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Fu J, Nguyen K. Reduction of Promiscuous Peptides-Enzyme Inhibition and Aggregation by Negatively Charged Biopolymers. ACS APPLIED BIO MATERIALS 2022; 5:1839-1845. [PMID: 34995072 DOI: 10.1021/acsabm.1c01128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, peptides selected from a microarray were found to inhibit β-gal with promiscuous mechanisms. Peptides inhibited the enzyme in a noncompetitive kinetics, and the inhibition of enzyme activities was reduced under high enzyme concentrations and the addition of detergent. Dynamic light scattering and atomic force microscope revealed that peptide/enzyme aggregation was related to inhibited enzyme activities. Positively charged residues of arginine and lysine were critical for the enzyme inhibition. The preincubation of peptide inhibitors with negatively charged biopolymers of polyphosphates, ssDNA, and low pI peptides could increase the residual activity of peptide-inhibited enzyme, possibly due to the disruption of the electrostatic interaction between positively charged peptide residues and the β-gal surface. Further, negative biopolymers were able to recover the activity of the aggregated peptide/β-gal complex. Negatively charged biopolymers could be used in high-throughput screening assays to reduce peptides/protein aggregation and thereby minimize promiscuous inhibitions.
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Affiliation(s)
- Jinglin Fu
- Department of Chemistry, Rutgers University-Camden, Camden, New Jersey 08102, United States.,Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey 08103, United States
| | - Kaitlyn Nguyen
- Department of Chemistry, Rutgers University-Camden, Camden, New Jersey 08102, United States
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2
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Qin X, Liu T. Recent Advances in Genetic Code Expansion Techniques for Protein Phosphorylation Studies. J Mol Biol 2021; 434:167406. [PMID: 34929199 DOI: 10.1016/j.jmb.2021.167406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 12/22/2022]
Abstract
Protein phosphorylation is a reversible, residue-specific posttranslational modification that plays a pivotal role in cell signaling, and the phosphorylation state of proteins is tightly regulated by kinases and phosphatases. Malfunction of this regulation is often associated with human diseases, and therefore elucidation of the function and regulation of this posttranslational modification is important. Genetic code expansion, which allows for site-specific introduction of noncanonical amino acids directly into target proteins in response to a non-sense codon is a powerful method for preparing homogeneously phosphorylated proteins both in Escherichia coli and mammalian cells and therefore is useful for studying protein phosphorylation. Herein, we summarize recent developments in the application of genetic code expansion for protein phosphorylation studies.
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Affiliation(s)
- Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
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3
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Lin W, Gandhi S, Oviedo Lara AR, Thomas AK, Helbig R, Zhang Y. Controlling Surface Wettability for Automated In Situ Array Synthesis and Direct Bioscreening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102349. [PMID: 34309086 DOI: 10.1002/adma.202102349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Indexed: 06/13/2023]
Abstract
The in situ synthesis of biomolecules on glass surfaces for direct bioscreening can be a powerful tool in the fields of pharmaceutical sciences, biomaterials, and chemical biology. However, it is still challenging to 1) achieve this conventional multistep combinatorial synthesis on glass surfaces with small feature sizes and high yields and 2) develop a surface which is compatible with solid-phase syntheses, as well as the subsequent bioscreening. This work reports an amphiphilic coating of a glass surface on which small droplets of polar aprotic organic solvents can be deposited with an enhanced contact angle and inhibited motion to permit fully automated multiple rounds of the combinatorial synthesis of small-molecule compounds and peptides. This amphiphilic coating can be switched into a hydrophilic network for protein- and cell-based screening. Employing this in situ synthesis method, chemical space can be probed via array technology with unprecedented speed for various applications, such as lead discovery/optimization in medicinal chemistry and biomaterial development.
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Affiliation(s)
- Weilin Lin
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Shanil Gandhi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alan Rodrigo Oviedo Lara
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alvin K Thomas
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Ralf Helbig
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Hohe Strasse 6, 01069, Dresden, Germany
| | - Yixin Zhang
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence "Physics of Life", Technische Universität Dresden, 01062, Dresden, Germany
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4
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Saei AA, Beusch CM, Sabatier P, Wells JA, Gharibi H, Meng Z, Chernobrovkin A, Rodin S, Näreoja K, Thorsell AG, Karlberg T, Cheng Q, Lundström SL, Gaetani M, Végvári Á, Arnér ESJ, Schüler H, Zubarev RA. System-wide identification and prioritization of enzyme substrates by thermal analysis. Nat Commun 2021; 12:1296. [PMID: 33637753 PMCID: PMC7910609 DOI: 10.1038/s41467-021-21540-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.
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Affiliation(s)
- Amir Ata Saei
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Christian M Beusch
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pierre Sabatier
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juan Astorga Wells
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hassan Gharibi
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Zhaowei Meng
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alexey Chernobrovkin
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Pelago Bioscience AB, Solna, Sweden
| | - Sergey Rodin
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Katja Näreoja
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ann-Gerd Thorsell
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Tobias Karlberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanna L Lundström
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Massimiliano Gaetani
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
- Chemical Proteomics Core Facility, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ákos Végvári
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Proteomics Biomedicum, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Herwig Schüler
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
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5
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Recent advance on PTP1B inhibitors and their biomedical applications. Eur J Med Chem 2020; 199:112376. [DOI: 10.1016/j.ejmech.2020.112376] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]
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6
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Dissecting the sequence determinants for dephosphorylation by the catalytic subunits of phosphatases PP1 and PP2A. Nat Commun 2020; 11:3583. [PMID: 32681005 PMCID: PMC7367873 DOI: 10.1038/s41467-020-17334-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 06/22/2020] [Indexed: 12/16/2022] Open
Abstract
The phosphatases PP1 and PP2A are responsible for the majority of dephosphorylation reactions on phosphoserine (pSer) and phosphothreonine (pThr), and are involved in virtually all cellular processes and numerous diseases. The catalytic subunits exist in cells in form of holoenzymes, which impart substrate specificity. The contribution of the catalytic subunits to the recognition of substrates is unclear. By developing a phosphopeptide library approach and a phosphoproteomic assay, we demonstrate that the specificity of PP1 and PP2A holoenzymes towards pThr and of PP1 for basic motifs adjacent to the phosphorylation site are due to intrinsic properties of the catalytic subunits. Thus, we dissect this amino acid specificity of the catalytic subunits from the contribution of regulatory proteins. Furthermore, our approach enables discovering a role for PP1 as regulator of the GRB-associated-binding protein 2 (GAB2)/14-3-3 complex. Beyond this, we expect that this approach is broadly applicable to detect enzyme-substrate recognition preferences. The substrate specificity of phosphoprotein phosphatases PP1 and PP2A depends on their catalytic and regulatory subunits. Using proteomics approaches, the authors here provide insights into the sequence specificity of the catalytic subunits and their distinct contributions to PP1 and PP2A selectivity.
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7
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Nitrogen-doped carbon dots-V2O5 nanobelts sensing platform for sensitive detection of ascorbic acid and alkaline phosphatase activity. Anal Chim Acta 2019; 1089:131-143. [DOI: 10.1016/j.aca.2019.08.061] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/30/2019] [Accepted: 08/25/2019] [Indexed: 02/07/2023]
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8
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Huang CF, Mrksich M. Profiling Protein Tyrosine Phosphatase Specificity with Self-Assembled Monolayers for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry and Peptide Arrays. ACS COMBINATORIAL SCIENCE 2019; 21:760-769. [PMID: 31553163 PMCID: PMC6848775 DOI: 10.1021/acscombsci.9b00152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The opposing activities of phosphatases and kinases determine the phosphorylation status of proteins, yet kinases have received disproportionate attention in studies of cellular processes, with the roles of phosphatases remaining less understood. This Research Article describes the use of phosphotyrosine-containing peptide arrays together with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to directly profile phosphatase substrate selectivities. Twenty-two protein tyrosine phosphatases were characterized with the arrays to give a profile of their specificities. An analysis of the data revealed that certain residues in the substrates had a conserved effect on activity for all enzymes tested, including the general rule that inclusion of a basic lysine or arginine residue on either side of the phosphotyrosine decreased activity. This insight also provides a new perspective on the role of a R1152Q mutant in the insulin receptor, which is known to exhibit a lower phosphorylation level and which this work suggests may be due to an increased activity toward phosphatase enzymes. The use of self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) to provide a rapid and quantitative assay of phosphatase enzymes will be important to gaining a more complete understanding of the biochemistry and biology of this important enzyme class.
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Affiliation(s)
- Che-Fan Huang
- Department of Chemistry, Northwestern University, Evanston, IL 60208, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, IL 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, United States
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9
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Hogan M, Bahta M, Tsuji K, Nguyen TX, Cherry S, Lountos GT, Tropea JE, Zhao BM, Zhao XZ, Waugh DS, Burke TR, Ulrich RG. Targeting Protein-Protein Interactions of Tyrosine Phosphatases with Microarrayed Fragment Libraries Displayed on Phosphopeptide Substrate Scaffolds. ACS COMBINATORIAL SCIENCE 2019; 21:158-170. [PMID: 30629404 DOI: 10.1021/acscombsci.8b00122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemical library screening approaches that focus exclusively on catalytic events may overlook unique effects of protein-protein interactions that can be exploited for development of specific inhibitors. Phosphotyrosyl (pTyr) residues embedded in peptide motifs comprise minimal recognition elements that determine the substrate specificity of protein tyrosine phosphatases (PTPases). We incorporated aminooxy-containing amino acid residues into a 7-residue epidermal growth factor receptor (EGFR) derived phosphotyrosine-containing peptide and subjected the peptides to solution-phase oxime diversification by reacting with aldehyde-bearing druglike functionalities. The pTyr residue remained unmodified. The resulting derivatized peptide library was printed in microarrays on nitrocellulose-coated glass surfaces for assessment of PTPase catalytic activity or on gold monolayers for analysis of kinetic interactions by surface plasmon resonance (SPR). Focusing on amino acid positions and chemical features, we first analyzed dephosphorylation of the peptide pTyr residues within the microarrayed library by the human dual-specificity phosphatases (DUSP) DUSP14 and DUSP22, as well as by PTPases from poxviruses (VH1) and Yersinia pestis (YopH). In order to identify the highest affinity oxime motifs, the binding interactions of the most active derivatized phosphopeptides were examined by SPR using noncatalytic PTPase mutants. On the basis of high-affinity oxime fragments identified by the two-step catalytic and SPR-based microarray screens, low-molecular-weight nonphosphate-containing peptides were designed to inhibit PTP catalysis at low micromolar concentrations.
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Affiliation(s)
- Megan Hogan
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, United States
| | - Medhanit Bahta
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Kohei Tsuji
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Trung X. Nguyen
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Scott Cherry
- Macromolecular Crystallography Laboratory, National Cancer Institute, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - George T. Lountos
- Macromolecular Crystallography Laboratory, National Cancer Institute, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, National Cancer Institute, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Bryan M. Zhao
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, United States
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, National Cancer Institute, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Robert G. Ulrich
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, United States
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10
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Sakaguchi I, Fukasawa T, Fujimoto K, Inouye M. Immobilization of Crosslinked Peptides that Possess High Helical Contents and Their Binding to Target DNAs on Au Surfaces. CHEM LETT 2018. [DOI: 10.1246/cl.171153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ikumi Sakaguchi
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Toshiaki Fukasawa
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kazuhisa Fujimoto
- Department of Applied Chemistry and Biochemistry, Kyushu Sangyo University, Fukuoka 813-8503, Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
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11
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Shen M, Rusling J, Dixit CK. Site-selective orientated immobilization of antibodies and conjugates for immunodiagnostics development. Methods 2017; 116:95-111. [PMID: 27876681 PMCID: PMC5374010 DOI: 10.1016/j.ymeth.2016.11.010] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/11/2023] Open
Abstract
Immobilized antibody systems are the key to develop efficient diagnostics and separations tools. In the last decade, developments in the field of biomolecular engineering and crosslinker chemistry have greatly influenced the development of this field. With all these new approaches at our disposal, several new immobilization methods have been created to address the main challenges associated with immobilized antibodies. Few of these challenges that we have discussed in this review are mainly associated to the site-specific immobilization, appropriate orientation, and activity retention. We have discussed the effect of antibody immobilization approaches on the parameters on the performance of an immunoassay.
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Affiliation(s)
- Min Shen
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
| | - James Rusling
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269-3136
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 060
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
| | - Chandra K Dixit
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
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12
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Palma A, Tinti M, Paoluzi S, Santonico E, Brandt BW, Hooft van Huijsduijnen R, Masch A, Heringa J, Schutkowski M, Castagnoli L, Cesareni G. Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases. J Biol Chem 2017; 292:4942-4952. [PMID: 28159843 DOI: 10.1074/jbc.m116.757518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/31/2017] [Indexed: 01/19/2023] Open
Abstract
Reversible tyrosine phosphorylation is a widespread post-translational modification mechanism underlying cell physiology. Thus, understanding the mechanisms responsible for substrate selection by kinases and phosphatases is central to our ability to model signal transduction at a system level. Classical protein-tyrosine phosphatases can exhibit substrate specificity in vivo by combining intrinsic enzymatic specificity with the network of protein-protein interactions, which positions the enzymes in close proximity to their substrates. Here we use a high throughput approach, based on high density phosphopeptide chips, to determine the in vitro substrate preference of 16 members of the protein-tyrosine phosphatase family. This approach helped identify one residue in the substrate binding pocket of the phosphatase domain that confers specificity for phosphopeptides in a specific sequence context. We also present a Bayesian model that combines intrinsic enzymatic specificity and interaction information in the context of the human protein interaction network to infer new phosphatase substrates at the proteome level.
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Affiliation(s)
- Anita Palma
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Michele Tinti
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Serena Paoluzi
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Elena Santonico
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Bernd Willem Brandt
- the Centre for Integrative Bioinformatics, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands, and
| | | | - Antonia Masch
- the Institut für Biochemie & Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06108 Halle, Germany
| | - Jaap Heringa
- the Centre for Integrative Bioinformatics, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands, and
| | - Mike Schutkowski
- the Institut für Biochemie & Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06108 Halle, Germany
| | - Luisa Castagnoli
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gianni Cesareni
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy,
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13
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Tinti M, Panni S, Cesareni G. Profiling Phosphopeptide-Binding Domain Recognition Specificity Using Peptide Microarrays. Methods Mol Biol 2017; 1518:177-193. [PMID: 27873207 DOI: 10.1007/978-1-4939-6584-7_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cellular organization and response to internal and external stimuli are mediated by an intricate web of protein interactions. Some of these interactions are regulated by covalent posttranslational modifications such as phosphorylation and acetylation. These modifications can change the chemical nature of the interaction interfaces and modulate the binding affinity of the interacting partners. In signal transduction, the most frequent modification is reversible phosphorylation of tyrosine, serine or threonine residues. Protein phosphorylation may modulate the activity of enzymes by modifying their conformation, or regulate the formation of complexes by creating docking sites to recruit downstream effectors. Families of modular domains, such as SH2, PTB, and 14-3-3, act as "readers" of the modification event. Specificity between closely related domains of the same family is mediated by the chemical properties of the domain binding surface that, aside from offering a hydrophilic pocket for the phosphorylated residue, shows preference for specific sequences. Although the protein structure and the cell context are also important to ensure specificity, the amino acid sequence flanking the phosphorylation site defines the accuracy of the recognition process, and it is therefore essential to define the binding specificity of phosphopeptide binding domains in order to understand and to infer the interaction web mediated by phosphopeptides. Methods commonly used to discover new interactions (such as yeast two hybrid and phage display) are not suited to study interactions with phosphorylated proteins. On the other hand, peptide arrays are a powerful approach to precisely identify the binding preference of phosphopeptide recognition domains. Here we describe a detailed protocol to assemble arrays of hundreds to thousands phospho-peptides and to screen them with any modular domain of interest.
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Affiliation(s)
- Michele Tinti
- Division of Biochemical Chemistry and Drug Discovery, College of Life Science, Dundee University, Dow Street, Dundee, DD1 4HN, UK.
| | - Simona Panni
- Department of Biology, Ecology and Earth Science, DiBEST, University of Calabria, Rende, Italy.
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.,Istituto Ricovero e Cura a Carattere Scientifico, Fondazione Santa Lucia, Rome, Italy
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14
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Abstract
Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening throughput and versatility. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules in high density on a flat surface, one is able to interrogate all possible interactions with desired targets, in just a single step. SMMs have become established as the choice platform for screening, lead discovery, and molecular characterization. This introduction describes the principles governing microarray construction and use, focusing on practical challenges faced when conducting SMM experiments. It will explain the key design considerations and lay the foundation for the chapters that follow. (An earlier version of this chapter appeared in Small Molecule Microarrays: Methods and Protocols, published in 2010.).
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Affiliation(s)
- Mahesh Uttamchandani
- Defence Medical and Environmental Research Institute, DMERI, DSO National Laboratories, #09-01, 27 Medical Drive, Singapore, Singapore, 117510. .,Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, Singapore, 117543.
| | - Shao Q Yao
- Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, Singapore, 117543.
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15
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Na Z, Pan S, Uttamchandani M, Yao SQ. Protein-Protein Interaction Inhibitors of BRCA1 Discovered Using Small Molecule Microarrays. Methods Mol Biol 2017; 1518:139-156. [PMID: 27873205 DOI: 10.1007/978-1-4939-6584-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microarray screening technology has transformed the life sciences arena over the last decade. The platform is widely used in the area of mapping interaction networks, to molecular fingerprinting and small molecular inhibitor discovery. The technique has significantly impacted both basic and applied research. The microarray platform can likewise enable high-throughput screening and discovery of protein-protein interaction (PPI) inhibitors. Herein we demonstrate the application of microarray-guided PPI inhibitor discovery, using human BRCA1 as an example. Mutations in BRCA1 have been implicated in ~50 % of hereditary breast cancers. By targeting the (BRCT)2 domain, we showed compound 15a and its prodrug 15b inhibited BRCA1 activities in tumor cells. Unlike previously reported peptide-based PPI inhibitors of BRCA1, the compounds identified could be directly administered to tumor cells, thus making them useful in targeting BRCA1/PARP-related pathways involved in DNA damage and repair response, for cancer therapy.
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Affiliation(s)
- Zhenkun Na
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Mahesh Uttamchandani
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore, Singapore
| | - Shao Q Yao
- Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.
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16
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Abstract
Phosphatases play key roles in normal physiology and diseases. Studying phosphatases has been both essential and challenging, and the application of conventional genetic and biochemical methods has led to crucial but still limited understanding of their mechanisms, substrates, and exclusive functions within highly intricate networks. With the advances in technologies such as cellular imaging and molecular and chemical biology in terms of sensitive tools and methods, the phosphatase field has thrived in the past years and has set new insights for cell signaling studies and for therapeutic development. In this review, we give an overview of the existing interdisciplinary tools for phosphatases, give examples on how they have been applied to increase our understanding of these enzymes, and suggest how they-and other tools yet barely used in the phosphatase field-might be adapted to address future questions and challenges.
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Affiliation(s)
- Sara Fahs
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Pablo Lujan
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
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17
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Lei Z, Gao J, Liu X, Liu D, Wang Z. Poly(glycidyl methacrylate-co-2-hydroxyethyl methacrylate) Brushes as Peptide/Protein Microarray Substrate for Improving Protein Binding and Functionality. ACS APPLIED MATERIALS & INTERFACES 2016; 8:10174-10182. [PMID: 27049528 DOI: 10.1021/acsami.6b01156] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We developed a three-dimensional (3D) polymer-brush substrate for protein and peptide microarray fabrication, and this substrate was facilely prepared by copolymerization of glycidyl methacrylate (GMA) and 2-hydroxyethyl methacrylate (HEMA) monomers via surface-initiated atom transfer radical polymerization (SI-ATRP) on a glass slide. The performance of obtained poly(glycidyl methacrylate-co-2-hydroxyethyl methacrylate) (P(GMA-HEMA)) brush substrate was assessed by binding of human IgG with rabbit antihuman IgG antibodies on a protein microarray and by the determination of matrix metalloproteinase (MMP) activities on a peptide microarray. The P(GMA-HEMA) brush substrate exhibited higher immobilization capacities for proteins and peptides than those of a two-dimensional (2D) planar epoxy slide. Furthermore, the sensitivity of the P(GMA-HEMA) brush-based microarray on rabbit antihuman IgG antibody detection was much higher than that of its 2D counterpart. The enzyme activities of MMPs were determined specifically with a low detection limit of 6.0 pg mL(-1) for MMP-2 and 5.7 pg mL(-1) for MMP-9. By taking advantage of the biocompatibility of PHEMA, the P(GMA-HEMA) brush-based peptide microarray was also employed to evaluate the secretion of MMP-2 and MMP-9 by cells cultured off the chip or directly on the chip, and satisfactory results were obtained.
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Affiliation(s)
- Zhen Lei
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
- University of Chinese Academy of Sciences , Beijing 100049, P. R. China
| | - Jiaxue Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
- University of Chinese Academy of Sciences , Beijing 100049, P. R. China
| | - Xia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
| | - Dianjun Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
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18
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Li X, Köhn M. Prediction and verification of novel peptide targets of protein tyrosine phosphatase 1B. Bioorg Med Chem 2016; 24:3255-8. [PMID: 27025565 PMCID: PMC4957924 DOI: 10.1016/j.bmc.2016.03.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 11/26/2022]
Abstract
Phosphotyrosine peptides are useful starting points for inhibitor design and for the search for protein tyrosine phosphatase (PTP) phosphoprotein substrates. To identify novel phosphopeptide substrates of PTP1B, we developed a computational prediction protocol based on a virtual library of protein sequences with known phosphotyrosine sites. To these we applied sequence-based methods, biologically meaningful filters and molecular docking. Five peptides were selected for biochemical testing of their potential as PTP1B substrates. All five peptides were equally good substrates for PTP1B compared to a known peptide substrate whereas appropriate control peptides were not recognized, showing that our protocol can be used to identify novel peptide substrates of PTP1B.
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Affiliation(s)
- Xun Li
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany; European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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19
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Pai J, Hyun S, Hyun JY, Park SH, Kim WJ, Bae SH, Kim NK, Yu J, Shin I. Screening of Pre-miRNA-155 Binding Peptides for Apoptosis Inducing Activity Using Peptide Microarrays. J Am Chem Soc 2016; 138:857-67. [PMID: 26771315 DOI: 10.1021/jacs.5b09216] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
MicroRNA-155, one of the most potent miRNAs that suppress apoptosis in human cancer, is overexpressed in numerous cancers, and it displays oncogenic activity. Peptide microarrays, constructed by immobilizing 185 peptides containing the C-terminal hydrazide onto epoxide-derivatized glass slides, were employed to evaluate peptide binding properties of pre-miRNA-155 and to identify its binding peptides. Two peptides, which were identified based on the results of peptide microarray and in vitro Dicer inhibition studies, were found to inhibit generation of mature miRNA-155 catalyzed by Dicer and to enhance expression of miRNA-155 target genes in cells. In addition, the results of cell experiments indicate that peptide inhibitors promote apoptotic cell death via a caspase-dependent pathway. Finally, observations made in NMR and molecular modeling studies suggest that a peptide inhibitor preferentially binds to the upper bulge and apical stem-loop region of pre-miRNA-155, thereby suppressing Dicer-mediated miRNA-155 processing.
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Affiliation(s)
- Jaeyoung Pai
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University , Seoul 03722, Korea
| | - Soonsil Hyun
- Department of Chemistry and Education, Seoul National University , Seoul 08826, Korea
| | - Ji Young Hyun
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University , Seoul 03722, Korea
| | - Seong-Hyun Park
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University , Seoul 03722, Korea
| | - Won-Je Kim
- Advanced Analysis Center, Korea Institute of Science and Technology , Seoul 02792, Korea
| | - Sung-Hun Bae
- CKD Research Institute , 315-20, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17006, Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology , Seoul 02792, Korea
| | - Jaehoon Yu
- Department of Chemistry and Education, Seoul National University , Seoul 08826, Korea
| | - Injae Shin
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University , Seoul 03722, Korea
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20
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Gao L, Lee SS, Chen J, Sun H, Zhao Y, Chai Z, Hu Y. High-Throughput Screening of Substrate Specificity for Protein Tyrosine Phosphatases (PTPs) on Phosphopeptide Microarrays. Methods Mol Biol 2016; 1368:181-196. [PMID: 26614076 DOI: 10.1007/978-1-4939-3136-1_13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Phosphatases are a family of enzymes responsible for the dephosphorylation of biomolecules. Phosphatases play essential roles in cell cycle regulation, signal transduction, and cellular communication. In recent years, one type of phosphatases, protein tyrosine phosphatases (PTPs), emerges as important therapeutic targets for complex and devastating diseases. Nevertheless, the physiological roles, substrate specificity, and downstream targets for PTPs remain largely unknown. To demonstrate how microarrays can be applied to characterizing PTPs, we describe here a phosphopeptide microarray strategy for activity-based high-throughput screening of PTPs substrate specificity. This is followed by a kinetic microarray assay and microplate assay to determine the rate constants of dephosphorylation by PTPs. This microarray strategy has been successfully applied to identifying several potent and selective substrates against different PTPs. These substrates could be used to design potent and selective PTPs inhibitors in the future.
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Affiliation(s)
- Liqian Gao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Singapore
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Singapore
| | - Jun Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Lab of Nuclear Radiation and Nuclear Energy Technology, Center for Multidisciplinary Research, Chinese Academy of Sciences (CAS), Institute of High Energy Physics, 19B Yuquan Road, Beijing, 100049, China
| | - Hongyan Sun
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, P.R. China.
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Lab of Nuclear Radiation and Nuclear Energy Technology, Center for Multidisciplinary Research, Chinese Academy of Sciences (CAS), Institute of High Energy Physics, 19B Yuquan Road, Beijing, 100049, China
| | - Zhifang Chai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Lab of Nuclear Radiation and Nuclear Energy Technology, Center for Multidisciplinary Research, Chinese Academy of Sciences (CAS), Institute of High Energy Physics, 19B Yuquan Road, Beijing, 100049, China
| | - Yi Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Lab of Nuclear Radiation and Nuclear Energy Technology, Center for Multidisciplinary Research, Chinese Academy of Sciences (CAS), Institute of High Energy Physics, 19B Yuquan Road, Beijing, 100049, China.
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21
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Gori A, Longhi R. Chemoselective Strategies to Peptide and Protein Bioprobes Immobilization on Microarray Surfaces. Methods Mol Biol 2016; 1352:145-56. [PMID: 26490473 DOI: 10.1007/978-1-4939-3037-1_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Ordered and reproducible bioprobe immobilization onto sensor surfaces is a critical step in the development of reliable analytical devices. A growing awareness of the impact of the immobilization scheme on the consistency of the generated data is driving the demand for chemoselective approaches to immobilize biofunctional ligands, such as peptides, in a predetermined and uniform fashion. Herein, the most intriguing strategies to selective and oriented peptide immobilization are described and discussed. The aim of the current work is to provide the reader a general picture on recent advances made in this field, highlighting the potential associated with each chemoselective strategy. Case studies are described to provide illustrative examples, and cross-references to more topic-focused and exhaustive reviews are proposed throughout the text.
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Affiliation(s)
- Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), Consiglio Nazionale delle Ricerche (CNR), Via Mario Bianco 9, Milan, 20131, Italy.
| | - Renato Longhi
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), Consiglio Nazionale delle Ricerche (CNR), Via Mario Bianco 9, Milan, 20131, Italy
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22
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Wang P, Na Z, Fu J, Tan CYJ, Zhang H, Yao SQ, Sun H. Microarray immobilization of biomolecules using a fast trans-cyclooctene (TCO)–tetrazine reaction. Chem Commun (Camb) 2014; 50:11818-21. [DOI: 10.1039/c4cc03838j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Meyer C, Hoeger B, Temmerman K, Tatarek-Nossol M, Pogenberg V, Bernhagen J, Wilmanns M, Kapurniotu A, Köhn M. Development of accessible peptidic tool compounds to study the phosphatase PTP1B in intact cells. ACS Chem Biol 2014; 9:769-76. [PMID: 24387659 DOI: 10.1021/cb400903u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play crucial roles in health and disease. Chemical modulators of their activity are vital tools to study their function. An important aspect is the accessibility of these tools, which is usually limited or not existent due to the required, often complex synthesis of the molecules. We describe here a strategy for the development of cellular active inhibitors and in-cell detection tools for PTP1B as a model PTP, which plays important roles in diabetes, obesity, and cancer. The tool compounds are based on a peptide sequence from PTP1B's substrate Src, and the resulting compounds are commercially accessible through standard peptide synthesis. The peptide inhibitor is remarkably selective against a panel of PTPs. We provide the co-crystal structure of PTP1B with the sequence from Src and the optimized peptide inhibitor, showing the molecular basis of the interaction of PTP1B with part of its natural substrate and explaining the crucial interactions to enhance binding affinity, which are made possible by simple optimization of the sequence. Our approach enables the broad accessibility of PTP1B tools to researchers and has the potential for the systematic development of accessible PTP modulators to enable the study of PTPs.
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Affiliation(s)
- Christoph Meyer
- Genome
Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Birgit Hoeger
- Genome
Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Koen Temmerman
- Hamburg
Outstation, European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany
| | - Marianna Tatarek-Nossol
- Institute
of Biochemistry and Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Vivian Pogenberg
- Hamburg
Outstation, European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany
| | - Jürgen Bernhagen
- Institute
of Biochemistry and Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Matthias Wilmanns
- Hamburg
Outstation, European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany
| | - Aphrodite Kapurniotu
- Division
of Peptide Biochemistry, Technische Universität München, Freising, Germany
| | - Maja Köhn
- Genome
Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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24
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Gray CJ, Weissenborn MJ, Eyers CE, Flitsch SL. Enzymatic reactions on immobilised substrates. Chem Soc Rev 2014; 42:6378-405. [PMID: 23579870 DOI: 10.1039/c3cs60018a] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Road, Manchester, M1 7DN, UK
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25
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Sun H, Chen GYJ, Yao SQ. Recent advances in microarray technologies for proteomics. ACTA ACUST UNITED AC 2013; 20:685-99. [PMID: 23706635 DOI: 10.1016/j.chembiol.2013.04.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/01/2013] [Accepted: 04/14/2013] [Indexed: 01/04/2023]
Abstract
Proteins are fundamental components of all living systems and critical drivers of biological functions. The large-scale study of proteins, their structures and functions, is defined as proteomics. This systems-wide analysis leads to a more comprehensive view of the intricate signaling transduction pathways that proteins engage in and improves the overall understanding of the complex processes supporting the living systems. Over the last two decades, the development of high-throughput analytical tools, such as microarray technologies, capable of rapidly analyzing thousands of protein-functioning and protein-interacting events, has fueled the growth of this important field. Herein, we review the most recent advancements in microarray technologies, with a special focus on peptide microarray, small molecule microarray, and protein microarray. These technologies have become prominent players in proteomics and have made significant changes to the landscape of life science and biomedical research. We will elaborate on their performance, advantages, challenges, and future directions.
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Affiliation(s)
- Hongyan Sun
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, PRC.
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26
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van Ameijde J, Overvoorde J, Knapp S, den Hertog J, Ruijtenbeek R, Liskamp RMJ. Real-Time Monitoring of the Dephosphorylating Activity of Protein Tyrosine Phosphatases Using Microarrays with 3-Nitrophosphotyrosine Substrates. Chempluschem 2013; 78:1349-1357. [PMID: 31986648 DOI: 10.1002/cplu.201300299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Indexed: 11/10/2022]
Abstract
Phosphatases and kinases regulate the crucial phosphorylation post-translational modification. In spite of their similarly important role in many diseases and therapeutic potential, phosphatases have received arguably less attention. One reason for this is a scarcity of high-throughput phosphatase assays. Herein, a new real-time, dynamic protein tyrosine phosphatase (PTP) substrate microarray assay measuring product formation is described. PTP substrates comprising a novel 3-nitrophosphotyrosine residue are immobilized in discrete spots. After reaction catalyzed by a PTP a 3-nitrotyrosine residue is formed that can be detected by specific, sequence-independent antibodies. The resulting microarray was successfully evaluated with a panel of recombinant PTPs and cell lysates, which afforded results comparable to data from other assays. Its parallel nature, convenience, and low sample requirements facilitate investigation of the therapeutically relevant PTP enzyme family.
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Affiliation(s)
- Jeroen van Ameijde
- Medicinal Chemistry and Chemical Biology, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht (The Netherlands), Fax: (+31) (0)30-253-6655.,Netherlands Proteomics Centre, Padualaan 8, 3584 CA Utrecht (The Netherlands)
| | - John Overvoorde
- Hubrecht Institute, KNAW and University Medical Centre, Uppsalalaan 8, 3508 AD Utrecht (The Netherlands)
| | - Stefan Knapp
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Headington, Oxford OX3 7DQ (U.K.)
| | - Jeroen den Hertog
- Hubrecht Institute, KNAW and University Medical Centre, Uppsalalaan 8, 3508 AD Utrecht (The Netherlands).,Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden (The Netherlands)
| | - Rob Ruijtenbeek
- Pamgene International Ltd. Wolvenhoek 10, 5200 BJ Den Bosch (The Netherlands)
| | - Rob M J Liskamp
- Medicinal Chemistry and Chemical Biology, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht (The Netherlands), Fax: (+31) (0)30-253-6655.,School of Chemistry, Joseph Black Building, Glasgow University, University Avenue, Glasgow G12 8QQ (U.K.)
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27
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Wang P, Zhang CJ, Chen G, Na Z, Yao SQ, Sun H. Site-specific immobilization of biomolecules by a biocompatible reaction between terminal cysteine and 2-cyanobenzothiazole. Chem Commun (Camb) 2013; 49:8644-6. [DOI: 10.1039/c3cc43566k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Pai J, Yoon T, Kim ND, Lee IS, Yu J, Shin I. High-throughput profiling of peptide-RNA interactions using peptide microarrays. J Am Chem Soc 2012; 134:19287-96. [PMID: 23110629 DOI: 10.1021/ja309760g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A rapid and quantitative method to evaluate binding properties of hairpin RNAs to peptides using peptide microarrays has been developed. The microarray technology was shown to be a powerful tool for high-throughput analysis of RNA-peptide interactions by its application to profiling interactions between 111 peptides and six hairpin RNAs. The peptide microarrays were also employed to measure hundreds of dissociation constants (K(d)) of RNA-peptide complexes. Our results reveal that both hydrophobic and hydrophilic faces of amphiphilic peptides are likely involved in interactions with RNAs. Furthermore, these results also show that most of the tested peptides bind hairpin RNAs with submicromolar K(d) values. One of the peptides identified by using this method was found to have good inhibitory activity against TAR-Tat interactions in cells. Because of their great applicability to evaluation of nearly all types of RNA-peptide interactions, peptide microarrays are expected to serve as robust tools for rapid assessment of peptide-RNA interactions and development of peptide ligands against RNA targets.
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Affiliation(s)
- Jaeyoung Pai
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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29
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Seaton DD, Krishnan J. Effects of multiple enzyme-substrate interactions in basic units of cellular signal processing. Phys Biol 2012; 9:045009. [PMID: 22872009 DOI: 10.1088/1478-3975/9/4/045009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covalent modification cycles are a ubiquitous feature of cellular signalling networks. In these systems, the interaction of an active enzyme with the unmodified form of its substrate is essential for signalling to occur. However, this interaction is not necessarily the only enzyme-substrate interaction possible. In this paper, we analyse the behaviour of a basic model of signalling in which additional, non-essential enzyme-substrate interactions are possible. These interactions include those between the inactive form of an enzyme and its substrate, and between the active form of an enzyme and its product. We find that these additional interactions can result in increased sensitivity and biphasic responses, respectively. The dynamics of the responses are also significantly altered by the presence of additional interactions. Finally, we evaluate the consequences of these interactions in two variations of our basic model, involving double modification of substrate and scaffold-mediated signalling, respectively. We conclude that the molecular details of protein-protein interactions are important in determining the signalling properties of enzymatic signalling pathways.
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Affiliation(s)
- D D Seaton
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, UK
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30
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Abstract
Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.
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31
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Current advances in peptide and small molecule microarray technologies. Curr Opin Chem Biol 2012; 16:234-42. [DOI: 10.1016/j.cbpa.2011.12.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/16/2011] [Accepted: 12/16/2011] [Indexed: 11/18/2022]
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32
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Peptide Arrays. MICROARRAYS IN DIAGNOSTICS AND BIOMARKER DEVELOPMENT 2012. [PMCID: PMC7193736 DOI: 10.1007/978-3-642-28203-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite the concern over the potential loss of structural information as a result of the use of peptides as opposed to proteins as molecular probes, peptide arrays have been implemented in a broad range of applications including antibody screening and epitope mapping, characterization of molecular interactions, and enzymatic activity profiling, and they have become a valuable tool for proteomics research. In this chapter, we first (Sect. 7.1) recapitulate the development of these arrays and highlight a couple of key improvements in the array production and the application in proteomics research. For clinical and biomarker development applications, it is important to measure entities that are directly related to physiological function (and dysfunction). In this respect, the assessment of enzymatic activities is obviously preferable to genotyping, expression profiling, or even measurement of protein amounts. In Sect. 7.2, an original technology based on peptides arrayed onto a porous support allows detailed profiling of kinase activities in a biological sample. The applications described range from kinase characterization to inhibition profiles, detection of off-target effects, and drug response prediction in a clinical setting, allowing rational choice of the drug to be used. Such directly functional approaches will have an important role in the transition to more personalized medicine. Finally, in Sect. 7.3, a recently developed method for “laser printing” of peptide arrays that will make these approaches much more practical is presented.
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33
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Gao L, Uttamchandani M, Yao SQ. Comparative proteomic profiling of mammalian cell lysates using phosphopeptide microarrays. Chem Commun (Camb) 2012; 48:2240-2. [DOI: 10.1039/c2cc17701c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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34
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H S Lu C, Liu K, Tan LP, Yao SQ. Current chemical biology tools for studying protein phosphorylation and dephosphorylation. Chemistry 2011; 18:28-39. [PMID: 22161995 DOI: 10.1002/chem.201103206] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Indexed: 12/12/2022]
Abstract
Amongst different posttranslational events involved in cellular-signaling pathways, phosphorylation and dephosphorylation of proteins are the most prevalent. Aberrant regulations in the cellular phosphoproteome network are implicated in most major human diseases. Consequently, kinases and phosphatases are two of the most important groups of drug targets in medicinal research today. A major challenge in the understanding of protein phosphorylation and dephosphorylation is the sheer complexity of the phosphoproteome network and the lack of tools capable of studying protein phosphorylation and dephosphorylation as they occur in cells. We highlight herein various chemical biology tools that have emerged in the last decade for such studies. First, we discuss the use of small-molecule mimics of phosphoamino acids and their use in elucidating the function of protein phosphorylation and dephosphorylation. We also introduce recent advances in the field of activity-based protein profiling (ABPP) for proteome-wide detection of protein phosphorylation and dephosphorylation. We next discuss the key concepts in the design of peptide- and protein-based biosensors capable of real-time reporting of phosphorylation/dephosphorylation events. Finally, we highlight the application of peptide and small-molecule microarrays (SMMs), and their applications in high-throughput screening and discovery of new compounds related to phosphorylation/dephosphorylation.
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Affiliation(s)
- Candy H S Lu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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35
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Shi H, Uttamchandani M, Yao SQ. Applying Small Molecule Microarrays and Resulting Affinity Probe Cocktails for Proteome Profiling of Mammalian Cell Lysates. Chem Asian J 2011; 6:2803-15. [DOI: 10.1002/asia.201100523] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Indexed: 12/22/2022]
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36
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Liu Q, Wu WH, Fang CL, Li RW, Liu P, Lei P, Hu J, Sun X, Zheng YZ, Zhao YF, Li YM. Mapping ApoE/Aβ binding regions to guide inhibitor discovery. MOLECULAR BIOSYSTEMS 2011; 7:1693-700. [PMID: 21409287 DOI: 10.1039/c1mb05019b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Blocking the interaction between the E4 isoform of apolipoprotein E (ApoE) and amyloid beta-peptide (Aβ) may be an avenue for pharmacological intervention in Alzheimer's disease (AD). The main regions of interaction of the two proteins are, respectively, ApoE244-272 and Aβ12-28. These protein segments are too large to facilitate the design of small molecule inhibitors. We mapped the primary components of ApoE/Aβ interaction to smaller peptide segments. Within the three motifs that are primarily responsible for ApoE/Aβ interaction, we identified four peptides that substantially block ApoE/Aβ interaction and further improved their inhibitory activity by rational hydrophobic amino acid substitution. Moreover, the mapping results provide the clue that the Aβ residues which interact with ApoE appear to be in the same region where Aβ self-interacts. According to this information, we found that Congo Red and X-34 could strongly inhibit ApoE/Aβ interaction. Our findings extend our understanding of ApoE/Aβ interaction and may guide the discovery of inhibitors that treat AD by antagonizing ApoE/Aβ interaction.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, PR China
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Ren L, Chen X, Luechapanichkul R, Selner NG, Meyer TM, Wavreille AS, Chan R, Iorio C, Zhou X, Neel BG, Pei D. Substrate specificity of protein tyrosine phosphatases 1B, RPTPα, SHP-1, and SHP-2. Biochemistry 2011; 50:2339-56. [PMID: 21291263 DOI: 10.1021/bi1014453] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We determined the substrate specificities of the protein tyrosine phosphatases (PTPs) PTP1B, RPTPα, SHP-1, and SHP-2 by on-bead screening of combinatorial peptide libraries and solution-phase kinetic analysis of individually synthesized phosphotyrosyl (pY) peptides. These PTPs exhibit different levels of sequence specificity and catalytic efficiency. The catalytic domain of RPTPα has very weak sequence specificity and is approximately 2 orders of magnitude less active than the other three PTPs. The PTP1B catalytic domain has modest preference for acidic residues on both sides of pY, is highly active toward multiply phosphorylated peptides, but disfavors basic residues at any position, a Gly at the pY-1 position, or a Pro at the pY+1 position. By contrast, SHP-1 and SHP-2 share similar but much narrower substrate specificities, with a strong preference for acidic and aromatic hydrophobic amino acids on both sides of the pY residue. An efficient SHP-1/2 substrate generally contains two or more acidic residues on the N-terminal side and one or more acidic residues on the C-terminal side of pY but no basic residues. Subtle differences exist between SHP-1 and SHP-2 in that SHP-1 has a stronger preference for acidic residues at the pY-1 and pY+1 positions and the two SHPs prefer acidic residues at different positions N-terminal to pY. A survey of the known protein substrates of PTP1B, SHP-1, and SHP-2 shows an excellent agreement between the in vivo dephosphorylation pattern and the in vitro specificity profiles derived from library screening. These results suggest that different PTPs have distinct sequence specificity profiles and the intrinsic activity/specificity of the PTP domain is an important determinant of the enzyme's in vivo substrate specificity.
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Affiliation(s)
- Lige Ren
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Wu H, Ge J, Yang PY, Wang J, Uttamchandani M, Yao SQ. A peptide aldehyde microarray for high-throughput profiling of cellular events. J Am Chem Soc 2011; 133:1946-54. [PMID: 21247160 DOI: 10.1021/ja109597v] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Microarrays provide exciting opportunities in the field of large-scale proteomics. With the aim to elucidate enzymatic activity and profiles within native biological samples, we developed a microarray comprising a focused positional-scanning library of enzyme inhibitors. The library was diversified across P(1)-P(4) positions, creating 270 different inhibitor sublibraries which were immobilized onto avidin slides. The peptide aldehyde-based small-molecule microarray (SMM) specifically targeted cysteine proteases, thereby enabling large-scale functional assessment of this subgroup of proteases, within fluorescently labeled samples, including pure proteins, cellular lysates, and infected samples. The arrays were shown to elicit binding fingerprints consistent with those of model proteins, specifically caspases and purified cysteine proteases from parasites (rhodesein and cruzain). When tested against lysates from apoptotic Hela and red blood cells infected with Plasmodium falciparum, clear signatures were obtained that were readily attributable to the activity of constituent proteases within these samples. Characteristic binding profiles were further able to distinguish various stages of the parasite infection in erythrocyte lysates. By converting one of our brightest microarray hits into a probe, putative protein markers were identified and pulled down from within apoptotic Hela lysates, demonstrating the potential of target validation and discovery. Taken together, these results demonstrate the utility of targeted SMMs in dissecting cellular biology in complex proteomic samples.
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Affiliation(s)
- Hao Wu
- Department of Chemistry, 3 Science Drive 3, National University of Singapore, Singapore 117543
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Wu H, Ge J, Uttamchandani M, Yao SQ. Small molecule microarrays: the first decade and beyond. Chem Commun (Camb) 2011; 47:5664-5670. [DOI: 10.1039/c1cc11464f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular Bits and Chips: Profiling and discovering the next generation of small molecule ligands.
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Affiliation(s)
- Hao Wu
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Jingyan Ge
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Mahesh Uttamchandani
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Department of Biological Sciences
- National University of Singapore
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Department of Biological Sciences
- National University of Singapore
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40
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Microarray-based enzyme profiling: Recent advances and applications (Review). Biointerphases 2010; 5:FA24-31. [DOI: 10.1116/1.3462969] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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41
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Gao L, Sun H, Yao SQ. Activity-based high-throughput determination of PTPs substrate specificity using a phosphopeptide microarray. Biopolymers 2010; 94:810-9. [DOI: 10.1002/bip.21533] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Fu J, Cai K, Johnston SA, Woodbury NW. Exploring peptide space for enzyme modulators. J Am Chem Soc 2010; 132:6419-24. [PMID: 20408521 DOI: 10.1021/ja100403a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A method is presented for screening high-density arrays to discover peptides that bind and modulate enzyme activity. A polyvinyl alcohol solution was applied to array surfaces to limit the diffusion of product molecules released from enzymatic reactions, allowing the simultaneous measurement of enzyme activity and binding at each peptide spot. For proof of concept, it was possible to identify peptides that bound to horseradish peroxidase, alkaline phosphatase, and beta-galactosidase and substantially altered enzyme activity by comparing the binding level of peptide to enzyme and bound enzyme activity. This basic technique may be generally applicable to find peptides or other small molecules that modify enzyme activity.
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Affiliation(s)
- Jinglin Fu
- Center for Single Molecule Biophysics, Arizona State University, Tempe, Arizona 85287, USA
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43
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Huang YY, Kuo CC, Chu CY, Huang YH, Hu YL, Lin JJ, Lo LC. Development of activity-based probes with tunable specificity for protein tyrosine phosphatase subfamilies. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.04.065] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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44
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Abstract
Speed and throughput are vital ingredients for discovery-driven, "-omics" research. The small molecule microarray is one such platform, which delivers phenomenal screening throughput and capabilities. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules at a high density on a flat surface, one is able to interrogate them quickly and conveniently, evaluating all possible interactions in a single step. SMMs have, over the last decade, been established as a robust platform for screening, lead discovery, and molecular characterization. In this chapter, we describe the ways in which microarrays have been constructed and applied, focusing on the practical challenges faced when designing and performing SMM experiments. This is written as an introduction for new readers to the field, explaining the key principles and laying the foundation for the chapters that follow.
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Affiliation(s)
- Mahesh Uttamchandani
- DSO National Laboratories, Defence Medical and Environmental Research Institute, Singapore, Singapore
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Kalesh KA, Tan LP, Lu K, Gao L, Wang J, Yao SQ. Peptide-based activity-based probes (ABPs) for target-specific profiling of proteintyrosine phosphatases (PTPs). Chem Commun (Camb) 2010; 46:589-91. [DOI: 10.1039/b919744c] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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46
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Vlad F, Rubio S, Rodrigues A, Sirichandra C, Belin C, Robert N, Leung J, Rodriguez PL, Laurière C, Merlot S. Protein phosphatases 2C regulate the activation of the Snf1-related kinase OST1 by abscisic acid in Arabidopsis. THE PLANT CELL 2009; 21:3170-84. [PMID: 19855047 PMCID: PMC2782292 DOI: 10.1105/tpc.109.069179] [Citation(s) in RCA: 367] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 09/12/2009] [Accepted: 09/29/2009] [Indexed: 05/18/2023]
Abstract
The plant hormone abscisic acid (ABA) orchestrates plant adaptive responses to a variety of stresses, including drought. This signaling pathway is regulated by reversible protein phosphorylation, and genetic evidence demonstrated that several related protein phosphatases 2C (PP2Cs) are negative regulators of this pathway in Arabidopsis thaliana. Here, we developed a protein phosphatase profiling strategy to define the substrate preferences of the HAB1 PP2C implicated in ABA signaling and used these data to screen for putative substrates. Interestingly, this analysis designated the activation loop of the ABA activated kinase OST1, related to Snf1 and AMPK kinases, as a putative HAB1 substrate. We experimentally demonstrated that HAB1 dephosphorylates and deactivates OST1 in vitro. Furthermore, HAB1 and the related PP2Cs ABI1 and ABI2 interact with OST1 in vivo, and mutations in the corresponding genes strongly affect OST1 activation by ABA. Our results provide evidence that PP2Cs are directly implicated in the ABA-dependent activation of OST1 and further suggest that the activation mechanism of AMPK/Snf1-related kinases through the inhibition of regulating PP2Cs is conserved from plants to human.
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Affiliation(s)
- Florina Vlad
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 91198 Gif-sur-Yvette Cedex, France
| | - Silvia Rubio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, ES-46022 Valencia, Spain
| | - Americo Rodrigues
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, ES-46022 Valencia, Spain
| | - Caroline Sirichandra
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 91198 Gif-sur-Yvette Cedex, France
| | - Christophe Belin
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 91198 Gif-sur-Yvette Cedex, France
| | - Nadia Robert
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 91198 Gif-sur-Yvette Cedex, France
| | - Jeffrey Leung
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 91198 Gif-sur-Yvette Cedex, France
| | - Pedro L. Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, ES-46022 Valencia, Spain
| | - Christiane Laurière
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 91198 Gif-sur-Yvette Cedex, France
- Address correspondence to
| | - Sylvain Merlot
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 91198 Gif-sur-Yvette Cedex, France
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Westerlind U, Schröder H, Hobel A, Gaidzik N, Kaiser A, Niemeyer C, Schmitt E, Waldmann H, Kunz H. Tumor-Associated MUC1 Tandem-Repeat Glycopeptide Microarrays to Evaluate Serum- and Monoclonal-Antibody Specificity. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902963] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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48
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Westerlind U, Schröder H, Hobel A, Gaidzik N, Kaiser A, Niemeyer C, Schmitt E, Waldmann H, Kunz H. Tumor-Associated MUC1 Tandem-Repeat Glycopeptide Microarrays to Evaluate Serum- and Monoclonal-Antibody Specificity. Angew Chem Int Ed Engl 2009; 48:8263-7. [DOI: 10.1002/anie.200902963] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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49
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Uttamchandani M, Lu CHS, Yao SQ. Next generation chemical proteomic tools for rapid enzyme profiling. Acc Chem Res 2009; 42:1183-92. [PMID: 19435360 DOI: 10.1021/ar9000586] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sequencing of the human genome provided a wealth of information about the genomic blueprint of a cell. But genes do not tell the entire story of life and living processes; identifying the roles of enzymes and mapping out their interactions is also crucial. Enzymes catalyze virtually every cellular process and metabolic exchange. They not only are instrumental in sustaining life but also are required for its regulation and diversification. Diseases such as cancer can be caused by minor changes in enzyme activities. In addition, the unique enzymes of pathogenic organisms are ripe targets for combating infections. Consequently, nearly one-third of all current drug targets are enzymes. An estimated 18-29% of eukaryotic genes encode enzymes, but only a limited proportion of enzymes have thus far been characterized. Therefore, little is understood about the physiological roles, substrate specificity, and downstream targets of the vast majority of these important proteins. A key step toward the biological characterization of enzymes, as well as their adoption as drug targets, is the development of global solutions that bridge the gap in understanding these proteins and their interactions. We herein present technological advances that facilitate the study of enzymes and their properties in a high-throughput manner. Over the years, our group has introduced and developed a variety of such enabling platforms for many classes of enzymes, including kinases, phosphatases, and proteases. For each of these different types of enzymes, specific design considerations are required to develop the appropriate chemical tools to characterize each class. These tools include activity-based probes and chemical compound libraries, which are rapidly assembled using efficient combinatorial synthesis or "click chemistry" strategies. The resulting molecular assortments may then be screened against the target enzymes in high-throughput using microplates or microarrays. These techniques offer powerful means to study, profile, and discover potent small molecules that can modulate enzyme activity. This Account will describe the concepts involved in designing chemical probes and libraries for comparative enzyme screening and drug discovery applications, as well as highlight how these technologies are changing the way in which enzymes may be rapidly profiled and characterized.
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Affiliation(s)
- Mahesh Uttamchandani
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510
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50
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Köhn M. Immobilization strategies for small molecule, peptide and protein microarrays. J Pept Sci 2009; 15:393-7. [PMID: 19308932 DOI: 10.1002/psc.1130] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protein, peptide and small molecule microarrays are valuable tools in biological research. In the last decade, substantial progress has been achieved to make these powerful technologies more reliable and available for researchers. This review describes chemical preparation methods for these microarrays with focus on site-selective and bioorthogonal immobilization reactions, particularly the Staudinger ligation and the thiol-ene reaction. In addition, the application of peptide microarrays, which were prepared by Staudinger ligation, to substrate specificity mapping is illustrated.
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Affiliation(s)
- Maja Köhn
- European Molecular Biology Laboratory, Gene Expression Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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