Pull-down Assay on Streptavidin Beads and Surface Plasmon Resonance Chips for SWATH-MS-based Interactomics

被引：7

作者：

Maryas, Josef ^{[1
,2
]}

Faktor, Jakub ^{[1
,2
]}

Capkova, Lenka ^{[1
]}

Mueller, Petr ^{[2
]}

Skladal, Petr ^{[1
]}

Bouchal, Pavel ^{[1
]}

机构：

[1] Masaryk Univ, Fac Sci, Dept Biochem, Kotlarska 2, CS-61137 Brno, Czech Republic

[2] Masaryk Mem Canc Inst, Reg Ctr Appl Mol Oncol, Brno, Czech Republic

来源：

CANCER GENOMICS & PROTEOMICS | 2018年 / 15卷 / 05期

关键词：

LC-SWATH-MS/MS; pull-down assay; PDLIM2; protein-protein interactions; SPR; PROTEIN-PROTEIN INTERACTIONS; DATA-INDEPENDENT ACQUISITION; MASS-SPECTROMETRY; RECOMBINANT PROTEINS; BREAST-CANCER; LC-MS/MS; SBP-TAG; PROTEOMICS; COMPLEX; CELLS;

D O I：

10.21873/cgp.20098

中图分类号：

R73 [肿瘤学];

学科分类号：

100214 ;

摘要：

Background/Aim: Pul-down assay is a popular in vitro method for identification of physical interactors of selected proteins. Here, for the first time, we compared three conventional variants of pull-down assay with the streptavidin-modified surface plasmon resonance (SPR) chips for the detection of PDZ and LIM domain protein 2 (PDLIM2) interaction partners. Materials and Methods: PDLIM2 protein-protein interactions were analysed by three variants of pull-down assay on streptavidin beads using LC-MS/MS in "Sequential Window Acquisition of all Theoretical fragment ion spectra (SWATH)" mode and compared with LC-SWATHMS/MS data from SPR chips. Results: The results showed that (i) the use of SPR chip led to comparable data compared to on-column streptavidin beads, (ii) gravity flow and microflow in wash and elution steps provided better results than centrifugation, and (iii) type and concentration of detergent did not significantly affect the interactome data of cancer-associated PDLIM2. Conclusion: Our study supports further application of SPR-based affinity purification with SWATH mass spectrometry for reproducible and controlled characterization of cancer-associated interactomes.

引用

页码：395 / 404

页数：10

共 36 条

[1]

Arany I, 2012, ANTICANCER RES, V32, P4759

[2] The structure of the SBP-Tag-streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits [J].

Barrette-Ng, Isabelle H. ;

Wu, Sau-Ching ;

Tjia, Wai-Mui ;

Wong, Sui-Lam ;

Ng, Kenneth K. S. .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2013, 69 :879-887

[3] Identification of protein phosphatase interacting proteins from normal and UVA-irradiated HaCaT cell lysates by surface plasmon resonance based binding technique using biotin-microcystin-LR as phosphatase capturing molecule [J].

Becsi, Balint ;

Dedinszki, Dora ;

Gyemant, Gyoengyi ;

Mathe, Csaba ;

Vasas, Gabor ;

Lontay, Beata ;

Erdodi, Ferenc .

JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 2014, 138 :240-248

[4] Methods for the detection and analysis of protein-protein interactions [J].

Berggard, Tord ;

Linse, Sara ;

James, Peter .

PROTEOMICS, 2007, 7 (16) :2833-2842

[5] Combinations of SPR arid MS for characterization of native and recombinant proteins in cell lysates [J].

Borch, Jonas ;

Roepstorff, Peter .

MOLECULAR BIOTECHNOLOGY, 2006, 33 (03) :179-190

[6] Combined Proteomics and Transcriptomics Identifies Carboxypeptidase B1 and Nuclear Factor κB (NF-κB) Associated Proteins as Putative Biomarkers of Metastasis in Low Grade Breast Cancer [J].

Bouchal, Pavel ;

Dvorakova, Monika ;

Roumeliotis, Theodoros ;

Bortlicek, Zbynek ;

Ihnatova, Ivana ;

Prochazkova, Iva ;

Ho, Jenny T. C. ;

Maryas, Josef ;

Imrichova, Hana ;

Budinska, Eva ;

Vyzula, Rostislav ;

Garbis, Spiros D. ;

Vojtesek, Borivoj ;

Nenutil, Rudolf .

MOLECULAR & CELLULAR PROTEOMICS, 2015, 14 (07) :1814-1830

[7] Development of a multifunctional tool for drug screening against plasmodial protein-protein interactions via surface plasmon resonance [J].

Boucher, Lauren E. ;

Bosch, Juergen .

JOURNAL OF MOLECULAR RECOGNITION, 2013, 26 (10) :496-500

[8] History of protein-protein interactions: From egg-white to complex networks [J].

Braun, Pascal ;

Gingras, Anne-Claude .

PROTEOMICS, 2012, 12 (10) :1478-1498

[9] Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues [J].

Bruderer, Roland ;

Bernhardt, Oliver M. ;

Gandhi, Tejas ;

Miladinovic, Sasa M. ;

Cheng, Lin-Yang ;

Messner, Simon ;

Ehrenberger, Tobias ;

Zanotelli, Vito ;

Butscheid, Yulia ;

Escher, Claudia ;

Vitek, Olga ;

Rinner, Oliver ;

Reiter, Lukas .

MOLECULAR & CELLULAR PROTEOMICS, 2015, 14 (05) :1400-1410

[10]

Collins BC, 2013, NAT METHODS, V10, P1246, DOI [10.1038/nmeth.2703, 10.1038/NMETH.2703]

← 1 2 3 4 →