1
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De Bakshi D, Chen YC, Wuerzberger-Davis SM, Ma M, Waters BJ, Li L, Suzuki A, Miyamoto S. Ectopic CH60 mediates HAPLN1-induced cell survival signaling in multiple myeloma. Life Sci Alliance 2023; 6:e202201636. [PMID: 36625202 PMCID: PMC9748848 DOI: 10.26508/lsa.202201636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Multiple myeloma (MM), the second most common hematological malignancy, is generally considered incurable because of the development of drug resistance. We previously reported that hyaluronan and proteoglycan link protein 1 (HAPLN1) produced by stromal cells induces activation of NF-κB, a tumor-supportive transcription factor, and promotes drug resistance in MM cells. However, the identity of the cell surface receptor that detects HAPLN1 and thereby engenders pro-tumorigenic signaling in MM cells remains unknown. Here, we performed an unbiased cell surface biotinylation assay and identified chaperonin 60 (CH60) as the direct binding partner of HAPLN1 on MM cells. Cell surface CH60 specifically interacted with TLR4 to evoke HAPLN1-induced NF-κB signaling, transcription of anti-apoptotic genes, and drug resistance in MM cells. Collectively, our findings identify a cell surface CH60-TLR4 complex as a HAPLN1 receptor and a potential molecular target to overcome drug resistance in MM cells.
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Affiliation(s)
- Debayan De Bakshi
- Cellular and Molecular Biology Graduate Program, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory of Cancer Research, University of Wisconsin, Madison, WI, USA
- Department of Oncology, University of Wisconsin, Madison, WI, USA
| | - Yu-Chia Chen
- McArdle Laboratory of Cancer Research, University of Wisconsin, Madison, WI, USA
- Department of Oncology, University of Wisconsin, Madison, WI, USA
| | - Shelly M Wuerzberger-Davis
- McArdle Laboratory of Cancer Research, University of Wisconsin, Madison, WI, USA
- Department of Oncology, University of Wisconsin, Madison, WI, USA
| | - Min Ma
- School of Pharmacy, University of Wisconsin, Madison, WI, USA
| | - Bayley J Waters
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Aussie Suzuki
- McArdle Laboratory of Cancer Research, University of Wisconsin, Madison, WI, USA
- Department of Oncology, University of Wisconsin, Madison, WI, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Shigeki Miyamoto
- McArdle Laboratory of Cancer Research, University of Wisconsin, Madison, WI, USA
- Department of Oncology, University of Wisconsin, Madison, WI, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
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2
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Benkovic SJ. From Bioorganic Models to Cells. Annu Rev Biochem 2021; 90:57-76. [PMID: 34153218 DOI: 10.1146/annurev-biochem-062320-062929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
I endeavor to share how various choices-some deliberate, some unconscious-and the unmistakable influence of many others shaped my scientific pursuits. I am fascinated by how two long-term, major streams of my research, DNA replication and purine biosynthesis, have merged with unexpected interconnections. If I have imparted to many of the talented individuals who have passed through my lab a degree of my passion for uncloaking the mysteries hidden in scientific research and an understanding of the honesty and rigor it demands and its impact on the world community, then my mentorship has been successful.
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Affiliation(s)
- Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
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3
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Huang R, Zhu W, Wu Y, Chen J, Yu J, Jiang B, Chen H, Chen W. A novel mass spectrometry-cleavable, phosphate-based enrichable and multi-targeting protein cross-linker. Chem Sci 2019; 10:6443-6447. [PMID: 31341596 PMCID: PMC6611067 DOI: 10.1039/c9sc00893d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Chemical cross-linking mass spectrometry (XL-MS) is a powerful technology for obtaining protein structural information and studying protein-protein interactions. We report phospho-bisvinylsulfone (pBVS) as a novel water-soluble, MS-cleavable, phosphate-based enrichable and multi-targeting cross-linker. In this approach, the fragmentation of pBVS cross-linked peptides occurs in situ through retro-Michael addition. The phosphate group is successfully used as a small affinity tag to isolate cross-linked peptides from the highly abundant non-cross-linked peptides. In addition, the linker targets multiple types of amino acid residues, including cysteine, lysine and histidine. This method was applied to cross-link bovine serum albumin (BSA), myoglobin and Lbcpf1 demonstrating the ability to yield accurate and abundant information to facilitate protein structure elucidation.
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Affiliation(s)
- Rong Huang
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
- University of Chinese Academy of Sciences , 19A Yuquan Road, Shijingshan District , Beijing , 100049 , China
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Yue Wu
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Jiakang Chen
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Jianghui Yu
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
- University of Chinese Academy of Sciences , 19A Yuquan Road, Shijingshan District , Beijing , 100049 , China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Hongli Chen
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Wenzhang Chen
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
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4
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Jiang Y, Suo H, Zhao Y, Li X, Sun Y, Li X, Dong W, Li W, Zhang W, Xu G. DBU-Promoted Cu(OAc)•H 2O-Catalysed Coupling Reactions of Aryl Iodides and Sodium Azide. JOURNAL OF CHEMICAL RESEARCH 2018. [DOI: 10.3184/174751918x15260507766192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
An efficient and simple protocol for the synthesis of aryl azides by the coupling of aryl iodides with sodium azide, in good to excellent yields in DMSO at 95 °C under catalysis by Cu(OAc)2-H2O and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), has been established. The optimised loadings of Cu(OAc)2-H2O and DBU were 10 mol% and 15 mol% respectively.
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Affiliation(s)
- Yuqin Jiang
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, PR. China
| | - Huajun Suo
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, PR. China
| | - Yaru Zhao
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, PR. China
| | - Xiyong Li
- Weihai Ocean Vocational College, Weihai, PR. China
| | - Yamin Sun
- Weihai Ocean Vocational College, Weihai, PR. China
| | - Xingfeng Li
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, PR. China
| | - Wenpei Dong
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, PR. China
| | - Wei Li
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, PR. China
| | - Weiwei Zhang
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, PR. China
| | - Guiqing Xu
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, PR. China
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5
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Chu F, Thornton DT, Nguyen HT. Chemical cross-linking in the structural analysis of protein assemblies. Methods 2018; 144:53-63. [PMID: 29857191 DOI: 10.1016/j.ymeth.2018.05.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
For decades, chemical cross-linking of proteins has been an established method to study protein interaction partners. The chemical cross-linking approach has recently been revived by mass spectrometric analysis of the cross-linking reaction products. Chemical cross-linking and mass spectrometric analysis (CXMS) enables the identification of residues that are close in three-dimensional (3D) space but not necessarily close in primary sequence. Therefore, this approach provides medium resolution information to guide de novo structure prediction, protein interface mapping and protein complex model building. The robustness and compatibility of the CXMS approach with multiple biochemical methods have made it especially appealing for challenging systems with multiple biochemical compositions and conformation states. This review provides an overview of the CXMS approach, describing general procedures in sample processing, data acquisition and analysis. Selection of proper chemical cross-linking reagents, strategies for cross-linked peptide identification, and successful application of CXMS in structural characterization of proteins and protein complexes are discussed.
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Affiliation(s)
- Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, United States.
| | - Daniel T Thornton
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
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6
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Lössl P, van de Waterbeemd M, Heck AJ. The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO J 2016; 35:2634-2657. [PMID: 27797822 PMCID: PMC5167345 DOI: 10.15252/embj.201694818] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes.
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Affiliation(s)
- Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
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7
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Zheng Q, Zhang H, Wu S, Chen H. Probing Protein 3D Structures and Conformational Changes Using Electrochemistry-Assisted Isotope Labeling Cross-Linking Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:864-875. [PMID: 26902947 PMCID: PMC4841728 DOI: 10.1007/s13361-016-1356-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
This study presents a new chemical cross-linking mass spectrometry (MS) method in combination with electrochemistry and isotope labeling strategy for probing both protein three-dimensional (3D) structures and conformational changes. For the former purpose, the target protein/protein complex is cross-linked with equal mole of premixed light and heavy isotope labeled cross-linkers carrying electrochemically reducible disulfide bonds (i.e., DSP-d0 and DSP-d8 in this study, DSP = dithiobis[succinimidyl propionate]), digested and then electrochemically reduced followed with online MS analysis. Cross-links can be quickly identified because of their reduced intensities upon electrolysis and the presence of doublet isotopic peak characteristics. In addition, electroreduction converts cross-links into linear peptides, facilitating MS/MS analysis to gain increased information about their sequences and modification sites. For the latter purpose of probing protein conformational changes, an altered procedure is adopted, in which the protein in two different conformations is cross-linked using DSP-d0 and DSP-d8 separately, and then the two protein samples are mixed in 1:1 molar ratio. The merged sample is subjected to digestion and electrochemical mass spectrometric analysis. In such a comparative cross-linking experiment, cross-links could still be rapidly recognized based on their responses to electrolysis. More importantly, the ion intensity ratios of light and heavy isotope labeled cross-links reveal the conformational changes of the protein, as exemplified by examining the effect of Ca(2+) on calmodulin conformation alternation. This new cross-linking MS method is fast and would have high value in structural biology. Graphical Abstract ᅟ.
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Affiliation(s)
- Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA
| | - Hao Zhang
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Shiyong Wu
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA.
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8
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Holding AN. XL-MS: Protein cross-linking coupled with mass spectrometry. Methods 2015; 89:54-63. [PMID: 26079926 DOI: 10.1016/j.ymeth.2015.06.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 11/29/2022] Open
Abstract
With the continuing trend to study larger and more complex systems, the application of protein cross-linking coupled with mass spectrometry (XL-MS) provides a varied toolkit perfectly suited to achieve these goals. By freezing the transient interactions through the formation of covalent bonds, XL-MS provides a vital insight into both the structure and organization of proteins in a wide variety of conditions. This review covers some of the established methods that underpin the field alongside the more recent developments that hold promise to further realize its potential in new directions.
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Affiliation(s)
- Andrew N Holding
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
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9
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Tran BQ, Goodlett DR, Goo YA. Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:123-9. [PMID: 26025770 DOI: 10.1016/j.bbapap.2015.05.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/07/2015] [Accepted: 05/18/2015] [Indexed: 01/12/2023]
Abstract
For the analysis of protein-protein interactions and protein conformations, cross-linking coupled with mass spectrometry (CXMS) has become an essential tool in recent years. A variety of cross-linking reagents are used to covalently link interacting amino acids to identify protein-binding partners. The spatial proximity of cross-linked amino acid residues is used to elucidate structural models of protein complexes. The main challenges for mapping protein-protein interaction are low stoichiometry and low frequency of cross-linked peptides relative to unmodified linear peptides as well as accurate and efficient matches to corresponding peptide sequences with low false discovery rates for identifying the site of cross-link. We evaluate the current state of chemical cross-linking and mass spectrometry applications with the special emphasis on the recent development of informatics data processing and analysis tools that help complexity of interpreting CXMS data. This article is part of a Special Issue entitled:Physiological Enzymology and Protein Functions.
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Affiliation(s)
- Bao Quoc Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
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10
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Zheng Q, Zhang H, Tong L, Wu S, Chen H. Cross-linking electrochemical mass spectrometry for probing protein three-dimensional structures. Anal Chem 2014; 86:8983-91. [PMID: 25141260 PMCID: PMC4165463 DOI: 10.1021/ac501526n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/20/2014] [Indexed: 12/27/2022]
Abstract
Chemical cross-linking combined with mass spectrometry (MS) is powerful to provide protein three-dimensional structure information but difficulties in identifying cross-linked peptides and elucidating their structures limit its usefulness. To tackle these challenges, this study presents a novel cross-linking MS in conjunction with electrochemistry using disulfide-bond-containing dithiobis[succinimidyl propionate] (DSP) as the cross-linker. In our approach, electrolysis of DSP-bridged protein/peptide products, as online monitored by desorption electrospray ionization mass spectrometry is highly informative. First, as disulfide bonds are electrochemically reducible, the cross-links are subject to pronounced intensity decrease upon electrolytic reduction, suggesting a new way to identify cross-links. Also, mass shift before and after electrolysis suggests the linkage pattern of cross-links. Electrochemical reduction removes disulfide bond constraints, possibly increasing sequence coverage for tandem MS analysis and yielding linear peptides whose structures are more easily determined than their cross-linked precursor peptides. Furthermore, this cross-linking electrochemical MS method is rapid, due to the fast nature of electrochemical conversion (much faster than traditional chemical reduction) and no need for chromatographic separation, which would be of high value for structural proteomics research.
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Affiliation(s)
- Qiuling Zheng
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States
| | - Hao Zhang
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Lingying Tong
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States
| | - Shiyong Wu
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States
| | - Hao Chen
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States
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11
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Vasicek L, O'Brien JP, Browning KS, Tao Z, Liu HW, Brodbelt JS. Mapping protein surface accessibility via an electron transfer dissociation selectively cleavable hydrazone probe. Mol Cell Proteomics 2012; 11:O111.015826. [PMID: 22393264 DOI: 10.1074/mcp.o111.015826] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A protein's surface influences its role in protein-protein interactions and protein-ligand binding. Mass spectrometry can be used to give low resolution structural information about protein surfaces and conformations when used in combination with derivatization methods that target surface accessible amino acid residues. However, pinpointing the resulting modified peptides upon enzymatic digestion of the surface-modified protein is challenging because of the complexity of the peptide mixture and low abundance of modified peptides. Here a novel hydrazone reagent (NN) is presented that allows facile identification of all modified surface residues through a preferential cleavage upon activation by electron transfer dissociation coupled with a collision activation scan to pinpoint the modified residue in the peptide sequence. Using this approach, the correlation between percent reactivity and surface accessibility is demonstrated for two biologically active proteins, wheat eIF4E and PARP-1 Domain C.
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Affiliation(s)
- Lisa Vasicek
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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12
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Tomohiro T, Kato K, Masuda S, Kishi H, Hatanaka Y. Photochemical Construction of Coumarin Fluorophore on Affinity-Anchored Protein. Bioconjug Chem 2011; 22:315-8. [DOI: 10.1021/bc100598r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takenori Tomohiro
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kenichi Kato
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Souta Masuda
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroyuki Kishi
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yasumaru Hatanaka
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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13
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Paramelle D, Enjalbal C, Amblard M, Forest E, Heymann M, Cantel S, Geourjon C, Martinez J, Subra G. Solid-Phase Cross-Linking (SPCL): A new tool for protein structure studies. Proteomics 2011; 11:1277-86. [DOI: 10.1002/pmic.201000029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 11/04/2010] [Accepted: 12/20/2010] [Indexed: 11/09/2022]
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14
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Popova TV, Reinbolt J, Ehresmann B, Shakirov MM, Serebriakova MV, Gerassimova YV, Knorre DG, Godovikova TS. Why do p-nitro-substituted aryl azides provide unintended dark reactions with proteins? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2010; 100:19-29. [PMID: 20570168 DOI: 10.1016/j.jphotobiol.2010.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 04/08/2010] [Accepted: 04/08/2010] [Indexed: 05/29/2023]
Abstract
Aryl azide-mediated photo cross-linking has been widely used to obtain structural features in biological systems, even though the reactive species generated upon photolysis in aqueous solution have not been well characterized. We have established a mechanistic framework for the formation of adducts between photoactivated 5-azido-2-nitrobenzoyl reagents and protein functional groups. Photolysis of the aryl azide tethered to biotin via an amide linkage yields a cross-link with streptavidin. The ability of the pre-irradiated reagent to form a similar cross-link indicates that it is the long-lived reactive intermediate that contributes to the cross-link formation. The reactive intermediate forms an adduct with tryptophan. The sequence of the labeled peptide is found to be GlyTrp(*)ThrValAlaTrp(*)LysAsn, corresponding to residues 74-81 of the streptavidin sequence, where Trp(*) designates the modified Trp-75 and Trp-79. A peak at m/z 1455.1 corresponding to the calculated [M(peptide)+aryl nitrene+2O](+) molecular ion value has been observed for the labeled peptide. Product structure identification experiments support the assignment that the long-lived reactive intermediate is a p-nitro-N-arylhydroxylamine, which undergoes a number of transformations in aqueous solution leading to nitroso derivatives. A plausible mechanism of the interaction between tryptophan and nitroso compound is discussed.
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Affiliation(s)
- Tatyana V Popova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian branch of the Russian Academy of Science, Novosibirsk 630090, Russia.
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15
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Tsai CS, Liu PY, Yen HY, Hsu TL, Wong CH. Development of trifunctional probes for glycoproteomic analysis. Chem Commun (Camb) 2010; 46:5575-7. [PMID: 20467665 DOI: 10.1039/c0cc00345j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new trifunctional probe, assembled using a cleavable linker, is useful for efficient enrichment and detection of alkynyl sugar-tagged biomolecules.
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Affiliation(s)
- Charng-Sheng Tsai
- Genomics Research Center, Academia Sinica, 128 Academia Road Section 2, Nankang, Taipei 115, Taiwan
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16
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Paramelle D, Cantel S, Enjalbal C, Amblard M, Forest E, Heymann M, Geourjon C, Martinez J, Subra G. A new generation of cross-linkers for selective detection by MALDI MS. Proteomics 2009; 9:5384-8. [DOI: 10.1002/pmic.200900562] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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17
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Chu F, Baker PR, Burlingame AL, Chalkley RJ. Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides. Mol Cell Proteomics 2009; 9:25-31. [PMID: 19809093 DOI: 10.1074/mcp.m800555-mcp200] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chemical cross-linking, followed by identification of the cross-linked residues, is a powerful approach to probe the topologies and interacting surfaces of protein assemblies. In this work, we demonstrate a new bioinformatics approach using multiple program modules within the software package "Protein Prospector" that greatly facilitates the discovery of cross-linked peptides in chemical cross-linking studies. Examples are given for how this approach has been used for defining interfaces in heterodimeric and homodimeric protein complexes, both of which provide results in close agreement with crystal structures, verifying the reliability of the approach.
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Affiliation(s)
- Feixia Chu
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
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18
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Lu Y, Tanasova M, Borhan B, Reid GE. Ionic reagent for controlling the gas-phase fragmentation reactions of cross-linked peptides. Anal Chem 2009; 80:9279-87. [PMID: 19551991 DOI: 10.1021/ac801625e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical cross-linking combined with proteolytic digestion and mass spectrometry (MS) is a promising approach to provide inter- and intramolecular distance constraints for the structural characterization of protein topologies and functional multiprotein complexes. Despite the relative straightforwardness of these methodologies, the identification and characterization of cross-linked proteins presents a significant analytical challenge, due to the complexity of the resultant peptide mixtures, as well as the array of inter-, intra-, or "dead-end"-cross-linked peptides that may be generated from a single cross-linking experiment. To address these issues, we describe here the synthesis, characterization, and initial evaluation of a novel "fixed charge" sulfonium ion-containing crosslinking reagent, S-methyl 5,5'-thiodipentanoylhydroxysuc-cinimide. The peptide products obtained by reaction with this reagent are all shown to fragment exclusively via facile cleavage of the C-S bond directly adjacent to the fixed charge during CID-MS/MS, resulting in the formation of characteristic product ions that enable the presence and type (i.e., inter, intra, or dead-end) of the cross-linked products to be readily determined, independently of the "proton mobility" of the precursor ion. Subsequent isolation and dissociation of these products by MS3 provides additional structural information required for identification of the peptide sequences involved in the cross-linking reactions, as well as for characterization of the specific site(s) at which cross-linking has occurred. The specificity of these gas-phase fragmentation reactions, as well as the solubility and stability of the cross-linking reagent under aqueous conditions, suggests that this strategy holds great promise for use in future studies aimed at the structural analysis of large proteins or multiprotein assemblies.
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Affiliation(s)
- Yali Lu
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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19
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Recombinant human SMOCs produced by in vitro refolding: Calcium-binding properties and interactions with serum proteins. Protein Expr Purif 2008; 62:75-82. [DOI: 10.1016/j.pep.2008.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 07/18/2008] [Accepted: 07/21/2008] [Indexed: 11/18/2022]
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20
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Kim Y, Ebright YW, Goodman AR, Reinberg D, Ebright RH. Nonradioactive, ultrasensitive site-specific protein-protein photocrosslinking: interactions of alpha-helix 2 of TATA-binding protein with general transcription factor TFIIA and transcriptional repressor NC2. Nucleic Acids Res 2008; 36:6143-54. [PMID: 18824481 PMCID: PMC2577341 DOI: 10.1093/nar/gkn612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We have developed an approach that enables nonradioactive, ultrasensitive (attamole sensitivity) site-specific protein–protein photocrosslinking, and we have applied the approach to the analysis of interactions of α-helix 2 (H2) of human TATA-element binding protein (TBP) with general transcription factor TFIIA and transcriptional repressor NC2. We have found that TBP H2 can be crosslinked to TFIIA in the TFIIA–TBP–DNA complex and in higher order transcription–initiation complexes, and we have mapped the crosslink to the ‘connector’ region of the TFIIA α/β subunit (TFIIAα/β). We further have found that TBP H2 can be crosslinked to NC2 in the NC2–TBP–DNA complex, and we have mapped the crosslink to the C-terminal ‘tail’ of the NC2 α-subunit (NC2α). Interactions of TBP H2 with the TFIIAα/β connector and the NC2α C-terminal tail were not observed in crystal structures of TFIIA–TBP–DNA and NC2–TBP–DNA complexes, since relevant segments of TFIIA and NC2 were not present in truncated TFIIA and NC2 derivatives used for crystallization. We propose that interactions of TBP H2 with the TFIIAα/β connector and the NC2α C-terminal tail provide an explanation for genetic results suggesting importance of TBP H2 in TBP–TFIIA interactions and TBP–NC2 interactions, and provide an explanation—steric exclusion—for competition between TFIIA and NC2.
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Affiliation(s)
- Younggyu Kim
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
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21
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Pourshahian S, Limbach PA. Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1081-1088. [PMID: 18320553 PMCID: PMC3008158 DOI: 10.1002/jms.1391] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A method has been developed to identify oligonucleotide-peptide heteroconjugates by accurate mass measurements using MS. The fractional mass (the decimal fraction mass value following the monoisotopic nominal mass) for peptides and oligonucleotides is different due to their differing molecular compositions. This property has been used to develop the general conditions necessary to differentiate peptides and oligonucleotides from oligonucleotide-peptide heteroconjugates. Peptides and oligonucleotides generated by the theoretical digestion of various proteins and nucleic acids were plotted as nominal mass versus fractional mass. Such plots reveal that three nucleotides cross-linked to a peptide produce enough change in the fractional mass to be recognized from non-cross-linked peptides at the same nominal mass. Experimentally, a Cytochrome c digest was spiked with an oligonucleotide-peptide heteroconjugate and conditions for analyzing the sample using liquid chromatography (LC)-MS were optimized. Upon analysis of this mixture, all detected masses were plotted on a fractional mass plot and the heteroconjugate could be readily distinguished from non-cross-linked peptides. The method developed here can be incorporated into a general proteomics-like scheme for identifying protein-nucleic acid cross-links, and this method is equally applicable to characterizing cross-links generated from protein-DNA and protein-RNA complexes.
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Affiliation(s)
| | - Patrick A. Limbach
- To whom correspondence should be addressed. Phone (513) 556-1871, Fax (513) 556-9239,
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22
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Ishmael FT, Fang X, Galdiero MR, Atasoy U, Rigby WF, Gorospe M, Cheadle C, Stellato C. Role of the RNA-binding protein tristetraprolin in glucocorticoid-mediated gene regulation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2008; 180:8342-53. [PMID: 18523301 PMCID: PMC2505276 DOI: 10.4049/jimmunol.180.12.8342] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Glucocorticoids (GCs) are the mainstay of anti-inflammatory therapy. Modulation of posttranscriptional regulation (PTR) of gene expression by GCs is a relevant yet poorly characterized mechanism of their action. The RNA-binding protein tristetraprolin (TTP) plays a central role in PTR by binding to AU-rich elements in the 3'-untranslated region of proinflammatory transcripts and accelerating their decay. We found that GCs induce TTP expression in primary and immortalized human bronchial epithelial cells. To investigate the importance of PTR and the role of TTP in GC function, we compared the effect of GC treatment on genome-wide gene expression using mouse embryonic fibroblasts (MEFs) obtained from wild-type and TTP(-/-) mice. We confirmed that GCs induce TTP in MEFs and observed in TTP(-/-) MEFs a striking loss of up to 85% of GC-mediated gene expression. Gene regulation by TNF-alpha was similarly affected, as was the antagonistic effect of GC on TNF-alpha-induced response. Inflammatory genes, including cytokines and chemokines, were among the genes whose sensitivity to GCs was affected by lack of TTP. Silencing of TTP in WT MEFs by small interfering RNA confirmed loss of GC response in selected targets. Immunoprecipitation of ribonucleoprotein complexes revealed binding of TTP to several validated transcripts. Changes in the rate of transcript degradation studied by actinomycin D were documented for only a subset of transcripts bound to TTP. These results reveal a strong and previously unrecognized contribution of PTR to the anti-inflammatory action of GCs and point at TTP as a key factor mediating this process through a complex mechanism of action.
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Affiliation(s)
- Faoud T. Ishmael
- Division of Allergy and Clinical Immunology, Johns Hopkins University, Baltimore, MD 21224
| | - Xi Fang
- Division of Allergy and Clinical Immunology, Johns Hopkins University, Baltimore, MD 21224
| | - Maria Rosaria Galdiero
- Division of Allergy and Clinical Immunology, Johns Hopkins University, Baltimore, MD 21224
| | - Ulus Atasoy
- University of Missouri-Columbia, Columbia, MO
| | | | - Myriam Gorospe
- Laboratory of Cellular and Molecular Biology, National Institute of Aging, NIH, Baltimore, MD 21224
| | - Chris Cheadle
- Division of Allergy and Clinical Immunology, Johns Hopkins University, Baltimore, MD 21224
| | - Cristiana Stellato
- Division of Allergy and Clinical Immunology, Johns Hopkins University, Baltimore, MD 21224
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23
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Qvit N, Monderer-Rothkoff G, Ido A, Shalev DE, Amster-Choder O, Gilon C. Development of bifunctional photoactivatable benzophenone probes and their application to glycoside substrates. Biopolymers 2008; 90:526-36. [DOI: 10.1002/bip.21010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Yang W, Steen H, Freeman MR. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics 2008; 8:832-51. [PMID: 18297654 DOI: 10.1002/pmic.200700650] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Signal transduction is one of the most active fields in modern biomedical research. Increasing evidence has shown that signaling proteins associate with each other in characteristic ways to form large signaling complexes. These diverse structures operate to boost signaling efficiency, ensure specificity and increase sensitivity of the biochemical circuitry. Traditional methods of protein analysis are inadequate to fully characterize and understand these structures, which are intricate, contain many components and are highly dynamic. Instead, proteomics technologies are currently being applied to investigate the nature and composition of multimeric signaling complexes. This review presents commonly used and potential proteomic methods of analyzing diverse protein complexes along with a discussion and a brief evaluation of alternative approaches. Challenges associated with proteomic analysis of signaling complexes are also discussed.
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Affiliation(s)
- Wei Yang
- The Urological Diseases Research Center, Department of Urology, Children's Hospital Boston, Boston, MA 02115, USA
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25
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Clavé G, Boutal H, Hoang A, Perraut F, Volland H, Renard PY, Romieu A. A novel heterotrifunctional peptide-based cross-linking reagent for facile access to bioconjugates. Applications to peptide fluorescent labelling and immobilisation. Org Biomol Chem 2008; 6:3065-78. [DOI: 10.1039/b807263a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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26
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Hiramatsu T, Guo Y, Hosoya T. 3-Azidodifluoromethyl-3H-diazirin-3-yl group as an all-in-one functional group for radioisotope-free photoaffinity labeling. Org Biomol Chem 2007; 5:2916-9. [PMID: 17728856 DOI: 10.1039/b710024h] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 3-azidodifluoromethyl-3H-diazirin-3-yl group was designed and synthesized as an all-in-one functional group for radioisotope-free photoaffinity labeling.
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Affiliation(s)
- Toshiyuki Hiramatsu
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology and SORST, Japan Science and Technology Agency (JST), 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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27
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Lascoux D, Paramelle D, Subra G, Heymann M, Geourjon C, Martinez J, Forest E. Discrimination and Selective Enhancement of Signals in the MALDI Mass Spectrum of a Protein by Combining a Matrix-Based Label for Lysine Residues with a Neutral Matrix. Angew Chem Int Ed Engl 2007; 46:5594-7. [PMID: 17591739 DOI: 10.1002/anie.200700811] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- David Lascoux
- Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, CEA, CNRS, UJF, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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28
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Lascoux D, Paramelle D, Subra G, Heymann M, Geourjon C, Martinez J, Forest E. Discrimination and Selective Enhancement of Signals in the MALDI Mass Spectrum of a Protein by Combining a Matrix-Based Label for Lysine Residues with a Neutral Matrix. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Sinz A. Isotope-Labeled Photoaffinity Reagents and Mass Spectrometry To Identify Protein–Ligand Interactions. Angew Chem Int Ed Engl 2007; 46:660-2. [PMID: 17167803 DOI: 10.1002/anie.200602549] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrea Sinz
- Biotechnological-Biomedical Center, Faculty of Chemistry and Mineralogy, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany.
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30
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Sinz A. Isotopenmarkierte Photoaffinitätsreagentien und Massenspektrometrie zur Identifizierung von Protein-Ligand-Wechselwirkungen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200602549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Bräse S, Gil C, Knepper K, Zimmermann V. Organic azides: an exploding diversity of a unique class of compounds. Angew Chem Int Ed Engl 2006; 44:5188-240. [PMID: 16100733 DOI: 10.1002/anie.200400657] [Citation(s) in RCA: 1636] [Impact Index Per Article: 90.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Since the discovery of organic azides by Peter Griess more than 140 years ago, numerous syntheses of these energy-rich molecules have been developed. In more recent times in particular, completely new perspectives have been developed for their use in peptide chemistry, combinatorial chemistry, and heterocyclic synthesis. Organic azides have assumed an important position at the interface between chemistry, biology, medicine, and materials science. In this Review, the fundamental characteristics of azide chemistry and current developments are presented. The focus will be placed on cycloadditions (Huisgen reaction), aza ylide chemistry, and the synthesis of heterocycles. Further reactions such as the aza-Wittig reaction, the Sundberg rearrangement, the Staudinger ligation, the Boyer and Boyer-Aubé rearrangements, the Curtius rearrangement, the Schmidt rearrangement, and the Hemetsberger rearrangement bear witness to the versatility of modern azide chemistry.
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Affiliation(s)
- Stefan Bräse
- Institut für Organische Chemie, Universität Karlsruhe TH, Germany.
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32
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Chu F, Mahrus S, Craik CS, Burlingame AL. Isotope-Coded and Affinity-Tagged Cross-Linking (ICATXL): An Efficient Strategy to Probe Protein Interaction Surfaces. J Am Chem Soc 2006; 128:10362-3. [PMID: 16895390 DOI: 10.1021/ja0614159] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemical cross-linking followed by identification of the cross-linked residues by mass spectrometry provides structural information on protein interaction surfaces. Nevertheless, accurate analysis of the digested, cross-linked proteins is often challenging. Herein, we describe a novel strategy that relies on the use of affinity-tagged cross-linkers and isotope coding on the cross-linker-modified species. Incorporation of O16 or O18 during the hydrolysis of the cross-linkers results in a characteristic "doublet" for the undesired products of a half-cross-linking reaction. Therefore, genuine cross-linked peptides are readily distinguished for further structural analysis. This strategy permits a sensitive and facile analysis on a dimeric protease inhibitor, ecotin, showing general applicability to other protein assemblies.
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Affiliation(s)
- Feixia Chu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-0446, USA
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33
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Sinz A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. MASS SPECTROMETRY REVIEWS 2006; 25:663-82. [PMID: 16477643 DOI: 10.1002/mas.20082] [Citation(s) in RCA: 514] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resolution methods for three-dimensional protein structure analysis, such as X-ray crystallography and NMR spectroscopy, consists of covalently connecting two functional groups of the protein(s) under investigation. The location of the created cross-links imposes a distance constraint on the location of the respective side chains and allows one to draw conclusions on the three-dimensional structure of the protein or a protein complex. Recently, chemical cross-linking of proteins has been combined with a mass spectrometric analysis of the created cross-linked products. This review article describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the different available strategies that employ chemical cross-linking and different mass spectrometric techniques. The challenges for mass spectrometry caused by the enormous complexity of the cross-linking reaction mixtures are emphasized. The various approaches described in the literature to facilitate the mass spectrometric detection of cross-linked products as well as computer software for data analyses are reviewed.
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Affiliation(s)
- Andrea Sinz
- Biotechnological-Biomedical Center, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany.
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34
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Kluger R, Alagic A. Chemical cross-linking and protein-protein interactions-a review with illustrative protocols. Bioorg Chem 2005; 32:451-72. [PMID: 15530987 DOI: 10.1016/j.bioorg.2004.08.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Indexed: 10/26/2022]
Abstract
The general term "protein-protein" interactions refers to the effects of proteins upon each other. The interactions can arise from co-existence in organized structural arrangements or in transient encounters. The latter are difficult to detect and define. Introduction of specific, stable chemical linkages can establish permanent relationships between what would normally be transiently associated species. The review covers the types and purposes of various linkers, including the comparative advantages of various approaches. The emphasis is on practical applications and thus includes methodology in the form of practical protocols for introducing the linkages and interpreting the outcomes.
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Affiliation(s)
- Ronald Kluger
- Department of Chemistry, University of Toronto, Ont, Canada M5S 3H6.
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35
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Bräse S, Gil C, Knepper K, Zimmermann V. Organische Azide - explodierende Vielfalt bei einer einzigartigen Substanzklasse. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200400657] [Citation(s) in RCA: 346] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Trakselis MA, Alley SC, Ishmael FT. Identification and Mapping of Protein−Protein Interactions by a Combination of Cross-Linking, Cleavage, and Proteomics. Bioconjug Chem 2005; 16:741-50. [PMID: 16029014 DOI: 10.1021/bc050043a] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions are vital for almost all cellular functions, and many require the formation of multiprotein complexes. Identification of the macroscopic and microscopic protein interactions within these complexes is essential in understanding their mechanisms, both under physiologic as well as pathologic conditions. This review describes the current technology available to investigate interactions between proteins utilizing chemical cross-linking and site-directed cleavage reagents, outlining the necessary steps involved in identifying interacting proteins both in vitro and in vivo. Once interacting proteins are identified, more information about the architecture of the assemblies is necessary. Unique separation techniques coupled with cross-linking and mass spectrometry can now identify specific interaction sites and lead to the development of quaternary structural protein models. Furthermore, combination of these methods with proteomic approaches enables the identification and analysis of complex interactions in vivo. Finally, future directions in cross-linking methodologies are discussed.
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Affiliation(s)
- Michael A Trakselis
- Medical Research Council, Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
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37
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Ishmael FT, Shier VK, Ishmael SS, Bond JS. Intersubunit and domain interactions of the meprin B metalloproteinase. Disulfide bonds and protein-protein interactions in the MAM and TRAF domains. J Biol Chem 2005; 280:13895-901. [PMID: 15695509 DOI: 10.1074/jbc.m414218200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Meprins, multimeric metalloproteases expressed in kidney and intestinal epithelial cells as well as in certain leukocytes and cancer cells, have the ability to hydrolyze a variety of growth factors, vasoactive peptides, cytokines, and extracellular matrix proteins. The meprin B isoform exists primarily as a cell-surface homooligomer composed of disulfide-linked, multidomain beta-subunits. To gain insight into how the tertiary and quaternary structure of meprin B affects function, the disulfide-bonding pattern and sites of domain-domain interactions were investigated using sedimentation equilibrium ultracentrifugation, cross-linking, and mass spectrometry techniques. Three symmetrical intersubunit disulfide bonds were identified in the noncatalytic interaction domains; two in the MAM (meprin, A-5 protein, protein-tyrosine phosphatase mu) domain and one in the TRAF (tumor necrosis factor receptor-associated factor) domain. These disulfide bridges are unique for the known homophilic interactions of these domains. Mutation of any of the intersubunit cysteine residues resulted in the inability of meprin B to form disulfide-linked dimers. The four cysteines of the protease domain formed intradomain disulfide bonds. The MAM domain also had one intradomain disulfide bond and one free cysteine. Cross-linking studies of the meprin B dimer with the amine-reactive cross-linker disuccinimidyl suberate revealed inter- and intradomain contacts within the protein, including prosequence-prosequence, protease-TRAF, protease-epidermal growth factor, and TRAF-TRAF interactions. From these observations, a model of the meprin B dimer structure is proposed that provides insight into the relationship between structure and function of this isoform.
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Affiliation(s)
- Faoud T Ishmael
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
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38
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Sinz A. Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:1225-1237. [PMID: 14696200 DOI: 10.1002/jms.559] [Citation(s) in RCA: 199] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.
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Affiliation(s)
- Andrea Sinz
- Biotechnological-Biomedical Center, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany.
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39
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Back JW, de Jong L, Muijsers AO, de Koster CG. Chemical cross-linking and mass spectrometry for protein structural modeling. J Mol Biol 2003; 331:303-13. [PMID: 12888339 DOI: 10.1016/s0022-2836(03)00721-6] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The growth of gene and protein sequence information is currently so rapid that three-dimensional structural information is lacking for the overwhelming majority of known proteins. In this review, efforts towards rapid and sensitive methods for protein structural characterization are described, complementing existing technologies. Based on chemical cross-linking and offering the analytical speed and sensitivity of mass spectrometry these methodologies are thought to contribute valuable tools towards future high throughput protein structure elucidation.
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Affiliation(s)
- Jaap Willem Back
- Swammerdam Institute for Life Sciences (SILS), Mass Spectrometry group, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV, Amsterdam, The Netherlands.
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40
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Trester-Zedlitz M, Kamada K, Burley SK, Fenyö D, Chait BT, Muir TW. A modular cross-linking approach for exploring protein interactions. J Am Chem Soc 2003; 125:2416-25. [PMID: 12603129 DOI: 10.1021/ja026917a] [Citation(s) in RCA: 165] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method is described for the elucidation of protein-protein interactions using novel cross-linking reagents and mass spectrometry. The method incorporates (1) a modular solid-phase synthetic strategy for generating the cross-linking reagents, (2) enrichment and digestion of cross-linked proteins using microconcentrators, (3) mass spectrometric analysis of cross-linked peptides, and (4) comprehensive computational analysis of the cross-linking data. This integrated approach has been applied to the study of cross-linking between the components of the heterodimeric protein complex negative cofactor 2.
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Affiliation(s)
- Michelle Trester-Zedlitz
- Laboratories of Synthetic Protein Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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41
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Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W. Bacteriophage T4 genome. Microbiol Mol Biol Rev 2003; 67:86-156, table of contents. [PMID: 12626685 PMCID: PMC150520 DOI: 10.1128/mmbr.67.1.86-156.2003] [Citation(s) in RCA: 562] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.
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Affiliation(s)
- Eric S Miller
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA.
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42
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Trakselis MA, Berdis AJ, Benkovic SJ. Examination of the role of the clamp-loader and ATP hydrolysis in the formation of the bacteriophage T4 polymerase holoenzyme. J Mol Biol 2003; 326:435-51. [PMID: 12559912 DOI: 10.1016/s0022-2836(02)01330-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Transient kinetic analyses further support the role of the clamp-loader in bacteriophage T4 as a catalyst which loads the clamp onto DNA through the sequential hydrolysis of two molecules of ATP before and after addition of DNA. Additional rapid-quench and pulse-chase experiments have documented this stoichiometry. The events of ATP hydrolysis have been related to the opening/closing of the clamp protein through fluorescence resonance energy transfer (FRET). In the absence of a hydrolysable form of ATP, the distance across the subunit interface of the clamp does not increase as measured by intramolecular FRET, suggesting gp45 cannot be loaded onto DNA. Therefore, ATP hydrolysis by the clamp-loader appears to open the clamp wide enough to encircle DNA easily. Two additional molecules of ATP then are hydrolyzed to close the clamp onto DNA. The presence of an intermolecular FRET signal indicated that the dissociation of the clamp-loader from this complex occurred after guiding the polymerase onto the correct face of the clamp bound to DNA. The final holoenzyme complex consists of the clamp, DNA, and the polymerase. Although this sequential assembly mechanism can be generally applied to most other replication systems studied to date, the specifics of ATP utilization seem to vary across replication systems.
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Affiliation(s)
- Michael A Trakselis
- Department of Chemistry, 415 Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
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43
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Ishmael FT, Trakselis MA, Benkovic SJ. Protein-protein interactions in the bacteriophage T4 replisome. The leading strand holoenzyme is physically linked to the lagging strand holoenzyme and the primosome. J Biol Chem 2003; 278:3145-52. [PMID: 12427736 DOI: 10.1074/jbc.m209858200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacteriophage T4 replication complex is composed of eight proteins that function together to replicate DNA. This replisome can be broken down into four basic units: a primosome composed of gp41, gp61, and gp59; a leading strand holoenzyme composed of gp43, gp44/62, and gp45; a lagging strand holoenzyme; and a single strand binding protein polymer. These units interact further to form the complete replisome. The leading and lagging strand polymerases are physically linked in the presence of DNA or an active replisome. The region of interaction was mapped to an extension of the finger domain, such that Cys-507 of one subunit is in close proximity to Cys-507 of a second subunit. The leading strand polymerase and the primosome also associate, such that gp59 mediates the contact between the two complexes. Binding of gp43 to the primosome complex causes displacement of gp32 from the gp59.gp61.gp41 primosome complex. The resultant species is a complex of proteins that may allow coordinated leading and lagging strand synthesis, helicase DNA unwinding activity, and polymerase nucleotide incorporation.
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Affiliation(s)
- Faoud T Ishmael
- Department of Biochemistry and Molecular Biology, Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania 17033, USA
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44
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Ishmael FT, Alley SC, Benkovic SJ. Assembly of the bacteriophage T4 helicase: architecture and stoichiometry of the gp41-gp59 complex. J Biol Chem 2002; 277:20555-62. [PMID: 11927580 DOI: 10.1074/jbc.m111951200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacteriophage T4 59 protein (gp59) plays an essential role in recombination and replication by mediating the assembly of the gene 41 helicase (gp41) onto DNA. gp59 is required to displace the gp32 single-stranded binding protein on the lagging strand to expose a site for helicase binding. To gain a better understanding of the mechanism of helicase assembly, the architecture and stoichiometry of the gp41-gp59 complex were investigated. Both the N and C termini of gp41 were found to lie close to or in the gp41-gp41 subunit interface and interact with gp59. The site of interaction of gp41 on gp59 is proximal to Cys-215 of gp59. Binding of gp41 to gp59 stimulates a conformational change in the protein resulting in hexamer formation of gp59, and gp59 likewise stimulates oligomer formation of gp41. The gp59 subunits in this complex are arranged in a head to head orientation, such that Cys-42 of one subunit is in close proximity to Cys-42 on an adjacent subunit, and Cys-215 on one subunit is close to Cys-215 on a neighboring subunit. As the helicase is loaded onto DNA, a conformational change in the gp41-gp59 complex occurs, which may serve to displace gp32 from the lagging strand and load the hexameric helicase in its place.
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Affiliation(s)
- Faoud T Ishmael
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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45
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Yegneswaran S, Fernández JA, Griffin JH, Dawson PE. Factor Va increases the affinity of factor Xa for prothrombin: a binding study using a novel photoactivable thiol-specific fluorescent probe. CHEMISTRY & BIOLOGY 2002; 9:485-94. [PMID: 11983337 DOI: 10.1016/s1074-5521(02)00132-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The multiprotein complex of factor Xa, factor Va, and prothrombin efficiently generates the blood-clotting agent, thrombin. Here, the formation of the factor Xa*prothrombin complex and the effects of factor Va on this complex were examined using a photoactivable thiol-specific fluorescent probe (LWB), which was synthesized and incorporated into the active site of factor Xa. The use of fluorescent LWB illustrated that factor Xa has an increased affinity for prothrombin in the presence of factor Va. Further exposure of these components to UV light resulted in a specific photocrosslinking of LWB-factor Xa to prothrombin, suggesting a physical association between these proteins. These data demonstrate that LWB can successfully function both as a spectroscopic probe and as a photocrosslinking reagent for studying protein-protein interactions.
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Affiliation(s)
- Subramanian Yegneswaran
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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46
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Valentine AM, Ishmael FT, Shier VK, Benkovic SJ. A zinc ribbon protein in DNA replication: primer synthesis and macromolecular interactions by the bacteriophage T4 primase. Biochemistry 2001; 40:15074-85. [PMID: 11735390 DOI: 10.1021/bi0108554] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gene product 61 primase protein from bacteriophage T4 was expressed as an intein fusion and purified to homogeneity. The primase binds one zinc ion, which is coordinated by four cysteine residues to form a zinc ribbon motif. Factors that influence the rate of priming were investigated, and a physiologically relevant priming rate of approximately 1 primer per second per primosome was achieved. Primase binding to the single-stranded binding protein (1 primase:4 gp32 monomers; K(d) approximately 860 nM) and to the helicase protein in the presence of DNA and ATP-gamma-S (1 primase:1 helicase monomer; K(d) approximately 100 nM) was investigated by isothermal titration calorimetry (ITC). Because the helicase is hexameric, the inferred stoichiometry of primase binding as part of the primosome is helicase hexamer:primase in a ratio of 1:6, suggesting that the active primase, like the helicase, might have a ring-like structure. The primase is a monomer in solution but binds to single-stranded DNA (ssDNA) primarily as a trimer (K(d) approximately 50-100 nM) as demonstrated by ITC and chemical cross-linking. Magnesium is required for primase-ssDNA binding. The minimum length of ssDNA required for stable binding is 22-24 bases, although cross-linking reveals transient interactions on oligonucleotides as short as 8 bases. The association is endothermic at physiologically relevant temperatures, which suggests an overall gain in entropy upon binding. Some possible sources of this gain in entropy are discussed.
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Affiliation(s)
- A M Valentine
- Department of Chemistry, The Pennsylvania State University, 415 Wartik Laboratory, University Park, Pennsylvania 16802, USA
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47
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Trakselis MA, Benkovic SJ. Intricacies in ATP-dependent clamp loading: variations across replication systems. Structure 2001; 9:999-1004. [PMID: 11709164 DOI: 10.1016/s0969-2126(01)00676-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA replication requires the coordinated effort of many proteins to create a highly processive biomachine able to replicate entire genomes in a single process. The clamp proteins confer on replisomes this property of processivity but in turn require clamp loaders for their functional assembly onto DNA. A more detailed view of the mechanisms for holoenzyme assembly in replication systems has been obtained from the advent of novel solution experiments and the appearance of low- and high-resolution structures for the clamp loaders.
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Affiliation(s)
- M A Trakselis
- Department of Chemistry, 414 Wartik Laboratory, Pennsylvania State University, University Park, PA 16802, USA
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48
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Alley SC, Trakselis MA, Mayer MU, Ishmael FT, Jones AD, Benkovic SJ. Building a replisome solution structure by elucidation of protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme. J Biol Chem 2001; 276:39340-9. [PMID: 11504721 DOI: 10.1074/jbc.m104956200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Assembly of DNA replication systems requires the coordinated actions of many proteins. The multiprotein complexes formed as intermediates on the pathway to the final DNA polymerase holoenzyme have been shown to have distinct structures relative to the ground-state structures of the individual proteins. By using a variety of solution-phase techniques, we have elucidated additional information about the solution structure of the bacteriophage T4 holoenzyme. Photocross-linking and mass spectrometry were used to demonstrate interactions between I107C of the sliding clamp and the DNA polymerase. Fluorescence resonance energy transfer, analytical ultracentrifugation, and isothermal titration calorimetry measurements were used to demonstrate that the C terminus of the DNA polymerase can interact at two distinct locations on the sliding clamp. Both of these binding modes may be used during holoenzyme assembly, but only one of these binding modes is found in the final holoenzyme. Present and previous solution interaction data were used to build a model of the holoenzyme that is consistent with these data.
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Affiliation(s)
- S C Alley
- Department of Chemistry, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
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49
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Trakselis MA, Mayer MU, Ishmael FT, Roccasecca RM, Benkovic SJ. Dynamic protein interactions in the bacteriophage T4 replisome. Trends Biochem Sci 2001; 26:566-72. [PMID: 11551794 DOI: 10.1016/s0968-0004(01)01929-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The bacteriophage T4 DNA replisome is a complex dynamic system employing a variety of proteins to orchestrate the synthesis of DNA on both the leading and lagging strands. Assembly of the protein complexes responsible for DNA synthesis and priming requires the coordination of transient biomolecular interactions. This interplay of proteins has been dissected through the use of small molecules including fluorescent probes and crosslinkers, enabling the development of a complex dynamic structural and kinetic model for DNA polymerase holoenzyme assembly and primosome formation.
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Affiliation(s)
- M A Trakselis
- Dept of Chemistry, 414 Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
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50
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Trakselis MA, Alley SC, Abel-Santos E, Benkovic SJ. Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 2001; 98:8368-75. [PMID: 11459977 PMCID: PMC37445 DOI: 10.1073/pnas.111006698] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The coordinated assembly of the DNA polymerase (gp43), the sliding clamp (gp45), and the clamp loader (gp44/62) to form the bacteriophage T4 DNA polymerase holoenzyme is a multistep process. A partially opened toroid-shaped gp45 is loaded around DNA by gp44/62 in an ATP-dependent manner. Gp43 binds to this complex to generate the holoenzyme in which gp45 acts to topologically link gp43 to DNA, effectively increasing the processivity of DNA replication. Stopped-flow fluorescence resonance energy transfer was used to investigate the opening and closing of the gp45 ring during holoenzyme assembly. By using two site-specific mutants of gp45 along with a previously characterized gp45 mutant, we tracked changes in distances across the gp45 subunit interface through seven conformational changes associated with holoenzyme assembly. Initially, gp45 is partially open within the plane of the ring at one of the three subunit interfaces. On addition of gp44/62 and ATP, this interface of gp45 opens further in-plane through the hydrolysis of ATP. Addition of DNA and hydrolysis of ATP close gp45 in an out-of-plane conformation. The final holoenzyme is formed by the addition of gp43, which causes gp45 to close further in plane, leaving the subunit interface open slightly. This open interface of gp45 in the final holoenzyme state is proposed to interact with the C-terminal tail of gp43, providing a point of contact between gp45 and gp43. This study further defines the dynamic process of bacteriophage T4 polymerase holoenzyme assembly.
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Affiliation(s)
- M A Trakselis
- Department of Chemistry, 414 Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
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