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Chang A, Leutert M, Rodriguez-Mias RA, Villén J. Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. J Proteome Res 2023; 22:1868-1880. [PMID: 37097255 PMCID: PMC10510590 DOI: 10.1021/acs.jproteome.2c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Phosphotyrosine (pY) enrichment is critical for expanding the fundamental and clinical understanding of cellular signaling by mass spectrometry-based proteomics. However, current pY enrichment methods exhibit a high cost per sample and limited reproducibility due to expensive affinity reagents and manual processing. We present rapid-robotic phosphotyrosine proteomics (R2-pY), which uses a magnetic particle processor and pY superbinders or antibodies. R2-pY can handle up to 96 samples in parallel, requires 2 days to go from cell lysate to mass spectrometry injections, and results in global proteomic, phosphoproteomic, and tyrosine-specific phosphoproteomic samples. We benchmark the method on HeLa cells stimulated with pervanadate and serum and report over 4000 unique pY sites from 1 mg of peptide input, strong reproducibility between replicates, and phosphopeptide enrichment efficiencies above 99%. R2-pY extends our previously reported R2-P2 proteomic and global phosphoproteomic sample preparation framework, opening the door to large-scale studies of pY signaling in concert with global proteome and phosphoproteome profiling.
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Affiliation(s)
- Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
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2
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Chang A, Leutert M, Rodriguez-Mias RA, Villén J. Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522335. [PMID: 36711935 PMCID: PMC9881991 DOI: 10.1101/2023.01.05.522335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Phosphotyrosine (pY) enrichment is critical for expanding fundamental and clinical understanding of cellular signaling by mass spectrometry-based proteomics. However, current pY enrichment methods exhibit a high cost per sample and limited reproducibility due to expensive affinity reagents and manual processing. We present rapid-robotic phosphotyrosine proteomics (R2-pY), which uses a magnetic particle processor and pY superbinders or antibodies. R2-pY handles 96 samples in parallel, requires 2 days to go from cell lysate to mass spectrometry injections, and results in global proteomic, phosphoproteomic and tyrosine specific phosphoproteomic samples. We benchmark the method on HeLa cells stimulated with pervanadate and serum and report over 4000 unique pY sites from 1 mg of peptide input, strong reproducibility between replicates, and phosphopeptide enrichment efficiencies above 99%. R2-pY extends our previously reported R2-P2 proteomic and global phosphoproteomic sample preparation framework, opening the door to large-scale studies of pY signaling in concert with global proteome and phosphoproteome profiling.
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Affiliation(s)
- Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
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3
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TIRAP-mediated activation of p38 MAPK in inflammatory signaling. Sci Rep 2022; 12:5601. [PMID: 35379857 PMCID: PMC8979995 DOI: 10.1038/s41598-022-09528-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/16/2022] [Indexed: 02/06/2023] Open
Abstract
AbstractThe role of TIRAP (toll/interleukin-1 receptor (TIR) domain-containing adapter protein) in macrophage inflammatory signalling has been significantly evolved since its discovery in 2001 due to its dynamic nature and subcellular localization to regulate multiple signaling through several protein–protein interactions (PPIs). Structural analysis of these interactions can reveal a better understanding of their conformational dynamics and the nature of their binding. Tyrosine phosphorylation in the TIR domain of TIRAP is very critical for its function. In toll-like receptor (TLR) 4/2 signalling, Bruton's tyrosine kinase (BTK) and Protein kinase C delta (PKCδ) are known to phosphorylate the Y86, Y106, Y159, and Y187 of TIRAP which is crucial for the downstream function of MAPKs (mitogen-activated protein kinases) activation. The objective of this study is to understand the interaction of TIRAP with p38 MAPK through molecular docking and identify the importance of TIRAP tyrosine phosphorylation in p38 MAPK interaction. In this structural study, we performed an in-silico molecular docking using HADDOCK 2.4, pyDockWEB, ClusPro 2.0, and ZDOCK 3.0.2 tools to unravel the interaction between TIRAP and p38 MAPK. Further, manual in-silico phosphorylations of TIRAP tyrosines; Y86, Y106, Y159, and Y187 was created in the Discovery Studio tool to study the conformational changes in protein docking and their binding affinities with p38 MAPK in comparison to non-phosphorylated state. Our molecular docking and 500 ns of molecular dynamic (MD) simulation study demonstrates that the Y86 phosphorylation (pY86) in TIRAP is crucial in promoting the higher binding affinity (∆Gbind) with p38 MAPK. The conformational changes due to the tyrosine phosphorylation mainly at the Y86 site pull the TIRAP closer to the active site in the kinase domain of p38 MAPK and plays a significant role at the interface site which is reversed in its dephosphorylated state. The heatmap of interactions between the TIRAP and p38 MAPK after the MD simulation shows that the TIRAP pY86 structure makes the highest number of stable hydrogen bonds with p38 MAPK residues. Our findings may further be validated in an in-vitro system and would be crucial for targeting the TIRAP and p38 MAPK interaction for therapeutic purposes against the chronic inflammatory response and associated diseases.
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4
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Dougherty PG, Karpurapu M, Koley A, Lukowski JK, Qian Z, Nirujogi TS, Rusu L, Chung S, Hummon AB, Li HW, Christman JW, Pei D. A Peptidyl Inhibitor that Blocks Calcineurin-NFAT Interaction and Prevents Acute Lung Injury. J Med Chem 2020; 63:12853-12872. [PMID: 33073986 PMCID: PMC8011862 DOI: 10.1021/acs.jmedchem.0c01236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Acute respiratory distress syndrome (ARDS) is an inflammatory lung disease with a high morbidity and mortality rate, for which no pharmacologic treatment is currently available. Our previous studies discovered that a pivotal step in the disease process is the activation of the nuclear factor of activated T cells (NFAT) c3 in lung macrophages, suggesting that inhibitors against the upstream protein phosphatase calcineurin should be effective for prevention/treatment of ARDS. Herein, we report the development of a highly potent, cell-permeable, and metabolically stable peptidyl inhibitor, CNI103, which selectively blocks the interaction between calcineurin and NFATc3, through computational and medicinal chemistry. CNI103 specifically inhibited calcineurin signaling in vitro and in vivo and exhibited a favorable pharmacokinetic profile, broad tissue distribution following different routes of administration, and minimal toxicity. Our data indicate that CNI103 is a promising novel treatment for ARDS and other inflammatory diseases.
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Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Entrada Therapeutics, 50 Northern Avenue, Boston, MA 02210, United States
| | - Manjula Karpurapu
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
| | - Jessica K. Lukowski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Entrada Therapeutics, 50 Northern Avenue, Boston, MA 02210, United States
| | - Teja Srinivas Nirujogi
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
- East Liverpool City Hospital, 425 W 5th Street, East Liverpool, Ohio 43920, United States
| | - Luiza Rusu
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Sangwoon Chung
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus OH, 43210, United States
| | - Hao W. Li
- Columbia Center for Translational Immunology, Columbia University, 650 W. 168 Street, New York, New York 10032, United States
| | - John W. Christman
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
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5
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An J, Zhai G, Guo Z, Bai X, Chen P, Dong H, Tian S, Ai D, Zhang Y, Zhang K. Combinatorial Peptide Ligand Library-Based Photoaffinity Probe for the Identification of Phosphotyrosine-Binding Domain Proteins. Anal Chem 2019; 91:3221-3226. [PMID: 30721620 DOI: 10.1021/acs.analchem.8b04781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphotyrosine (pY) serves as a docking site for the recognition proteins containing pY-binding (pYB) modules, such as the SH2 domain, to mediate cell signal transduction. Thus, it is vital to profile these binding proteins for understanding of signal regulation. However, identification of pYB proteins remains a significant challenge due to their low abundance and typically weak and transient interactions with pY sites. Herein, we designed and prepared a pY-peptide photoaffinity probe for the robust and specific enrichment and identification of its binding proteins. Using SHC1-pY317 as a paradigm, we showed that the developed probe enables to capture target protein with high selectivity and remarkable specificity even in a complex context. Notably, we expanded the strategy to a combinatorial pY-peptide-based photoaffinity probe by using combinatorial peptide ligand library (CPLL) technique and identified 24 SH2 domain proteins, which presents a deeper profiling of pYB proteins than previous reports using affinity probes. Moreover, the method can be used to mine putative pYB proteins and confirmed PKN2 as a selective binder to pY, expanding the repertoire of known domain proteins. Our approach provides a general strategy for rapid and robust interrogating pYB proteins and will promote the understanding of the signal transduction mechanism.
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Affiliation(s)
- Jinying An
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Guijin Zhai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Zhenchang Guo
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Xue Bai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Pu Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Hanyang Dong
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Ding Ai
- Tianjin Key Laboratory of Metabolic Diseases, Department of Physiology and Pathophysiology , Tianjin Medical University , Tianjin 300070 , China
| | - Yukui Zhang
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
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6
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Veggiani G, Huang H, Yates BP, Tong J, Kaneko T, Joshi R, Li SSC, Moran MF, Gish G, Sidhu SS. Engineered SH2 domains with tailored specificities and enhanced affinities for phosphoproteome analysis. Protein Sci 2018; 28:403-413. [PMID: 30431205 DOI: 10.1002/pro.3551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 02/05/2023]
Abstract
Protein phosphorylation is the most abundant post-translational modification in cells. Src homology 2 (SH2) domains specifically recognize phosphorylated tyrosine (pTyr) residues to mediate signaling cascades. A conserved pocket in the SH2 domain binds the pTyr side chain and the EF and BG loops determine binding specificity. By using large phage-displayed libraries, we engineered the EF and BG loops of the Fyn SH2 domain to alter specificity. Engineered SH2 variants exhibited distinct specificity profiles and were able to bind pTyr sites on the epidermal growth factor receptor, which were not recognized by the wild-type Fyn SH2 domain. Furthermore, mass spectrometry showed that SH2 variants with additional mutations in the pTyr-binding pocket that enhanced affinity were highly effective for enrichment of diverse pTyr peptides within the human proteome. These results showed that engineering of the EF and BG loops could be used to tailor SH2 domain specificity, and SH2 variants with diverse specificities and high affinities for pTyr residues enabled more comprehensive analysis of the human phosphoproteome. STATEMENT: Src Homology 2 (SH2) domains are modular domains that recognize phosphorylated tyrosine embedded in proteins, transducing these post-translational modifications into cellular responses. Here we used phage display to engineer hundreds of SH2 domain variants with altered binding specificities and enhanced affinities, which enabled efficient and differential enrichment of the human phosphoproteome for analysis by mass spectrometry. These engineered SH2 domain variants will be useful tools for elucidating the molecular determinants governing SH2 domains binding specificity and for enhancing analysis and understanding of the human phosphoproteome.
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Affiliation(s)
- Gianluca Veggiani
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Haiming Huang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Bradley P Yates
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Jiefei Tong
- Program in Molecular Structure and Function, The Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 0A4, Canada
| | - Tomonori Kaneko
- Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Rakesh Joshi
- Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Shawn S C Li
- Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Michael F Moran
- Program in Molecular Structure and Function, The Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 3E1, Canada.,The Hospital for Sick Children, SPARC Biocentre, Toronto, Ontario, M5G 0A4, Canada
| | - Gerald Gish
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Sachdev S Sidhu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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7
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Barnawi G, Noden M, Taylor R, Lohani C, Beriashvili D, Palmer M, Taylor SD. An entirely fmoc solid phase approach to the synthesis of daptomycin analogs. Biopolymers 2018; 111. [PMID: 29293268 DOI: 10.1002/bip.23094] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/29/2017] [Accepted: 12/03/2017] [Indexed: 02/06/2023]
Abstract
Daptomycin is an important Ca2+ -dependent cyclic lipodepsipeptide antibiotic used to treat serious gram-positive infections. The search for daptomycin analogs with improved activity and their application as tools for studying its mechanism of action has prompted us to develop an entirely Fmoc solid phase approach to the synthesis of daptomycin analogs. Key to the success of this approach was the development of conditions that allowed for the formation of the ester bond on resin-bound peptides consisting of residues 1-10 and the decanoyl lipid tail. The esterification reaction proceeded more efficiently on Tentagel resin as opposed to standard polystyrene resin. This approach was used to synthesize a series of analogs in which each position of Dap-E12-W13, a relatively active daptomycin analog, was individually substituted by alanine. Only positions 2, 6, and 11 were found to be amenable to substitution by alanine in that the corresponding alanine analogs were only 1.5- to 4-fold less active than Dap-E12-W13. We also found that the daptomycin analog, Dap-K6-E12-W13, exhibits in vitro activity approaching that of daptomycin at physiological Ca2+ concentration. Studies with Dap-K6-E12-W13 and model liposomes indicate that this analog interacts with membranes by the same mechanism as daptomycin. This analog is currently being used as a lead for the development daptomycin analogs with improved activity.
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Affiliation(s)
- Ghufran Barnawi
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Michael Noden
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Robert Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Chuda Lohani
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - David Beriashvili
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Michael Palmer
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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8
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Liao H, Pei D. Cell-permeable bicyclic peptidyl inhibitors against T-cell protein tyrosine phosphatase from a combinatorial library. Org Biomol Chem 2017; 15:9595-9598. [PMID: 29116277 PMCID: PMC5702537 DOI: 10.1039/c7ob02562a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein tyrosine phosphatases (PTPs) have been challenging targets for inhibitor design, because all PTPs share a highly conserved active site structure, which is positively charged and requires negatively charged moieties for tight binding. In this study, we developed cell-permeable bicyclic peptidyl inhibitors against T-cell PTP (TCPTP), which feature a cell-penetrating motif in one ring and a target-binding sequence in the second ring.
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Affiliation(s)
- Hui Liao
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.
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9
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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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10
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Lohani CR, Soley J, Kralt B, Palmer M, Taylor SD. α-Azido Esters in Depsipeptide Synthesis: C–O Bond Cleavage during Azido Group Reduction. J Org Chem 2016; 81:11831-11840. [PMID: 27934468 DOI: 10.1021/acs.joc.6b02309] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chuda Raj Lohani
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L
3G1, Canada
| | - Jacob Soley
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L
3G1, Canada
| | - Braden Kralt
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L
3G1, Canada
| | - Michael Palmer
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L
3G1, Canada
| | - Scott D. Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L
3G1, Canada
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11
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Lohani CR, Rasera B, Scott B, Palmer M, Taylor SD. α-Azido Acids in Solid-Phase Peptide Synthesis: Compatibility with Fmoc Chemistry and an Alternative Approach to the Solid Phase Synthesis of Daptomycin Analogs. J Org Chem 2016; 81:2624-8. [PMID: 26938305 DOI: 10.1021/acs.joc.5b02882] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Chuda Raj Lohani
- Department of Chemistry, University of Waterloo, 200 University
Avenue West, Waterloo, Ontario Canada, N2L 3G1
| | - Benjamin Rasera
- Department of Chemistry, University of Waterloo, 200 University
Avenue West, Waterloo, Ontario Canada, N2L 3G1
| | - Bradley Scott
- Department of Chemistry, University of Waterloo, 200 University
Avenue West, Waterloo, Ontario Canada, N2L 3G1
| | - Michael Palmer
- Department of Chemistry, University of Waterloo, 200 University
Avenue West, Waterloo, Ontario Canada, N2L 3G1
| | - Scott D. Taylor
- Department of Chemistry, University of Waterloo, 200 University
Avenue West, Waterloo, Ontario Canada, N2L 3G1
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12
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Wang Y, Han Y, Fan E, Zhang K. Analytical strategies used to identify the readers of histone modifications: A review. Anal Chim Acta 2015; 891:32-42. [PMID: 26388362 DOI: 10.1016/j.aca.2015.06.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
Abstract
The so-called "readers" of histone post-translational modifications (HPTMs) refer to proteins or complexes that are recruited to HPTMs thus eventually regulate gene transcription. To identify these "readers", mass spectrometry plays an essential role following various enriching strategies. These enriching methods include the use of modified histone peptides/proteins or chemically synthesized histones/nucleosomes containing desired HPTMs to enrich the readers of HPTMs. Despite the peptide- or protein-based assay is straightforward and easy to perform for most labs, this strategy has limited applications for those weak or combinational interactions among various HPTMs and false-positive results are a potential big problem. While the results derived from synthesized histone proteins/nucleosomes is more reliable as it mimics the real chromatic conditions thus is able to analyze the binders of those cross-talked HPTMs, usually the synthesis is so difficult that their applications are impeded for high throughput analysis. In this review, an overview of these analytical techniques is provided and their advantages and disadvantages are discussed.
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Affiliation(s)
- Ye Wang
- Department of Chemistry, Nankai University, 300071 Tianjin, China
| | - Yanpu Han
- Department of Chemistry, Nankai University, 300071 Tianjin, China
| | - Enguo Fan
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Stefan-Meier-Straße 17, 79104 Freiburg, Germany; School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Jungong Road No. 516, 200093 Shanghai, China.
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, 300070 Tianjin, China; Department of Chemistry, Nankai University, 300071 Tianjin, China.
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13
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Witucki LA, Borowicz LS, Pedley AM, Curtis-Fisk J, Kuszpit EG. Identification of FAK substrate peptides via colorimetric screening of a one-bead one-peptide combinatorial library. J Pept Sci 2015; 21:302-11. [PMID: 25728406 DOI: 10.1002/psc.2751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/19/2014] [Accepted: 12/30/2014] [Indexed: 11/09/2022]
Abstract
Focal adhesion kinase (FAK) is a protein tyrosine kinase that is associated with regulating cellular functions such as cell adhesion and migration and has emerged as an important target for cancer research. Short peptide substrates that are selectively and efficiently phosphorylated by FAK have not been previously identified and tested. Here we report the synthesis and screening of a one-bead one-peptide combinatorial library to identify novel substrates for FAK. Using a solid-phase colorimetric antibody tagging detection platform, the peptide beads phosphorylated by FAK were sequenced via Edman degradation and then validated through radioisotope kinetic studies with [γ-(32)P] ATP to derive Michaelis-Menton constants. The combination of results gathered from both colorimetric and radioisotope kinase assays led to the rational design of a second generation of FAK peptide substrates. Out of all the potential peptide substrates evaluated, the most active was GDYVEFKKK with a K(M) = 92 μM and a Vmax = 1920 nmol/min/mg. Peptide substrates discovered within this study may be useful diagnostic tools for future kinase investigations and may lead to novel therapeutic agents.
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Affiliation(s)
- Laurie A Witucki
- Department of Chemistry, Grand Valley State University, Allendale, MI, 49401, USA
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14
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Zaretsky S, Tan J, Hickey JL, Yudin AK. Macrocyclic templates for library synthesis of peptido-conjugates. Methods Mol Biol 2015; 1248:67-80. [PMID: 25616326 DOI: 10.1007/978-1-4939-2020-4_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cyclic peptides have wide utility in the biological sciences. As conformationally locked analogs of the parent linear peptides, they possess greater stability under physiological conditions and increased binding affinity for their targets. As investigations of biological processes often require reporter molecules and functional readouts, chemical probes are commonly appended with functional groups that allow for conjugation to biological entities. Herein we describe the functionalization of cyclic peptides prepared via aziridine aldehyde-mediated macrocyclization. These cyclic peptides contain an aziridine ring that can be further functionalized by ring opening with nucleophiles. We report on the methodology used to produce a cyclic peptide analog of Pro-Gly-Leu-Gly-Phe with either azido or sulfhydryl functionality.
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Affiliation(s)
- Serge Zaretsky
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada, M5S 3H6
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15
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Zhao B, Tan PH, Li SSC, Pei D. Systematic characterization of the specificity of the SH2 domains of cytoplasmic tyrosine kinases. J Proteomics 2013; 81:56-69. [PMID: 23313216 DOI: 10.1016/j.jprot.2012.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 12/18/2012] [Accepted: 12/29/2012] [Indexed: 01/26/2023]
Abstract
Cytoplasmic tyrosine kinases (CTK) generally contain a Src-homology 2 (SH2) domain, whose role in the CTK family is not fully understood. Here we report the determination of the specificity of 25 CTK SH2 domains by screening one-bead-one-compound (OBOC) peptide libraries. Based on the peptide sequences selected by the SH2 domains, we built Support Vector Machine (SVM) models for the prediction of binding ligands for the SH2 domains. These models yielded support for the progressive phosphorylation model for CTKs in which the overlapping specificity of the CTK SH2 and kinase domains has been proposed to facilitate targeting of the CTK substrates with at least two potential phosphotyrosine (pTyr) sites. We curated 93 CTK substrates with at least two pTyr sites catalyzed by the same CTK, and showed that 71% of these substrates had at least two pTyr sites predicted to bind a common CTK SH2 domain. More importantly, we found 34 instances where there was at least one pTyr site predicted to be recognized by the SH2 domain of the same CTK, suggesting that the SH2 and kinase domains of the CTKs may cooperate to achieve progressive phosphorylation of a protein substrate. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Bing Zhao
- Department of Biochemistry and Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada N6A 5C1
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16
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Kaneko T, Joshi R, Feller SM, Li SS. Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Cell Commun Signal 2012; 10:32. [PMID: 23134684 PMCID: PMC3507883 DOI: 10.1186/1478-811x-10-32] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022] Open
Abstract
SH2 domains are long known prominent players in the field of phosphotyrosine recognition within signaling protein networks. However, over the years they have been joined by an increasing number of other protein domain families that can, at least with some of their members, also recognise pTyr residues in a sequence-specific context. This superfamily of pTyr recognition modules, which includes substantial fractions of the PTB domains, as well as much smaller, or even single member fractions like the HYB domain, the PKCδ and PKCθ C2 domains and RKIP, represents a fascinating, medically relevant and hence intensely studied part of the cellular signaling architecture of metazoans. Protein tyrosine phosphorylation clearly serves a plethora of functions and pTyr recognition domains are used in a similarly wide range of interaction modes, which encompass, for example, partner protein switching, tandem recognition functionalities and the interaction with catalytically active protein domains. If looked upon closely enough, virtually no pTyr recognition and regulation event is an exact mirror image of another one in the same cell. Thus, the more we learn about the biology and ultrastructural details of pTyr recognition domains, the more does it become apparent that nature cleverly combines and varies a few basic principles to generate a sheer endless number of sophisticated and highly effective recognition/regulation events that are, under normal conditions, elegantly orchestrated in time and space. This knowledge is also valuable when exploring pTyr reader domains as diagnostic tools, drug targets or therapeutic reagents to combat human diseases.
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Affiliation(s)
- Tomonori Kaneko
- Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
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17
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18
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Kaneko T, Huang H, Cao X, Li X, Li C, Voss C, Sidhu SS, Li SSC. Superbinder SH2 Domains Act as Antagonists of Cell Signaling. Sci Signal 2012; 5:ra68. [DOI: 10.1126/scisignal.2003021] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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19
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Barua D, Hlavacek WS, Lipniacki T. A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. THE JOURNAL OF IMMUNOLOGY 2012; 189:646-58. [PMID: 22711887 DOI: 10.4049/jimmunol.1102003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BCR signaling regulates the activities and fates of B cells. BCR signaling encompasses two feedback loops emanating from Lyn and Fyn, which are Src family protein tyrosine kinases (SFKs). Positive feedback arises from SFK-mediated trans phosphorylation of BCR and receptor-bound Lyn and Fyn, which increases the kinase activities of Lyn and Fyn. Negative feedback arises from SFK-mediated cis phosphorylation of the transmembrane adapter protein PAG1, which recruits the cytosolic protein tyrosine kinase Csk to the plasma membrane, where it acts to decrease the kinase activities of Lyn and Fyn. To study the effects of the positive and negative feedback loops on the dynamical stability of BCR signaling and the relative contributions of Lyn and Fyn to BCR signaling, we consider in this study a rule-based model for early events in BCR signaling that encompasses membrane-proximal interactions of six proteins, as follows: BCR, Lyn, Fyn, Csk, PAG1, and Syk, a cytosolic protein tyrosine kinase that is activated as a result of SFK-mediated phosphorylation of BCR. The model is consistent with known effects of Lyn and Fyn deletions. We find that BCR signaling can generate a single pulse or oscillations of Syk activation depending on the strength of Ag signal and the relative levels of Lyn and Fyn. We also show that bistability can arise in Lyn- or Csk-deficient cells.
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Affiliation(s)
- Dipak Barua
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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20
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Kaneko T, Sidhu SS, Li SSC. Evolving specificity from variability for protein interaction domains. Trends Biochem Sci 2011; 36:183-90. [PMID: 21227701 DOI: 10.1016/j.tibs.2010.12.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 12/07/2010] [Accepted: 12/08/2010] [Indexed: 12/18/2022]
Abstract
An important question in modular domain-peptide interactions, which play crucial roles in many biological processes, is how the diverse specificities exhibited by different members of a domain family are encoded in a common scaffold. Analysis of the Src homology (SH) 2 family has revealed that its specificity is determined, in large part, by the configuration of surface loops that regulate ligand access to binding pockets. In a distinct manner, SH3 domains employ loops for ligand recognition. The PDZ domain, in contrast, achieves specificity by co-evolution of binding-site residues. Thus, the conformational and sequence variability afforded by surface loops and binding sites provides a general mechanism by which to encode the wide spectrum of specificities observed for modular protein interaction domains.
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Affiliation(s)
- Tomonori Kaneko
- Department of Biochemistry and the Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
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21
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Hard RL, Liu J, Shen J, Zhou P, Pei D. HDAC6 and Ubp-M BUZ domains recognize specific C-terminal sequences of proteins. Biochemistry 2010; 49:10737-46. [PMID: 21090589 PMCID: PMC3005221 DOI: 10.1021/bi101014s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The BUZ/Znf-UBP domain is a protein module found in the cytoplasmic deacetylase HDAC6, E3 ubiquitin ligase BRAP2/IMP, and a subfamily of ubiquitin-specific proteases. Although several BUZ domains have been shown to bind ubiquitin with high affinity by recognizing its C-terminal sequence (RLRGG-COOH), it is currently unknown whether the interaction is sequence-specific or whether the BUZ domains are capable of binding to proteins other than ubiquitin. In this work, the BUZ domains of HDAC6 and Ubp-M were subjected to screening against a one-bead-one-compound (OBOC) peptide library that exhibited random peptide sequences with free C-termini. Sequence analysis of the selected binding peptides as well as alanine scanning studies revealed that the BUZ domains require a C-terminal Gly-Gly motif for binding. At the more N-terminal positions, the two BUZ domains have distinct sequence specificities, allowing them to bind to different peptides and/or proteins. A database search of the human proteome on the basis of the BUZ domain specificities identified 11 and 24 potential partner proteins for Ubp-M and HDAC6 BUZ domains, respectively. Peptides corresponding to the C-terminal sequences of four of the predicted binding partners (FBXO11, histone H4, PTOV1, and FAT10) were synthesized and tested for binding to the BUZ domains by fluorescence polarization. All four peptides bound to the HDAC6 BUZ domain with low micromolar K(D) values and less tightly to the Ubp-M BUZ domain. Finally, in vitro pull-down assays showed that the Ubp-M BUZ domain was capable of binding to the histone H3-histone H4 tetramer protein complex. Our results suggest that BUZ domains are sequence-specific protein-binding modules, with each BUZ domain potentially binding to a different subset of proteins.
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Affiliation(s)
| | | | | | | | - Dehua Pei
- To whom correspondence should be addressed. Phone: 614-688-4068; Fax: 614-292-1532
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22
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Waterman PM, Cambier JC. The conundrum of inhibitory signaling by ITAM-containing immunoreceptors: potential molecular mechanisms. FEBS Lett 2010; 584:4878-82. [PMID: 20875413 PMCID: PMC2998577 DOI: 10.1016/j.febslet.2010.09.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 09/14/2010] [Accepted: 09/17/2010] [Indexed: 11/28/2022]
Abstract
Immunoreceptor signals must be appropriately transduced and regulated to achieve effective immunity while controlling inflammation and autoimmunity. It is generally held that these processes are mediated by the interplay of distinct activating and inhibitory receptors via conserved activating (ITAM) and inhibitory (ITIM) signaling motifs. However, recent evidence indicates that under certain conditions incomplete phosphorylation of ITAM tyrosines leads to inhibitory signaling. This new regulatory function of ITAMs has been termed ITAMi (inhibitory ITAM). Here we discuss the potential molecular mechanisms of inhibitory signaling by ITAM-containing receptors.
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Affiliation(s)
- Paul M Waterman
- Integrated Department of Immunology, University of Colorado School of Medicine, Denver CO 80206, USA
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23
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Chen X, Tan PH, Zhang Y, Pei D. On-bead screening of combinatorial libraries: reduction of nonspecific binding by decreasing surface ligand density. ACTA ACUST UNITED AC 2010; 11:604-11. [PMID: 19397369 DOI: 10.1021/cc9000168] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
On-bead screening of one-bead-one-compound (OBOC) libraries provides a powerful method for the rapid identification of active compounds against molecular or cellular targets. However, on-bead screening is susceptible to interference from nonspecific binding, which results in biased screening data and false positives. In this work, we have found that a major source of nonspecific binding is derived from the high ligand loading on the library beads, which permits a macromolecular target (e.g., a protein) to simultaneously interact with multiple ligands on the bead surface. To circumvent this problem, we have synthesized a phosphotyrosyl (pY)-containing peptide library on spatially segregated TentaGel microbeads, which feature a 10-fold reduced peptide loading on the bead surface but a normal peptide loading in the bead interior. The library was screened against a panel of 10 Src homology 2 (SH2) domains including those of Csk and Fyn kinases and adaptor protein SLAP, and the specific recognition motif(s) was successfully identified for each of the domains. In contrast, when the SH2 domains were screened against a control library that contained unaltered (high) ligand loading at the bead surface, six of them exhibited varying degrees of sequence biases, ranging from minor perturbation in the relative abundance of different sequences to the exclusive selection of false positive sequences that have no measurable affinity to the target protein. These results indicate that reduction of the ligand loading on the bead surface represents a simple, effective strategy to largely eliminate the interference from nonspecific binding, while preserving sufficient amounts of materials in the bead interior for compound identification. This finding should further expand the utility of OBOC libraries in biomedical research.
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Affiliation(s)
- Xianwen Chen
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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24
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Thakkar A, Cohen AS, Connolly MD, Zuckermann RN, Pei D. High-throughput sequencing of peptoids and peptide-peptoid hybrids by partial edman degradation and mass spectrometry. ACTA ACUST UNITED AC 2010; 11:294-302. [PMID: 19154119 DOI: 10.1021/cc8001734] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A method for the rapid sequence determination of peptoids [oligo(N-substituted glycines)] and peptide-peptoid hybrids selected from one-bead-one-compound combinatorial libraries has been developed. In this method, beads carrying unique peptoid (or peptide-peptoid) sequences were subjected to multiple cycles of partial Edman degradation (PED) by treatment with a 1:3 (mol/mol) mixture of phenyl isothiocyanate (PITC) and 9-fluorenylmethyl chloroformate (Fmoc-Cl) to generate a series of N-terminal truncation products for each resin-bound peptoid. After PED, the Fmoc group was removed from the N-terminus and any reacted side chains via piperidine treatment. The resulting mixture of the full-length peptoid and its truncation products was analyzed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry, to reveal the sequence of the full-length peptoid. With a slight modification, the method was also effective in the sequence determination of peptide-peptoid hybrids. This rapid, high-throughput, sensitive, and inexpensive sequencing method should greatly expand the utility of combinatorial peptoid libraries in biomedical and materials research.
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Affiliation(s)
- Amit Thakkar
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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25
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Kaneko T, Huang H, Zhao B, Li L, Liu H, Voss CK, Wu C, Schiller MR, Li SSC. Loops govern SH2 domain specificity by controlling access to binding pockets. Sci Signal 2010; 3:ra34. [PMID: 20442417 DOI: 10.1126/scisignal.2000796] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cellular functions require specific protein-protein interactions that are often mediated by modular domains that use binding pockets to engage particular sequence motifs in their partners. Yet, how different members of a domain family select for distinct sequence motifs is not fully understood. The human genome encodes 120 Src homology 2 (SH2) domains (in 110 proteins), which mediate protein-protein interactions by binding to proteins with diverse phosphotyrosine (pTyr)-containing sequences. The structure of the SH2 domain of BRDG1 bound to a peptide revealed a binding pocket that was blocked by a loop residue in most other SH2 domains. Analysis of 63 SH2 domain structures suggested that the SH2 domains contain three binding pockets, which exhibit selectivity for the three positions after the pTyr in a peptide, and that SH2 domain loops defined the accessibility and shape of these pockets. Despite sequence variability in the loops, we identified conserved structural features in the loops of SH2 domains responsible for controlling access to these surface pockets. We engineered new loops in an SH2 domain that altered specificity as predicted. Thus, selective blockage of binding subsites or pockets by surface loops provides a molecular basis by which the diverse modes of ligand recognition by the SH2 domain may have evolved and provides a framework for engineering SH2 domains and designing SH2-specific inhibitors.
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Affiliation(s)
- Tomonori Kaneko
- Department of Biochemistry and the Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada N6A 5C1
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26
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Combinatorial profiling of chromatin binding modules reveals multisite discrimination. Nat Chem Biol 2010; 6:283-90. [PMID: 20190764 PMCID: PMC2922993 DOI: 10.1038/nchembio.319] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 12/17/2009] [Indexed: 11/08/2022]
Abstract
Specific interactions between post-translational modifications (PTMs) and chromatin-binding proteins are central to the idea of a 'histone code'. Here, we used a 5,000-member, PTM-randomized, combinatorial peptide library based on the N terminus of histone H3 to interrogate the multisite specificity of six chromatin binding modules, which read the methylation status of Lys4. We found that Thr3 phosphorylation, Arg2 methylation and Thr6 phosphorylation are critical additional PTMs that modulate the ability to recognize and bind histone H3. Notably, phosphorylation of Thr6 yielded the most varied effect on protein binding, suggesting an important regulatory mechanism for readers of the H3 tail. Mass spectrometry and antibody-based evidence indicate that this previously uncharacterized modification exists on native H3, and NMR analysis of ING2 revealed the structural basis for discrimination. These investigations reveal a continuum of binding affinities in which multisite PTM recognition involves both switch- and rheostat-like properties, yielding graded effects that depend on the inherent 'reader' specificity.
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27
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Ekici OD, Zhu J, Wah Chung IY, Paetzel M, Dalbey RE, Pei D. Profiling the substrate specificity of viral protease VP4 by a FRET-based peptide library approach. Biochemistry 2009; 48:5753-9. [PMID: 19435306 DOI: 10.1021/bi900461e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Knowing the substrate specificity of a protease is useful in determining its physiological substrates, developing robust assays, and designing specific inhibitors against the enzyme. In this work, we report the development of a combinatorial peptide library method for systematically profiling the substrate specificity of endopeptidases. A fluorescent donor (Edans) and quencher (Dabcyl) pair was added to the C- and N-termini of a support-bound peptide. Protease cleavage of the peptide removed the N-terminal quencher, resulting in fluorescent beads, which were isolated and individually sequenced by partial Edman degradation and mass spectrometry (PED-MS) to reveal the peptide sequence, as well as the site of proteolytic cleavage. The method was validated with bovine trypsin and Escherichia coli leader peptidase and subsequently applied to determine the substrate specificity of a viral protease, VP4, derived from the blotched snakehead virus (BSNV). The results show that VP4 cleaves peptides with a consensus sequence of (Abu/Ala/Pro)-X-Ala downward arrowX, in agreement with the previously observed cleavage sites in its protein substrates. Resynthesis and a solution-phase assay of several representative sequences against VP4 confirmed the library screening results.
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Affiliation(s)
- Ozlem Dogan Ekici
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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28
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Cady CT, Rice JS, Ott VL, Cambier JC. Regulation of hematopoietic cell function by inhibitory immunoglobulin G receptors and their inositol lipid phosphatase effectors. Immunol Rev 2008; 224:44-57. [PMID: 18759919 DOI: 10.1111/j.1600-065x.2008.00663.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Numerous autoimmune and inflammatory disorders stem from the dysregulation of hematopoietic cell activation. The activity of inositol lipid and protein tyrosine phosphatases, and the receptors that recruit them, is critical for prevention of these disorders. Balanced signaling by inhibitory and activating receptors is now recognized to be an important factor in tuning cell function and inflammatory potential. In this review, we provide an overview of current knowledge of membrane proximal events in signaling by inhibitory/regulatory receptors focusing on structural and functional characteristics of receptors and their effectors Src homology 2 (SH2) domain-containing tyrosine phosphatase 1 and SH2 domain-containing inositol 5-phosphatase-1. We review use of new strategies to identify novel regulatory receptors and effectors. Finally, we discuss complementary actions of paired inhibitory and activating receptors, using Fc gammaRIIA and Fc gammaRIIB regulation human basophil activation as a prototype.
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Affiliation(s)
- Carol T Cady
- Department of Immunology, University of Colorado Denver School of Medicine, Denver, CO, USA
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29
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Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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30
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Mitra S, Barrios AM. Identifying selective protein tyrosine phosphatase substrates and inhibitors from a fluorogenic, combinatorial peptide library. Chembiochem 2008; 9:1216-9. [PMID: 18412190 DOI: 10.1002/cbic.200800046] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sayantan Mitra
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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31
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Zhang Y, Zhou S, Wavreille AS, DeWille J, Pei D. Cyclic peptidyl inhibitors of Grb2 and tensin SH2 domains identified from combinatorial libraries. ACTA ACUST UNITED AC 2008; 10:247-55. [PMID: 18257540 DOI: 10.1021/cc700185g] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic peptides provide attractive lead compounds for drug discovery and excellent molecular probes in biomedical research. In this work, a novel method has been developed for the high-throughput synthesis, screening, and identification of cyclic peptidyl ligands against macromolecular targets. Support-bound cyclic phosphotyrosyl peptide libraries containing randomized amino acid sequences and different ring sizes (theoretical diversity of 3.2 x 10(6)) were synthesized and screened against the SH2 domains of Grb2 and tensin. Potent, selective inhibitors were identified from the libraries and were generally more effective than the corresponding linear peptides. One of the inhibitors selected against the Grb2 SH2 domain inhibited human breast cancer cell growth and disrupted actin filaments. This method should be applicable to the development of cyclic peptidyl inhibitors against other protein domains, enzymes, and receptors.
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Affiliation(s)
- Yanyan Zhang
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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32
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Joo SH, Pei D. Synthesis and screening of support-bound combinatorial peptide libraries with free C-termini: determination of the sequence specificity of PDZ domains. Biochemistry 2008; 47:3061-72. [PMID: 18232644 DOI: 10.1021/bi7023628] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Preparation of support-bound combinatorial peptide libraries with free C-termini has been challenging in the past because solid-phase peptide synthesis usually starts from the C-terminus, which must be covalently attached to the solid support. In this work, we have developed a general methodology to synthesize and screen one-bead-one-compound peptide libraries containing free C-termini. TentaGel microbeads (90 mum) were spatially segregated into outer and inner layers, and peptides were synthesized on the beads in the conventional C --> N manner, with their C-termini attached to the support through an ester linkage on the bead surface but through an amide bond in the bead interior. The surface peptides were cyclized between their N-terminal amine and a carboxyl group installed at a C-terminal linker sequence, while the internal peptides were kept in the linear form. Base hydrolysis of the ester linkage in the cyclic peptides regenerated linear peptides that contained a free alpha-carboxyl group at their C-termini but remained covalently attached to the resin via the N-termini ("inverted" peptides). An inverted peptide library containing five random residues (theoretical diversity of 3.2 x 10 (6)) was synthesized and screened for binding to four postsynaptic density-95/discs large/zona occluden-1 (PDZ) domains of sodium-hydrogen exchanger regulatory factor-1 (NHERF1) and channel-interacting PDZ domain protein (CIPP). The identity of the binding peptides was determined by sequencing the linear encoding peptides inside the bead by partial Edman degradation/mass spectrometry. Consensus recognition motifs were identified for the PDZ domains, and representative peptides were resynthesized and confirmed for binding to their cognate PDZ domains. This method should be generally applicable to all PDZ domains as well as other protein domains and enzymes that recognize the C-terminus of their target proteins.
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Affiliation(s)
- Sang Hoon Joo
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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