W, Koudelka T, Anastasi C, Becker A, Moali C, Tholey A (2016) Characterization of post-translational modifications in full-length human BMP-1 confirms the presence of a rare vicinal disulfide linkage in the catalytic domain and highlights novel features of the EGF domain. J Proteomics 138:136-145

Itakura M, Iwashina M, Mizuno T, Ito T, Hagiwara H, Hirose S (1994) Mutational analysis of disulfide bridges in the type C atrial natriuretic peptide receptor. J Biol Chem 269:8314-8318

Liu F, van Breukelen B, Heck AJ (2014) Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Mol Cell Proteomics 13:2776-2786

Liu Y, Sun W, Shan B, Zhang K (2017a) DISC: DISulfide linkage Characterization from tandem mass spectra. Bioinformatics 33:3861-3870

Liu Y, Xiao W, Shinde M, Field J, Templeton DM (2017b) Cadmium favors F-actin depolymerization in rat renal mesangial cells by site-specific, disulfide-based dimerization of the CAP1 protein. Arch Toxicol, 1-16

Lu S, Fan S-B, Yang B, Li Y-X, Meng J-M, Wu L, Li P, Zhang K, Zhang M-J, Fu Y (2015) Mapping native disulfide bonds at a proteome scale. Nat Methods 12:329

Mauney CH, Rogers LC, Harris RS, Daniel LW, Devarie-Baez NO, Wu H, Furdui CM, Poole LB, Perrino FW, Hollis T (2017) The SAMHD1 dNTP triphosphohydrolase is controlled by a redox switch. Antioxid Redox Signal 27:1317-1331

McCarthy AA, Haebel PW, Tö rrönen A, Rybin V, Baker EN, Metcalf P (2000) Crystal structure of the protein disulfide bond isomerase, DsbC, from Escherichia coli. Nat Struct Mol Biol 7:196

McDonagh B (2009) Diagonal electrophoresis for detection of protein disulphide bridges. In: Two-Dimensional Electrophoresis Protocols. Springer, pp. 305-310

Murad W, Singh R (2013) MS2DB +: a software for determination of disulfide bonds using multi-ion analysis. IEEE Trans Nanobiosci 12:69-71

Sharma D, Rajarathnam K (2000) 13C NMR chemical shifts can predict disulfide bond formation. J Biomol NMR 18:165-171

Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N (2014) Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Mol Cell Proteomics 13:1128-1136

Wang T, Liang L, Xue Y, Jia P-F, Chen W, Zhang M-X, Wang Y-C, Li H-J, Yang W-C (2016) A receptor heteromer mediates the male perception of female attractants in plants. Nature 531:241

Wefing S, Schnaible V, Hoffmann D (2006) SearchXLinks. A program for the identification of disulfide bonds in proteins from mass spectra. Anal Chem 78:1235-1241

Wu S-L, Jiang H, Lu Q, Dai S, Hancock WS, Karger BL (2008) Mass spectrometric determination of disulfide linkages in recombinant therapeutic proteins using online LC-MS with electron-transfer dissociation. Anal Chem 81:112-122

Wu J, Yan Z, Li Z, Qian X, Lu S, Dong M, Zhou Q, Yan N (2016) Structure of the voltage-gated calcium channel Ca v 1.1 at 3.6 Å resolution. Nature 537:191

Wu Y, Zhu Y, Gao F, Jiao Y, Oladejo BO, Chai Y, Bi Y, Lu S, Dong M, Zhang C (2017) Structures of phlebovirus glycoprotein Gn and identification of a neutralizing antibody epitope. Proc Natl Acad Sci 114:E7564-E7573

Xu H, Zhang L, Freitas MA (2007) Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine. J Proteome Res 7:138-144

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