101
|
Abstract
The traditional sample preparation workflow for mass spectrometry (MS)-based phosphoproteomics is time consuming and usually requires multiple steps, e.g., lysis, protein precipitation, reduction, alkylation, digestion, fractionation, and phosphopeptide enrichment. Each step can introduce chemical artifacts, in vitro protein and peptide modifications, and contaminations. Those often result in sample loss and affect the sensitivity, dynamic range and accuracy of the mass spectrometric analysis. Here we describe a simple and reproducible phosphoproteomics protocol, where lysis, denaturation, reduction, and alkylation are performed in a single step, thus reducing sample loss and increasing reproducibility. Moreover, unlike standard cell lysis procedures the cell harvesting is performed at high temperatures (99 °C) and without detergents and subsequent need for protein precipitation. Phosphopeptides are enriched using TiO2 beads and the orbitrap mass spectrometer is operated in a sensitive mode with higher energy collisional dissociation (HCD).
Collapse
Affiliation(s)
- Rosa R Jersie-Christensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Abida Sultan
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark.
| |
Collapse
|
102
|
Abstract
Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture.
Collapse
Affiliation(s)
- Tine E Thingholm
- Division of Translational Cancer Research, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark.
| |
Collapse
|
103
|
Thingholm TE, Larsen MR. Sequential Elution from IMAC (SIMAC): An Efficient Method for Enrichment and Separation of Mono- and Multi-phosphorylated Peptides. Methods Mol Biol 2016; 1355:147-160. [PMID: 26584924 DOI: 10.1007/978-1-4939-3049-4_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Phosphoproteomics relies on methods for efficient purification and sequencing of phosphopeptides from highly complex biological systems, especially when using low amounts of starting material. Current methods for phosphopeptide enrichment, e.g., Immobilized Metal ion Affinity Chromatography and titanium dioxide chromatography provide varying degrees of selectivity and specificity for phosphopeptide enrichment. The number of multi-phosphorylated peptides identified in most published studies is rather low. Here we describe a protocol for a strategy that separates mono-phosphorylated peptides from multiply phosphorylated peptides using Sequential elution from Immobilized Metal ion Affinity Chromatography. The method relies on the initial enrichment and separation of mono- and multi-phosphorylated peptides using Immobilized Metal ion Affinity Chromatography and a subsequent enrichment of the mono-phosphorylated peptides using titanium dioxide chromatography. The two separate phosphopeptide fractions are then subsequently analyzed by mass spectrometric methods optimized for mono-phosphorylated and multi-phosphorylated peptides, respectively, resulting in improved identification of especially multi-phosphorylated peptides from a minimum amount of starting material.
Collapse
Affiliation(s)
- Tine E Thingholm
- Division of Translational Cancer Research, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
| |
Collapse
|
104
|
Abstract
Titanium dioxide (TiO2) has very high affinity for phosphopeptides and in recent years it has become one of the most popular methods for phosphopeptide enrichment from complex biological samples. Peptide loading onto TiO2 resin in a highly acidic environment in the presence of 2,5-dihydroxybenzoic acid (DHB), phthalic acid, lactic acid, or glycolic acid has been shown to improve selectivity significantly by reducing unspecific binding of non-phosphorylated peptides. The phosphopeptides bound to the TiO2 are subsequently eluted from the chromatographic material using an alkaline buffer. TiO2 chromatography is extremely tolerant towards most buffers used in biological experiments, highly robust and as such it has become the method of choice in large-scale phosphoproteomics. Here we describe a batch mode protocol for phosphopeptide enrichment using TiO2 chromatographic material followed by desalting and concentration of the sample by reversed phase micro-columns prior to downstream MS and LC-MS/MS analysis.
Collapse
Affiliation(s)
- Tine E Thingholm
- Division of Translational Cancer Research, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
| |
Collapse
|
105
|
Abstract
Magnetic nanocomposites are hybrid structures consisting of an iron oxide (Fe3O4/γ-Fe2O3) superparamagnetic core and a coating shell which presents affinity for a specific target molecule. Within the scope of phosphopeptide enrichment, the magnetic core is usually first functionalized with an intermediate layer of silica or carbon to improve dispersibility and increase specific area, and then with an outer layer of a phosphate-affinity material. Fe3O4-coating materials include metal oxides, rare earth metal-based compounds, immobilized-metal ions, polymers, and many others. This chapter provides a generic overview of the different materials that can be found in literature and their advantages and drawbacks.
Collapse
Affiliation(s)
- Íris L Batalha
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK.
| | - Ana Cecília A Roque
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| |
Collapse
|
106
|
Abstract
Reversible protein phosphorylation plays essential roles in coordinating cell division and many other biological processes. Cell cycle regulation by opposing kinase and protein phosphatase activities is often complex and major challenges exist in identifying the direct substrates of these enzymes and the specific sites at which they act. While cell cycle kinases are known to exhibit strict substrate specificities important for coordinating the complex events of cell division, phosphatases have only recently been recognized to exert similarly precise regulatory control over cell cycle events through timely dephosphorylation of specific substrates. The molecular determinants for substrate recognition by many phosphatases that function in cell division are still poorly delineated. To understand phosphatase specificity, it is critical to employ methods that monitor the dephosphorylation of individual phosphorylation sites on physiologically relevant substrates. Here, using the cell cycle phosphatase Cdc14 as an example, we describe two methods for studying phosphatase specificity, one using synthetic phosphopeptide substrates and the other using intact phosphoprotein substrates. These methods are useful for targeted characterization of small substrate sets and are also adaptable to large-scale applications for global specificity studies.
Collapse
Affiliation(s)
- Brendan L Powers
- Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | | | | |
Collapse
|
107
|
Abstract
In recent years, mass spectrometry-based phosphoproteomics has propelled our knowledge about the regulation of cellular pathways. Nevertheless, typically applied bottom-up strategies have several limitations. Trypsin, the preferentially used proteolytic enzyme shows impaired cleavage efficiency in the vicinity of phosphorylation sites. Moreover, depending on the frequency and distribution of tryptic cleavage sites (Arg/Lys), generated peptides can be either too short or too long for confident identification using standard LC-MS approaches. To overcome these limitations, we introduce an alternative and simple approach based on the usage of the nonspecific serine protease subtilisin, which enables a fast and reproducible digestion and provides access to "hidden" areas of the proteome. Thus, in a single LC-MS experiment >1800 phosphopeptides were confidently identified and localized from 125 μg of HeLa digest, compared to >2100 sites after tryptic digestion. While the overlap was less than 20 %, subtilisin allowed the identification of many phosphorylation sites that are theoretically not accessible via tryptic digestion, thus considerably increasing the coverage of the phosphoproteome.
Collapse
Affiliation(s)
- Humberto Gonczarowska-Jorge
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- CAPES Foundation, Ministry of Education of Brazil, Caixa Postal 250, Brasília - DF, 70040-020, Brazil
| | - Margherita Dell'Aica
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Clarissa Dickhut
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.
| |
Collapse
|
108
|
Shi J, Yuan D, Haburcak R, Zhang Q, Zhao C, Zhang X, Xu B. Enzymatic Dissolution of Biocomposite Solids Consisting of Phosphopeptides to Form Supramolecular Hydrogels. Chemistry 2015; 21:18047-51. [PMID: 26462722 PMCID: PMC4743537 DOI: 10.1002/chem.201504087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Indexed: 11/06/2022]
Abstract
Enzyme-catalyzed dephosphorylation is essential for biomineralization and bone metabolism. Here we report the exploration of using enzymatic reaction to transform biocomposites of phosphopeptides and calcium (or strontium) ions to supramolecular hydrogels as a mimic of enzymatic dissolution of biominerals. (31) P NMR shows that strong affinity between the phosphopeptides and alkaline metal ions (e.g., Ca(2+) or Sr(2+) ) induces the formation of biocomposites as precipitates. Electron microscopy reveals that the enzymatic reaction regulates the morphological transition from particles to nanofibers. Rheology confirms the formation of a rigid hydrogel. As the first example of enzyme-instructed dissolution of a solid to form supramolecular nanofibers/hydrogels, this work provides an approach to generate soft materials with desired properties, expands the application of supramolecular hydrogelators, and offers insights to control the demineralization of calcified soft tissues.
Collapse
Affiliation(s)
- Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA), Fax: (+1) 781-736-2516
| | - Dan Yuan
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA), Fax: (+1) 781-736-2516
| | - Richard Haburcak
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA), Fax: (+1) 781-736-2516
| | - Qiang Zhang
- Division of Physical Science & Engineering and Core Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia)
| | - Chao Zhao
- Division of Physical Science & Engineering and Core Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia)
| | - Xixiang Zhang
- Division of Physical Science & Engineering and Core Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia)
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA), Fax: (+1) 781-736-2516.
| |
Collapse
|
109
|
Chen Y, Xiong Z, Peng L, Gan Y, Zhao Y, Shen J, Qian J, Zhang L, Zhang W. Facile Preparation of Core-Shell Magnetic Metal-Organic Framework Nanoparticles for the Selective Capture of Phosphopeptides. ACS Appl Mater Interfaces 2015; 7:16338-16347. [PMID: 26156207 DOI: 10.1021/acsami.5b03335] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In regard to the phosphoproteome, highly specific and efficient capture of heteroideous kinds of phosphopeptides from intricate biological sample attaches great significance to comprehensive and in-depth phosphorylated proteomics research. However, until now, it has been a challenge. In this study, a new-fashioned porous immobilized metal ion affinity chromatography (IMAC) material was designed and fabricated to promote the selectivity and detection limit for phosphopeptides by covering a metal-organic frameworks (MOFs) shell onto Fe3O4 nanoparticles, taking advantage of layer-by-layer method (the synthesized nanoparticle denoted as Fe3O4@MIL-100 (Fe)). The thick layer renders the nanoparticles with perfect hydrophilic character, super large surface area, large immobilization of the Fe(3+) ions and the special porous structure. Specifically, the as-synthesized MOF-decorated magnetic nanoparticles own an ultra large surface area which is up to 168.66 m(2) g(-1) as well as two appropriate pore sizes of 1.93 and 3.91 nm with a narrow grain-size distribution and rapid separation under the magnetic circumstance. The unique features vested the synthesized nanoparticles an excellent ability for phosphopeptides enrichment with high selectivity for β-casein (molar ratio of β-casein/BSA, 1:500), large enrichment capacity (60 mg g(-1)), low detection limit (0.5 fmol), excellent phosphopeptides recovery (above 84.47%), fine size-exclusion of high molecular weight proteins, good reusability, and desirable batch-to-batch repeatability. Furthermore, encouraged by the experimental results, we successfully performed the as-prepared porous IMAC nanoparticle in the specific capture of phosphopeptides from the human serum (both the healthy and unhealthy) and nonfat milk, which proves itself to be a good candidate for the enrichment and detection of the low-abundant phosphopeptides from complicated biological samples.
Collapse
Affiliation(s)
- Yajing Chen
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhichao Xiong
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Li Peng
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yangyang Gan
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yiman Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jie Shen
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Junhong Qian
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lingyi Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
110
|
García-Nebot MJ, Alegría A, Barberá R, Gaboriau F, Bouhallab S. Effect of Caseinophosphopeptides from αs- and β-Casein on Iron Bioavailability in HuH7 Cells. J Agric Food Chem 2015; 63:6757-6763. [PMID: 26154705 DOI: 10.1021/acs.jafc.5b02424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two pools of caseinophosphopeptides (CPPs) obtained from αs- and β-casein fractions (α-CPPs and β-CPPs) were characterized. A total of 16 CPPs were identified in the α-CPPs pool, 9 of them derived from αs1-casein and 7 from αs2-casein. A total of 18 CPPs were identified in the β-CPPs pool. Four of the identified CPPs contained the characteristic phosphoseryl-glutamic acid cluster SpSpSpEE. Calcein assay was used to compare the iron-binding capacity of the α- and β-CPPs pools. At the concentration of 12.5 μM CPPs used in the iron bioavailability assays, β-CPPs pools show greater iron-binding capacity than α-CPPs pools. HuH7 human hepatoma cells show many differentiated functions of liver cells in vivo and can be used to evaluate iron bioavailability (ferritin content and soluble transferrin receptor) from Fe-α-CPPs and Fe-β-CPPs complexes. The α-CPPs and β-CPPs pools did not improve ferritin content or soluble transferrin receptor in HuH7 cells.
Collapse
Affiliation(s)
- María José García-Nebot
- †Nutrition and Food Chemistry, Faculty of Pharmacy, University of Valencia, Avenida Vicente Andrés Estellés s/n, 46100 Burjassot (Valencia), Spain
| | - Amparo Alegría
- †Nutrition and Food Chemistry, Faculty of Pharmacy, University of Valencia, Avenida Vicente Andrés Estellés s/n, 46100 Burjassot (Valencia), Spain
| | - Reyes Barberá
- †Nutrition and Food Chemistry, Faculty of Pharmacy, University of Valencia, Avenida Vicente Andrés Estellés s/n, 46100 Burjassot (Valencia), Spain
| | - François Gaboriau
- §INSERM, UMR991, Université de Rennes 1, Hôpital Pontchaillou, 2 Avenue Henri le Guilloux, F-35033 Rennes Cedex, France
| | | |
Collapse
|
111
|
Kim JH, Ku B, Lee KS, Kim SJ. Structural analysis of the polo-box domain of human Polo-like kinase 2. Proteins 2015; 83:1201-8. [PMID: 25846005 PMCID: PMC7720676 DOI: 10.1002/prot.24804] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/03/2015] [Accepted: 03/20/2015] [Indexed: 12/25/2022]
Abstract
Polo-like kinases (Plks) are the key regulators of cell cycle progression, the members of which share a kinase domain and a polo-box domain (PBD) that serves as a protein-binding module. While Plk1 is a promising target for antitumor therapy, Plk2 is regarded as a tumor suppressor even though the two Plks commonly recognize the S-pS/T-P motif through their PBD. Herein, we report the crystal structure of the PBD of Plk2 at 2.7 Å. Despite the overall structural similarity with that of Plk1 reflecting their high sequence homology, the crystal structure also contains its own features including the highly ordered loop connecting two subdomains and the absence of 310 -helices in the N-terminal region unlike the PBD of Plk1. Based on the three-dimensional structure, we furthermore could model its interaction with two types of phosphopeptides, one of which was previously screened as the optimal peptide for the PBD of Plk2.
Collapse
Affiliation(s)
- Ju Hee Kim
- Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Bonsu Ku
- Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Kyung S. Lee
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Seung Jun Kim
- Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| |
Collapse
|
112
|
Brown R, Stuart SA, Houel S, Ahn NG, Old WM. Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation. J Am Soc Mass Spectrom 2015; 26:1128-42. [PMID: 25851653 PMCID: PMC4509682 DOI: 10.1007/s13361-015-1109-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 05/14/2023]
Abstract
Collision-induced dissociation (CID) remains the predominant mass spectrometry-based method for identifying phosphorylation sites in complex mixtures. Unfortunately, the gas-phase reactivity of phosphoester bonds results in MS/MS spectra dominated by phosphoric acid (H3PO4) neutral loss events, suppressing informative peptide backbone cleavages. To understand the major drivers of H3PO4 neutral loss, we performed robust nonparametric statistical analysis of local and distal sequence effects on the magnitude and variability of neutral loss, using a collection of over 35,000 unique phosphopeptide MS/MS spectra. In contrast to peptide amide dissociation pathways, which are strongly influenced by adjacent amino acid side chains, we find that neutral loss of H3PO4 is affected by both proximal and distal sites, most notably basic residues and the peptide N-terminal primary amine. Previous studies have suggested that protonated basic residues catalyze neutral loss through direct interactions with the phosphate. In contrast, we find that nearby basic groups decrease neutral loss regardless of mobility class, an effect only seen by stratifying spectra by charge-mobility. The most inhibitory bases are those immediately N-terminal to the phosphate, presumably because of steric hindrances in catalyzing neutral loss. Further evidence of steric effects is shown by the presence of proline, which can dramatically reduce the presence of neutral loss when between the phosphate and a possible charge donor. In mobile proton spectra, the N-terminus is the strongest predictor of high neutral loss, with proximity to the N-terminus essential for peptides to exhibit the highest levels of neutral loss.
Collapse
Affiliation(s)
- Robert Brown
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Scott A. Stuart
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | | | - Natalie G. Ahn
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309
| | - William M. Old
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
- Corresponding author: William M. Old, Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, Phone: 303-492-5519, Fax: 303-492-2439,
| |
Collapse
|
113
|
Wijeratne AB, Wijesundera DN, Paulose M, Ahiabu IB, Chu WK, Varghese OK, Greis KD. Phosphopeptide separation using radially aligned titania nanotubes on titanium wire. ACS Appl Mater Interfaces 2015; 7:11155-64. [PMID: 25941752 DOI: 10.1021/acsami.5b00799] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Phosphoproteomic analysis offers a unique view of cellular function and regulation in biological systems by providing global measures of a key cellular regulator in the form of protein phosphorylation. Understanding the phosphorylation changes between normal and diseased cells or tissues offers a window into the mechanism of disease and thus potential targets for therapeutic intervention. A key step in these studies is the enrichment of phosphorylated peptides that are typically separated and analyzed by using liquid chromatography mass spectrometry. The mesoporous titania beads/particles (e.g., Titansphere TiO2 beads from GL Sciences Inc., Japan) that are widely used for phosphopeptide enrichment are expensive and offer very limited opportunities for further performance improvement. Titiania nanotube arrays have shown promising characteristics for phosphopeptide separation. Here we report a proof-of-concept study to evaluate the efficacy of nanotubes on Ti-wire for phosphoproteomics research. We used titania nanotubes radially grown on titanium wires as well as the commercial beads to separate phosphopeptides generated from mouse liver complex tissue extracts. Our studies revealed that the nanotubes on metal wire provide comparable efficacy for enrichment of phophopeptides and offer an ease of use advantage versus mesoporous beads, thus having the potential to become a low cost and more practical material/methodology for phosphopeptide enrichment in biological studies.
Collapse
Affiliation(s)
- Aruna B Wijeratne
- †Department of Cancer Biology, The University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States
| | | | | | | | | | | | - Kenneth D Greis
- †Department of Cancer Biology, The University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States
| |
Collapse
|
114
|
Kim D, Pai PJ, Creese AJ, Jones AW, Russell DH, Cooper HJ. Probing the electron capture dissociation mass spectrometry of phosphopeptides with traveling wave ion mobility spectrometry and molecular dynamics simulations. J Am Soc Mass Spectrom 2015; 26:1004-13. [PMID: 25832028 PMCID: PMC4422852 DOI: 10.1007/s13361-015-1094-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/05/2015] [Accepted: 02/05/2015] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation mass spectrometry offers several advantages for the analysis of peptides, most notably that backbone c and z fragments typically retain labile modifications such as phosphorylation. We have shown previously that, in some cases, the presence of phosphorylation has a deleterious effect on peptide sequence coverage, and hypothesized that intramolecular interactions involving the phosphate group were preventing separation of backbone fragments. In the present work, we seek to rationalize the observed ECD behavior through a combination of ECD of model peptides, traveling wave ion mobility mass spectrometry and molecular dynamics simulations. The results suggest that for doubly protonated ions of phosphopeptide APLpSFRGSLPKSYVK a salt-bridge structure is favored, whereas for the doubly-protonated ions of APLSFRGSLPKpSYVK ionic hydrogen bonds predominate.
Collapse
Affiliation(s)
- Doyong Kim
- Department of Chemistry, Texas A&M University, College Station, TX 77840 USA
| | - Pei-Jing Pai
- Department of Chemistry, Texas A&M University, College Station, TX 77840 USA
| | - Andrew J. Creese
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Andrew W. Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77840 USA
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| |
Collapse
|
115
|
Krásný L, Pompach P, Strnadová M, Hynek R, Vališ K, Havlíček V, Novák P, Volný M. High-throughput workflow for identification of phosphorylated peptides by LC-MALDI-TOF/TOF-MS coupled to in situ enrichment on MALDI plates functionalized by ion landing. J Mass Spectrom 2015; 50:802-811. [PMID: 26169134 DOI: 10.1002/jms.3586] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 06/04/2023]
Abstract
We report an MS-based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high-throughput sample analysis. The workflow is based on an in situ enrichment on matrix-assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO2 using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO2 into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high-performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn-based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal-to-noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12-myristate 13-acetate. These phosphorylations concerned the mitogen-activated protein kinase/extracellular signal-regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non-activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high-performance liquid chromatography gradient.
Collapse
Affiliation(s)
- Lukáš Krásný
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Institute of Chemical Technology, Technická 5, Prague, 16628, Czech Republic
| | - Petr Pompach
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Marcela Strnadová
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Radovan Hynek
- Institute of Chemical Technology, Technická 5, Prague, 16628, Czech Republic
| | - Karel Vališ
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Vladimír Havlíček
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, 17.listopadu 12, Olomouc, 771 46, Czech Republic
| | - Petr Novák
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Michael Volný
- Applied Physics Laboratory, University of Washington, 1013 NE 40th St, Seattle, WA, 98105, USA
| |
Collapse
|
116
|
Schönberg A, Baginsky S. The Peptide Microarray ChloroPhos1.0: A Screening Tool for the Identification of Arabidopsis thaliana Chloroplast Protein Kinase Substrates. Methods Mol Biol 2015; 1306:147-57. [PMID: 25930700 DOI: 10.1007/978-1-4939-2648-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
We designed the peptide microarray ChloroPhos1.0 to screen for substrates of chloroplast protein kinases. The peptides represented on the microarray were selected from phosphoproteomics data, and the identified chloroplast phosphopeptides were spotted as 15-mers on a glass slide with the phosphorylation site centered. Altogether, 905 distinct peptides from chloroplast proteins are present on the array. Here we describe how the array can be used to identify the target protein spectrum of chloroplast kinases. We present the method and discuss limitations and challenges associated with the determination of phosphorylation activity on peptide substrates in vitro.
Collapse
Affiliation(s)
- Anna Schönberg
- Department of Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, Halle (Saale), 06120, Germany
| | | |
Collapse
|
117
|
Alpert AJ, Hudecz O, Mechtler K. Anion-exchange chromatography of phosphopeptides: weak anion exchange versus strong anion exchange and anion-exchange chromatography versus electrostatic repulsion-hydrophilic interaction chromatography. Anal Chem 2015; 87:4704-11. [PMID: 25827581 PMCID: PMC4423237 DOI: 10.1021/ac504420c] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/31/2015] [Indexed: 02/08/2023]
Abstract
Most phosphoproteomics experiments rely on prefractionation of tryptic digests before online liquid chromatography-mass spectrometry. This study compares the potential and limitations of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and anion-exchange chromatography (AEX). At a pH higher than 5, phosphopeptides have two negative charges per residue and are well-retained in AEX. However, peptides with one or two phosphate groups are not separated from peptides with multiple Asp or Glu residues, interfering with the identification of phosphopeptides. At a pH of 2, phosphate residues have just a single negative charge but Asp and Glu are uncharged. This facilitates the separation of phosphopeptides from unmodified acidic peptides. Singly phosphorylated peptides are retained weakly under these conditions, due to electrostatic repulsion, unless hydrophilic interaction is superimposed in the ERLIC mode. Weak anion-exchange (WAX) and strong anion-exchange (SAX) columns were compared, with both peptide standards and a HeLa cell tryptic digest. The SAX column exhibited greater retention at pH 6 than did the WAX column. However, only about 60% as many phosphopeptides were identified with SAX at pH 6 than via ERLIC at pH 2. In one ERLIC run, 12 467 phosphopeptides were identified, including 4233 with more than one phosphate. We conclude that chromatography of phosphopeptides is best performed at low pH in the ERLIC mode. Under those conditions, the performances of the SAX and WAX materials were comparable. The data have been deposited with the ProteomeXchange with identifier PXD001333.
Collapse
Affiliation(s)
- Andrew J. Alpert
- PolyLC
Inc., 9151 Rumsey Road,
Ste. 175, Columbia, Maryland 21045, United States
| | - Otto Hudecz
- Research
Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
- Institute
of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Karl Mechtler
- Research
Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
- Institute
of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| |
Collapse
|
118
|
Herring LE, Grant KG, Blackburn K, Haugh JM, Goshe MB. Development of a tandem affinity phosphoproteomic method with motif selectivity and its application in analysis of signal transduction networks. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 988:166-74. [PMID: 25777480 PMCID: PMC4489695 DOI: 10.1016/j.jchromb.2015.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/02/2015] [Accepted: 02/07/2015] [Indexed: 11/26/2022]
Abstract
Phosphorylation is an important post-translational modification that is involved in regulating many signaling pathways. Of particular interest are the growth factor mediated Ras and phosphoinositide 3-kinase (PI3K) signaling pathways which, if misregulated, can contribute to the progression of cancer. Phosphoproteomic methods have been developed to study regulation of signaling pathways; however, due to the low stoichiometry of phosphorylation, understanding these pathways is still a challenge. In this study, we have developed a multi-dimensional method incorporating electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) with tandem IMAC/TiO2 enrichment for subsequent phosphopeptide identification by LC/MS/MS. We applied this method to PDGF-stimulated NIH 3T3 cells to provide over 11,000 unique phosphopeptide identifications. Upon motif analysis, IMAC was found to enrich for basophilic kinase substrates while the subsequent TiO2 step enriched for acidophilic kinase substrates, suggesting that both enrichment methods are necessary to capture the full complement of kinase substrates. Biological functions that were over-represented at each PDGF stimulation time point, together with the phosphorylation dynamics of several phosphopeptides containing known kinase phosphorylation sites, illustrate the feasibility of this approach in quantitative phosphoproteomic studies.
Collapse
Affiliation(s)
- Laura E Herring
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, United States
| | - Kyle G Grant
- Gene Therapy Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-73522, United States
| | - Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, United States
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States
| | - Michael B Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, United States.
| |
Collapse
|
119
|
Lee DG, Kwon J, Eom CY, Kang YM, Roh SW, Lee KB, Choi JS. Directed analysis of cyanobacterial membrane phosphoproteome using stained phosphoproteins and titanium-enriched phosphopeptides. J Microbiol 2015; 53:279-87. [PMID: 25845541 DOI: 10.1007/s12275-015-5021-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 11/26/2022]
Abstract
Gel-free shotgun phosphoproteomics of unicellular cyanobacterium Synechocystis sp. PCC 6803 has not been reported up to now. The purpose of this study is to develop directed membrane phosphoproteomic method in Synechocystis sp. Total Synechocystis membrane proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and phosphoprotein-stained gel bands were selectively subjected to in-gel trypsin digestion. The phosphorylation sites of the resulting peptides were determined by assigning the neutral loss of [M-H(3)PO(4)] to Ser, Thr, and Tyr residues using nano-liquid chromatography 7 Tesla Fourier transform mass spectrometry. As an initial application, 111 proteins and 33 phosphoproteins were identified containing 11 integral membrane proteins. Identified four unknown phosphoproteins with transmembrane helices were suggested to be involved in membrane migration or transporters based on BLASTP search annotations. The overall distribution of hydrophobic amino acids in pTyr was lower in frequency than that of pSer or pThr. Positively charged amino acids were abundantly revealed in the surrounding amino acids centered on pTyr. A directed shotgun membrane phosphoproteomic strategy provided insight into understanding the fundamental regulatory processes underlying Ser, Thr, and Tyr phosphorylation in multi-layered membranous cyanobacteria.
Collapse
Affiliation(s)
- Dong-Gi Lee
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
120
|
Pellach M, Atsmon-Raz Y, Simonovsky E, Gottlieb H, Jacoby G, Beck R, Adler-Abramovich L, Miller Y, Gazit E. Spontaneous structural transition in phospholipid-inspired aromatic phosphopeptide nanostructures. ACS Nano 2015; 9:4085-4095. [PMID: 25802000 DOI: 10.1021/acsnano.5b00133] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phospholipid membranes could be considered a prime example of the ability of nature to produce complex yet ordered structures, by spontaneous and efficient self-assembly. Inspired by the unique properties and architecture of phospholipids, we designed simple amphiphilic decapeptides, intended to fold in the center of the peptide sequence, with a phosphorylated serine "head" located within a central turn segment, and two hydrophobic "tails". The molecular design also included the integration of the diphenylalanine motif, previously shown to facilitate self-assembly and increase nanostructure stability. Secondary structure analysis of the peptides indeed indicated the presence of stabilized conformations in solution, with a central turn connecting two hydrophobic "tails", and interactions between the hydrophobic strands. The mechanisms of assembly into supramolecular structures involved structural transitions between different morphologies, which occurred over several hours, leading to the formation of distinctive nanostructures, including half-elliptical nanosheets and curved tapes. The phosphopeptide building blocks appear to self-assemble via a particular combination of aromatic, hydrophobic and ionic interactions, as well as hydrogen bonding, as demonstrated by proposed constructed simulated models of the peptides and self-assembled nanostructures. Molecular dynamics simulations also gave insight into mechanisms of structural transitions of the nanostructures at a molecular level. Because of the biocompatibility of peptides, the phosphopeptide assemblies allow for expansion of the library of biomolecular nanostructures available for future design and application of biomedical devices.
Collapse
Affiliation(s)
- Michal Pellach
- †Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yoav Atsmon-Raz
- ‡Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
- §Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Eyal Simonovsky
- ‡Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
- §Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Hugo Gottlieb
- ⊥Department of Chemistry, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Guy Jacoby
- ∥The Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Roy Beck
- ∥The Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Lihi Adler-Abramovich
- †Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yifat Miller
- ‡Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
- §Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Ehud Gazit
- †Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- #Department of Materials Science and Engineering Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
121
|
Ithychanda SS, Fang X, Mohan ML, Zhu L, Tirupula KC, Naga Prasad SV, Wang YX, Karnik SS, Qin J. A mechanism of global shape-dependent recognition and phosphorylation of filamin by protein kinase A. J Biol Chem 2015; 290:8527-38. [PMID: 25666618 PMCID: PMC4375502 DOI: 10.1074/jbc.m114.633446] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/27/2015] [Indexed: 12/23/2022] Open
Abstract
Protein phosphorylation mediates essentially all aspects of cellular life. In humans, this is achieved by ∼500 kinases, each recognizing a specific consensus motif (CM) in the substrates. The majority of CMs are surface-exposed and are thought to be accessible to kinases for phosphorylation. Here we investigated the archetypical protein kinase A (PKA)-mediated phosphorylation of filamin, a major cytoskeletal protein that can adopt an autoinhibited conformation. Surprisingly, autoinhibited filamin is refractory to phosphorylation by PKA on a known Ser(2152) site despite its CM being exposed and the corresponding isolated peptide being readily phosphorylated. Structural analysis revealed that although the CM fits into the PKA active site its surrounding regions sterically clash with the kinase. However, upon ligand binding, filamin undergoes a conformational adjustment, allowing rapid phosphorylation on Ser(2152). These data uncover a novel ligand-induced conformational switch to trigger filamin phosphorylation. They further suggest a substrate shape-dependent filtering mechanism that channels specific exposed CM/kinase recognition in diverse signaling responses.
Collapse
Affiliation(s)
- Sujay Subbayya Ithychanda
- From the Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Xianyang Fang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI, National Institutes of Health, Frederick, Maryland 21702, and
| | - Maradumane L Mohan
- From the Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Liang Zhu
- From the Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Kalyan C Tirupula
- From the Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Sathyamangla V Naga Prasad
- From the Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI, National Institutes of Health, Frederick, Maryland 21702, and
| | - Sadashiva S Karnik
- From the Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Jun Qin
- From the Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| |
Collapse
|
122
|
Chen X, Li S, Zhang X, Min Q, Zhu JJ. Weaving a two-dimensional fishing net from titanoniobate nanosheets embedded with Fe₃O₄ nanocrystals for highly efficient capture and isotope labeling of phosphopeptides. Nanoscale 2015; 7:5815-5825. [PMID: 25757497 DOI: 10.1039/c4nr07041k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Qualitative and quantitative characterization of phosphopeptides by means of mass spectrometry (MS) is the main goal of MS-based phosphoproteomics, but suffers from their low abundance in the large haystack of various biological molecules. Herein, we introduce two-dimensional (2D) metal oxides to tackle this biological separation issue. A nanocomposite composed of titanoniobate nanosheets embedded with Fe₃O₄ nanocrystals (Fe₃O₄-TiNbNS) is constructed via a facile cation-exchange approach, and adopted for the capture and isotope labeling of phosphopeptides. In this nanoarchitecture, the 2D titanoniobate nanosheets offer enlarged surface area and a spacious microenvironment for capturing phosphopeptides, while the Fe₃O₄ nanocrystals not only incorporate a magnetic response into the composite but, more importantly, also disrupt the restacking process between the titanoniobate nanosheets and thus preserve a greater specific surface for binding phosphopeptides. Owing to the extended active surface, abundant Lewis acid sites and excellent magnetic controllability, Fe₃O₄-TiNbNS demonstrates superior sensitivity, selectivity and capacity over homogeneous bulk metal oxides, layered oxides, and even restacked nanosheets in phosphopeptide enrichment, and further allows in situ isotope labeling to quantify aberrantly-regulated phosphopeptides from sera of leukemia patients. This composite nanosheet greatly contributes to the MS analysis of phosphopeptides and gives inspiration in the pursuit of 2D structured materials for separation of other biological molecules of interests.
Collapse
Affiliation(s)
- Xueqin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China.
| | | | | | | | | |
Collapse
|
123
|
Maes E, Brusten W, Beutels F, Baggerman G, Mertens I, Valkenborg D, Landuyt B, Schoofs L, Tirez K. The benefits and limitations of reaction cell and sector field inductively coupled plasma mass spectrometry in the detection and quantification of phosphopeptides. Rapid Commun Mass Spectrom 2015; 29:35-44. [PMID: 25462361 DOI: 10.1002/rcm.7079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 10/16/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE The phosphorylation of proteins is one of the most important post-translational modifications in nature. Knowledge of the quantity or degree of protein phosphorylation in biological samples is extremely important. A combination of liquid chromatography (LC) and inductively coupled plasma mass spectrometry (ICP-MS) allows the absolute and relative quantification of the phosphorus signal. METHODS A comparison between dynamic reaction cell quadrupole ICP-MS (DRC-Q-ICP-MS) and high-resolution sector field ICP-MS (SF-ICP-MS) in detecting signals of phosphorus-containing species using identical capillary LC (reversed-phase technology) and nebulizer settings was performed. RESULTS A method to diminish the reversed-phase gradient-related signal instability in phosphorus detection with LC/ICP-MS applications was developed. Bis(4-nitrophenyl)phosphate (BNPP) was used as a standard to compare signal-to-noise ratios and limits of detection (LODs) between the two instrumental setups. The LOD reaches a value of 0.8 µg L(-1) when applying the DRC technology in Q-ICP-MS and an LOD of 0.09 µg L(-1) was found with the SF-ICP-MS setup. This BNPP standard was further used to compare the absolute quantification possibilities of phosphopeptides in these two setups. CONCLUSIONS This one-to-one comparison of two interference-reducing ICP-MS instruments demonstrates that absolute quantification of individual LC-separated phosphopeptides is possible. However, based on the LOD values, SF-ICP-MS has a higher sensitivity in detecting phosphorus signals and thus is preferred in phosphopeptide analysis.
Collapse
Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium; KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
124
|
Mukherjee G, Claudia Röwer C, Koy C, Protzel C, Lorenz P, Thiesen HJ, Hakenberg OW, Glocker MO. Ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for phosphopeptide analysis with a solidified ionic liquid matrix. Eur J Mass Spectrom (Chichester) 2015; 21:65-77. [PMID: 26181280 DOI: 10.1255/ejms.1362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A solidified ionic liquid matrix (SILM) consisting of 3-aminoquinoline, α-cyano-4- hydroxycinnamic acid and ammonium dihydrogen phosphate combines the benefits of liquid and solid MALDI matrices and proves to be well suitable for phosphopeptide analysis using MALDI-MS in the low femtomole range. Desalting and buffer exchange that typically follow after phosphopeptide elution from metal oxide affinity chromatography (MOAC) materials can be omitted. Shifting the pH from acidic to basic during target preparation causes slow matrix crystallization and homogeneous embedding of the analyte molecules, forming a uniform preparation from which (phospho)peptides can be ionized in high yields over long periods of time. The novel combination of MOAC-based phosphopeptide enrichment with SILM preparation has been developed with commercially available standard phosphopeptides and with α-casein as phosphorylated standard protein. The applicability of the streamlined phosphopeptide analysis procedure to cell biological and clinical samples has been tested (i) using affinity-enriched endogenous TRIM28 from cell cultures and (ii) by analysis of a two-dimensional gel-separated protein spot from a bladder cancer sample.
Collapse
Affiliation(s)
| | | | - Cornelia Koy
- Proteome Center Rostock, University of Rostock, Germany..
| | - Chris Protzel
- Urology Clinic and Polyclinic, University Medicine Rostock, Germany..
| | - Peter Lorenz
- Institute of Immunology, University Medicine Rostock, Germany..
| | | | - Oliver W Hakenberg
- Urology Clinic and Polyclinic, University Medicine Rostock, Germany. - rostock.de
| | | |
Collapse
|
125
|
Abstract
Polo-like kinase 1 (PLK1) plays crucial functions in multiple stages of mitosis and is considered to be a potential drug target for cancer therapy. The functions of PLK1 are mediated by its N-terminal kinase domain and C-terminal polo-box domain (PBD). Most inhibitors targeting the kinase domain of PLK1 have a selectivity issue because of a high degree of structural conservation within kinase domains of all protein kinases. Here, we combined virtual and experimental screenings to identify green tea catechins as potent inhibitors of the PLK1 PBD. Initially, (-)-epigallocatechin, one of the main components of green tea polyphenols, was found to significantly block the binding of fluorescein-labeled phosphopeptide to the PBD at a concentration of 10 μm. Next, additional catechins were evaluated for their dose-dependent inhibition of the PBD and preliminary structure-activity relationships were derived. Cellular analysis further showed that catechins interfere with the proper subcellular localization of PLK1, lead to cell-cycle arrest in the S and G2M phases, and induce growth inhibition of several human cancer cell types, such as breast adenocarcinoma (MCF7), lung adenocarcinoma (A549), and cervical adenocarcinoma (HeLa). Our data provides new insight into understanding the anticancer activities of green tea catechins.
Collapse
Affiliation(s)
- Hong-Mei Shan
- Key Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055 (China)
| | | | | |
Collapse
|
126
|
Menegatti ACO, Vernal J, Terenzi H. The unique serine/threonine phosphatase from the minimal bacterium Mycoplasma synoviae: biochemical characterization and metal dependence. J Biol Inorg Chem 2015; 20:61-75. [PMID: 25370051 DOI: 10.1007/s00775-014-1209-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 10/24/2014] [Indexed: 01/12/2023]
Abstract
Serine/threonine protein phosphatases have been described in many pathogenic bacteria as essential enzymes involved in phosphorylation-dependent signal transduction pathways and frequently associated with the virulence of these organisms. An inspection of Mycoplasma synoviae genome revealed the presence of a gene (prpC) encoding a putative protein phosphatase of the protein phosphatase 2C (PP2C) subfamily. Here, we report a complete biochemical characterization of M. synoviae phosphatase (PrpC) and the particular role of metal ions in the structure-function relationship of this enzyme. PrpC amino acid sequence analysis revealed that all the residues involved in the dinuclear metal center and the putative third metal ion-coordinating residues, conserved in PP2C phosphatases, are present in PrpC. PrpC is a monomeric protein able to dephosphorylate phospho-substrates with Mn(2+) ions' dependence. Thermal stability analysis demonstrated the enzyme stability at mild temperatures and the influence of Mn(2+) ions in this property. Mass spectrometry analysis suggested that three metal ions bind to PrpC, two of which with an apparent high-affinity constant. Mutational analysis of the putative third metal-coordinating residues, Asp122 and Arg164, revealed that these variants exhibited a weaker binding of manganese ions, and that both mutations affected PrpC phosphatase activity. According to these results, PrpC is a metal-dependent protein phosphatase member with an improved stability in the holo form and with Asp122, possibly implicated in the third metal-binding site, essential to catalytic activity.
Collapse
Affiliation(s)
- Angela C O Menegatti
- Departamento de Bioquímica-CCB, Centro de Biologia Molecular Estrutural, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Javier Vernal
- Departamento de Bioquímica-CCB, Centro de Biologia Molecular Estrutural, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Hernán Terenzi
- Departamento de Bioquímica-CCB, Centro de Biologia Molecular Estrutural, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil.
| |
Collapse
|
127
|
Thomas M, Huck N, Hoehenwarter W, Conrath U, Beckers GJM. Combining Metabolic ¹⁵N Labeling with Improved Tandem MOAC for Enhanced Probing of the Phosphoproteome. Methods Mol Biol 2015; 1306:81-96. [PMID: 25930695 DOI: 10.1007/978-1-4939-2648-0_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In eukaryotic cells many diverse cellular functions are regulated by reversible protein phosphorylation. In recent years, phosphoproteomics has become a powerful tool for studying protein phosphorylation because it enables unbiased localization, and site-specific quantification of in vivo phosphorylation of hundreds of proteins in a single experiment. A common strategy for identifying phosphoproteins and their phosphorylation sites from complex biological samples is the enrichment of phosphopeptides from digested cellular lysates followed by mass spectrometry. However, despite high sensitivity of modern mass spectrometers the large dynamic range of protein abundance and the transient nature of protein phosphorylation remained major pitfalls in MS-based phosphoproteomics. This is particularly true for plants in which the presence of secondary metabolites and endogenous compounds, the overabundance of ribulose-1,5-bisphosphate carboxylase and other components of the photosynthetic apparatus, and the concurrent difficulties in protein extraction necessitate two-step phosphoprotein/phosphopeptide enrichment strategies (Nakagami et al., Plant Cell Physiol 53:118-124, 2012).Approaches for label-free peptide quantification are advantageous due to their low cost and experimental simplicity, but they lack precision. These drawbacks can be overcome by metabolic labeling of whole plants with heavy nitrogen ((15)N) which allows combining two samples very early in the phosphoprotein enrichment workflow. This avoids sample-to-sample variation introduced by the analytical procedures and it results in robust relative quantification values that need no further standardization. The integration of (15)N metabolic labeling into tandem metal-oxide affinity chromatography (MOAC) (Hoehenwarter et al., Mol Cell Proteomics 12:369-380, 2013) presents an improved and highly selective approach for the identification and accurate site-specific quantification of low-abundance phosphoproteins that is based on the successive enrichment of light and heavy nitrogen-labeled phosphoproteins and peptides. This improved strategy combines metabolic labeling of whole plants with the stable heavy nitrogen isotope ((15)N), protein extraction under denaturing conditions, phosphoprotein enrichment using Al(OH)3-based MOAC, and tryptic digest of enriched phosphoproteins followed by TiO2-based MOAC of phosphopeptides and quantitative phosphopeptide measurement by liquid chromatography (LC) and high-resolution accurate mass (HR/AM) mass spectrometry (MS). Thus, tandem MOAC effectively targets the phosphate moiety of phosphoproteins and phosphopeptides and allows probing of the phosphoproteome to unprecedented depth, while (15)N metabolic labeling enables accurate relative quantification of measured peptides and direct comparison between samples.
Collapse
Affiliation(s)
- Martin Thomas
- Plant Biochemistry and Molecular Biology Group, Department of Plant Physiology, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany
| | | | | | | | | |
Collapse
|
128
|
Ho HP, Rathod P, Louis M, Tada CK, Rahaman S, Mark KJ, Leng J, Dana D, Kumar S, Lichterfeld M, Chang EJ. Studies on quantitative phosphopeptide analysis by matrix-assisted laser desorption/ionization mass spectrometry without label, chromatography or calibration curves. Rapid Commun Mass Spectrom 2014; 28:2681-9. [PMID: 25380489 PMCID: PMC4225566 DOI: 10.1002/rcm.7063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/23/2014] [Accepted: 09/23/2014] [Indexed: 05/12/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry combined with isotope labeling methods are effective for protein and peptide quantification, but limited in their multiplexing capacity, cost-effectiveness and dynamic range. This study investigates MALDI-MS-based quantification of peptide phosphorylation without labeling, and aims to overcome the shot-to-shot variability of MALDI using a mathematical transformation and extended data acquisition times. METHODS A linear relationship between the reciprocal of phosphopeptide mole fraction and the reciprocal of phosphorylated-to-unphosphorylated signal ratio is derived, and evaluated experimentally using three separate phosphopeptide systems containing phosphorylated serine, threonine and tyrosine residues: mixtures of phosphopeptide and its des-phospho-analog with known stoichiometry measured by vacuum MALDI-linear ion trap mass spectrometry and fit to the linear model. The model is validated for quantifying in vitro phosphorylation assays with inhibition studies on Cdk2/cyclinA. RESULTS Dynamic range of picomoles to femtomoles, good accuracy (deviations of 1.5-3.0% from expected values) and reproducibility (relative standard deviation (RSD) = 4.3-6.3%) are achieved. Inhibition of cyclin-dependent kinase phosphorylation by the classical inhibitors olomoucine and r-roscovitine was evaluated and IC50 values found to be in agreement with reported literature values. These results, achieved with single-point calibration, without isotope or chromatography, compare favorably to those arrived at using isotope dilution (p > 0.5 for accuracy). CONCLUSIONS The mathematical relationship derived here can be applied to a method that we term Double Reciprocal Isotope-free Phosphopeptide Quantification (DRIP-Q), as a strategy for quantification of in vitro phosphorylation assays, the first MALDI-based, isotope- and calibration curve-free method of its type. These results also pave the way for further systematic studies investigating the effect of peptide composition and experimental conditions on quantitative, label-free MALDI.
Collapse
Affiliation(s)
- Hsin-Pin Ho
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Pratikkumar Rathod
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Marissa Louis
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Christine K. Tada
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Sherida Rahaman
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Kevin J. Mark
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
- Department of Natural Sciences, LaGuardia Community College, The City University of New York, Long Island City, NY, USA
| | - Jin Leng
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA and Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Dibyendu Dana
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, Queens, NY USA
| | - Sanjai Kumar
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, Queens, NY USA
- Department of Biochemistry, The Graduate Center, The City University of New York, New York, NY, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA and Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Emmanuel J. Chang
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
- Department of Biochemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Address reprint requests to Emmanuel Chang; York College, 94-20 Guy R. Brewer Blvd, Jamaica, NY 11451, 718-262-3778 (phone), 718-262-2652 (fax),
| |
Collapse
|
129
|
Xiong Z, Chen Y, Zhang L, Ren J, Zhang Q, Ye M, Zhang W, Zou H. Facile synthesis of guanidyl-functionalized magnetic polymer microspheres for tunable and specific capture of global phosphopeptides or only multiphosphopeptides. ACS Appl Mater Interfaces 2014; 6:22743-22750. [PMID: 25466400 DOI: 10.1021/am506882b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The highly selective and efficient capture of heterogeneous types of phosphopeptides is critical for comprehensive and in-depth phosphoproteome analysis, but it still remains a challenge since the lack of affinity material with large binding capacity and controllable specificity. Here, a new affinity material was prepared to improve the enrichment capacity and endue the tunable specificity by introducing guanidyl onto poly(glycidyl methacrylate) (PGMA) modified Fe3O4 microsphere (denoted as Fe3O4@PGMA-Guanidyl). The thick polymer shell endows the composite microsphere with large amount of guanidyl and is beneficial to enhancing the affinity interaction between phosphopeptides and the material. Interestingly, the Fe3O4@PGMA-Guanidyl possesses tunable enriching ability for global phosphopeptides or only multiphosphopeptides through simple regulation of buffer composition. The composite has large enrichment capacity (200 mg g(-1)), extremely high detection sensitivity (0.5 fmol), high enrichment recovery (91.30%), great specificity, and rapid magnetic separation. Moreover, the result of the application to capture of phosphopeptides from tryptic digest of nonfat milk has demonstrated the great potential of Fe3O4@PGMA-Guanidyl in detection and identification of low-abundance phosphopeptides of interest in biological sample.
Collapse
Affiliation(s)
- Zhichao Xiong
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology , Shanghai 200237, China
| | | | | | | | | | | | | | | |
Collapse
|
130
|
Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
Collapse
Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
131
|
Yang C, Zhong X, Li L. Recent advances in enrichment and separation strategies for mass spectrometry-based phosphoproteomics. Electrophoresis 2014; 35:3418-29. [PMID: 24687451 PMCID: PMC4849134 DOI: 10.1002/elps.201400017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/21/2014] [Accepted: 03/21/2014] [Indexed: 12/29/2022]
Abstract
Due to the significance of protein phosphorylation in various biological processes and signaling events, new analytical techniques for enhanced phosphoproteomics have been rapidly introduced in the recent years. The combinatorial use of the phospho-specific enrichment techniques and prefractionation methods prior to MS analysis enable comprehensive profiling of the phosphoproteome and facilitate deciphering the critical roles that phosphorylation plays in signaling pathways in various biological systems. This review places special emphasis on the recent five-year (2009-2013) advances for enrichment and separation techniques that have been utilized for phosphopeptides prior to MS analysis.
Collapse
Affiliation(s)
- Chenxi Yang
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| |
Collapse
|
132
|
Zhao R, Peng X, Li Q, Song W. Effects of phosphorylatable short peptide-conjugated chitosan-mediated IL-1Ra and igf-1 gene transfer on articular cartilage defects in rabbits. PLoS One 2014; 9:e112284. [PMID: 25390659 PMCID: PMC4229204 DOI: 10.1371/journal.pone.0112284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/10/2014] [Indexed: 11/25/2022] Open
Abstract
Previously, we reported an improvement in the transfection efficiency of the plasmid DNA-chitosan (pDNA/CS) complex by the utilization of phosphorylatable short peptide-conjugated chitosan (pSP-CS). In this study, we investigated the effects of pSP-CS-mediated gene transfection of interleukin-1 receptor antagonist protein (IL-1Ra) combined with insulin-like growth factor-1 (IGF-1) in rabbit chondrocytes and in a rabbit model of cartilage defects. pBudCE4.1-IL-1Ra+igf-1, pBudCE4.1-IL-1Ra and pBudCE4.1-igf-1 were constructed and combined with pSP-CS to form pDNA/pSP-CS complexes. These complexes were transfected into rabbit primary chondrocytes or injected into the joint cavity. Seven weeks after treatment, all rabbits were sacrificed and analyzed. High levels of IL-1Ra and igf-1 expression were detected both in the cell culture supernatant and in the synovial fluid. In vitro, the transgenic complexes caused significant proliferation of chondrocytes, promotion of glycosaminoglycan (GAG) and collagen II synthesis, and inhibition of chondrocyte apoptosis and nitric oxide (NO) synthesis. In vivo, the exogenous genes resulted in increased collagen II synthesis and reduced NO and GAG concentrations in the synovial fluid; histological studies revealed that pDNA/pSP-CS treatment resulted in varying degrees of hyaline-like cartilage repair and Mankin score decrease. The co-expression of both genes produced greater effects than each single gene alone both in vitro and in vivo. The results suggest that pSP-CS is a good candidate for use in gene therapy for the treatment of cartilage defects and that igf-1 and IL-1Ra co-expression produces promising biologic effects on cartilage defects.
Collapse
Affiliation(s)
- Ronglan Zhao
- Department of Medical Laboratory, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University, Weifang, Shandong, China
| | - Xiaoxiang Peng
- Department of Medical Laboratory, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University, Weifang, Shandong, China
- * E-mail:
| | - Qian Li
- Department of Medical Laboratory, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University, Weifang, Shandong, China
| | - Wei Song
- Department of Medical Laboratory, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University, Weifang, Shandong, China
| |
Collapse
|
133
|
Qian WJ, Park JE, Lim D, Lai CC, Kelley JA, Park SY, Lee KW, Yaffe MB, Lee KS, Burke TR. Mono-anionic phosphopeptides produced by unexpected histidine alkylation exhibit high Plk1 polo-box domain-binding affinities and enhanced antiproliferative effects in HeLa cells. Biopolymers 2014; 102:444-55. [PMID: 25283071 PMCID: PMC4895914 DOI: 10.1002/bip.22569] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/12/2014] [Accepted: 09/27/2014] [Indexed: 11/07/2022]
Abstract
Binding of polo-like kinase 1 (Plk1) polo-box domains (PBDs) to phosphothreonine (pThr)/phosphoserine (pSer)-containing sequences is critical for the proper function of Plk1. Although high-affinity synthetic pThr-containing peptides provide starting points for developing PBD-directed inhibitors, to date the efficacy of such peptides in whole cell assays has been poor. This potentially reflects limited cell membrane permeability arising, in part, from the di-anionic nature of the phosphoryl group or its mimetics. In our current article we report the unanticipated on-resin N(τ)-alkylation of histidine residues already bearing a N(π)- alkyl group. This resulted in cationic imidazolium-containing pThr peptides, several of which exhibit single-digit nanomolar PBD-binding affinities in extracellular assays and improved antimitotic efficacies in intact cells. We enhanced the cellular efficacies of these peptides further by applying bio-reversible pivaloyloxymethyl (POM) phosphoryl protection. New structural insights presented in our current study, including the potential utility of intramolecular charge masking, may be useful for the further development of PBD-binding peptides and peptide mimetics.
Collapse
Affiliation(s)
- Wen-Jian Qian
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Dan Lim
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U. S. A
| | - Christopher C. Lai
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - James A. Kelley
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - Suk-Youl Park
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 443-270, Republic of Korea
| | - Ki-Won Lee
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 443-270, Republic of Korea
- World Class University Biomodulation Major and Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Michael B. Yaffe
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U. S. A
| | - Kyung S. Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| |
Collapse
|
134
|
Abstract
The c-Jun N-terminal kinases (JNKs) are ubiquitous proteins that phosphorylate their substrates, such as transcription factors, in response to physical stress, cytokines or UV radiation. This leads to changes in gene expression, ensuing either cell cycle progression or apoptosis. Active phospho JNK1 is the main in vivo kinase component of the JNK cascade, whereas JNK2 is presumed not to participate as a kinase during JNK signalling. However, there is evidence that JNK isoforms interact functionally in vivo. Also, a recent chemical genetics investigation has confirmed that JNK transient activation leads to cellular proliferation, whereas a sustained one is pro-apoptotic. Here we investigate the phosphorylation pattern of JNK2, with protein biochemistry tools and tandem mass spectrometry. We choose to focus on JNK2 because of its reported constitutive activity in glioma cells. Our results indicate that purified JNK2 from transfected nonstressed 293T cells is a mixture of the mono-sites pThr183 and pTyr185 of its activation loop and of pThr386 along its unique C-terminal region. Upon UV stimulation, its phosphorylation stoichiometry is upregulated on the activation loop, generating a mixture of mono-pTyr185 and the expected dual-pThr183/pTyr185 species, with the pThr386 specie present but unaltered respect to the basal conditions.
Collapse
Affiliation(s)
- Genaro Pimienta
- Inflammation and Infectious Diseases Center, Burnham Institute for Medical Research, La Jolla, California 92037 USA
| | | | | | | | | | | | | |
Collapse
|
135
|
Tape C, Worboys JD, Sinclair J, Gourlay R, Vogt J, McMahon KM, Trost M, Lauffenburger DA, Lamont DJ, Jørgensen C. Reproducible automated phosphopeptide enrichment using magnetic TiO2 and Ti-IMAC. Anal Chem 2014; 86:10296-302. [PMID: 25233145 PMCID: PMC4206527 DOI: 10.1021/ac5025842] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/18/2014] [Indexed: 12/28/2022]
Abstract
Reproducible, comprehensive phosphopeptide enrichment is essential for studying phosphorylation-regulated processes. Here, we describe the application of hyper-porous magnetic TiO2 and Ti-IMAC microspheres for uniform automated phosphopeptide enrichment. Combining magnetic microspheres with a magnetic particle-handling robot enables rapid (45 min), reproducible (r2 ≥ 0.80) and high-fidelity (>90% purity) phosphopeptide purification in a 96-well format. Automated phosphopeptide enrichment demonstrates reproducible synthetic phosphopeptide recovery across 2 orders of magnitude, "well-to-well" quantitative reproducibility indistinguishable to internal SILAC standards, and robust "plate-to-plate" reproducibility across 5 days of independent enrichments. As a result, automated phosphopeptide enrichment enables statistical analysis of label-free phosphoproteomic samples in a high-throughput manner. This technique uses commercially available, off-the-shelf components and can be easily adopted by any laboratory interested in phosphoproteomic analysis. We provide a free downloadable automated phosphopeptide enrichment program to facilitate uniform interlaboratory collaboration and exchange of phosphoproteomic data sets.
Collapse
Affiliation(s)
- Christopher
J. Tape
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan D. Worboys
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - John Sinclair
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - Robert Gourlay
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Janis Vogt
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kelly M. McMahon
- Cancer
Research UK Manchester Institute, The University
of Manchester, Wilmslow
Road, Manchester M20 4BX, United Kingdom
| | - Matthias Trost
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Douglas A. Lauffenburger
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Douglas J. Lamont
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Claus Jørgensen
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
- Cancer
Research UK Manchester Institute, The University
of Manchester, Wilmslow
Road, Manchester M20 4BX, United Kingdom
| |
Collapse
|
136
|
Xu Q, Deller MC, Nielsen TK, Grant JC, Lesley SA, Elsliger MA, Deacon AM, Wilson IA. Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin. PLoS One 2014; 9:e107309. [PMID: 25197798 PMCID: PMC4157861 DOI: 10.1371/journal.pone.0107309] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/09/2014] [Indexed: 01/15/2023] Open
Abstract
Kanadaptin is a nuclear protein of unknown function that is widely expressed in mammalian tissues. The crystal structure of the forkhead-associated (FHA) domain of human kanadaptin was determined to 1.6 Å resolution. The structure reveals an asymmetric dimer in which one monomer is complexed with a phosphopeptide mimic derived from a peptide segment from the N-terminus of a symmetry-related molecule as well as a sulfate bound to the structurally conserved phosphothreonine recognition cleft. This structure provides insights into the molecular recognition features utilized by this family of proteins and represents the first evidence that kanadaptin is likely involved in a phosphorylation-mediated signaling pathway. These results will be of use for designing experiments to further probe the function of kanadaptin.
Collapse
Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Marc C. Deller
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tine K. Nielsen
- Protein Production Facility, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joanna C. Grant
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Scott A. Lesley
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Ian A. Wilson
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
137
|
Abstract
Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. Several algorithms have been proposed to uncover phosphorylation motifs, whereas the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. Here we present a novel notion called conditional phosphorylation motifs. Through this new concept, the motifs whose over-expressiveness mainly benefits from its constituting parts can be filtered out effectively. To discover conditional phosphorylation motifs, we propose an algorithm called C-Motif for a non-redundant identification of significant phosphorylation motifs. C-Motif is implemented under the Apriori framework, and it tests the statistical significance together with the frequency of candidate motifs in a single stage. Experiments demonstrate that C-Motif outperforms some current algorithms such as MMFPh and Motif-All in terms of coverage and non-redundancy of the results and efficiency of the execution. The source code of C-Motif is available at: https://sourceforge. net/projects/cmotif/.
Collapse
|
138
|
Sadygov RG. Use of singular value decomposition analysis to differentiate phosphorylated precursors in strong cation exchange fractions. Electrophoresis 2014; 35:3498-503. [PMID: 24913822 DOI: 10.1002/elps.201400053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/13/2014] [Accepted: 05/20/2014] [Indexed: 01/26/2023]
Abstract
We studied the use of peak deviations (PDs) for application in phosphoproteomics. Due to the differences in the mass defects, the PDs of samples containing mixtures of phosphorylated and nonphosphorylated peptides show bimodal distributions. The ratios of peak heights accurately predict the phosphoproteome content of a sample. In this work, we apply a signal-processing tool, singular value decomposition, to reveal characteristic features of the phosphorylated, nonphosphorylated, and mixed samples. We show that a simple application of singular value decomposition to the PD matrix (i) detects transitions from mostly phosphorylated samples to mostly nonphosphorylated samples, (ii) reveals modes of low-abundance species in the presence of the high-abundance species (e.g., phosphorylated peptides), and (iii) simplifies the interpretation of the clustering of a covariance matrix obtained from PDs. As the eigenfunctions of the inner-product of the data matrix (made from the PDs) are Hermite functions, we observe a change of sign in the transition from samples enriched in phosphorylated peptides to samples containing fewer phosphorylated peptides. The ordering of the singular values of the data matrix points in the direction of changes to the phosphorylation content. No peptide identifications from a database were used for this study.
Collapse
Affiliation(s)
- Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
| |
Collapse
|
139
|
Cao H, Deterding LJ, Blackshear PJ. Identification of a major phosphopeptide in human tristetraprolin by phosphopeptide mapping and mass spectrometry. PLoS One 2014; 9:e100977. [PMID: 25010646 PMCID: PMC4091943 DOI: 10.1371/journal.pone.0100977] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/02/2014] [Indexed: 11/18/2022] Open
Abstract
Tristetraprolin/zinc finger protein 36 (TTP/ZFP36) binds and destabilizes some pro-inflammatory cytokine mRNAs. TTP-deficient mice develop a profound inflammatory syndrome due to excessive production of pro-inflammatory cytokines. TTP expression is induced by various factors including insulin and extracts from cinnamon and green tea. TTP is highly phosphorylated in vivo and is a substrate for several protein kinases. Multiple phosphorylation sites are identified in human TTP, but it is difficult to assign major vs. minor phosphorylation sites. This study aimed to generate additional information on TTP phosphorylation using phosphopeptide mapping and mass spectrometry (MS). Wild-type and site-directed mutant TTP proteins were expressed in transfected human cells followed by in vivo radiolabeling with [32P]-orthophosphate. Histidine-tagged TTP proteins were purified with Ni-NTA affinity beads and digested with trypsin and lysyl endopeptidase. The digested peptides were separated by C18 column with high performance liquid chromatography. Wild-type and all mutant TTP proteins were localized in the cytosol, phosphorylated extensively in vivo and capable of binding to ARE-containing RNA probes. Mutant TTP with S90 and S93 mutations resulted in the disappearance of a major phosphopeptide peak. Mutant TTP with an S197 mutation resulted in another major phosphopeptide peak being eluted earlier than the wild-type. Additional mutations at S186, S296 and T271 exhibited little effect on phosphopeptide profiles. MS analysis identified the peptide that was missing in the S90 and S93 mutant protein as LGPELSPSPTSPTATSTTPSR (corresponding to amino acid residues 83–103 of human TTP). MS also identified a major phosphopeptide associated with the first zinc-finger region. These analyses suggest that the tryptic peptide containing S90 and S93 is a major phosphopeptide in human TTP.
Collapse
Affiliation(s)
- Heping Cao
- U. S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Leesa J. Deterding
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Perry J. Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America and Departments of Biochemistry and Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| |
Collapse
|
140
|
SidAhmed-Mezi M, Kurcewicz I, Rose C, Louvel J, Sokoloff P, Pumain R, Laschet JJ. Mass spectrometric detection and characterization of atypical membrane-bound zinc-sensitive phosphatases modulating GABAA receptors. PLoS One 2014; 9:e100612. [PMID: 24967814 PMCID: PMC4072668 DOI: 10.1371/journal.pone.0100612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/29/2014] [Indexed: 12/17/2022] Open
Abstract
Background GABAA receptor (GABAAR) function is maintained by an endogenous phosphorylation mechanism for which the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is the kinase. This phosphorylation is specific to the long intracellular loop I2 of the α1 subunit at two identified serine and threonine residues. The phosphorylation state is opposed by an unknown membrane-bound phosphatase, which inhibition favors the phosphorylated state of the receptor and contributes to the maintenance of its function. In cortical nervous tissue from epileptogenic areas in patients with drug-resistant epilepsies, both the endogenous phosphorylation and the functional state of the GABAAR are deficient. Methodology/Principal Findings The aim of this study is to characterize the membrane-bound phosphatases counteracting the endogenous phosphorylation of GABAAR. We have developed a new analytical tool for in vitro detection of the phosphatase activities in cortical washed membranes by liquid chromatography coupled to mass spectrometry. The substrates are two synthetic phosphopeptides, each including one of the identified endogenous phosphorylation sites of the I2 loop of GABAAR α1 subunit. We have shown the presence of multiple and atypical phosphatases sensitive to zinc ions. Patch-clamp studies of the rundown of the GABAAR currents on acutely isolated rat pyramidal cells using the phosphatase inhibitor okadaic acid revealed a clear heterogeneity of the phosphatases counteracting the function of the GABAAR. Conclusion/Significance Our results provide new insights on the regulation of GABAAR endogenous phosphorylation and function by several and atypical membrane-bound phosphatases specific to the α1 subunit of the receptor. By identifying specific inhibitors of these enzymes, novel development of antiepileptic drugs in patients with drug-resistant epilepsies may be proposed.
Collapse
Affiliation(s)
- Mounia SidAhmed-Mezi
- Inserm, Infantile Epilepsies and Brain Plasticity U1129, Paris, France
- University Paris Descartes, Paris, France
- CEA, Gif sur Yvette, France
- * E-mail: (MS); (JJL)
| | - Irène Kurcewicz
- University Paris Descartes, Paris, France
- Inserm, Centre de Psychiatrie et de Neurosciences U894, Paris, France
| | - Christiane Rose
- University Paris Descartes, Paris, France
- Inserm, Centre de Psychiatrie et de Neurosciences U894, Paris, France
| | - Jacques Louvel
- University Paris Descartes, Paris, France
- Inserm, Centre de Psychiatrie et de Neurosciences U894, Paris, France
| | - Pierre Sokoloff
- Institut de Recherche Pierre Fabre, Neurologie & Psychiatrie, Castres, France
| | - René Pumain
- Inserm, Infantile Epilepsies and Brain Plasticity U1129, Paris, France
- University Paris Descartes, Paris, France
- CEA, Gif sur Yvette, France
| | - Jacques J. Laschet
- Inserm, Infantile Epilepsies and Brain Plasticity U1129, Paris, France
- University Paris Descartes, Paris, France
- CEA, Gif sur Yvette, France
- * E-mail: (MS); (JJL)
| |
Collapse
|
141
|
Ma WF, Zhang C, Zhang YT, Yu M, Guo J, Zhang Y, Lu HJ, Wang CC. Magnetic MSP@ZrO₂ microspheres with yolk-shell structure: designed synthesis and application in highly selective enrichment of phosphopeptides. Langmuir 2014; 30:6602-6611. [PMID: 24835108 DOI: 10.1021/la501381v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Magnetic yolk-shell MSP@ZrO2 microspheres consisting of a movable magnetic supraparticle (MSP) core and a crystalline ZrO2 shell were synthesized via a two-step controlled "sol-gel" approach for the first time. First, a large amount of the generated hydrolyzate Zr(OH)4 was firmly fixed onto the surface of the cross-linked polymethylacrylic acid matrix via a strong hydrogen-bonding interaction between Zr(OH)4 and the carboxyl groups. Then a calcination process was adopted to convert the Zr(OH)4 into a continuous ZrO2 shell and simultaneously make the ZrO2 shell crystallized. At the same time, the polymer matrix could be selectively removed to form a yolk-shell structure, which has better dispersibility and higher adsorbing efficiency of phosphopeptides than its solid counterpart. The formation mechanism of such yolk-shell microspheres could be reasonably proved by the results of TEM, TGA, VSM, XRD, and FT-IR characterization. By taking advantage of the unique properties, the yolk-shell MSP@ZrO2 exhibited high specificity and great capability in selective enrichment of phosphopeptides, and a total of 33 unique phosphopeptides mapped to 33 different phosphoproteins had been identified from 1 mL of human saliva. This result clearly demonstrated that the yolk-shell MSP@ZrO2 has great performance in purifying and identifying the low-abundant phosphopeptides from real complex biological samples. Moreover, the synthetic method can be used to produce hybrid yolk-shell MSP@ZrO2-TiO2.
Collapse
Affiliation(s)
- Wan-Fu Ma
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University , Shanghai 200433, China
| | | | | | | | | | | | | | | |
Collapse
|
142
|
Zhang Y, Ma W, Zhang C, Wang C, Lu H. Titania composite microspheres endowed with a size-exclusive effect toward the highly specific revelation of phosphopeptidome. ACS Appl Mater Interfaces 2014; 6:6290-6299. [PMID: 24745367 DOI: 10.1021/am501339e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The efficient isolation of low-abundance phosphopeptides from complicated biological samples containing a significant quantity of nonphosphopeptides and proteins is essential for phosphopeptidome research but remains a great challenge. In this Article, magnetic composite microspheres comprising a magnetic colloidal nanocrystal cluster core and a mesoporous titania shell with an average pore diameter of 3.4 nm were modified by directly coating an amorphous titania shell onto the magnetite core, followed by converting the amorphous titania shell into a crystalline structure via a hydrothermal process at 80 °C. The as-prepared magnetic mesoporous titania microspheres possess a remarkable specific surface area that is as high as 603.5 m2/g, which is an appropriate pore size with a narrow size distribution and a high magnetic responsiveness. These outstanding features imply that the composite microspheres exhibit extraordinary performance in phosphopeptidome research, including high specificity toward phosphopeptides, an excellent size-exclusion effect against phosphoproteins, exceptional enrichment capacity, and efficient separation from mixtures. Encouraged by the experimental results, we employed this method to investigate the phosphopeptidome of snake venom for the first time. A total of 35 phosphopeptides was identified from the snake venom from the family Viperidae, accounting for 75% of the total identified peptides. This result represents the largest data set of the phosphopeptidome in snake venom from the family Viperidae.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University , Shanghai 200032, China
| | | | | | | | | |
Collapse
|
143
|
Boex-Fontvieille E, Daventure M, Jossier M, Hodges M, Zivy M, Tcherkez G. Phosphorylation pattern of Rubisco activase in Arabidopsis leaves. Plant Biol (Stuttg) 2014. [PMID: 24119201 DOI: 10.1111/plb.12100mid:24119201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Rubisco activase (RCA) is an ancillary photosynthetic protein essential for Rubisco activity. Some data suggest that post-translational modifications (such as reduction of disulphide bridges) are involved in the regulation of RCA activity. However, despite the key role of protein phosphorylation in general metabolic regulation, RCA phosphorylation has not been well characterised. We took advantage of phosphoproteomics and gas exchange analyses with instant sampling adapted to Arabidopsis rosettes to examine the occurrence and variations of phosphopeptides associated with RCA in different photosynthetic contexts (CO2 mole fraction, light and dark). We detected two phosphopeptides from RCA corresponding to residues Thr 78 and Ser 172, and show that the former is considerably more phosphorylated in the dark than in the light, while the latter show no light/dark pattern. The CO2 mole fraction did not influence phosphorylation of either residue. Phosphorylation thus appears to be a potential mechanism associated with RCA dark inactivation, when Rubisco-catalysed carboxylation is arrested. Since Thr 78 and Ser 172 are located in the N and Walker domains of the protein, respectively, the involvement of phosphorylation in protein-protein interaction and catalysis is likely.
Collapse
Affiliation(s)
- E Boex-Fontvieille
- Institut de biologie des plantes, CNRS UMR 8618, Université Paris-Sud, Orsay, France
| | | | | | | | | | | |
Collapse
|
144
|
Boex-Fontvieille E, Daventure M, Jossier M, Hodges M, Zivy M, Tcherkez G. Phosphorylation pattern of Rubisco activase in Arabidopsis leaves. Plant Biol (Stuttg) 2014; 16:550-7. [PMID: 24119201 DOI: 10.1111/plb.12100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/20/2013] [Indexed: 05/09/2023]
Abstract
Rubisco activase (RCA) is an ancillary photosynthetic protein essential for Rubisco activity. Some data suggest that post-translational modifications (such as reduction of disulphide bridges) are involved in the regulation of RCA activity. However, despite the key role of protein phosphorylation in general metabolic regulation, RCA phosphorylation has not been well characterised. We took advantage of phosphoproteomics and gas exchange analyses with instant sampling adapted to Arabidopsis rosettes to examine the occurrence and variations of phosphopeptides associated with RCA in different photosynthetic contexts (CO2 mole fraction, light and dark). We detected two phosphopeptides from RCA corresponding to residues Thr 78 and Ser 172, and show that the former is considerably more phosphorylated in the dark than in the light, while the latter show no light/dark pattern. The CO2 mole fraction did not influence phosphorylation of either residue. Phosphorylation thus appears to be a potential mechanism associated with RCA dark inactivation, when Rubisco-catalysed carboxylation is arrested. Since Thr 78 and Ser 172 are located in the N and Walker domains of the protein, respectively, the involvement of phosphorylation in protein-protein interaction and catalysis is likely.
Collapse
Affiliation(s)
- E Boex-Fontvieille
- Institut de biologie des plantes, CNRS UMR 8618, Université Paris-Sud, Orsay, France
| | | | | | | | | | | |
Collapse
|
145
|
Yan Y, Zhang X, Deng C. Designed synthesis of titania nanoparticles coated hierarchially ordered macro/mesoporous silica for selective enrichment of phosphopeptides. ACS Appl Mater Interfaces 2014; 6:5467-5471. [PMID: 24666404 DOI: 10.1021/am500412v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Metal oxide affinity chromatography (MOAC) is a powerful technique in phosphoproteome research. However, the achievement of highly specific enrichment and sensitive detection of phosphopeptide by MOAC remains a big challenge since the lack of high specificity and large binding capacity of conventional MOAC materials. In this work, a new MOAC material, TiO2-coated hierarchically ordered macro/mesoporous silica (denoted as HOMMS@TiO2) composites, was prepared via a facile process. The HOMMS@TiO2 composites were demonstrated to have low limit of detection (8 fmol) and great specificity with a very rapid enrichment speed (within 1 min). These experimental results have demonstrated that the HOMMS@TiO2 exhibit great potential in phosphoproteome research.
Collapse
Affiliation(s)
- Yinghua Yan
- Department of Chemistry, Fudan University , Shanghai 200433, China
| | | | | |
Collapse
|
146
|
Li S, Mhamdi A, Trotta A, Kangasjärvi S, Noctor G. The protein phosphatase subunit PP2A-B'γ is required to suppress day length-dependent pathogenesis responses triggered by intracellular oxidative stress. New Phytol 2014; 202:145-160. [PMID: 24299221 DOI: 10.1111/nph.12622] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 11/03/2013] [Indexed: 05/09/2023]
Abstract
Oxidative stress responses are influenced by growth day length, but little is known about how this occurs. A combined reverse genetics, metabolomics and proteomics approach was used to address this question in Arabidopsis thaliana. A catalase-deficient mutant (cat2), in which intracellular oxidative stress drives pathogenesis-related responses in a day length-dependent manner, was crossed with a knockdown mutant for a specific type 2A protein phosphatase subunit (pp2a-b'γ). In long days (LD), the pp2a-b'γ mutation reinforced cat2-triggered pathogenesis responses. In short days (SD), conditions in which pathogenesis-related responses were not activated in cat2, the additional presence of the pp2a-b'γ mutation allowed lesion formation, PATHOGENESIS-RELATED GENE1 (PR1) induction, salicylic acid (SA) and phytoalexin accumulation and the establishment of metabolite profiles that were otherwise observed in cat2 only in LD. Lesion formation in cat2 pp2a-b'γ in SD was genetically dependent on SA synthesis, and was associated with decreased PHYTOCHROME A transcripts. Phosphoproteomic analyses revealed that several potential protein targets accumulated in the double mutant, including recognized players in pathogenesis and key enzymes of primary metabolism. We conclude that the cat2 and pp2a-b'γ mutations interact synergistically, and that PP2A-B'γ is an important player in controlling day length-dependent responses to intracellular oxidative stress, possibly through phytochrome-linked pathways.
Collapse
Affiliation(s)
- Shengchun Li
- Institut de Biologie des Plantes, UMR8618 CNRS, Université de Paris sud, 91405, Orsay Cedex, France
| | - Amna Mhamdi
- Institut de Biologie des Plantes, UMR8618 CNRS, Université de Paris sud, 91405, Orsay Cedex, France
| | - Andrea Trotta
- Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | | | - Graham Noctor
- Institut de Biologie des Plantes, UMR8618 CNRS, Université de Paris sud, 91405, Orsay Cedex, France
| |
Collapse
|
147
|
Najam-ul-Haq M, Saeed A, Jabeen F, Maya F, Ashiq MN, Sharif A. Newly developed poly(allyl glycidyl ether/divinyl benzene) polymer for phosphopeptides enrichment and desalting of biofluids. ACS Appl Mater Interfaces 2014; 6:3536-3545. [PMID: 24533437 DOI: 10.1021/am405718j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The polymeric materials have contributed significantly in the area of bioanalytical science. The functionalization of polymeric backbone after its development brings unique selectivity towards the target biomolecules. In present work, the functionalities of choice have been introduced through the ring-opening of allyl glycidyl ether. The utility of polymer is widened through derivatizations to immobilized metal ion affinity chromatographic (IMAC) material for the phosphopeptides enrichment and Reversed Phase (C-18) for the desalting prior to MALDI-MS analysis. The polymer-IMAC in addition to Fe(3+) is also immobilized with lanthanide ions like La(3+), Eu(3+), and Er(3+). The amount of Fe(3+) immobilized is determined as 0.7928 mg/g. Spherical morphology with narrow particle size dispersion is revealed by scanning electron microscopy (SEM). The surface area, pore volume and size distribution is determined by nitrogen adsorption porosimetery. The elemental composition and purity level is confirmed by energy dispersive X-ray spectroscopy (EDX) data. The derivatization to IMAC and RP is evaluated by Fourier transform infrared (FT-IR) spectroscopy. The polymer enables the efficient phosphopeptide enrichment to equal degree from casein variants, non-fat milk, egg yolk, human serum, and HeLa cell extract. The identification of phosphorylation sites can lead to the phosphorylation pathways to understand the post-translational modifications. The identification with their sequence coverage is made using Mascot and Phosphosite Plus. It is sensitive to enrich the phosphopeptides down to 2 femtomoles with very high selectivity of 1:2000 with BSA background. These attributes are linked to the higher surface area (173.1554 m(2)/g) of the designed polymer. The non-specific bindings, particularly the Fe(3+) linked acidic residues are also avoided. Four characteristic phosphopeptides (fibrinopeptide A and their hydrolytic products) from fibrinogen α-chain are identified from the human serum after the enrichment, which have link to the hepatocellular carcinoma (HCC). The proportions of fibrinogen and their phosphorylation products enriched by poly(AGE/DVB)-IMAC open new horizons in the biomarker discovery.
Collapse
Affiliation(s)
- Muhammad Najam-ul-Haq
- Institute of Chemical Sciences, Bahauddin Zakariya University , Multan 60800, Pakistan
| | | | | | | | | | | |
Collapse
|
148
|
Casado P, Bilanges B, Rajeeve V, Vanhaesebroeck B, Cutillas PR. Environmental stress affects the activity of metabolic and growth factor signaling networks and induces autophagy markers in MCF7 breast cancer cells. Mol Cell Proteomics 2014; 13:836-48. [PMID: 24425749 PMCID: PMC3945912 DOI: 10.1074/mcp.m113.034751] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/13/2013] [Indexed: 11/06/2022] Open
Abstract
Phosphoproteomic techniques are contributing to our understanding of how signaling pathways interact and regulate biological processes. This technology is also being used to characterize how signaling networks are remodeled during disease progression and to identify biomarkers of signaling pathway activity and of responses to cancer therapy. A potential caveat in these studies is that phosphorylation is a very dynamic modification that can substantially change during the course of an experiment or the retrieval and processing of cellular samples. Here, we investigated how exposure of cells to ambient conditions modulates phosphorylation and signaling pathway activity in the MCF7 breast cancer cell line. About 1.5% of 3,500 sites measured showed a significant change in phosphorylation extent upon exposure of cells to ambient conditions for 15 min. The effects of this perturbation in modifying phosphorylation patterns did not involve random changes due to stochastic activation of kinases and phosphatases. Instead, exposure of cells to ambient conditions elicited an environmental stress reaction that involved a coordinated response to a metabolic stress situation, which included: (1) the activation of AMPK; (2) the inhibition of PI3K, AKT, and ERK; (3) an increase in markers of protein synthesis inhibition at the level of translation elongation; and (4) an increase in autophagy markers. We also observed that maintaining cells in ice modified but did not completely abolish this metabolic stress response. In summary, exposure of cells to ambient conditions affects the activity of signaling networks previously implicated in metabolic and growth factor signaling. Mass spectrometry data have been deposited to the ProteomeXchange with identifier PXD000472.
Collapse
Affiliation(s)
- Pedro Casado
- From the ‡Analytical Signalling Group and
- ¶ Current affiliation: Integrative Cell Signaling and Proteomics Group, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry
| | - Benoit Bilanges
- §Cell Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London EC1B 6BQ, UK
| | - Vinothini Rajeeve
- From the ‡Analytical Signalling Group and
- ¶ Current affiliation: Integrative Cell Signaling and Proteomics Group, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry
| | - Bart Vanhaesebroeck
- §Cell Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London EC1B 6BQ, UK
| | - Pedro R. Cutillas
- From the ‡Analytical Signalling Group and
- ¶ Current affiliation: Integrative Cell Signaling and Proteomics Group, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry
| |
Collapse
|
149
|
Lanucara F, Chi Hoo Lee D, Eyers CE. Unblocking the sink: improved CID-based analysis of phosphorylated peptides by enzymatic removal of the basic C-terminal residue. J Am Soc Mass Spectrom 2014; 25:214-225. [PMID: 24297471 PMCID: PMC3899453 DOI: 10.1007/s13361-013-0770-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 06/02/2023]
Abstract
A one-step enzymatic reaction for improving the collision-induced dissociation (CID)-based tandem mass spectrometry (MS/MS) analysis of phosphorylated peptides in an ion trap is presented. Carboxypeptidase-B (CBP-B) was used to selectively remove C-terminal arginine or lysine residues from phosphorylated tryptic/Lys-C peptides prior to their MS/MS analysis by CID with a Paul-type ion trap. Removal of this basic C-terminal residue served to limit the extent of gas-phase neutral loss of phosphoric acid (H3PO4), favoring the formation of diagnostic b and y ions as determined by an increase in both the number and relative intensities of the sequence-specific product ions. Such differential fragmentation is particularly valuable when the H3PO4 elimination is so predominant that localizing the phosphorylation site on the peptide sequence is hindered. Improvement in the quality of tandem mass spectral data generated by CID upon CBP-B treatment resulted in greater confidence both in assignment of the phosphopeptide primary sequence and for pinpointing the site of phosphorylation. Higher Mascot ion scores were also generated, combined with lower expectation values and higher delta scores for improved confidence in site assignment; Ascore values also improved. These results are rationalized in accordance with the accepted mechanisms for the elimination of H3PO4 upon low energy CID and insights into the factors dictating the observed dissociation pathways are presented. We anticipate this approach will be of utility in the MS analysis of phosphorylated peptides, especially when alternative electron-driven fragmentation techniques are not available.
Collapse
Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Dave Chi Hoo Lee
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
| | - Claire E. Eyers
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| |
Collapse
|
150
|
Fredens J, Engholm-Keller K, Møller-Jensen J, Larsen MR, Færgeman NJ. Identification of novel protein functions and signaling mechanisms by genetics and quantitative phosphoproteomics in Caenorhabditis elegans. Methods Mol Biol 2014; 1188:107-124. [PMID: 25059608 DOI: 10.1007/978-1-4939-1142-4_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Stable isotope labeling by amino acids combined with mass spectrometry is a widely used methodology for measuring relative changes in protein and phosphorylation levels at a global level. We have applied this method to the model organism Caenorhabditis elegans in combination with RNAi-mediated gene knockdown by feeding the nematode on pre-labeled lysine auxotroph Escherichia coli. In this chapter, we describe in details the generation of the E. coli strain, incorporation of heavy isotope-labeled lysine in C. elegans, and the procedure for a comprehensive global phosphoproteomic experiment.
Collapse
Affiliation(s)
- Julius Fredens
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | | | | | | | | |
Collapse
|