1
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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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2
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Li J, Li N, Hou Y, Fan M, Zhang Y, Zhang Q, Dang F. Facile fabrication of Ti 4+-immobilized magnetic nanoparticles by phase-transitioned lysozyme nanofilms for enrichment of phosphopeptides. Anal Bioanal Chem 2024; 416:1657-1665. [PMID: 38319356 DOI: 10.1007/s00216-024-05170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 02/07/2024]
Abstract
In this study, titanium (IV)-immobilized magnetic nanoparticles (Ti4+-PTL-MNPs) were firstly synthesized via a one-step aqueous self-assembly of lysozyme nanofilms for efficient phosphopeptide enrichment. Under physiological conditions, lysozymes readily self-organized into phase-transitioned lysozyme (PTL) nanofilms on Fe3O4@SiO2 and Fe3O4@C MNP surfaces with abundant functional groups, including -NH2, -COOH, -OH, and -SH, which can be used as multiple linkers to efficiently chelate Ti4+. The obtained Ti4+-PTL-MNPs possessed high sensitivity of 0.01 fmol μL-1 and remarkable selectivity even at a mass ratio of β-casein to BSA as low as 1:400 for phosphopeptide enrichment. Furthermore, the synthesized Ti4+-PTL-MNPs can also selectively identify low-abundance phosphopeptides from extremely complicated human serum samples and their rapid separation, good reproducibility, and excellent recovery were also proven. This one-step self-assembly of PTL nanofilms facilitated the facile and efficient surface functionalization of various nanoparticles for proteomes/peptidomes.
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Affiliation(s)
- Jianru Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Nan Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an, 710072, China.
| | - Yawen Hou
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Miao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Yuxiu Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Qiqi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Fuquan Dang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China.
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3
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Wang J, Zhao X, Zhang H, Chen Y, Bie Z. In situ digestion-assisted multi-template imprinted nanoparticles for efficient analysis of protein phosphorylation. Mikrochim Acta 2023; 190:490. [PMID: 38030869 DOI: 10.1007/s00604-023-06081-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/29/2023] [Indexed: 12/01/2023]
Abstract
A new general approach called in situ digestion-assisted multi-template imprinting is proposed for preparation of phospho-specific molecularly imprinted nanoparticles. Through the novel templating strategy and controllable imprinting process, imprinted nanoparticles specific to the intact phosphoprotein and its phosphopeptides were synthesized. The prepared imprinted nanoparticles exhibited excellent specificity (cross reactivity < 10%), high affinity (10-6 M), high efficiency (47.5%), and good generality (both intact phosphoprotein and phosphopeptides). We also realized the fine tuning of the recognition at peptide level of the imprinted nanoparticles by adjusting the imprinting time. Based on the selective enrichment of the imprinted nanoparticles, the MS identification of both the intact phosphoprotein (Tau) and phosphopeptides (angiotensin II and peptides of Tau) in real complex samples could be achieved. Therefore, we believe that the in situ digestion-assisted multi-template imprinting strategy holds promising future in both phosphorylation analysis and proteomics applications.
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Affiliation(s)
- Jie Wang
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
| | - Xiuling Zhao
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China
| | - Hui Zhang
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
| | - Yang Chen
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China
| | - Zijun Bie
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China.
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China.
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4
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Wang Q, Fang F, Sun L. Pilot investigation of magnetic nanoparticle-based immobilized metal affinity chromatography for efficient enrichment of phosphoproteoforms for mass spectrometry-based top-down proteomics. Anal Bioanal Chem 2023; 415:4521-4531. [PMID: 37017721 PMCID: PMC10540245 DOI: 10.1007/s00216-023-04677-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/06/2023]
Abstract
Protein phosphorylation is a vital and common post-translational modification (PTM) in cells, modulating various biological processes and diseases. Comprehensive top-down proteomics of phosphorylated proteoforms (phosphoproteoforms) in cells and tissues is essential for a better understanding of the roles of protein phosphorylation in fundamental biological processes and diseases. Mass spectrometry (MS)-based top-down proteomics of phosphoproteoforms remains challenging due to their relatively low abundance. Herein, we investigated magnetic nanoparticle-based immobilized metal affinity chromatography (IMAC, Ti4+, and Fe3+) for selective enrichment of phosphoproteoforms for MS-based top-down proteomics. The IMAC method achieved reproducible and highly efficient enrichment of phosphoproteoforms from simple and complex protein mixtures. It outperformed one commercial phosphoprotein enrichment kit regarding the capture efficiency and recovery of phosphoproteins. Reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) analyses of yeast cell lysates after IMAC (Ti4+ or Fe3+) enrichment produced roughly 100% more phosphoproteoform identifications compared to without IMAC enrichment. Importantly, the phosphoproteoforms identified after Ti4+-IMAC or Fe3+-IMAC enrichment correspond to proteins with much lower overall abundance compared to that identified without the IMAC treatment. We also revealed that Ti4+-IMAC and Fe3+-IMAC could enrich different pools of phosphoproteoforms from complex proteomes and the combination of those two methods will be useful for further improving the phosphoproteoform coverage from complex samples. The results clearly demonstrate the value of our magnetic nanoparticle-based Ti4+-IMAC and Fe3+-IMAC for advancing top-down MS characterization of phosphoproteoforms in complex biological systems.
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Affiliation(s)
- Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA.
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5
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Kong Q, Weng Y, Zheng Z, Chen W, Li P, Cai Z, Tian R. Integrated and High-Throughput Approach for Sensitive Analysis of Tyrosine Phosphoproteome. Anal Chem 2022; 94:13728-13736. [PMID: 36179360 DOI: 10.1021/acs.analchem.2c01807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine phosphorylation (pTyr) regulates various signaling pathways under normal and cancerous states. Due to their low abundance and transient and dynamic natures, systematic profiling of pTyr sites is challenging. Antibody and engineered binding domain-based approaches have been well applied to pTyr peptide enrichment. However, traditional methods have the disadvantage of a long sample preparation process, which makes them unsuitable for processing limited amount of samples, especially in a high-throughput manner. In this study we developed a 96-well microplate-based approach to integrate all the sample preparation steps starting from cell culture to MS-compatible pTyr peptide enrichment in three consecutive 96-well microplates. By assembling an engineered SH2 domain onto a microplate, nonspecific adsorption of phosphopeptides is greatly reduced, which allows us to remove the Ti-IMAC purification and three C18 desalting steps (after digestion, pTyr enrichment, and Ti-IMAC purification) and, therefore, greatly simplifies the entire pTyr peptide enrichment workflow, especially when processing a large number of samples. Starting with 96-well microplate-cultured, pervanadate-stimulated cells, our approach could enrich 21% more pTyr sites than the traditional serial pTyr enrichment approach and showed good sensitivity and reproducibility in the range of 200 ng to 200 μg peptides. Importantly, we applied this approach to profile tyrosine kinase inhibitor-mediated EGFR signaling pathway and could well differentiate the distinct response of different pTyr sites. Collectively, the integrated 96-well microplate-based approach is valuable for profiling pTyr sites from limited biological samples and in a high-throughput manner.
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Affiliation(s)
- Qian Kong
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Yicheng Weng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zhendong Zheng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Wendong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Pengfei Li
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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6
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Xiao K, Zhu R, Du C, Zheng H, Zhang X, Chen J. Zinc-Air Battery-Assisted Self-Powered PEC Sensors for Sensitive Assay of PTP1B Activity Based on Perovskite Quantum Dots Encapsulated in Vinyl-Functionalized Covalent Organic Frameworks. Anal Chem 2022; 94:9844-9850. [PMID: 35749712 DOI: 10.1021/acs.analchem.2c01702] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The self-powered sensors have attracted widespread attention in the analysis field due to a huge demand of point-of-care testing (POCT) in the early diagnosis of diseases. However, the output voltage of the reported self-powered sensors is always small, resulting in a narrow linear detection range and low assay sensitivity. Herein, a self-powered photoelectrochemical (PEC) sensor with zinc-air batteries as a power source was developed for activity assay of protein tyrosine phosphatase 1B (PTP1B) based on perovskite quantum dots encapsulated in the vinyl-functionalized covalent organic framework (COF-V). CsPbBr3 nanocrystals were stabilized by the confinement effect of the COF-V cage without aggregation, and the resulting CsPbBr3@COF-V composite was used as the cathodic photoelectric material to construct the zinc-air battery with a large open-circuit voltage (OCV, 1.556 V). Before PTP1B activity assay, an auxiliary peptide-polyamidoamine-phosphopeptide (P2-PAMAM-P1) hybrid was introduced into the photocathode via thiol-ene click reaction between the thiol group on the P1 and the vinyl group on the COF-V. The steric hindrance effect of the P1-PAMAM-P2 hybrid inhibited the PEC performance of the photocathode, resulting in a small OCV of the zinc-air battery. When the PTP1B existed, PTP1B-catalyzed dephosphorylation of tyrosine on P1 facilitated the cleavage process of P1 by chymotrypsin, leading to the removal of the P2-PAMAM-P1 hybrid from the photocathode and consequently the enhancement of the OCV. Therefore, the activity of PTP1B was sensitively detected. The developed self-powered PEC sensor showed superior performance for PTP1B activity assay (broad linear response range, 0.1 pM to 10 nM and low detection limit, 0.032 pM) due to the large output voltage of the constructed zinc-air battery and has great potential in POCT of protein phosphatase-related diseases and the discovery of protein phosphatase-targeted drugs.
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Affiliation(s)
- Ke Xiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Rong Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Cuicui Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Hejie Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xiaohua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jinhua Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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7
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Zhao J, He H, Guo Z, Liu Z. Molecularly Imprinted and Cladded Nanoparticles Provide Better Phosphorylation Recognition. Anal Chem 2021; 93:16194-16202. [PMID: 34839654 DOI: 10.1021/acs.analchem.1c04070] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Phosphorylation is one of the most frequently occurring post-translation modifications in mammals. Because abnormal protein phosphorylation is related to many diseases, phosphorylation analysis is essential for a sound understanding of protein phosphorylation and its relationship with diseases. Among several types of reagents for phosphorylation recognition, molecularly imprinted polymers (MIPs), as synthetic mimics of antibodies, have exhibited unique strengths that can overcome the drawbacks of biological reagents. However, the performance of current MIPs has remained unideal. Meanwhile, while the currently existing imprinting methods have permitted the production of several material formats, such as crushed particles and mesoporous nanoparticles, a general method allowing for the preparation of monodispersed molecularly imprinted nanoparticles has not been developed yet. Herein, we report a new approach called reverse microemulsion template docking surface imprinting and cladding (RMTD-SIC) for facile preparation of monodispersed imprinted nanoparticles for better phosphorylation recognition. Through rational design and controllable engineering, monodisperse imprinted and cladded nanoparticles specific to general phosphorylation and tyrosine phosphorylation were synthesized, which yield the highest imprinting factors as compared with published studies. The prepared nanomaterials exhibited excellent specificity and affinity, allowing for specific enrichment and improved mass spectrometric identification of target phosphorylated peptides from complex samples containing 100-fold more abundant interfering peptides. Therefore, the RMTD-SIC approach holds great potential for phosphorylation analysis and phosphorylation recognition-based applications.
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Affiliation(s)
- Jialing Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hui He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhanchen Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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8
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Wang Z, Li Z, Su T, Han X, Hou Z, Zheng Y, Liu J, Xu J, Yang J, Liu H. BirA*-protein A fusion protein based BioEnhancer amplifies western blot immunosignal. Electrophoresis 2021; 42:793-799. [PMID: 33354816 DOI: 10.1002/elps.202000167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 11/08/2022]
Abstract
Western blot (protein immunoblot) is a widely used analytical technique in molecular biology. Utilizing the specific recognizing primary antibody, proteins immobilized on various matrix are investigated by subsequent visualization steps, for example, by the horse radish peroxidase conjugated secondary antibody incubation. Methods to improve the sensitivity in protein identification or quantification are appreciated by biochemists. Herein, we report a new strategy to amplify Western blot signals by constructing a probe with proximal labeling and IgG targeting abilities. The R118G mutation attenuated the biotin-AMP binding affinity of the bacterial biotin ligase BirA*, offering a proximity-dependent labeling ability, which could be used as a signal amplifier. We built a BirA*-protein A fusion protein (BioEnhancer) that specifically binds to IgG and adds biotin tags to its proximal amine groups, enhancing the immunosignal of target proteins. In our experiments, the BioEnhancer system amplified the immunosignal by tenfold compared to the standard western blot. Additionally, our strategy could couple with other signal enhancement methods to further increase the western blot sensitivity.
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Affiliation(s)
- Zhen Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Ziyang Li
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Tian Su
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Xiao Han
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Yupeng Zheng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Jiachen Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Jun Xu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Jeffy Yang
- Sulich Medicine and Dentistry, Western University, London, Canada
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
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9
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Li M, Xiong Y, Lu W, Wang X, Liu Y, Na B, Qin H, Tang M, Qin H, Ye M, Liang X, Qing G. Functional Nanochannels for Sensing Tyrosine Phosphorylation. J Am Chem Soc 2020; 142:16324-16333. [PMID: 32894673 DOI: 10.1021/jacs.0c06510] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Tyrosine phosphorylation (pTyr), much of which occurred on localized multiple sites, initiates cellular signaling, governs cellular functions, and its dysregulation is implicated in many diseases, especially cancers. pTyr-specific sensing is of great significance for understanding disease states and developing targeted anticancer drugs, however, it is very challenging due to the slight difference from serine (pSer) or threonine phosphorylation (pThr). Here we present polyethylenimine-g-phenylguanidine (PEI-PG)-modified nanochannels that can address the challenge. Rich guanidinium groups enabled PEI-PG to form multiple interactions with phosphorylated residues, especially pTyr residue, which triggered the conformational change of PEI-PG. By taking advantage of the "OFF-ON" change of the ion flux arising from the conformational shrinkage of the grafted PEI-PG, the nanochannels could distinguish phosphorylated peptide (PP) from nonmodified peptide, recognize PPs with pSer, pThr, or pTyr residue and PPs with different numbers of identical residues, and importantly could sense pTyr peptides in a biosample. Benefiting from the strong interaction between the guanidinium group and the pTyr side-chain, the specific sensing of pTyr peptide was achieved by performing a simple logic operation based on PEI-PG-modified nanochannels when Ca2+ was introduced as an interferent. The excellent pTyr sensing capacity makes the nanochannels available for real-time monitoring of the pTyr process by c-Abl kinase on a peptide substrate, even under complicated conditions, and the proof-of-concept study of monitoring the kinase activity demonstrates its potential in kinase inhibitor screening.
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Affiliation(s)
- Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, East China University of Technology, Nanchang 330013, P. R. China
| | - Yuting Xiong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, East China University of Technology, Nanchang 330013, P. R. China
| | - Wenqi Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xue Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yunhai Liu
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, East China University of Technology, Nanchang 330013, P. R. China
| | - Bing Na
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, East China University of Technology, Nanchang 330013, P. R. China
| | - Haijuan Qin
- Research Centre of Modern Analytical Technology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Mingliang Tang
- College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
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10
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Ahsan N, Wilson RS, Rao RSP, Salvato F, Sabila M, Ullah H, Miernyk JA. Mass Spectrometry-Based Identification of Phospho-Tyr in Plant Proteomics. J Proteome Res 2020; 19:561-571. [PMID: 31967836 DOI: 10.1021/acs.jproteome.9b00550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
O-Phosphorylation (phosphorylation of the hydroxyl-group of S, T, and Y residues) is among the first described and most thoroughly studied posttranslational modification (PTM). Y-Phosphorylation, catalyzed by Y-kinases, is a key step in both signal transduction and regulation of enzymatic activity in mammalian systems. Canonical Y-kinase sequences are absent from plant genomes/kinomes, often leading to the assumption that plant cells lack O-phospho-l-tyrosine (pY). However, recent improvements in sample preparation, coupled with advances in instrument sensitivity and accessibility, have led to results that unequivocally disproved this assumption. Identification of hundreds of pY-peptides/proteins, followed by validation using genomic, molecular, and biochemical approaches, implies previously unappreciated roles for this "animal PTM" in plants. Herein, we review extant results from studies of pY in plants and propose a strategy for preparation and analysis of pY-peptides that will allow a depth of coverage of the plant pY-proteome comparable to that achieved in mammalian systems.
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Affiliation(s)
- Nagib Ahsan
- Division of Biology and Medicine , Brown University , Providence , Rhode Island 02903 , United States.,Center for Cancer Research Development, Proteomics Core Facility , Rhode Island Hospital , Providence , Rhode Island 02903 , United States
| | - Rashaun S Wilson
- Keck Mass Spectrometry & Proteomics Resource , Yale University , New Haven , Connecticut 06511 , United States
| | - R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center , Yenepoya University , Mangalore 575018 , India
| | - Fernanda Salvato
- Department of Plant and Microbial Biology, College of Agriculture and Life Sciences , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Mercy Sabila
- Department of Biology , Howard University , Washington , D.C. 20059 , United States
| | - Hemayet Ullah
- Department of Biology , Howard University , Washington , D.C. 20059 , United States
| | - Ján A Miernyk
- Division of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
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A polymer monolith composed of a perovskite and cucurbit[6]uril hybrid for highly selective enrichment of phosphopeptides prior to mass spectrometric analysis. Mikrochim Acta 2019; 187:68. [PMID: 31853651 DOI: 10.1007/s00604-019-4054-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022]
Abstract
A hybrid monolith was prepared from perovskite and cucurbit[6]uril [poly(hydroxyethyl methacrylate-pentaerythritol triacrylate) monolith] for the enrichment of phosphopeptides. By coupling with mass spectrometry, three goals were simultaneously realized, viz. (a) selective enrichment of phosphopeptides from non-phosphopeptides, (b) identification of mono- and multi-phosphopeptides, and (c) recognition of tyrosine phosphopeptides. The perovskite introduced into the monolith warrants high selectivity for phosphopeptides even at a high (10,000:1) ratio of non-phosphopeptides to phosphopeptides, and and enables identification of eight mono- and multi-phosphopeptides from standard β-casein tryptic digests. Tyrosine phosphopeptides were specifically detected via the recognition capability of cucurbit[6]uril integrated into the monolith. The method has remarkably specific enrichment capacity for phosphopeptides from samples including human serum, nonfat milk, and human acute myelocytic leukemia cell lysate. Graphical abstractSchematic representation of a monolith integrated with perovskite and cucurbit[6]uril. The monolithic column was coupled with mass spectrometry and applied to the enrichment of phosphopeptides. The method has remarkably specific enrichment capacity for phosphopeptides from complex biological samples.
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Zheng Z, Chu B, Kong Q, Chen X, Ke M, Qin Y, Lu Y, Feng S, Tian R. High-Throughput Phosphotyrosine Protein Complexes Screening by Photoaffinity-Engineered Protein Scaffold-Based Forward-Phase Protein Array. Anal Chem 2019; 91:10026-10032. [PMID: 31282657 DOI: 10.1021/acs.analchem.9b01845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Low-abundance phosphotyrosine (pTyr)-mediated signaling protein complexes play critical roles in cancer signaling. The precise and comprehensive profiling of these pTyr-mediated protein complexes remains challenging because of their dynamic nature and weak binding affinity. Taking advantage of the SH2 domains modified with trifunctional chemical probes and genetic mutations (termed Photo-pTyr-scaffold), we developed a Photo-pTyr-scaffold-based forward-phase protein array that can be used to specifically capture complexes by developing an engineered SH2 domain, photoaffinity cross-linking, and antibody-based measuring weak pTyr-mediated protein complexes from complex biological samples in a 96-well microplate format. This platform demonstrated good precision for quantitation (R2 = 0.99) and high sensitivity by which only 5 μg of whole cell lysates is needed. We successfully applied the technology for profiling the dynamic EGF-stimulation-dependent EGFR signaling protein complexes across four different time courses (i.e., 0, 2, 5, 10, and 30 min) in a high-throughput manner. We further evaluated the modulation of EGFR-GRB2-SHC1 protein complexes by FDA-approved EGFR kinase inhibitor erlotinib, demonstrating the feasibility of this approach for high-throughput drug screening. The Photo-pTyr-scaffold-based forward-phase protein array could be generically applicable for exploring the dynamic pTyr signaling complexes in various biological systems and screening for related drugs in a high-throughput manner.
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Affiliation(s)
- Zhendong Zheng
- Key Laboratory of Oil Gas and Fine Chemicals, Ministry of Education and Xinjiang Uyghur Autonomous Region, College of Chemistry and Chemical Engineering , Xinjiang University , Urumqi 830046 , China.,Department of Chemistry , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Bizhu Chu
- Department of Chemistry , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Qian Kong
- Department of Chemistry , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Xiong Chen
- Department of Chemistry , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Mi Ke
- Department of Chemistry , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Yunqiu Qin
- Department of Chemistry , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Yi Lu
- Key Laboratory of Oil Gas and Fine Chemicals, Ministry of Education and Xinjiang Uyghur Autonomous Region, College of Chemistry and Chemical Engineering , Xinjiang University , Urumqi 830046 , China
| | - Shun Feng
- School of Life Science and Engineering , Southwest Jiaotong University , Chengdu 610031 , China
| | - Ruijun Tian
- Department of Chemistry , Southern University of Science and Technology , Shenzhen 518055 , China.,Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research , Shenzhen 518055 , China
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Núñez C, Chantada-Vázquez MDP, Bravo SB, Vázquez-Estévez S. Novel functionalized nanomaterials for the effective enrichment of proteins and peptides with post-translational modifications. J Proteomics 2018; 181:170-189. [DOI: 10.1016/j.jprot.2018.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
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