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Mitochondrial HSP70 Chaperone System-The Influence of Post-Translational Modifications and Involvement in Human Diseases. Int J Mol Sci 2021; 22:ijms22158077. [PMID: 34360841 PMCID: PMC8347752 DOI: 10.3390/ijms22158077] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/25/2023] Open
Abstract
Since their discovery, heat shock proteins (HSPs) have been identified in all domains of life, which demonstrates their importance and conserved functional role in maintaining protein homeostasis. Mitochondria possess several members of the major HSP sub-families that perform essential tasks for keeping the organelle in a fully functional and healthy state. In humans, the mitochondrial HSP70 chaperone system comprises a central molecular chaperone, mtHSP70 or mortalin (HSPA9), which is actively involved in stabilizing and importing nuclear gene products and in refolding mitochondrial precursor proteins, and three co-chaperones (HSP70-escort protein 1-HEP1, tumorous imaginal disc protein 1-TID-1, and Gro-P like protein E-GRPE), which regulate and accelerate its protein folding functions. In this review, we summarize the roles of mitochondrial molecular chaperones with particular focus on the human mtHsp70 and its co-chaperones, whose deregulated expression, mutations, and post-translational modifications are often considered to be the main cause of neurological disorders, genetic diseases, and malignant growth.
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Wang S, Huang M, Hua J, Wei L, Lin S, Xiao L. Digital counting of single semiconducting polymer nanoparticles for the detection of alkaline phosphatase. NANOSCALE 2021; 13:4946-4955. [PMID: 33629092 DOI: 10.1039/d0nr09232k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Alkaline phosphatase (ALP) as a necessary hydrolase in phosphate metabolism is closely related to various diseases. Ultrasensitive detection of ALP with a convenient and sensitive method is of fundamental importance. In this work, a fluorescence resonance energy transfer (FRET)-based single-particle enumeration (SPE) method is proposed for the quantitative analysis of ALP. This strategy is based on the effective fluorescence suppression by a polydopamine (PDA) shell on the surface of semiconducting polymer nanoparticles (SPNs). PDA with broadband absorption in the UV-vis region can serve as an excellent quencher for SPNs. However, ascorbic acid (AA), the product of the hydrolysis of 2-phosphate-l-ascorbic acid trisodium salt (AAP) in the presence of ALP, can effectively inhibit the self-polymerization of dopamine (DA) to form a PDA layer. Therefore, ALP can be accurately quantified by counting the concentration-related fluorescent particles in the fluorescence image. A linear range from 0.031 to 12.4 μU mL-1 and a limit-of-detection (LOD) of 0.01 μU mL-1 for ALP determination are achieved. The spiked recoveries for ALP determination in a human serum sample are between 90% and 108% with RSD less than 3.1%. In summary, this convenient and sensitive approach proposed here provides promising prospects for ALP detection in a complex biological matrix.
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Affiliation(s)
- Shumin Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China. and State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Mengna Huang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.
| | - Jianhao Hua
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Lin Wei
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.
| | - Shen Lin
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
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Chau DDL, Yung KWY, Chan WWL, An Y, Hao Y, Chan HYE, Ngo JCK, Lau KF. Attenuation of amyloid-β generation by atypical protein kinase C-mediated phosphorylation of engulfment adaptor PTB domain containing 1 threonine 35. FASEB J 2019; 33:12019-12035. [PMID: 31373844 DOI: 10.1096/fj.201802825rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amyloid-β (Aβ) is derived from the proteolytic processing of amyloid precursor protein (APP), and the deposition of extracellular Aβ to form amyloid plaques is a pathologic hallmark of Alzheimer's disease (AD). Although reducing Aβ generation and accumulation has been proposed as a means of treating the disease, adverse side effects and unsatisfactory efficacy have been reported in several clinical trials that sought to lower Aβ levels. Engulfment adaptor phosphotyrosine-binding (PTB) domain containing 1 (GULP1) is a molecular adaptor that has been shown to interact with APP to alter Aβ production. Therefore, the modulation of the GULP1-APP interaction may be an alternative approach to reducing Aβ. However, the mechanisms that regulate GULP1-APP binding remain elusive. As GULP1 is a phosphoprotein, and because phosphorylation is a common mechanism that regulates protein interaction, we anticipated that GULP1 phosphorylation would influence GULP1-APP interaction and thereby Aβ production. We show here that the phosphorylation of GULP1 threonine 35 (T35) reduces GULP1-APP interaction and suppresses the stimulatory effect of GULP1 on APP processing. The residue is phosphorylated by an isoform of atypical PKC (PKCζ). Overexpression of PKCζ reduces both GULP1-APP interaction and GULP1-mediated Aβ generation. Moreover, the activation of PKCζ via insulin suppresses APP processing. In contrast, GULP1-mediated APP processing is enhanced in PKCζ knockout cells. Similarly, PKC ι, another member of atypical PKC, also decreases GULP1-mediated APP processing. Intriguingly, our X-ray crystal structure of GULP1 PTB-APP intracellular domain (AICD) peptide reveals that GULP1 T35 is not located at the GULP1-AICD binding interface; rather, it immediately precedes the β1-α2 loop that forms a portion of the binding groove for the APP helix αC. Phosphorylating the residue may induce an allosteric effect on the conformation of the binding groove. Our results indicate that GULP1 T35 phosphorylation is a mechanism for the regulation of GULP1-APP interaction and thereby APP processing. Moreover, the activation of atypical PKC, such as by insulin, may confer a beneficial effect on AD by lowering GULP1-mediated Aβ production.-Chau, D. D.-L., Yung, K. W.-Y., Chan, W. W.-L., An, Y., Hao, Y., Chan, H.-Y. E., Ngo, J. C.-K., Lau, K.-F. Attenuation of amyloid-β generation by atypical protein kinase C-mediated phosphorylation of engulfment adaptor PTB domain containing 1 threonine 35.
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Affiliation(s)
- Dennis Dik-Long Chau
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kristen Wing-Yu Yung
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - William Wai-Lun Chan
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ying An
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yan Hao
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho-Yin Edwin Chan
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jacky Chi-Ki Ngo
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwok-Fai Lau
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Identification of Phosphorylated Cyclin-Dependent Kinase 1 Associated with Colorectal Cancer Survival Using Label-Free Quantitative Analyses. PLoS One 2016; 11:e0158844. [PMID: 27383761 PMCID: PMC4934865 DOI: 10.1371/journal.pone.0158844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 06/22/2016] [Indexed: 01/16/2023] Open
Abstract
Colorectal cancer is the most common form of cancer in the world, and the five-year survival rate is estimated to be almost 90% in the early stages. Therefore, the identification of potential biomarkers to assess the prognosis of early stage colorectal cancer patients is critical for further clinical treatment. Dysregulated tyrosine phosphorylation has been found in several diseases that play a significant regulator of signaling in cellular pathways. In this study, this strategy was used to characterize the tyrosine phosphoproteome of colorectal cell lines with different progression abilities (SW480 and SW620). We identified a total of 280 phosphotyrosine (pTyr) peptides comprising 287 pTyr sites from 261 proteins. Label-free quantitative analysis revealed the differential level of a total of 103 pTyr peptides between SW480 and SW620 cells. We showed that cyclin-dependent kinase I (CDK1) pTyr15 level in SW480 cells was 3.3-fold greater than in SW620 cells, and these data corresponded with the label-free mass spectrometry-based proteomic quantification analysis. High level CDK1 pTyr15 was associated with prolonged disease-free survival for stage II colorectal cancer patients (n = 79). Taken together, our results suggest that the CDK1 pTyr15 protein is a potential indicator of the progression of colorectal cancer.
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Liu NY, Lee HH, Chang ZF, Tsay YG. Examination of segmental average mass spectra from liquid chromatography-tandem mass spectrometric (LC-MS/MS) data enables screening of multiple types of protein modifications. Anal Chim Acta 2015; 892:115-22. [PMID: 26388481 DOI: 10.1016/j.aca.2015.07.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/13/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023]
Abstract
It has been observed that a modified peptide and its non-modified counterpart, when analyzed with reverse phase liquid chromatography, usually share a very similar elution property [1-3]. Inasmuch as this property is common to many different types of protein modifications, we propose an informatics-based approach, featuring the generation of segmental average mass spectra ((sa)MS), that is capable of locating different types of modified peptides in two-dimensional liquid chromatography-mass spectrometric (LC-MS) data collected for regular protease digests from proteins in gels or solutions. To enable the localization of these peptides in the LC-MS map, we have implemented a set of computer programs, or the (sa)MS package, that perform the needed functions, including generating a complete set of segmental average mass spectra, compiling the peptide inventory from the Sequest/TurboSequest results, searching modified peptide candidates and annotating a tandem mass spectrum for final verification. Using ROCK2 as an example, our programs were applied to identify multiple types of modified peptides, such as phosphorylated and hexosylated ones, which particularly include those peptides that could have been ignored due to their peculiar fragmentation patterns and consequent low search scores. Hence, we demonstrate that, when complemented with peptide search algorithms, our approach and the entailed computer programs can add the sequence information needed for bolstering the confidence of data interpretation by the present analytical platforms and facilitate the mining of protein modification information out of complicated LC-MS/MS data.
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Affiliation(s)
- Nai-Yu Liu
- Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Hsiao-Hui Lee
- Department of Life Science & Institute of Genome Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Zee-Fen Chang
- Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yeou-Guang Tsay
- Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan; Proteomics Research Center, National Yang-Ming University, Taipei, 112, Taiwan.
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Wei SC, Fattet L, Tsai JH, Guo Y, Pai VH, Majeski HE, Chen AC, Sah RL, Taylor SS, Engler AJ, Yang J. Matrix stiffness drives epithelial-mesenchymal transition and tumour metastasis through a TWIST1-G3BP2 mechanotransduction pathway. Nat Cell Biol 2015; 17:678-88. [PMID: 25893917 PMCID: PMC4452027 DOI: 10.1038/ncb3157] [Citation(s) in RCA: 625] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/11/2015] [Indexed: 12/15/2022]
Abstract
Matrix stiffness potently regulates cellular behaviour in various biological contexts. In breast tumours, the presence of dense clusters of collagen fibrils indicates increased matrix stiffness and correlates with poor survival. It is unclear how mechanical inputs are transduced into transcriptional outputs to drive tumour progression. Here we report that TWIST1 is an essential mechanomediator that promotes epithelial-mesenchymal transition (EMT) in response to increasing matrix stiffness. High matrix stiffness promotes nuclear translocation of TWIST1 by releasing TWIST1 from its cytoplasmic binding partner G3BP2. Loss of G3BP2 leads to constitutive TWIST1 nuclear localization and synergizes with increasing matrix stiffness to induce EMT and promote tumour invasion and metastasis. In human breast tumours, collagen fibre alignment, a marker of increasing matrix stiffness, and reduced expression of G3BP2 together predict poor survival. Our findings reveal a TWIST1-G3BP2 mechanotransduction pathway that responds to biomechanical signals from the tumour microenvironment to drive EMT, invasion and metastasis.
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Affiliation(s)
- Spencer C Wei
- 1] Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA [2] The Biomedical Sciences Graduate Program, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Laurent Fattet
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Jeff H Tsai
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Yurong Guo
- Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Vincent H Pai
- 1] Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA [2] The Biomedical Sciences Graduate Program, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Hannah E Majeski
- 1] Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA [2] The Biomedical Sciences Graduate Program, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Albert C Chen
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Robert L Sah
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Susan S Taylor
- 1] Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA [2] Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA [3] Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
| | - Jing Yang
- 1] Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA [2] Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive La Jolla, California 92093-0819, USA
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Automatisierte Detektion von Proteinphosphorylierung durch Nanoliter-Enzymreaktionen auf Mikroarrays. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Screening for protein phosphorylation using nanoscale reactions on microdroplet arrays. Angew Chem Int Ed Engl 2014; 54:1671-5. [PMID: 25504774 DOI: 10.1002/anie.201409440] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/25/2022]
Abstract
We present a novel and straightforward screening method to detect protein phosphorylations in complex protein mixtures. A proteolytic digest is separated by a conventional nanoscale liquid chromatography (nano-LC) separation and the eluate is immediately compartmentalized into microdroplets, which are spotted on a microarray MALDI plate. Subsequently, the enzyme alkaline phosphatase is applied to every second microarray spot to remove the phosphate groups from phosphorylated peptides, which results in a mass shift of n×-80 Da. The MALDI-MS scan of the microarray is then evaluated by a software algorithm to automatically identify the phosphorylated peptides by exploiting the characteristic chromatographic peak profile induced by the phosphatase treatment. This screening method does not require extensive MS/MS experiments or peak list evaluation and can be easily extended to other enzymatic or chemical reactions.
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Affiliation(s)
- Simon K Küster
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich (Switzerland)
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Yang TH, Chang HT, Hsiao ES, Sun JL, Wang CC, Wu HY, Liao PC, Wu WS. iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation. BMC Bioinformatics 2014; 15 Suppl 16:S10. [PMID: 25521246 PMCID: PMC4290636 DOI: 10.1186/1471-2105-15-s16-s10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Background Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research. But the low abundance of phosphopeptides among the total proteome in cells remains an obstacle in mass spectrometry-based proteomic analysis. To provide a solution, an alternative analytic strategy to confidently identify phosphorylated peptides by using the alkaline phosphatase (AP) treatment combined with high-resolution mass spectrometry was provided. While the process is applicable, the key integration along the pipeline was mostly done by tedious manual work. Results We developed a software toolkit, iPhos, to facilitate and streamline the work-flow of AP-assisted phosphoproteome characterization. The iPhos tookit includes one assister and three modules. The iPhos Peak Extraction Assister automates the batch mode peak extraction for multiple liquid chromatography mass spectrometry (LC-MS) runs. iPhos Module-1 can process the peak lists extracted from the LC-MS analyses derived from the original and dephosphorylated samples to mine out potential phosphorylated peptide signals based on mass shift caused by the loss of some multiples of phosphate groups. And iPhos Module-2 provides customized inclusion lists with peak retention time windows for subsequent targeted LC-MS/MS experiments. Finally, iPhos Module-3 facilitates to link the peptide identifications from protein search engines to the quantification results from pattern-based label-free quantification tools. We further demonstrated the utility of the iPhos toolkit on the data of human metastatic lung cancer cells (CL1-5). Conclusions In the comparison study of the control group of CL1-5 cell lysates and the treatment group of dasatinib-treated CL1-5 cell lysates, we demonstrated the applicability of the iPhos toolkit and reported the experimental results based on the iPhos-facilitated phosphoproteome investigation. And further, we also compared the strategy with pure DDA-based LC-MS/MS phosphoproteome investigation. The results of iPhos-facilitated targeted LC-MS/MS analysis convey more thorough and confident phosphopeptide identification than the results of pure DDA-based analysis.
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Wang MC, Lee YH, Liao PC. Optimization of titanium dioxide and immunoaffinity-based enrichment procedures for tyrosine phosphopeptide using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Bioanal Chem 2014; 407:1343-56. [PMID: 25486920 DOI: 10.1007/s00216-014-8352-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 11/06/2014] [Accepted: 11/17/2014] [Indexed: 01/25/2023]
Abstract
Tyrosine phosphorylation is an important regulator of signaling in cellular pathways, and dysregulated tyrosine phosphorylation causes several diseases. Mass spectrometry has revealed the importance of global phosphoproteomic characterization. Analysis of tyrosine phosphorylation by studying the mass-spectrometry (MS)-determined phosphoproteome remains difficult because of the relatively low abundance of tyrosine phosphoproteins. To effectively evaluate tyrosine-phosphopeptide enrichment and reduce ion suppression from non-phosphorylated peptides in MS analysis, three trypsin-digested BSA peptides and 14 standard phosphopeptides, including six tyrosine phosphopeptides, four serine phosphopeptides, and four threonine phosphopeptides, were subjected to titanium dioxide immunoaffinity-based enrichment and also to combined enrichment using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-mass spectrometry (LC-MS) analyses. The enrichment factors were evaluated to determine the efficiency of each enrichment procedure. Comparison of five optimized enrichment methods, including TiO2-based immunoaffinity purification in Tris and MOPS buffer systems, TiO2-immunoaffinity enrichment, and immunoaffinity-TiO2 enrichment for total tyrosine, serine and threonine phosphopeptides, revealed that the order of the enrichment factors for total tyrosine phosphopeptides is: (i) immunoaffinity-TiO2 (enrichment factor = 38,244), (ii) TiO2-immunoaffinity (enrichment factor = 24,987), (iii) TiO2 micro-column (enrichment factor = 10,305), (iv) immunoaffinity in Tris buffer system (enrichment factor = 1450), and (v) immunoaffinity in the MOPS buffer system (enrichment factor = 32). These results reveal that an alternative enrichment scheme before use of a TiO2 micro-column, using immunoaffinity 4G10 and PY99 antibody enrichment under optimized conditions, can provide greater selectivity for tyrosine-phosphopeptide enrichment.
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Affiliation(s)
- Ming-Chuan Wang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan, 70428, Taiwan, Republic of China
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Mitulović G. New HPLC Techniques for Proteomics Analysis: A Short Overview of Latest Developments. J LIQ CHROMATOGR R T 2014. [DOI: 10.1080/10826076.2014.941266] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Goran Mitulović
- a Clinical Institute of Laboratory Medicine and Proteomics Core Facility , Medical University of Vienna , Wien , Austria
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Chen CJ, Lai CC, Tseng MC, Liu YC, Liu YH, Chiou LW, Tsai FJ. A novel titanium dioxide-polydimethylsiloxane plate for phosphopeptide enrichment and mass spectrometry analysis. Anal Chim Acta 2014; 812:105-13. [DOI: 10.1016/j.aca.2014.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/25/2013] [Accepted: 01/06/2014] [Indexed: 01/01/2023]
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Yalak G, Vogel V. Extracellular phosphorylation and phosphorylated proteins: not just curiosities but physiologically important. Sci Signal 2012; 5:re7. [PMID: 23250399 DOI: 10.1126/scisignal.2003273] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mining of the literature and high-throughput mass spectrometry data from both healthy and diseased tissues and from body fluids reveals evidence that various extracellular proteins can exist in phosphorylated states. Extracellular kinases and phosphatases (ectokinases and ectophosphatases) are active in extracellular spaces during times of sufficiently high concentrations of adenosine triphosphate. There is evidence for a role of extracellular phosphorylation in various physiological functions, including blood coagulation, immune cell activation, and the formation of neuronal networks. Ectokinase activity is increased in some diseases, including cancer, Alzheimer's disease, and some microbial infections. We summarize the literature supporting the physiological and pathological roles of extracellularly localized protein kinases, protein phosphatases, and phosphorylated proteins and provide an analysis of the available mass spectrometry data to annotate potential extracellular phosphorylated proteins.
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Affiliation(s)
- Garif Yalak
- Department of Health Sciences and Technology, ETH Zurich, Wolfgang Pauli Strasse 10, HCI F443, CH-8093 Zurich, Switzerland
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Choi H, Lee S, Jun CD, Park ZY. Development of an off-line capillary column IMAC phosphopeptide enrichment method for label-free phosphorylation relative quantification. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:2991-7. [PMID: 21930439 DOI: 10.1016/j.jchromb.2011.08.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 07/29/2011] [Accepted: 08/24/2011] [Indexed: 11/26/2022]
Abstract
Immobilized metal affinity chromatography (IMAC) and metal oxide type affinity chromatography (MOAC) techniques have been widely used for mass spectrometry-based phosphorylation analysis. Unlike MOAC techniques, IMAC requires rather complete removals of buffering reagents, salts and high concentrations of denaturant prior to sample loading in order for the successful enrichment of phosphopeptides. In this study, a simple off-line capillary column-based IMAC phosphopeptide enrichment method can shorten sample preparation time by eliminating the speed-vac step from the desalting process. Tryptic digest peptide samples containing 2M urea can be directly processed and the entire IMAC procedure can be completed within 6 h. When tryptic digest peptide samples prepared from mouse whole brain tissues were analyzed using our method, an average of 249 phosphoproteins and 463 unique phosphopeptides were identified from single 2-h RPLC-MS/MS analysis (~88% specificity). An additional advantage of this method is the significantly improved reproducibility of the phosphopeptide enrichment results. When four independent phosphopeptide enrichment experiments were carried out, the peak areas of phosphopeptides identified among four enrichment experiments were relatively similar (less than 16.2% relative standard dev.). Because of this increased reproducibility, relative phosphorylation quantification analysis of major phosphoproteins appears to be feasible without the need for stable isotope labeling techniques.
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Affiliation(s)
- Hyunwoo Choi
- School of Life Sciences, Gwangju Institute of Science & Technology, 1 Oryong-Dong, Buk-Gu, Gwangju 500-712, Republic of Korea
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Wu HY, Tseng VS, Chen LC, Chang HY, Chuang IC, Tsay YG, Liao PC. Identification of Tyrosine-Phosphorylated Proteins Associated with Lung Cancer Metastasis using Label-Free Quantitative Analyses. J Proteome Res 2010; 9:4102-12. [DOI: 10.1021/pr1006153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hsin-Yi Wu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, Institute of Information Science, Academia Sinica, Taipei, Taiwan, Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, and Institute of Medical Informatics, National Cheng Kung
| | - Vincent S. Tseng
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, Institute of Information Science, Academia Sinica, Taipei, Taiwan, Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, and Institute of Medical Informatics, National Cheng Kung
| | - Lien-Chin Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, Institute of Information Science, Academia Sinica, Taipei, Taiwan, Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, and Institute of Medical Informatics, National Cheng Kung
| | - Hui-Yin Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, Institute of Information Science, Academia Sinica, Taipei, Taiwan, Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, and Institute of Medical Informatics, National Cheng Kung
| | - I-Chi Chuang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, Institute of Information Science, Academia Sinica, Taipei, Taiwan, Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, and Institute of Medical Informatics, National Cheng Kung
| | - Yeou-Guang Tsay
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, Institute of Information Science, Academia Sinica, Taipei, Taiwan, Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, and Institute of Medical Informatics, National Cheng Kung
| | - Pao-Chi Liao
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, Institute of Information Science, Academia Sinica, Taipei, Taiwan, Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, and Institute of Medical Informatics, National Cheng Kung
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