1
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Bailey BL, Nguyen W, Cowman AF, Sleebs BE. Chemo-proteomics in antimalarial target identification and engagement. Med Res Rev 2023; 43:2303-2351. [PMID: 37232495 PMCID: PMC10947479 DOI: 10.1002/med.21975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Humans have lived in tenuous battle with malaria over millennia. Today, while much of the world is free of the disease, areas of South America, Asia, and Africa still wage this war with substantial impacts on their social and economic development. The threat of widespread resistance to all currently available antimalarial therapies continues to raise concern. Therefore, it is imperative that novel antimalarial chemotypes be developed to populate the pipeline going forward. Phenotypic screening has been responsible for the majority of the new chemotypes emerging in the past few decades. However, this can result in limited information on the molecular target of these compounds which may serve as an unknown variable complicating their progression into clinical development. Target identification and validation is a process that incorporates techniques from a range of different disciplines. Chemical biology and more specifically chemo-proteomics have been heavily utilized for this purpose. This review provides an in-depth summary of the application of chemo-proteomics in antimalarial development. Here we focus particularly on the methodology, practicalities, merits, and limitations of designing these experiments. Together this provides learnings on the future use of chemo-proteomics in antimalarial development.
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Affiliation(s)
- Brodie L. Bailey
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
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2
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Glashauser J, Camelo C, Hollmann M, Backer W, Jacobs T, Sanchez JI, Schleutker R, Förster D, Berns N, Riechmann V, Luschnig S. Acute manipulation and real-time visualization of membrane trafficking and exocytosis in Drosophila. Dev Cell 2023; 58:709-723.e7. [PMID: 37023749 DOI: 10.1016/j.devcel.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 01/05/2023] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Intracellular trafficking of secretory proteins plays key roles in animal development and physiology, but so far, tools for investigating the dynamics of membrane trafficking have been limited to cultured cells. Here, we present a system that enables acute manipulation and real-time visualization of membrane trafficking through the reversible retention of proteins in the endoplasmic reticulum (ER) in living multicellular organisms. By adapting the "retention using selective hooks" (RUSH) approach to Drosophila, we show that trafficking of GPI-linked, secreted, and transmembrane proteins can be controlled with high temporal precision in intact animals and cultured organs. We demonstrate the potential of this approach by analyzing the kinetics of ER exit and apical secretion and the spatiotemporal dynamics of tricellular junction assembly in epithelia of living embryos. Furthermore, we show that controllable ER retention enables tissue-specific depletion of secretory protein function. The system is broadly applicable to visualizing and manipulating membrane trafficking in diverse cell types in vivo.
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Affiliation(s)
- Jade Glashauser
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Carolina Camelo
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Manuel Hollmann
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Wilko Backer
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Thea Jacobs
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Jone Isasti Sanchez
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Raphael Schleutker
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Dominique Förster
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Nicola Berns
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Veit Riechmann
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Stefan Luschnig
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany.
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3
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Cai B, Mhetre AB, Krusemark CJ. Selection methods for proximity-dependent enrichment of ligands from DNA-encoded libraries using enzymatic fusion proteins. Chem Sci 2023; 14:245-250. [PMID: 36687357 PMCID: PMC9811540 DOI: 10.1039/d2sc05495g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
Herein, we report a selection approach to enrich ligands from DNA-encoded libraries (DELs) based on proximity to an enzymatic tag on the target protein. This method involves uncaging or installation of a biotin purification tag on the DNA construct either through photodeprotection of a protected biotin group using a light emitting protein tag (nanoluciferase) or by acylation using an engineered biotin ligase (UltraID). This selection does not require purification of the target protein and results in improved recovery and enrichment of DNA-linked ligands. This approach should serve as a general and convenient tool for molecular discovery with DELs.
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Affiliation(s)
- Bo Cai
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
| | - Amol B. Mhetre
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
| | - Casey J. Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
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4
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Liu Z, Xie X, Huang Z, Lin F, Liu S, Chen Z, Qin S, Fan X, Chen PR. Spatially resolved cell tagging and surfaceome labeling via targeted photocatalytic decaging. Chem 2022. [DOI: 10.1016/j.chempr.2022.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Huang HJ, Lin YT, Chung MC, Chen YH, Tan KT. Glucose and Ethanol Detection with an Affinity-Switchable Lateral Flow Assay. Anal Chem 2022; 94:5084-5090. [PMID: 35297623 DOI: 10.1021/acs.analchem.1c05316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The lateral flow assay (LFA) is one of the most successful analytical platforms for rapid on-site detection of target substances. This type of assay has been used in many rapid diagnoses, for example, pregnancy tests and infectious disease prevention. However, applications of LFAs for very small molecules remain a demanding challenge due to the problem of obtaining the corresponding binding partners to form sandwich complexes. In this paper, we report an affinity-switchable (AS) LFA (ASLFA) for the rapid and selective detection of hydrogen peroxide (H2O2), glucose, and ethanol in blood serum and urine samples. Unlike classical LFAs, which rely on the "always on" interaction between the antigen and the antibody, the working principle of ASLFA is based on the gold nanoparticle-conjugated AS biotin probe Au@H2O2-ASB, which can be activated by H2O2 for binding with the streptavidin (SA) protein. In the presence of glucose and ethanol, glucose oxidase and alcohol oxidase can react with the substrate to generate H2O2 and thereby activate Au@H2O2-ASB for binding with SA. Therefore, this ASLFA approach can be an alternative for classical glucose and ethanol detection methods in a wide variety of samples, where simple and rapid on-site detection is essential.
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Affiliation(s)
- Hsiao-Jung Huang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan
| | - Yu-Ting Lin
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan
| | - Min-Chi Chung
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan
| | - Yu-Hsuan Chen
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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6
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Torabi M, Zolfigol MA, Yarie M, Gu Y. Application of ammonium acetate as a dual rule reagent-catalyst in synthesis of new symmetrical terpyridines. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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7
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Chen YH, Gupta NK, Huang HJ, Lam CH, Huang CL, Tan KT. Affinity-Switchable Lateral Flow Assay. Anal Chem 2021; 93:5556-5561. [DOI: 10.1021/acs.analchem.1c00138] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yu-Hsuan Chen
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Nitesh K. Gupta
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Hsiao-Jung Huang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Chak Hin Lam
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Ching-Lan Huang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan, Republic of China
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8
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Shu P, Niu H, Zhang L, Xu H, Yu M, Li J, Yang X, Fei Y, Liu H, Ju Z, Xu Z. Regioselective Dechloroacetylations Mediated by Ammonium Acetate: Practical Syntheses of 2,3,4,6‐Tetra‐
O
‐chloroacetyl‐glycopyranoses and Cinnamoyl Glucose Esters. ChemistrySelect 2020. [DOI: 10.1002/slct.202001955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Penghua Shu
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Haoying Niu
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Lingxiang Zhang
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Haichang Xu
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Mengzhu Yu
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Junping Li
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Xue Yang
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Yingying Fei
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Hao Liu
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Zhiyu Ju
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
| | - Zhihong Xu
- School of Chemistry and Chemical EngineeringXuchang University Xuchang 461000 China
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9
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Chen YH, Chien WC, Lee DC, Tan KT. Signal Amplification and Detection of Small Molecules via the Activation of Streptavidin and Biotin Recognition. Anal Chem 2019; 91:12461-12467. [DOI: 10.1021/acs.analchem.9b03144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | - Kui-Thong Tan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan (ROC)
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10
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On-cell catalysis by surface engineering of live cells with an artificial metalloenzyme. Commun Chem 2018. [DOI: 10.1038/s42004-018-0087-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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11
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Chung TH, Wu YP, Chew CY, Lam CH, Tan KT. Imaging and Quantification of Secreted Peroxynitrite at the Cell Surface by a Streptavidin-Biotin-Controlled Binding Probe. Chembiochem 2018; 19:2584-2590. [PMID: 30352141 DOI: 10.1002/cbic.201800542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Indexed: 12/13/2022]
Abstract
The ability to detect and image secreted peroxynitrite (ONOO- ) along the extracellular surface of a single cell is biologically significant, as ONOO- generally exerts its function for host defense and signal transductions at the plasma membrane. However, as a result of the short lifetime and fast diffusion rate of small ONOO- , precise determination of the ONOO- level at the cell surface remains a challenging task. In this paper, the use of a membrane-anchored streptavidin-biotin-controlled binding probe (CBP), ONOO-CBP, to determine quantitatively the ONOO- level at the cell surface and to investigate the effect of different stimulants on the production of ONOO- along the plasma membrane of macrophages is reported. Our results revealed that the combination of NO synthase (iNOS) and NADPH oxidase (NOX) activators was highly effective in inducing ONOO- secretion, achieving more than a 25-fold increase in ONOO- relative to untreated cells. After 1 h of phorbol-12-myristate-13-acetate (PMA) stimulation, the amount of ONOO- secreted by RAW264.7 macrophages was similar to the condition treated with 25 μm 3-morpholinosydnonimine hydrochloride (SIN-1), which was estimated to release about 20 μm of ONOO- into Dulbecco's modified Eagle's medium (DMEM) in 1 h. This novel approach should open up new opportunities to image various reactive oxygen and nitrogen species secreted at the plasma membrane that cannot be simply achieved by conventional analytical methods.
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Affiliation(s)
- Tzu-Hsuan Chung
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu, 30013, Taiwan
| | - Yung-Peng Wu
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu, 30013, Taiwan
| | - Chee Ying Chew
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu, 30013, Taiwan
| | - Chak Hin Lam
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu, 30013, Taiwan
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu, 30013, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu, 30013, Taiwan
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12
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering von Proteinen an Oberflächen: Von komplementärer Charakterisierung zu Materialoberflächen mit maßgeschneiderten Funktionen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Svenja Morsbach
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Grazia Gonella
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Volker Mailänder
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Dermatologie; Universitätsmedizin der Johannes Gutenberg-Universität Mainz; Langenbeckstraße 1 55131 Mainz Deutschland
| | - Seraphine Wegner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Si Wu
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tobias Weidner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Chemie; Universität Aarhus; Langelandsgade 140 8000 Aarhus C Dänemark
| | - Rüdiger Berger
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kaloian Koynov
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Doris Vollmer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Noemí Encinas
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Seah Ling Kuan
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tristan Bereau
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kurt Kremer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Hans-Jürgen Butt
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Katharina Landfester
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
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13
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions. Angew Chem Int Ed Engl 2018; 57:12626-12648. [PMID: 29663610 PMCID: PMC6391961 DOI: 10.1002/anie.201712448] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/13/2018] [Indexed: 01/17/2023]
Abstract
Once materials come into contact with a biological fluid containing proteins, proteins are generally—whether desired or not—attracted by the material's surface and adsorb onto it. The aim of this Review is to give an overview of the most commonly used characterization methods employed to gain a better understanding of the adsorption processes on either planar or curved surfaces. We continue to illustrate the benefit of combining different methods to different surface geometries of the material. The thus obtained insight ideally paves the way for engineering functional materials that interact with proteins in a predetermined manner.
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Affiliation(s)
- Svenja Morsbach
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Dermatology, University Medical Center Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Seraphine Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Si Wu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Doris Vollmer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Noemí Encinas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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14
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Bartelt SM, Chervyachkova E, Steinkühler J, Ricken J, Wieneke R, Tampé R, Dimova R, Wegner SV. Dynamic blue light-switchable protein patterns on giant unilamellar vesicles. Chem Commun (Camb) 2018; 54:948-951. [DOI: 10.1039/c7cc08758f] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The photoswitchable iLID/Nano interaction allows for specific, non-invasive, reversible and dynamic protein photopatterning on GUVs with high spatiotemporal control.
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Affiliation(s)
- S. M. Bartelt
- Max Planck Institute for Polymer Research
- Mainz
- Germany
| | | | - J. Steinkühler
- Department of Theory and Biosystems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
| | - J. Ricken
- Max Planck Institute for Polymer Research
- Mainz
- Germany
| | - R. Wieneke
- Institut für Biochemie, Biozentrum
- Cluster of Excellence Frankfurt
- Goethe-Universität Frankfurt
- Frankfurt
- Germany
| | - R. Tampé
- Institut für Biochemie, Biozentrum
- Cluster of Excellence Frankfurt
- Goethe-Universität Frankfurt
- Frankfurt
- Germany
| | - R. Dimova
- Department of Theory and Biosystems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
| | - S. V. Wegner
- Max Planck Institute for Polymer Research
- Mainz
- Germany
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15
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Wu YP, Chew CY, Li TN, Chung TH, Chang EH, Lam CH, Tan KT. Target-activated streptavidin-biotin controlled binding probe. Chem Sci 2017; 9:770-776. [PMID: 29629147 PMCID: PMC5872805 DOI: 10.1039/c7sc04014h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/16/2017] [Indexed: 11/21/2022] Open
Abstract
Target-activated chemical probes are important tools in basic biological research and medical diagnosis for monitoring enzyme activities and reactive small molecules. Based on the fluorescence turn-on mechanism, they can be divided into two classes: dye-based fluorescent probes and caged-luciferin. In this paper, we introduce a new type of chemical probe in which the fluorescence turn-on is based on controlled streptavidin-biotin binding. Compared to conventional probes, the streptavidin-biotin controlled binding probe has several advantages, such as minimal background at its "OFF" state, multiple signal amplification steps, and unlimited selection of the optimal dyes for detection. To expand the scope, a new synthetic method was developed, through which a wider range of analyte recognition groups can be easily introduced to construct the binding probe. This probe design was successfully applied to image and study secreted peroxynitrite (ONOO-) at the cell surface of macrophages where information on ONOO- is difficult to obtain. As the signals are generated upon the binding of streptavidin to the biotin probe, this highly versatile design can not only be used in fluorescence detection but can also be applied in various other detection modes, such as electrochemical and enzyme-amplified luminescence detection.
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Affiliation(s)
- Yung-Peng Wu
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of China .
| | - Chee Ying Chew
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of China .
| | - Tian-Neng Li
- Institute of Molecular and Cellular Biology , Department of Life Science , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of China
| | - Tzu-Hsuan Chung
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of China .
| | - En-Hao Chang
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of China .
| | - Chak Hin Lam
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of China .
| | - Kui-Thong Tan
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of China .
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16
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Structural Characterization of the Avidin Interactions with Fluorescent Pyrene-Conjugates: 1-Biotinylpyrene and 1-Desthiobiotinylpyrene. Molecules 2016; 21:molecules21101270. [PMID: 27689976 PMCID: PMC6274289 DOI: 10.3390/molecules21101270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/07/2016] [Accepted: 09/17/2016] [Indexed: 11/28/2022] Open
Abstract
Avidin is a tetrameric protein that belongs to the calycin superfamily. It has been studied mainly because of its extraordinary affinity to biotin, which led to a wide range of applications based on the avidin-biotin system. In the present study, we report the first crystal structures of avidin in a complex with two novel fluorescent pyrene derivatives: 1-biotinylpyrene (B9P) and 1-desthiobiotinylpyrene (D9P). The crystal structures were solved by molecular replacement using the coordinates of avidin molecule as a starting model and the final models of avidin/B9P and avidin/D9P were refined to resolutions of 2.0 Å and 2.1 Å, respectively. Our data reveal changes in loop conformation as well as in overall fold and quaternary arrangement of the avidin upon the binding of these fluorescent probes. Moreover, the crystal structures allowed analysis of the details of the interactions between the protein and the pyrene derivatives. Structural description of the complexes will contribute to the design of conjugates for expanding the capabilities of avidin–biotin technology.
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17
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Yamaguchi S, Ura M, Izuta S, Okamoto A. Chemically Activatable Alkyne Tag for Low pH-Enhanced Molecular Labeling on Living Cells. Bioconjug Chem 2016; 27:1976-80. [DOI: 10.1021/acs.bioconjchem.6b00399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Satoshi Yamaguchi
- Research
Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Manami Ura
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shin Izuta
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akimitsu Okamoto
- Research
Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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18
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Błauż A, Rychlik B, Makal A, Szulc K, Strzelczyk P, Bujacz G, Zakrzewski J, Woźniak K, Plażuk D. Ferrocene-Biotin Conjugates: Synthesis, Structure, Cytotoxic Activity and Interaction with Avidin. Chempluschem 2016; 81:1191-1201. [DOI: 10.1002/cplu.201600320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Andrzej Błauż
- Cytometry Lab; Department of Molecular Biophysics; Faculty of Biology and Environmental Protection; University of Łódź; 141/143 Pomorska St. 90-236 Łódź Poland
| | - Błażej Rychlik
- Cytometry Lab; Department of Molecular Biophysics; Faculty of Biology and Environmental Protection; University of Łódź; 141/143 Pomorska St. 90-236 Łódź Poland
| | - Anna Makal
- Department of Chemistry; University of Warsaw; Pasteura, 1 02-093 Warszawa Poland
| | - Katarzyna Szulc
- Cytometry Lab; Department of Molecular Biophysics; Faculty of Biology and Environmental Protection; University of Łódź; 141/143 Pomorska St. 90-236 Łódź Poland
| | - Paweł Strzelczyk
- Institute of Technical Biochemistry; Łódź University of Technology; Stefanowskiego 4/10 90-924 Łódź Poland
| | - Grzegorz Bujacz
- Institute of Technical Biochemistry; Łódź University of Technology; Stefanowskiego 4/10 90-924 Łódź Poland
| | - Janusz Zakrzewski
- Department of Organic Chemistry; Faculty of Chemistry; University of Łódź; Tamka 12 41-403 Łódź Poland
| | - Krzysztof Woźniak
- Department of Chemistry; University of Warsaw; Pasteura, 1 02-093 Warszawa Poland
| | - Damian Plażuk
- Department of Organic Chemistry; Faculty of Chemistry; University of Łódź; Tamka 12 41-403 Łódź Poland
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19
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Strzelczyk P, Bujacz G. Crystal structure and ligand affinity of avidin in the complex with 4′-hydroxyazobenzene-2-carboxylic acid. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Terai T, Kohno M, Boncompain G, Sugiyama S, Saito N, Fujikake R, Ueno T, Komatsu T, Hanaoka K, Okabe T, Urano Y, Perez F, Nagano T. Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport. J Am Chem Soc 2015; 137:10464-7. [DOI: 10.1021/jacs.5b05672] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | - Shigeru Sugiyama
- Graduate
School of Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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21
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Yamamoto T, Aoki K, Sugiyama A, Doi H, Kodama T, Shimizu Y, Kanai M. Design and synthesis of biotin analogues reversibly binding with streptavidin. Chem Asian J 2015; 10:1071-8. [PMID: 25691069 DOI: 10.1002/asia.201500120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Indexed: 11/06/2022]
Abstract
Two new biotin analogues, biotin carbonate 5 and biotin carbamate 6, have been synthesized. These molecules were designed to reversibly bind with streptavidin by replacing the hydrogen-bond donor NH group(s) of biotin's cyclic urea moiety with oxygen. Biotin carbonate 5 was synthesized from L-arabinose (7), which furnishes the desired stereochemistry at the 3,4-cis-dihydroxy groups, in 11% overall yield (over 10 steps). Synthesis of biotin carbamate 6 was accomplished from L-cysteine-derived chiral aldehyde 33 in 11% overall yield (over 7 steps). Surface plasmon resonance analysis of water-soluble biotin carbonate analogue 46 and biotin carbamate analogue 47 revealed that KD values of these compounds for binding to streptavidin were 6.7×10(-6) M and 1.7×10(-10) M, respectively. These values were remarkably greater than that of biotin (KD =10(-15) M), and thus indicate the importance of the nitrogen atoms for the strong binding between biotin and streptavidin.
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Affiliation(s)
- Tomohiro Yamamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
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22
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Custódio CA, San Miguel-Arranz V, Gropeanu RA, Gropeanu M, Wirkner M, Reis RL, Mano JF, del Campo A. Photopatterned antibodies for selective cell attachment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:10066-10071. [PMID: 25076392 DOI: 10.1021/la502688h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present a phototriggerable system that allows for the spatiotemporal controlled attachment of selected cell types to a biomaterial using immobilized antibodies that specifically target individual cell phenotypes. o-Nitrobenzyl caged biotin was used to functionalize chitosan membranes and mediate site-specific coupling of streptavidin and biotinylated antibodies after light activation. The ability of this system to capture and immobilize specific cells on a surface was tested using endothelial-specific biotinylated antibodies and nonspecific ones as controls. Homogeneous patterned monolayers of human umbilical vein endothelial cells were obtained on CD31-functionalized surfaces. This is a simple and generic approach that is applicable to other ligands, materials, and cell types and shows the flexibility of caged ligands to trigger and control the interaction between cells and biomaterials.
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Affiliation(s)
- C A Custódio
- Max-Planck-Institut für Polymerforschung , Ackermannweg 10, 55128 Mainz, Germany
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23
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Fairhead M, Shen D, Chan LKM, Lowe ED, Donohoe TJ, Howarth M. Love-Hate ligands for high resolution analysis of strain in ultra-stable protein/small molecule interaction. Bioorg Med Chem 2014; 22:5476-86. [PMID: 25128469 DOI: 10.1016/j.bmc.2014.07.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 12/19/2022]
Abstract
The pathway of ligand dissociation and how binding sites respond to force are not well understood for any macromolecule. Force effects on biological receptors have been studied through simulation or force spectroscopy, but not by high resolution structural experiments. To investigate this challenge, we took advantage of the extreme stability of the streptavidin-biotin interaction, a paradigm for understanding non-covalent binding as well as a ubiquitous research tool. We synthesized a series of biotin-conjugates having an unchanged strong-binding biotin moiety, along with pincer-like arms designed to clash with the protein surface: 'Love-Hate ligands'. The Love-Hate ligands contained various 2,6-di-ortho aryl groups, installed using Suzuki coupling as the last synthetic step, making the steric repulsion highly modular. We determined binding affinity, as well as solving 1.1-1.6Å resolution crystal structures of streptavidin bound to Love-Hate ligands. Striking distortion of streptavidin's binding contacts was found for these complexes. Hydrogen bonds to biotin's ureido and thiophene rings were preserved for all the ligands, but biotin's valeryl tail was distorted from the classic conformation. Streptavidin's L3/4 loop, normally forming multiple energetically-important hydrogen bonds to biotin, was forced away by clashes with Love-Hate ligands, but Ser45 from L3/4 could adapt to hydrogen-bond to a different part of the ligand. This approach of preparing conflicted ligands represents a direct way to visualize strained biological interactions and test protein plasticity.
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Affiliation(s)
- Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Di Shen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Louis K M Chan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ed D Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Timothy J Donohoe
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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24
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Chen N, Hong FL, Wang HH, Yuan QH, Ma WY, Gao XN, Shi R, Zhang RJ, Sun CS, Wang SB. Modified recombinant proteins can be exported via the Sec pathway in Escherichia coli. PLoS One 2012; 7:e42519. [PMID: 22912705 PMCID: PMC3418276 DOI: 10.1371/journal.pone.0042519] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 07/10/2012] [Indexed: 01/29/2023] Open
Abstract
The correct folding of a protein is a pre-requirement for its proper posttranslational modification. The Escherichia coli Sec pathway, in which preproteins, in an unfolded, translocation-competent state, are rapidly secreted across the cytoplasmic membrane, is commonly assumed to be unfavorable for their modification in the cytosol. Whether posttranslationally modified recombinant preproteins can be efficiently transported via the Sec pathway, however, remains unclear. ACP and BCCP domain (BCCP87) are carrier proteins that can be converted into active phosphopantetheinylated ACP (holo-ACP) and biotinylated-BCCP (holo-BCCP) by AcpS and BirA, respectively. In the present study, we show that, when ACP or BCCP87 is fused to the C-terminus of secretory protein YebF or MBP, the resulting fusion protein preYebF-ACP, preYebF-BCCP87, preMBP-ACP or preMBP-BCCP87 can be modified and then secreted. Our data demonstrate that posttranslational modification of preYebF-ACP, preYebF-BCCP87 preMBP-ACP and preMBP-BCCP87 can take place in the cytosol prior to translocation, and the Sec machinery accommodates these previously modified fusion proteins. High levels of active holo-ACP and holo-BCCP87 are achieved when AcpS or BirA is co-expressed, especially when sodium azide is used to retard their translocation across the inner membrane. Our results also provide an alternative to achieve a high level of modified recombinant proteins expressed extracellularly.
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Affiliation(s)
- Nan Chen
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Fu-Lin Hong
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Hai-Hong Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Qi-Hang Yuan
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Wan-Yan Ma
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Xu-Na Gao
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Rui Shi
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Rui-Juan Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Chang-Sheng Sun
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Sheng-Bin Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
- * E-mail:
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