1
|
Hori M, Steinauer A, Tetter S, Hälg J, Manz EM, Hilvert D. Stimulus-responsive assembly of nonviral nucleocapsids. Nat Commun 2024; 15:3576. [PMID: 38678040 PMCID: PMC11055949 DOI: 10.1038/s41467-024-47808-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fusing maltose binding protein to the subunits of NC-4, an engineered protein cage that encapsulates its own encoding mRNA, we successfully blocked spontaneous capsid assembly, allowing isolation of the individual monomers in soluble form. To initiate RNA-templated nucleocapsid formation, the steric block can be simply removed by selective proteolysis. Analyses by transmission and cryo-electron microscopy confirmed that the resulting assemblies are structurally identical to their RNA-containing counterparts produced in vivo. Enzymatically triggered cage formation broadens the range of RNA molecules that can be encapsulated by NC-4, provides unique opportunities to study the co-assembly of capsid and cargo, and could be useful for studying other nonviral and viral assemblies.
Collapse
Affiliation(s)
- Mao Hori
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, Japan
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LIBN, Lausanne, Switzerland
| | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Jamiro Hälg
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Eva-Maria Manz
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
2
|
Ogunbowale A, Georgieva ER. Engineered Chimera Protein Constructs to Facilitate the Production of Heterologous Transmembrane Proteins in E. coli. Int J Mol Sci 2024; 25:2354. [PMID: 38397029 PMCID: PMC10889703 DOI: 10.3390/ijms25042354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
To delve into the structure-function relationship of transmembrane proteins (TMPs), robust protocols are needed to produce them in a pure, stable, and functional state. Among all hosts that express heterologous TMPs, E. coli has the lowest cost and fastest turnover. However, many of the TMPs expressed in E. coli are misfolded. Several strategies have been developed to either direct the foreign TMPs to E. coli's membrane or retain them in a cytosolic soluble form to overcome this deficiency. Here, we summarize protein engineering methods to produce chimera constructs of the desired TMPs fused to either a signal peptide or precursor maltose binding protein (pMBP) to direct the entire construct to the periplasm, therefore depositing the fused TMP in the plasma membrane. We further describe strategies to produce TMPs in soluble form by utilizing N-terminally fused MBP without a signal peptide. Depending on its N- or C-terminus location, a fusion to apolipoprotein AI can either direct the TMP to the membrane or shield the hydrophobic regions of the TMP, maintaining the soluble form. Strategies to produce G-protein-coupled receptors, TMPs of Mycobacterium tuberculosis, HIV-1 Vpu, and other TMPs are discussed. This knowledge could increase the scope of TMPs' expression in E. coli.
Collapse
Affiliation(s)
| | - Elka R. Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| |
Collapse
|
3
|
Fisher K, Halliwell T, Payne KAP, Ragala G, Hay S, Rigby SEJ, Leys D. Efficient NADPH-dependent dehalogenation afforded by a self-sufficient reductive dehalogenase. J Biol Chem 2023; 299:105086. [PMID: 37495113 PMCID: PMC10463259 DOI: 10.1016/j.jbc.2023.105086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Reductive dehalogenases are corrinoid and iron-sulfur cluster-containing enzymes that catalyze the reductive removal of a halogen atom. The oxygen-sensitive and membrane-associated nature of the respiratory reductive dehalogenases has hindered their detailed kinetic study. In contrast, the evolutionarily related catabolic reductive dehalogenases are oxygen tolerant, with those that are naturally fused to a reductase domain with similarity to phthalate dioxygenase presenting attractive targets for further study. We present efficient heterologous expression of a self-sufficient catabolic reductive dehalogenase from Jhaorihella thermophila in Escherichia coli. Combining the use of maltose-binding protein as a solubility-enhancing tag with the btuCEDFB cobalamin uptake system affords up to 40% cobalamin occupancy and a full complement of iron-sulfur clusters. The enzyme is able to efficiently perform NADPH-dependent dehalogenation of brominated and iodinated phenolic compounds, including the flame retardant tetrabromobisphenol, under both anaerobic and aerobic conditions. NADPH consumption is tightly coupled to product formation. Surprisingly, corresponding chlorinated compounds only act as competitive inhibitors. Electron paramagnetic resonance spectroscopy reveals loss of the Co(II) signal observed in the resting state of the enzyme under steady-state conditions, suggesting accumulation of Co(I)/(III) species prior to the rate-limiting step. In vivo reductive debromination activity is readily observed, and when the enzyme is expressed in E. coli strain W, supports growth on 3-bromo-4-hydroxyphenylacetic as a sole carbon source. This demonstrates the potential for catabolic reductive dehalogenases for future application in bioremediation.
Collapse
Affiliation(s)
- Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Tom Halliwell
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl A P Payne
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Gabriel Ragala
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Stephen E J Rigby
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| |
Collapse
|
4
|
Lee S. Peptide ligand interaction with maltose-binding protein tagged to the calcitonin gene-related peptide receptor: The inhibitory role of receptor N-glycosylation. Peptides 2022; 150:170735. [PMID: 35007660 DOI: 10.1016/j.peptides.2022.170735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022]
Abstract
Calcitonin gene-related peptide (CGRP) and adrenomedullin (AM) are peptide hormones and their receptors play a critical role in migraine progression and blood pressure control, respectively. CGRP and AM receptors are structurally related since they are the complex of the calcitonin receptor-like receptor (CLR) with the different types of receptor activity-modifying protein (RAMP). Several crystal structures of the CGRP and AM receptor extracellular domain (ECD) used maltose-binding protein (MBP) as a tag protein to facilitate crystallization. Unexpectedly, the recent crystal structures of CGRP receptor ECD showed that the N-terminal tag MBP located in proximity of bound/mutated peptide ligands. This study provided evidence that MBP N-terminally tagged to the CGRP receptor ECD formed chemical interaction with the mutated peptide ligands. Interestingly, N-glycosylation of the CGRP receptor ECD was predicted to prevent MBP docking to the mutated peptide ligands. I found that the N-glycosylation of CLR ECD N123 was the most critical for inhibiting MBP interaction with the mutated peptide ligands. The MBP tag protein interaction was also dependent on the sequence of the peptide ligands. In contrast to the CGRP receptor, the MBP tag was not involved in peptide ligand binding at AM receptor ECD. Here, I provided evidence that N-glycosylation of the CGRP receptor ECD inhibited the tag protein interaction suggesting an additional function of N-glycosylation in the MBP-fused CGRP receptor ECD. This study reveals the importance of using tag protein-free versions of the CGRP receptor for the accurate assessment of peptide binding affinity.
Collapse
Affiliation(s)
- Sangmin Lee
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, High Point, NC 27268, USA.
| |
Collapse
|
5
|
Salmen W. Positive and Negative Affinity Chromatography to Purify Norovirus P-Domain Protein. Methods Mol Biol 2022; 2466:83-92. [PMID: 35585312 DOI: 10.1007/978-1-0716-2176-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Affinity chromatography enables the separation and isolation of proteins of interest from complex milieu of biochemicals. Nickel-charged affinity resins and amylose resins are two commonly used matrices for the isolation of proteins with histidine tag (6× His-tag) and maltose binding protein (MBP) tag, respectively. Herein we describe the isolation of the Protruding domain (P-domain) of Norovirus's major capsid protein, VP1, through a highly efficient batch purification technique. By fusing the P-domain to a 6×His-MBP tag followed by a TEV cleavage site, we can effectively purify the P-domain in three chromatography steps (positive nickel affinity, negative nickel affinity, and negative amylose affinity).
Collapse
Affiliation(s)
- Wilhelm Salmen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
6
|
Cantrell MS, Wall JD, Pu X, Turner M, Woodbury L, Fujise K, McDougal OM, Warner LR. Expression and purification of a cleavable recombinant fortilin from Escherichia coli for structure activity studies. Protein Expr Purif 2022; 189:105989. [PMID: 34626801 PMCID: PMC8557625 DOI: 10.1016/j.pep.2021.105989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/11/2021] [Accepted: 10/04/2021] [Indexed: 01/03/2023]
Abstract
Complications related to atherosclerosis account for approximately 1 in 4 deaths in the United States and treatment has focused on lowering serum LDL-cholesterol levels with statins. However, approximately 50% of those diagnosed with atherosclerosis have blood cholesterol levels within normal parameters. Human fortilin is an anti-apoptotic protein and a factor in macrophage-mediated atherosclerosis and is hypothesized to protect inflammatory macrophages from apoptosis, leading to subsequent cardiac pathogenesis. Fortilin is unique because it provides a novel drug target for atherosclerosis that goes beyond lowering cholesterol and utilization of a solution nuclear magnetic resonance (NMR) spectroscopy, structure-based drug discovery approach requires milligram quantities of pure, bioactive, recombinant fortilin. Here, we designed expression constructs with different affinity tags and protease cleavage sites to find optimal conditions to obtain the quantity and purity of protein necessary for structure activity relationship studies. Plasmids encoding fortilin with maltose binding protein (MBP), 6-histidine (6His) and glutathione-S-transferase (GST), N- terminal affinity tags were expressed and purified from Escherichia coli (E. coli). Cleavage sites with tobacco etch virus (TEV) protease and human rhinovirus (HRV) 3C protease were assessed. Despite high levels of expression of soluble protein, the fusion constructs were resistant to proteinases without the inclusion of amino acids between the cleavage site and N-terminus. We surveyed constructs with increasing lengths of glycine/serine (GGS) linkers between the cleavage site and fortilin and found that inclusion of at least one GGS insert led to successful protease cleavage and pure fortilin with conserved binding to calcium as measured by NMR.
Collapse
Affiliation(s)
- Maranda S Cantrell
- Biomolecular Sciences Ph.D. Program, Boise State University, Boise, ID, 83725, USA; Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA
| | - Jackson D Wall
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA
| | - Xinzhu Pu
- Biomolecular Research Center, Boise State University, Boise, ID, 83725, USA
| | - Matthew Turner
- Biomolecular Research Center, Boise State University, Boise, ID, 83725, USA
| | - Luke Woodbury
- Biomolecular Research Center, Boise State University, Boise, ID, 83725, USA
| | - Ken Fujise
- Harborview Medical Center, University of Washington, Seattle, WA, 98104-2499, USA
| | - Owen M McDougal
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA
| | - Lisa R Warner
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA.
| |
Collapse
|
7
|
Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. eLife 2021; 10:e70236. [PMID: 34623258 PMCID: PMC8500717 DOI: 10.7554/elife.70236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022] Open
Abstract
With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.
Collapse
Affiliation(s)
- William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Brandon S Sim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Anthony K Nhim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Marium M Raza
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Eric Gb Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Chloe M Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| |
Collapse
|
8
|
Nguyen TKO, Vu TL, Nguyen MQ, Ta HKK, Park KS, Kim SH, Kim CJ, Jang YJ, Choe H. Soluble Prokaryotic Overexpression and Purification of Human GM-CSF Using the Protein Disulfide Isomerase b'a' Domain. Int J Mol Sci 2021; 22:ijms22105267. [PMID: 34067755 PMCID: PMC8156066 DOI: 10.3390/ijms22105267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/06/2021] [Accepted: 05/15/2021] [Indexed: 12/30/2022] Open
Abstract
Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a member of the colony-stimulating factor (CSF) family, which functions to enhance the proliferation and differentiation of hematopoietic stem cells and other hematopoietic lineages such as neutrophils, dendritic cells, or macrophages. These proteins have thus generated considerable interest in clinical therapy research. A current obstacle to the prokaryotic production of human GM-CSF (hGM-CSF) is its low solubility when overexpressed and subsequent complex refolding processes. In our present study, the solubility of hGM-CSF was examined when combined with three N-terminal fusion tags in five E. coli strains at three different expression temperatures. In the five E. coli strains BL21 (DE3), ClearColi BL21 (DE3), LOBSTR, SHuffle T7 and Origami2 (DE3), the hexahistidine-tagged hGM-CSF showed the best expression but was insoluble in all cases at each examined temperature. Tagging with the maltose-binding protein (MBP) and the b'a' domain of protein disulfide isomerase (PDIb'a') greatly improved the soluble overexpression of hGM-CSF at 30 °C and 18 °C. The solubility was not improved using the Origami2 (DE3) and SHuffle T7 strains that have been engineered for disulfide bond formation. Two conventional chromatographic steps were used to purify hGM-CSF from the overexpressed PDIb'a'-hGM-CSF produced in ClearColi BL21 (DE3). In the experiment, 0.65 mg of hGM-CSF was isolated from a 0.5 L flask culture of these E. coli and showed a 98% purity by SDS-PAGE analysis and silver staining. The bioactivity of this purified hGM-CSF was measured at an EC50 of 16.4 ± 2 pM by a CCK8 assay in TF-1 human erythroleukemia cells.
Collapse
Affiliation(s)
- Thi Kieu Oanh Nguyen
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Thi Luong Vu
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Minh Quan Nguyen
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Huynh Kim Khanh Ta
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Kyoung Sun Park
- Wide River Institute of Immunology, Seoul National University College of Medicine, Seoul 25159, Korea; (K.S.P.); (S.H.K.)
| | - Soo Hyeon Kim
- Wide River Institute of Immunology, Seoul National University College of Medicine, Seoul 25159, Korea; (K.S.P.); (S.H.K.)
| | - Chong Jai Kim
- Department of Pathology, Asan-Minnesota Institute for Innovating Transplantation, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea;
| | - Yeon Jin Jang
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Han Choe
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
- Correspondence: ; Tel.: +82-2-3010-4292
| |
Collapse
|
9
|
Kohno M, Arakawa T, Sunagawa N, Mori T, Igarashi K, Nishimoto T, Fushinobu S. Molecular analysis of cyclic α-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway. PLoS One 2020; 15:e0241912. [PMID: 33211750 PMCID: PMC7676653 DOI: 10.1371/journal.pone.0241912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022] Open
Abstract
Cyclic α-maltosyl-(1→6)-maltose (CMM) is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. Here, we report functional and structural analyses on CMM-binding protein (CMMBP), which is a substrate-binding protein (SBP) of an ABC importer system of the bacteria Arthrobacter globiformis. Isothermal titration calorimetry analysis revealed that CMMBP specifically bound to CMM with a Kd value of 9.6 nM. The crystal structure of CMMBP was determined at a resolution of 1.47 Å, and a panose molecule was bound in a cleft between two domains. To delineate its structural features, the crystal structure of CMMBP was compared with other SBPs specific for carbohydrates, such as cyclic α-nigerosyl-(1→6)-nigerose and cyclodextrins. These results indicate that A. globiformis has a unique metabolic pathway specialized for CMM.
Collapse
Affiliation(s)
- Masaki Kohno
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- R&D Division, HAYASHIBARA CO., LTD., Okayama, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
| | - Tetsuya Mori
- R&D Division, HAYASHIBARA CO., LTD., Okayama, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
- * E-mail:
| |
Collapse
|
10
|
Byrne NJ, Lee AC, Kostas J, Reid JC, Partridge AT, So SS, Cowan JE, Abeywickrema P, Huang H, Zebisch M, Barker JJ, Soisson SM, Brooun A, Su HP. Development of a robust crystallization platform for immune receptor TREM2 using a crystallization chaperone strategy. Protein Expr Purif 2020; 179:105796. [PMID: 33221505 DOI: 10.1016/j.pep.2020.105796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/15/2020] [Accepted: 11/13/2020] [Indexed: 11/18/2022]
Abstract
TREM2 has been identified by genomic analysis as a potential and novel target for the treatment of Alzheimer's disease. To enable structure-based screening of potential small molecule therapeutics, we sought to develop a robust crystallization platform for the TREM2 Ig-like domain. A systematic set of constructs containing the structural chaperone, maltose binding protein (MBP), fused to the Ig domain of TREM2, were evaluated in parallel expression and purification, followed by crystallization studies. Using protein crystallization and high-resolution diffraction as a readout, a MBP-TREM2 Ig fusion construct was identified that generates reproducible protein crystals diffracting at 2.0 Å, which makes it suitable for soaking of potential ligands. Importantly, analysis of crystal packing interfaces indicates that most of the surface of the TREM2 Ig domain is available for small molecule binding. A proof of concept co-crystallization study with a small library of fragments validated potential utility of this system for the discovery of new TREM2 therapeutics.
Collapse
Affiliation(s)
- Noel J Byrne
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA.
| | - Amy C Lee
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - James Kostas
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - John C Reid
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - Andrea T Partridge
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - Sung-Sau So
- Department of Computational and Structural Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Joseph E Cowan
- Department of Discovery Sample Management, Merck & Co., Inc., Rahway, NJ, USA
| | - Pravien Abeywickrema
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | | | | | | | - Stephen M Soisson
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - Alexei Brooun
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - Hua-Poo Su
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| |
Collapse
|
11
|
Nguyen MT, Heo Y, Do BH, Baek S, Kim CJ, Jang YJ, Lee W, Choe H. Bacterial overexpression and purification of soluble recombinant human serum albumin using maltose-binding protein and protein disulphide isomerase. Protein Expr Purif 2019; 167:105530. [PMID: 31698036 DOI: 10.1016/j.pep.2019.105530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022]
Abstract
Human serum albumin (HSA), the most abundant serum protein in healthy humans, plays important roles in many physiological processes and has wide clinical and research applications. Despite several efforts to obtain recombinant HSA (rHSA) from bacterial and eukaryotic expression systems, a low-cost and high-yield method for rHSA production is not available. The large molecular weight and high disulphide content hamper the expression and production of rHSA using bacterial hosts. Hence, a strategy that uses a fusion technique and engineered Escherichia coli strains was employed to improve the expression of soluble rHSA in the bacterial cytoplasm. The solubilities of the b'a' domain of human protein disulphide isomerase (PDIb'a')- and maltose-binding protein (MBP)-tagged rHSA expressed in Origami 2 at 18 °C were notably increased by up to 90.1% and 96%, respectively. A simple and efficient protocol for rHSA purification was established and approximately 9.46 mg rHSA was successfully obtained from a 500-mL culture at 97% purity. However, rHSA was mostly obtained in soluble oligomeric form. By introducing a simple refolding and size-exclusion chromatography step, monomeric rHSA was obtained at 34% yield. Native polyacrylamide gel electrophoresis confirmed the similarity in the molecular weights between E. coli-derived monomeric rHSA and commercial monomeric HSA.
Collapse
Affiliation(s)
- Minh Tan Nguyen
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, South Korea; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Yunseok Heo
- Department of Biochemistry, Yonsei University, Seoul, 03722, South Korea
| | - Bich Hang Do
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Sangki Baek
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, South Korea
| | - Chong Jai Kim
- Department of Pathology, Asan-Minnesota Institute for Innovating Transplantation, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, South Korea
| | - Yeon Jin Jang
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, South Korea
| | - Weontae Lee
- Department of Biochemistry, Yonsei University, Seoul, 03722, South Korea.
| | - Han Choe
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, South Korea.
| |
Collapse
|
12
|
Abstract
Tyrosine nitration is a protein post-translational modification that is predominantly non-enzymatic and is observed to be increased under conditions of nitrosative stress and in numerous disease states. A small protein motif (14-18 amino acids) responsive to tyrosine nitration has been developed. In this design, nitrotyrosine replaced the conserved Glu12 of an EF-hand metal-binding motif. Thus, the non-nitrated peptide bound terbium weakly. In contrast, tyrosine nitration resulted in a 45-fold increase in terbium affinity. Nuclear magnetic resonance spectroscopy indicated direct binding of nitrotyrosine to the metal and EF-hand-like metal contacts in this designed peptide. Nitrotyrosine is an efficient quencher of fluorescence. To develop a sensor of tyrosine nitration, the initial design was modified to incorporate Glu residues at EF-hand positions 9 and 16 as additional metal-binding residues, to increase the terbium affinity of the peptide with unmodified tyrosine. This peptide with a tyrosine at residue 12 bound terbium and effectively sensitized terbium luminescence. Tyrosine nitration resulted in a 180-fold increase in terbium affinity ( Kd = 1.6 μM) and quenching of terbium luminescence. This sequence was incorporated as an encoded protein tag and applied as a turn-off fluorescent protein sensor of tyrosine nitration. The sensor was responsive to nitration by peroxynitrite, with fluorescence quenched upon nitration. The greater terbium affinity upon tyrosine nitration resulted in a large dynamic range and sensitivity to substoichiometric nitration. An improved approach for the synthesis of peptides containing nitrotyrosine was also developed, via the in situ silyl protection of nitrotyrosine. This work represents the first designed, encodable protein motif that is responsive to tyrosine nitration.
Collapse
Affiliation(s)
- Andrew R. Urmey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| |
Collapse
|
13
|
Xu H, Wang Q, Zhang Z, Yi L, Ma L, Zhai C. A simplified method to remove fusion tags from a xylanase of Bacillus sp. HBP8 with HRV 3C protease. Enzyme Microb Technol 2019; 123:15-20. [PMID: 30686346 DOI: 10.1016/j.enzmictec.2019.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 10/19/2018] [Accepted: 01/04/2019] [Indexed: 02/06/2023]
Abstract
Human rhinovirus 3C protease (HRV 3C protease) is commonly used as a tool to remove fusion tags from recombinant proteins in gene engineering due to its distinguished specificity and high activity at low temperature. This paper is aimed to simplify the strategy of removing epitope tags from target proteins with HRV 3C protease. Fusion proteins composed of a xylanase from Bacillus sp. HBP8 (xylHB) and double tags (MBP/Nus and 6×His, with an HRV 3C protease recognition site between them) were applied as substrates. To perform the cleavage and purification, strains expressing HRV 3C protease and the substrates were mixed before (co-fermentation method) or after (post-fermentation method) inducing with IPTG, followed by cell disruption and incubation at 4℃, overnight for cleavage. The soluble cytoplasmic fraction was added to Ni-NTA resin to recover the cleaved target protein. Because the process was carried out in the cell lysate, it was named as cell lysate purification system based on HRV 3C protease (CLP3C). Our data indicated small number of cells expressing HRV 3C protease was enough to remove the fusion tags efficiently with both co-fermentation and post-fermentation methods. More importantly, the tags were cleaved precisely with no obvious non-specific degradation to the target protein. Hence, active xylanase was recovered easily with this strategy.
Collapse
Affiliation(s)
- Hu Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China; School of Chucai honors, Hubei University, Wuhan, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China; School of Chucai honors, Hubei University, Wuhan, People's Republic of China
| | - Zhiwei Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China.
| |
Collapse
|
14
|
Selmke B, Borbat PP, Nickolaus C, Varadarajan R, Freed JH, Trommer WE. Open and Closed Form of Maltose Binding Protein in Its Native and Molten Globule State As Studied by Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2018; 57:5507-5512. [PMID: 30004675 PMCID: PMC6211580 DOI: 10.1021/acs.biochem.8b00322] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An intensively investigated intermediate state of protein folding is the molten globule (MG) state, which contains secondary but hardly any tertiary structure. In previous work, we have determined the distances between interacting spins within maltose binding protein (MBP) in its native state using continuous wave and double electron-electron resonance (DEER) electron paramagnetic resonance (EPR) spectroscopy. Seven double mutants had been employed to investigate the structure within the two domains of MBP. DEER data nicely corroborated the previously available X-ray data. Even in its MG state, MBP is known to still bind its ligand maltose. We therefore hypothesized that there must be a defined structure around the binding pocket of MBP already in the absence of tertiary structure. Here we have investigated the functional and structural difference between native and MG state in the open and closed form with a new set of MBP mutants. In these, the spin-label positions were placed near the active site. Binding of its ligands leads to a conformational change from open to closed state, where the two domains are more closely together. The complete set of MBP mutants was analyzed at pH 3.2 (MG) and pH 7.4 (native state) using double-quantum coherence EPR. The values were compared with theoretical predictions of distances between the labels in biradicals constructed by molecular modeling from the crystal structures of MBP in open and closed form and were found to be in excellent agreement. Measurements show a defined structure around the binding pocket of MBP in MG, which explains maltose binding. A new and important finding is that in both states ligand-free MBP can be found in open and closed form, while ligand-bound MBP appears only in closed form because of maltose binding.
Collapse
Affiliation(s)
- Benjamin Selmke
- Department of Chemistry, TU Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
| | - Peter P. Borbat
- Department of Chemistry and Chemical Biology, ACERT National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Chen Nickolaus
- Department of Chemistry, TU Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
| | | | - Jack H. Freed
- Department of Chemistry and Chemical Biology, ACERT National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Wolfgang E. Trommer
- Department of Chemistry, TU Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
| |
Collapse
|
15
|
Abstract
Plant receptor-like kinases (RLKs) are regulated by posttranscriptional modification and by interaction with regulatory proteins. A common modification of RLKs is (auto)phosphorylation, and a common regulatory protein is the calcium sensor calmodulin (CaM). We have developed protocols to detect the interaction of an RLK with CaM. The interaction with CaM was shown by bimolecular fluorescence complementation (BiFC) (see Chapter 14) and pull-down assay (this chapter). Both methods offer unique advantages. BiFC is useful in showing interaction of soluble as well as of membrane-bound proteins in planta. Pull-down assays are restricted to soluble proteins and provide in vitro data. The pull-down assay provides the advantage that proteins can be modified prior to binding and that experimental conditions such as the concentration of Ca2+ or other divalent cations can be controlled. This chapter provides a pull-down protocol to study RLK-CaM interaction with optional steps to investigate the impact of RLK phosphorylation or of Ca2+.
Collapse
Affiliation(s)
- Christine Kaufmann
- Plant Developmental Biology and Plant Physiology, University of Kiel, Am Botanischen Garten 5, 24118, Kiel, Germany
| | - Margret Sauter
- Plant Developmental Biology and Plant Physiology, University of Kiel, Am Botanischen Garten 5, 24118, Kiel, Germany.
| |
Collapse
|
16
|
Liu G, Zhai X, Zhou H, Yang X, Zhang N, Tai G, Ni W. The combination of maltose-binding protein and BCG-induced Th1 activation is involved in TLR2/9-mediated upregulation of MyD88-TRAF6 and TLR4-mediated downregulation of TRIF-TRAF3. Cell Immunol 2018; 325:56-63. [PMID: 29452695 DOI: 10.1016/j.cellimm.2018.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/23/2018] [Accepted: 02/10/2018] [Indexed: 01/05/2023]
Abstract
Our previous study demonstrated that maltose-binding protein (MBP) activated Th1 through the TLR2-mediated MyD88-dependent pathway and the TLR4-mediated TRIF-dependent pathway. The combination of MBP and BCG synergistically induced Th1 activation, and the TLR2/9-mediated MyD88-dependent pathway is involved in this process. To further explore this mechanism, we stimulated purified mouse CD4+ T cells with MBP and BCG in vitro. The results demonstrated that MBP combined with BCG synergistically increased IFN-γ production and TLR2/4/9 expression, suggesting the involvement of TLR2/4/9 in the combination-induced Th1 activation. Next, TLRs 2/4/9 were blocked to analyze the effects of TLRs on Th1 activation. The results demonstrated that MBP induced a low level of Th1 activation by upregulating TLR2-mediated MyD88-TRAF6 and TLR4-mediated TRIF-TRAF3 expression, whereas MBP combined with BCG induced synergistic Th1 activation, which was not only triggered by strong upregulation of TLR2/9-mediated MyD88-TRAF6 expression but also by shifting TLR4-mediated TRIF-TRAF3 into the TRIF-TRAF6 pathway. Moreover, we observed that a TLR4 antibody upregulated MyD88 expression and a TLR9 inhibitor downregulated TRIF expression, indicating that there was cross-talk between TLRs 2/4/9 in MBP combined with BCG-induced Th1 activation. Our findings may expand the knowledge regarding TLR cross-talk involved in regulating the Th1 response.
Collapse
Affiliation(s)
- Guomu Liu
- Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Xiaoyu Zhai
- Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Hongyue Zhou
- Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Xiaoyu Yang
- Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Nannan Zhang
- Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Guixiang Tai
- Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Weihua Ni
- Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China.
| |
Collapse
|
17
|
Lee SB, Park SK, Kim YS. Maltose binding protein-fusion enhances the bioactivity of truncated forms of pig myostatin propeptide produced in E. coli. PLoS One 2017; 12:e0174956. [PMID: 28369115 PMCID: PMC5378391 DOI: 10.1371/journal.pone.0174956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/18/2017] [Indexed: 11/18/2022] Open
Abstract
Myostatin (MSTN) is a potent negative regulator of skeletal muscle growth. MSTN propeptide (MSTNpro) inhibits MSTN binding to its receptor through complex formation with MSTN, implying that MSTNpro can be a useful agent to improve skeletal muscle growth in meat-producing animals. Four different truncated forms of pig MSTNpro containing N-terminal maltose binding protein (MBP) as a fusion partner were expressed in E. coli, and purified by the combination of affinity chromatography and gel filtration. The MSTN-inhibitory capacities of these proteins were examined in an in vitro gene reporter assay. A MBP-fused, truncated MSTNpro containing residues 42-175 (MBP-Pro42-175) exhibited the same MSTN-inhibitory potency as the full sequence MSTNpro. Truncated MSTNpro proteins containing either residues 42-115 (MBP-Pro42-115) or 42-98 (MBP-Pro42-98) also exhibited MSTN-inhibitory capacity even though the potencies were significantly lower than that of full sequence MSTNpro. In pull-down assays, MBP-Pro42-175, MBP-Pro42-115, and MBP-Pro42-98 demonstrated their binding to MSTN. MBP was removed from the truncated MSTNpro proteins by incubation with factor Xa to examine the potential role of MBP on MSTN-inhibitory capacity of those proteins. Removal of MBP from MBP-Pro42-175 and MBP-Pro42-98 resulted in 20-fold decrease in MSTN-inhibitory capacity of Pro42-175 and abolition of MSTN-inhibitory capacity of Pro42-98, indicating that MBP as fusion partner enhanced the MSTN-inhibitory capacity of those truncated MSTNpro proteins. In summary, this study shows that MBP is a very useful fusion partner in enhancing MSTN-inhibitory potency of truncated forms of MSTNpro proteins, and MBP-fused pig MSTNpro consisting of amino acid residues 42-175 is sufficient to maintain the full MSTN-inhibitory capacity.
Collapse
Affiliation(s)
- Sang Beum Lee
- Wide River Institute of Immunology, Seoul National University College of Medicine, Hongcheon, Gangwon-do, South Korea
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Sung Kwon Park
- National Institute of Animal Science, RDA, Suwon, South Korea
| | - Yong Soo Kim
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, United States of America
- * E-mail:
| |
Collapse
|
18
|
Rush MD, Walker EM, Prehna G, Burton T, van Breemen RB. Development of a Magnetic Microbead Affinity Selection Screen (MagMASS) Using Mass Spectrometry for Ligands to the Retinoid X Receptor-α. J Am Soc Mass Spectrom 2017; 28:479-485. [PMID: 27966173 PMCID: PMC5352471 DOI: 10.1007/s13361-016-1564-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 11/07/2016] [Accepted: 11/20/2016] [Indexed: 05/21/2023]
Abstract
To overcome limiting factors in mass spectrometry-based screening methods such as automation while still facilitating the screening of complex mixtures such as botanical extracts, magnetic microbead affinity selection screening (MagMASS) was developed. The screening process involves immobilization of a target protein on a magnetic microbead using a variety of possible chemistries, incubation with mixtures of molecules containing possible ligands, a washing step that removes non-bound compounds while a magnetic field retains the beads in the microtiter well, and an organic solvent release step followed by LC-MS analysis. Using retinoid X receptor-α (RXRα) as an example, which is a nuclear receptor and target for anti-inflammation therapy as well as cancer treatment and prevention, a MagMASS assay was developed and compared with an existing screening assay, pulsed ultrafiltration (PUF)-MS. Optimization of MagMASS involved evaluation of multiple protein constructs and several magnetic bead immobilization chemistries. The full-length RXRα construct immobilized with amylose beads provided optimum results. Additional enhancements of MagMASS were the application of 96-well plates to enable automation, use of UHPLC instead of HPLC for faster MS analyses, and application of metabolomics software for faster, automated data analysis. Performance of MagMASS was demonstrated using mixtures of synthetic compounds and known ligands spiked into botanical extracts. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Michael D Rush
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Chicago, IL, USA
| | - Elisabeth M Walker
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Chicago, IL, USA
| | - Gerd Prehna
- Center for Structural Biology Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, USA
| | - Tristesse Burton
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Chicago, IL, USA
| | - Richard B van Breemen
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Chicago, IL, USA.
| |
Collapse
|
19
|
Min D, Arbing MA, Jefferson RE, Bowie JU. A simple DNA handle attachment method for single molecule mechanical manipulation experiments. Protein Sci 2016; 25:1535-44. [PMID: 27222403 PMCID: PMC4972209 DOI: 10.1002/pro.2952] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
Manipulating single molecules and systems of molecules with mechanical force is a powerful technique to examine their physical properties. Applying force requires attachment of the target molecule to larger objects using some sort of molecular tether, such as a strand of DNA. DNA handle attachment often requires difficult manipulations of the target molecule, which can preclude attachment to unstable, hard to obtain, and/or large, complex targets. Here we describe a method for covalent DNA handle attachment to proteins that simply requires the addition of a preprepared reagent to the protein and a short incubation. The handle attachment method developed here provides a facile approach for studying the biomechanics of biological systems.
Collapse
Affiliation(s)
- Duyoung Min
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - Robert E Jefferson
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| |
Collapse
|
20
|
Raran-Kurussi S, Waugh DS. A dual protease approach for expression and affinity purification of recombinant proteins. Anal Biochem 2016; 504:30-7. [PMID: 27105777 PMCID: PMC4877217 DOI: 10.1016/j.ab.2016.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/01/2016] [Accepted: 04/07/2016] [Indexed: 11/29/2022]
Abstract
We describe a new method for affinity purification of recombinant proteins using a dual protease protocol. Escherichia coli maltose binding protein (MBP) is employed as an N-terminal tag to increase the yield and solubility of its fusion partners. The MBP moiety is then removed by rhinovirus 3C protease, prior to purification, to yield an N-terminally His6-tagged protein. Proteins that are only temporarily rendered soluble by fusing them to MBP are readily identified at this stage because they will precipitate after the MBP tag is removed by 3C protease. The remaining soluble His6-tagged protein, if any, is subsequently purified by immobilized metal affinity chromatography (IMAC). Finally, the N-terminal His6 tag is removed by His6-tagged tobacco etch virus (TEV) protease to yield the native recombinant protein, and the His6-tagged contaminants are removed by adsorption during a second round of IMAC, leaving only the untagged recombinant protein in the column effluent. The generic strategy described here saves time and effort by removing insoluble aggregates at an early stage in the process while also reducing the tendency of MBP to "stick" to its fusion partners during affinity purification.
Collapse
Affiliation(s)
- Sreejith Raran-Kurussi
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - David S Waugh
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| |
Collapse
|
21
|
Gholizadeh A. Differential expression of a cysteine proteinase and cystatin pair as sidebyside fusion forms in Escherichia coli. Tsitol Genet 2016; 50:16-25. [PMID: 30480414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
As a basic study, the fusion expressions of two functionally related proteins were described. The side by side fusion construction, expression, purification and functional characterization of Arabidopsis papain-like cysteine proteinase (CP) and cysteine proteinase inhibitor (CPI) were successfully carried out by using an Escherichia coli expression system without affecting the recombinant bacterial growth. The purification products of two different fused constructs designated as «R1: H2N-maltose binding protein-CPI-CP-COOH and R2: H2N-maltose binding protein-CP-CPI-COOH» showed inverse enzymatic/inhibitory activities, in vitro. Analysis of the constructs by using computational tools revealed that the arrangement of CP/CPI pair in fusion forms might be the important criteria for proper tertiary organization, structural folding and functional property. The overall results showed that the C-terminally located molecule could be the active folded structure in each fusion construct. The achievements of the present work may be utilized in a specific protein engineering application such as manufacturing the novel switchable expression systems in the future.
Collapse
|
22
|
Abstract
Sialyltransferases (STs) are disulfide-containing, type II transmembrane glycoproteins that catalyze the transfer of sialic acid to proteins and lipids and participate in the synthesis of the core structure oligosaccharides of human milk. Sialic acids are found at the outermost position of glycostructures, playing a key role in health and disease. Sialylation is also essential for the production of recombinant therapeutic proteins (RTPs). Despite their importance, availability of sialyltransferases is limited due to the low levels of stable, soluble and active protein produced in bacterial expression systems, which hampers biochemical and structural studies on these enzymes and restricts biotechnological applications. We report the successful expression of active human sialyltransferases ST3Gal1 and ST6Gal1 in commercial Escherichia coli strains designed for production of disulfide-containing proteins. Fusion of hST3Gal1 with different solubility enhancers and substitution of exposed hydrophobic amino acids by negatively charged residues (supercharging-like approach) were performed to promote solubility and folding. Co-expression of sialyltransferases with the chaperon/foldases sulfhydryl oxidase, protein disulfide isomerase and disulfide isomerase C was explored to improve the formation of native disulfide bonds. Active sialyltransferases fused with maltose binding protein (MBP) were obtained in sufficient amounts for biochemical and structural studies when expressed under oxidative conditions and co-expression of folding factors increased the yields of active and properly folded sialyltransferases by 20%. Mutation of exposed hydrophobic amino acids increased recovery of active enzyme by 2.5-fold, yielding about 7 mg of purified protein per liter culture. Functionality of recombinant enzymes was evaluated in the synthesis of sialosides from the β-d-galactoside substrates lactose, N-acetyllactosamine and benzyl 2-acetamido-2-deoxy-3-O-(β-d-galactopyranosyl)-α-d-galactopyranoside.
Collapse
Affiliation(s)
- Maria Elena Ortiz-Soto
- Institut für Organische Chemie, Julius-Maximilians-Universität, Am Hubland, 97074, Würzburg, Germany
| | - Jürgen Seibel
- Institut für Organische Chemie, Julius-Maximilians-Universität, Am Hubland, 97074, Würzburg, Germany
| |
Collapse
|
23
|
Cohen DO, Duchin S, Feldman M, Zarivach R, Aharoni A, Levy D. Engineering of Methylation State Specific 3xMBT Domain Using ELISA Screening. PLoS One 2016; 11:e0154207. [PMID: 27111853 PMCID: PMC4844143 DOI: 10.1371/journal.pone.0154207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/10/2016] [Indexed: 01/08/2023] Open
Abstract
The ε-amino group of lysine residues may be mono-, di- or tri-methylated by protein lysine methyltransferases. In the past few years it has been highly considered that methylation of both histone and non-histone proteins has fundamental role in development and progression of various human diseases. Thus, the establishment of tools to study lysine methylation that will distinguish between the different states of methylation is required to elucidate their cellular functions. The 3X malignant brain tumor domain (3XMBT) repeats of the Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1) have been utilized in the past as an affinity reagent for the identification of mono- and di-methylated lysine residues on individual proteins and on a proteomic scale. Here, we have utilized the 3XMBT domain to develop an enzyme-linked immunosorbent assay (ELISA) that allows the high-throughput detection of 3XMBT binding to methylated lysines. We demonstrated that this system allows the detection of methylated peptides, methylated proteins and PKMT activity on both peptides and proteins. We also optimized the assay to detect 3XMBT binding in crude E. coli lysates which facilitated the high throughput screening of 3XMBT mutant libraries. We have utilized protein engineering tools and generated a double site saturation 3XMBT library of residues 361 and 411 that were shown before to be important for binding mono and di-methylated substrates and identified variants that can exclusively recognize only di-methylated peptides. Together, our results demonstrate a powerful new approach that will contribute to deeper understanding of lysine methylation biology and that can be utilized for the engineering of domains for specific binders of other post-translational modifications.
Collapse
Affiliation(s)
- Dan Od Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Shai Duchin
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
- * E-mail: (DL); (AA)
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
- * E-mail: (DL); (AA)
| |
Collapse
|
24
|
Bokhove M, Sadat Al Hosseini H, Saito T, Dioguardi E, Gegenschatz-Schmid K, Nishimura K, Raj I, de Sanctis D, Han L, Jovine L. Easy mammalian expression and crystallography of maltose-binding protein-fused human proteins. J Struct Biol 2016; 194:1-7. [PMID: 26850170 PMCID: PMC4771870 DOI: 10.1016/j.jsb.2016.01.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/28/2016] [Accepted: 01/31/2016] [Indexed: 01/19/2023]
Abstract
We present a strategy to obtain milligrams of highly post-translationally modified eukaryotic proteins, transiently expressed in mammalian cells as rigid or cleavable fusions with a mammalianized version of bacterial maltose-binding protein (mMBP). This variant was engineered to combine mutations that enhance MBP solubility and affinity purification, as well as provide crystal-packing interactions for increased crystallizability. Using this cell type-independent approach, we could increase the expression of secreted and intracellular human proteins up to 200-fold. By molecular replacement with MBP, we readily determined five novel high-resolution structures of rigid fusions of targets that otherwise defied crystallization.
Collapse
Affiliation(s)
- Marcel Bokhove
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Hamed Sadat Al Hosseini
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Takako Saito
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Elisa Dioguardi
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Katharina Gegenschatz-Schmid
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Kaoru Nishimura
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Isha Raj
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | | | - Ling Han
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Luca Jovine
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden.
| |
Collapse
|
25
|
Abstract
SUMO-specific proteases, known as Ulps in baker's yeast and SENPs in humans, have important roles in controlling the dynamics of SUMO-modified proteins. They display distinct modes of action and specificity, in that they may act on the SUMO precursor, mono-sumoylated, and/or polysumoylated proteins, and they might be specific for substrates with certain SUMO paralogs. SUMO chains may be dismantled either by endo or exo mechanisms. Biochemical characterization of a protease usually requires purification of the protein of interest. Developing a purification protocol, however, can be very difficult, and in some cases, isolation of a protease in its pure form may go along with a substantial loss of activity. To characterize the reaction mechanism of Ulps, we have developed an in vitro assay, which makes use of substrates endowed with artificial poly-SUMO chains of defined lengths, and S. cerevisiae Ulp enzymes in crude extract from E. coli. This fast and economic approach should be applicable to SUMO-specific proteases from other species as well.
Collapse
Affiliation(s)
- Julia Eckhoff
- Institute for Genetics, Biocenter, University of Cologne, 50674, Cologne, Germany
| | - R Jürgen Dohmen
- Institute for Genetics, Biocenter, University of Cologne, 50674, Cologne, Germany.
| |
Collapse
|
26
|
Fogen D, Wu SC, Ng KKS, Wong SL. Engineering Streptavidin and a Streptavidin-Binding Peptide with Infinite Binding Affinity and Reversible Binding Capability: Purification of a Tagged Recombinant Protein to High Purity via Affinity-Driven Thiol Coupling. PLoS One 2015; 10:e0139137. [PMID: 26406477 PMCID: PMC4583386 DOI: 10.1371/journal.pone.0139137] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/08/2015] [Indexed: 12/02/2022] Open
Abstract
To extend and improve the utility of the streptavidin-binding peptide tag (SBP-tag) in applications ranging from affinity purification to the reversible immobilization of recombinant proteins, a cysteine residue was introduced to the streptavidin mutein SAVSBPM18 and the SBP-tag to generate SAVSBPM32 and SBP(A18C), respectively. This pair of derivatives is capable of forming a disulfide bond through the newly introduced cysteine residues. SAVSBPM32 binds SBP-tag and biotin with binding affinities (Kd ~ 10-8M) that are similar to SAVSBPM18. Although SBP(A18C) binds to SAVSBPM32 more weakly than SBP-tag, the binding affinity is sufficient to bring the two binding partners together efficiently before they are locked together via disulfide bond formation–a phenomenon we have named affinity-driven thiol coupling. Under the condition with SBP(A18C) tags in excess, two SBP(A18C) tags can be captured by a tetrameric SAVSBPM32. The stoichiometry of the disulfide-bonded SAVSBPM32-SBP(A18C) complex was determined using a novel two-dimensional electrophoresis method which has general applications for analyzing the composition of disulfide-bonded protein complexes. To illustrate the application of this reversible immobilization technology, optimized conditions were established to use the SAVSBPM32-affinity matrix for the purification of a SBP(A18C)-tagged reporter protein to high purity. Furthermore, we show that the SAVSBPM32-affinity matrix can also be applied to purify a biotinylated protein and a reporter protein tagged with the unmodified SBP-tag. The dual (covalent and non-covalent) binding modes possible in this system offer great flexibility to many different applications which need reversible immobilization capability.
Collapse
Affiliation(s)
- Dawson Fogen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sau-Ching Wu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Kenneth Kai-Sing Ng
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sui-Lam Wong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
| |
Collapse
|
27
|
Russo A, Scognamiglio PL, Hong Enriquez RP, Santambrogio C, Grandori R, Marasco D, Giordano A, Scoles G, Fortuna S. In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands. PLoS One 2015; 10:e0133571. [PMID: 26252476 PMCID: PMC4529233 DOI: 10.1371/journal.pone.0133571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/27/2015] [Indexed: 12/25/2022] Open
Abstract
Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.
Collapse
Affiliation(s)
- Anna Russo
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- Department of Medical Biotechnology, University of Siena, Policlinico Le Scotte, Viale Bracci, Siena, Italy
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples “Federico II”, DFM-Scarl, Naples, Italy
| | | | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples “Federico II”, DFM-Scarl, Naples, Italy
- * E-mail: (SF); (DM)
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine & Center for Biotechnology Temple University Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Surgery & Neuroscience University of Siena, Strada delle Scotte n. 6, Siena, Italy
| | - Giacinto Scoles
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sara Fortuna
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- * E-mail: (SF); (DM)
| |
Collapse
|
28
|
Nauen R, Wölfel K, Lueke B, Myridakis A, Tsakireli D, Roditakis E, Tsagkarakou A, Stephanou E, Vontas J. Development of a lateral flow test to detect metabolic resistance in Bemisia tabaci mediated by CYP6CM1, a cytochrome P450 with broad spectrum catalytic efficiency. Pestic Biochem Physiol 2015; 121:3-11. [PMID: 26047106 DOI: 10.1016/j.pestbp.2014.12.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/25/2014] [Accepted: 12/26/2014] [Indexed: 06/04/2023]
Abstract
Cotton whitefly, Bemisia tabaci (Genn.) (Homoptera: Aleyrodidae) is a major sucking pest in many agricultural and horticultural cropping systems globally. The frequent use of insecticides of different mode of action classes resulted in populations resisting treatments used to keep numbers under economic damage thresholds. Recently it was shown that resistance to neonicotinoids such as imidacloprid is linked to the over-expression of CYP6CM1, a cytochrome P450 monooxygenase detoxifying imidacloprid and other neonicotinoid insecticides when recombinantly expressed in insect cells. However over-expression of CYP6CM1 is also known to confer cross-resistance to pymetrozine, an insecticide not belonging to the chemical class of neonicotinoids. In addition we were able to demonstrate by LC-MS/MS analysis the metabolisation of pyriproxyfen by recombinantly expressed CYP6CM1. Based on our results CYP6CM1 is one of the most versatile detoxification enzymes yet identified in a pest of agricultural importance, as it detoxifies a diverse range of chemical classes used to control whiteflies. Therefore we developed a field-diagnostic antibody-based lateral flow assay which detects CYP6CM1 protein at levels providing resistance to neonicotinoids and other insecticides. The ELISA based test kit can be used as a diagnostic tool to support resistance management strategies based on the alternation of different modes of action of insecticides.
Collapse
Affiliation(s)
- Ralf Nauen
- Bayer CropScience AG, R&D Pest Control Biology, Alfred Nobel Str. 50, Monheim D-40789, Germany.
| | - Katharina Wölfel
- Bayer CropScience AG, R&D Pest Control Biology, Alfred Nobel Str. 50, Monheim D-40789, Germany
| | - Bettina Lueke
- Bayer CropScience AG, R&D Pest Control Biology, Alfred Nobel Str. 50, Monheim D-40789, Germany
| | - Antonis Myridakis
- Environmental Chemical Processes Laboratory (ECPL), Department of Chemistry, University of Crete, Heraklion 71003, Greece
| | | | - Emmanouil Roditakis
- Hellenic Agricultural Organisation "Demeter", NAGREF, Plant Protection Institute of Heraklion, Heraklion 71003, Greece
| | - Anastasia Tsagkarakou
- Hellenic Agricultural Organisation "Demeter", NAGREF, Plant Protection Institute of Heraklion, Heraklion 71003, Greece
| | - Euripides Stephanou
- Environmental Chemical Processes Laboratory (ECPL), Department of Chemistry, University of Crete, Heraklion 71003, Greece
| | - John Vontas
- Pesticide Science Lab, Department of Crop Science, Agricultural University of Athens, Athens 11855, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 71003, Greece.
| |
Collapse
|
29
|
Zheng S, Vuong BQ, Vaidyanathan B, Lin JY, Huang FT, Chaudhuri J. Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA. Cell 2015; 161:762-73. [PMID: 25957684 PMCID: PMC4426339 DOI: 10.1016/j.cell.2015.03.020] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/31/2014] [Accepted: 02/27/2015] [Indexed: 12/20/2022]
Abstract
Transcription through immunoglobulin switch (S) regions is essential for class switch recombination (CSR), but no molecular function of the transcripts has been described. Likewise, recruitment of activation-induced cytidine deaminase (AID) to S regions is critical for CSR; however, the underlying mechanism has not been fully elucidated. Here, we demonstrate that intronic switch RNA acts in trans to target AID to S region DNA. AID binds directly to switch RNA through G-quadruplexes formed by the RNA molecules. Disruption of this interaction by mutation of a key residue in the putative RNA-binding domain of AID impairs recruitment of AID to S region DNA, thereby abolishing CSR. Additionally, inhibition of RNA lariat processing leads to loss of AID localization to S regions and compromises CSR; both defects can be rescued by exogenous expression of switch transcripts in a sequence-specific manner. These studies uncover an RNA-mediated mechanism of targeting AID to DNA.
Collapse
Affiliation(s)
- Simin Zheng
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Bao Q Vuong
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Biology, City College of New York, New York, NY 10031, USA
| | - Bharat Vaidyanathan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Jia-Yu Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Feng-Ting Huang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
| |
Collapse
|
30
|
Elvitigala DAS, Priyathilaka TT, Whang I, Nam BH, Lee J. A teleostan homolog of catalase from black rockfish (Sebastes schlegelii): insights into functional roles in host antioxidant defense and expressional responses to septic conditions. Fish Shellfish Immunol 2015; 44:321-331. [PMID: 25707597 DOI: 10.1016/j.fsi.2015.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 06/04/2023]
Abstract
Antioxidative defense renders a significant protection against environmental stress in organisms and maintains the correct redox balance in cells, thereby supporting proper immune function. Catalase is an indispensable antioxidant in organisms that detoxifies hydrogen peroxides produced in cellular environments. In this study, we sought to molecularly characterize a homolog of catalase (RfCat), identified from black rockfish (Sebastes schlegelii). RfCat consists of a 1581 bp coding region for a protein of 527 amino acids, with a predicted molecular weight of 60 kD. The protein sequence of RfCat harbored similar domain architecture to known catalases, containing a proximal active site signature and proximal heme ligand signature, and further sharing prominent homology with its teleostan counterparts. As affirmed by multiple sequence alignments, most of the functionally important residues were well conserved in RfCat. Furthermore, our phylogenetic analysis indicates its common vertebrate ancestral origin and a close evolutionary relationship with teleostan catalases. Recombinantly expressed RfCat demonstrated prominent peroxidase activity that varied with different substrate and protein concentrations, and protected against DNA damage. RfCat mRNA was ubiquitously expressed among different tissues examined, as detected by qPCR. In addition, RfCat mRNA expression was modulated in response to pathogenic stress elicited by Streptococcus iniae and poly I:C in blood and spleen tissues. Collectively, our findings indicate that RfCat may play an indispensable role in host response to oxidative stress and maintain a correct redox balance after a pathogen invasion.
Collapse
Affiliation(s)
- Don Anushka Sandaruwan Elvitigala
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Special Self-Governing Province 690-756, Republic of Korea
| | - Thanthrige Thiunuwan Priyathilaka
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Special Self-Governing Province 690-756, Republic of Korea
| | - Ilson Whang
- Fish Vaccine Research Center, Jeju National University, Jeju Special Self-Governing Province 690-756, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Fisheries Research and Development Institute, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan 619-705, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Special Self-Governing Province 690-756, Republic of Korea.
| |
Collapse
|
31
|
Coyle BL, Baneyx F. A cleavable silica-binding affinity tag for rapid and inexpensive protein purification. Biotechnol Bioeng 2014; 111:2019-26. [PMID: 24777569 DOI: 10.1002/bit.25257] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/27/2014] [Accepted: 03/31/2014] [Indexed: 01/03/2023]
Abstract
We describe a new affinity purification tag called Car9 that confers proteins to which it is fused micromolar affinity for unmodified silica. When appended to the C-terminus of GFPmut2 through a flexible linker, Car9 promotes efficient adsorption to silica gel and the fusion protein can be released from the particles by incubation with L-lysine. Using a silica gel column and the lysine elution approach in fast protein liquid chromatography (FPLC) mode, Car9-tagged versions of GFPmut2, mCherry and maltose binding protein (MBP) can be recovered from clarified lysates with a purity of 80-90%. Capitalizing on silica's ability to handle large pressure drops, we further show that it is possible to go from cell lysates to purified protein in less than 15 min using a fully disposable device. Finally, we demonstrate that the linker-Car9 region is susceptible to proteolysis by E. coli OmpT and take advantage of this observation to excise the C-terminal extension of GFPmut2-Car9 by incubating purified fusion protein with cells that overproduce the outer membrane protease OmpT. The set of strategies described herein, should reduce the cost of affinity purification by at least 10-fold, cut down purification times to minutes, and allow for the production of proteins with native (or nearly native) termini from their C-terminally-tagged versions.
Collapse
Affiliation(s)
- Brandon L Coyle
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington, 98195-1750
| | | |
Collapse
|
32
|
Xu Y, He Z, He Q, Qiu Y, Chen B, Chen J, Liu X. Use of cloneable peptide-MBP fusion protein as a mimetic coating antigen in the standardized immunoassay for mycotoxin ochratoxin A. J Agric Food Chem 2014; 62:8830-8836. [PMID: 25127400 DOI: 10.1021/jf5028922] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The quality of mycotoxin conjugates is essential to the development of reliability of immunoassays for mycotoxins. However, conventional mycotoxin conjugates are usually synthesized by chemical methods, which are harmful to the environment and yield unwanted cross-reactions. In this study, using ochratoxin A (OTA) as a model system, a selected OTA mimotope (phage-displayed peptide) that specifically binds to anti-OTA antibody was expressed as soluble and monovalent fusions to maltose binding protein (MBP). These prepared fusion proteins can serve as a mimetic coating antigen in both a quantitative chemiluminescent enzyme-linked immunoassay (CLEIA) and a qualitative dot immunoassay for OTA. One of the prepared mimetic coating antigen (L12-206-MBP)-based CLEIAs exhibited a half-inhibition concentration (IC50) of 0.82 ng/mL and a working range of 0.30-2.17 ng/mL, which resemble those of the conventional OTA-OVA conjugate-based immunoassay. The dot immunoassay developed with both the OTA-OVA conjugate and the mimetics showed identical visual cutoff values of 5 ng/mL. The mimetic coating antigen proposed here is an OTA-free product and can be prepared reproducibly as a homogeneous product and facilitates standardization of immunoassays for the mycotoxin OTA.
Collapse
Affiliation(s)
- Yang Xu
- State Key Laboratory of Food Science and Technology, Sino-Germany Joint Research Institute, Nanchang University , No. 235 Nanjing East Road, Nanchang 330047, China
| | | | | | | | | | | | | |
Collapse
|
33
|
Gromek KA, Suchy FP, Meddaugh HR, Wrobel RL, LaPointe LM, Chu UB, Primm JG, Ruoho AE, Senes A, Fox BG. The oligomeric states of the purified sigma-1 receptor are stabilized by ligands. J Biol Chem 2014; 289:20333-44. [PMID: 24847081 PMCID: PMC4106346 DOI: 10.1074/jbc.m113.537993] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 04/29/2014] [Indexed: 12/05/2022] Open
Abstract
Sigma-1 receptor (S1R) is a mammalian member of the ERG2 and sigma-1 receptor-like protein family (pfam04622). It has been implicated in drug addiction and many human neurological disorders, including Alzheimer and Parkinson diseases and amyotrophic lateral sclerosis. A broad range of synthetic small molecules, including cocaine, (+)-pentazocine, haloperidol, and small endogenous molecules such as N,N-dimethyltryptamine, sphingosine, and steroids, have been identified as regulators of S1R. However, the mechanism of activation of S1R remains obscure. Here, we provide evidence in vitro that S1R has ligand binding activity only in an oligomeric state. The oligomeric state is prone to decay into an apparent monomeric form when exposed to elevated temperature, with loss of ligand binding activity. This decay is suppressed in the presence of the known S1R ligands such as haloperidol, BD-1047, and sphingosine. S1R has a GXXXG motif in its second transmembrane region, and these motifs are often involved in oligomerization of membrane proteins. Disrupting mutations within the GXXXG motif shifted the fraction of the higher oligomeric states toward smaller states and resulted in a significant decrease in specific (+)-[(3)H]pentazocine binding. Results presented here support the proposal that S1R function may be regulated by its oligomeric state. Possible mechanisms of molecular regulation of interacting protein partners by S1R in the presence of small molecule ligands are discussed.
Collapse
Affiliation(s)
| | | | | | | | | | - Uyen B Chu
- Neuroscience, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | | | - Arnold E Ruoho
- Neuroscience, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | | | - Brian G Fox
- From the Transmembrane Protein Center, Departments of Biochemistry and
| |
Collapse
|
34
|
Tong J, Yang H, Im YJ. Crystallization and preliminary X-ray crystallographic analysis of the C-terminal domain of guanylate kinase-associated protein from Rattus norvegicus. Acta Crystallogr F Struct Biol Commun 2014; 70:949-54. [PMID: 25005096 PMCID: PMC4089539 DOI: 10.1107/s2053230x1401187x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/22/2014] [Indexed: 11/11/2022] Open
Abstract
Guanylate kinase-associated protein (GKAP) is a scaffolding protein that plays a role in protein-protein interactions at the synaptic junction such as linking the NMDA receptor-PSD-95 complex to the Shank-Homer complex. In this study, the C-terminal helical domain of GKAP from Rattus norvegicus was purified and crystallized by the vapour-diffusion method. To improve the diffraction quality of the GKAP crystals, a flexible loop in GKAP was truncated and an MBP (maltose-binding protein)-GKAP fusion was constructed in which the last C-terminal helix of MBP is fused to the N-terminus of the GKAP domain. The MBP-GKAP crystals diffracted to 2.0 Å resolution using synchrotron radiation. The crystal was orthorhombic, belonging to space group P2₁2₁2, with unit-cell parameters a=99.1, b=158.7, c=65.5 Å. The Matthews coefficient was determined to be 2.44 Å3 Da(-1) (solvent content 49.5%) with two molecules in the asymmetric unit. Initial attempts to solve the structure by molecular replacement using the MBP structure were successful.
Collapse
Affiliation(s)
- Junsen Tong
- College of Pharmacy, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Huiseon Yang
- College of Pharmacy, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Young Jun Im
- College of Pharmacy, Chonnam National University, Gwangju 500-757, Republic of Korea
| |
Collapse
|
35
|
Zhou C, Yan Y, Fang J, Cheng B, Fan J. A new fusion protein platform for quantitatively measuring activity of multiple proteases. Microb Cell Fact 2014; 13:44. [PMID: 24649897 PMCID: PMC4000059 DOI: 10.1186/1475-2859-13-44] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombinant proteins fused with specific cleavage sequences are widely used as substrate for quantitatively analyzing the activity of proteases. Here we propose a new fusion platform for multiple proteases, by using diaminopropionate ammonia-lyase (DAL) as the fusion protein. It was based on the finding that a fused His6-tag could significantly decreases the activities of DAL from E. coli (eDAL) and Salmonella typhimurium (sDAL). Previously, we have shown that His6GST-tagged eDAL could be used to determine the activity of tobacco etch virus protease (TEVp) under different temperatures or in the denaturant at different concentrations. In this report, we will assay different tags and cleavage sequences on DAL for expressing yield in E. coli, stability of the fused proteins and performance of substrate of other common proteases. RESULTS We tested seven different protease cleavage sequences (rhinovirus 3C, TEV protease, factor Xa, Ssp DnaB intein, Sce VMA1 intein, thrombin and enterokinase), three different tags (His6, GST, CBD and MBP) and two different DALs (eDAL and sDAL), for their performance as substrate to the seven corresponding proteases. Among them, we found four active DAL-fusion substrates suitable for TEVp, factor Xa, thrombin and DnaB intein. Enterokinase cleaved eDAL at undesired positions and did not process sDAL. Substitution of GST with MBP increase the expression level of the fused eDAL and this fusion protein was suitable as a substrate for analyzing activity of rhinovirus 3C. We demonstrated that SUMO protease Ulp1 with a N-terminal His6-tag or MBP tag displayed different activity using the designed His6SUMO-eDAL as substrate. Finally, owing to the high level of the DAL-fusion protein in E. coli, these protein substrates can also be detected directly from the crude extract. CONCLUSION The results show that our designed DAL-fusion proteins can be used to quantify the activities of both sequence- and conformational-specific proteases, with sufficient substrate specificity.
Collapse
Affiliation(s)
- Chengdong Zhou
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, 130#, Changjiang West Road, Hefei City, Anhui Province 230036, PR. China
| | - Yanping Yan
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, 130#, Changjiang West Road, Hefei City, Anhui Province 230036, PR. China
| | - Jie Fang
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, 130#, Changjiang West Road, Hefei City, Anhui Province 230036, PR. China
| | - Beijiu Cheng
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, 130#, Changjiang West Road, Hefei City, Anhui Province 230036, PR. China
| | - Jun Fan
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, 130#, Changjiang West Road, Hefei City, Anhui Province 230036, PR. China
| |
Collapse
|
36
|
Do BH, Ryu HB, Hoang P, Koo BK, Choe H. Soluble prokaryotic overexpression and purification of bioactive human granulocyte colony-stimulating factor by maltose binding protein and protein disulfide isomerase. PLoS One 2014; 9:e89906. [PMID: 24594699 PMCID: PMC3940694 DOI: 10.1371/journal.pone.0089906] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/24/2014] [Indexed: 01/17/2023] Open
Abstract
Human granulocyte colony-stimulating factor (hGCSF), a neutrophil-promoting cytokine, is an effective therapeutic agent for neutropenia patients who have undergone several cancer treatments. Efficient production of hGCSF using E. coli is challenging because the hormone tends to aggregate and forms inclusion bodies. This study examined the ability of seven different N-terminal fusion tags to increase expression of soluble hGCSF in E. coli. Four tag proteins, namely maltose-binding protein (MBP), N-utilization substance protein A, protein disulfide isomerase (PDI), and the b'a' domain of PDI (PDIb'a'), increased the solubility of hGCSF under normal conditions. Lowering the expression temperature from 30°C to 18°C also increased the solubility of thioredoxin-tagged and glutathione S-transferase-tagged hGCSF. By contrast, hexahistidine-tagged hGCSF was insoluble at both temperatures. Simple conventional chromatographic methods were used to purify hGCSF from the overexpressed PDIb'a'-hGCSF and MBP-hGCSF proteins. In total, 11.3 mg or 10.2 mg of pure hGCSF were obtained from 500 mL cultures of E. coli expressing PDIb'a'-hGCSF or MBP-hGCSF, respectively. SDS-PAGE analysis and silver staining confirmed high purity of the isolated hGCSF proteins, and the endotoxin levels were less than 0.05 EU/µg of protein. Subsequently, the bioactivity of the purified hGCSF proteins similar to that of the commercially available hGCSF was confirmed using the mouse M-NFS-60 myelogenous leukemia cell line. The EC50s of the cell proliferation dose-response curves for hGCSF proteins purified from MBP-hGCSF and PDIb'a'-hGCSF were 2.83±0.31 pM, and 3.38±0.41 pM, respectively. In summary, this study describes an efficient method for the soluble overexpression and purification of bioactive hGCSF in E. coli.
Collapse
Affiliation(s)
- Bich Hang Do
- Department of Physiology and Biomedical Institute of Technology, University of Ulsan College of Medicine, Seoul, Korea
| | - Han-Bong Ryu
- Department of Physiology and Biomedical Institute of Technology, University of Ulsan College of Medicine, Seoul, Korea
| | - Phuong Hoang
- Department of Physiology and Biomedical Institute of Technology, University of Ulsan College of Medicine, Seoul, Korea
| | - Bon-Kyung Koo
- Department of Physiology and Biomedical Institute of Technology, University of Ulsan College of Medicine, Seoul, Korea
| | - Han Choe
- Department of Physiology and Biomedical Institute of Technology, University of Ulsan College of Medicine, Seoul, Korea
- * E-mail:
| |
Collapse
|
37
|
Abstract
Isolating spliceosomes at a specific assembly stage requires a means to stall or enrich for one of the intermediate splicing complexes. We describe strategies to arrest spliceosomes at different points of complex formation and provide a detailed protocol developed for isolating intact splicing complexes arrested between the first and second chemical steps of splicing. Briefly, spliceosomes are assembled on a radiolabeled in vitro-transcribed splicing substrate from components present in nuclear extract of HeLa cells. Spliceosome progression is arrested after the first step of splicing chemistry by mutating the pre-mRNA substrate at the 3' splice site. The substrate also contains binding sites for the MS2 protein, which serve as an affinity tag. Purification of arrested spliceosomes is carried out in two steps: (1) size exclusion chromatography and (2) affinity selection via a fusion of MS2 and maltose-binding protein (MBP). Complex assembly and purification are analyzed by denaturing polyacrylamide gel electrophoresis.
Collapse
Affiliation(s)
- Janine O Ilagan
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
| | | |
Collapse
|
38
|
Miyazawa-Onami M, Takeuchi K, Takano T, Sugiki T, Shimada I, Takahashi H. Perdeuteration and methyl-selective (1)H, (13)C-labeling by using a Kluyveromyces lactis expression system. J Biomol NMR 2013; 57:297-304. [PMID: 24146206 DOI: 10.1007/s10858-013-9789-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/07/2013] [Indexed: 06/02/2023]
Abstract
The production of stable isotope-labeled proteins is critical in structural analyses of large molecular weight proteins using NMR. Although prokaryotic expression systems using Escherichia coli have been widely used for this purpose, yeast strains have also been useful for the expression of functional eukaryotic proteins. Recently, we reported a cost-effective stable isotope-labeled protein expression using the hemiascomycete yeast Kluyveromyces lactis (K. lactis), which allow us to express exogenous proteins at costs comparable to prokaryotic expression systems. Here, we report the successful production of highly deuterated (>90 %) protein in the K. lactis system. We also examined the methyl-selective (1)H, (13)C-labeling of Ile, Leu, and Val residues using commonly used amino acid precursors. The efficiency of (1)H-(13)C-incorporation varied significantly based on the amino acid. Although a high level of (1)H-(13)C-incorporation was observed for the Ile δ1 position, (1)H, (13)C-labeling rates of Val and Leu methyl groups were limited due to the mitochondrial localization of enzymes involved in amino acid biosynthesis and the lack of transporters for α-ketoisovalerate in the mitochondrial membrane. In line with this notion, the co-expression with branched-chain-amino-acid aminotransferase in the cytosol significantly improved the incorporation rates of amino acid precursors. Although it would be less cost-effective, addition of (13)C-labeled valine can circumvent problems associated with precursors and achieve high level (1)H, (13)C-labeling of Val and Leu. Taken together, the K. lactis system would be a good alternative for expressing large eukaryotic proteins that need deuteration and/or the methyl-selective (1)H, (13)C-labeling for the sensitive detection of NMR resonances.
Collapse
Affiliation(s)
- Mayumi Miyazawa-Onami
- Research and Development Department, Japan Biological Informatics Consortium, Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
39
|
Shen Ni L, Allaudin ZNB, Mohd Lila MAB, Othman AMB, Othman FB. Selective apoptosis induction in MCF-7 cell line by truncated minimal functional region of Apoptin. BMC Cancer 2013; 13:488. [PMID: 24144306 PMCID: PMC4015422 DOI: 10.1186/1471-2407-13-488] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 09/30/2013] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Chicken Anemia Virus (CAV) VP3 protein (also known as Apoptin), a basic and proline-rich protein has a unique capability in inducing apoptosis in cancer cells but not in normal cells. Five truncated Apoptin proteins were analyzed to determine their selective ability to migrate into the nucleus of human breast adenocarcinoma MCF-7 cells for inducing apoptosis. METHODS For identification of the minimal selective domain for apoptosis, the wild-type Apoptin gene had been reconstructed by PCR to generate segmental deletions at the N' terminal and linked with nuclear localization sites (NLS1 and NLS2). All the constructs were fused with maltose-binding protein gene and individually expressed by in vitro Rapid Translation System. Standardized dose of proteins were delivered into human breast adenocarcinoma MCF-7 cells and control human liver Chang cells by cytoplasmic microinjection, and subsequently observed for selective apoptosis effect. RESULTS Three of the truncated Apoptin proteins with N-terminal deletions spanning amino acid 32-83 retained the cancer selective nature of wild-type Apoptin. The proteins were successfully translocated to the nucleus of MCF-7 cells initiating apoptosis, whereas non-toxic cytoplasmic retention was observed in normal Chang cells. Whilst these truncated proteins retained the tumour-specific death effector ability, the specificity for MCF-7 cells was lost in two other truncated proteins that harbor deletions at amino acid 1-31. The detection of apoptosing normal Chang cells and MCF-7 cells upon cytoplasmic microinjection of these proteins implicated a loss in Apoptin's signature targeting activity. CONCLUSIONS Therefore, the critical stretch spanning amino acid 1-31 at the upstream of a known hydrophobic leucine-rich stretch (LRS) was strongly suggested as one of the prerequisite region in Apoptin for cancer targeting. Identification of this selective domain provides a platform for developing small targets to facilitating carrier-mediated-transport across cellular membrane, simultaneously promoting protein delivery for selective and effective breast cancer therapy.
Collapse
Affiliation(s)
- Lim Shen Ni
- Institute of Biosciences, Universiti Putra, Serdang, Malaysia
| | - Zeenathul Nazariah bt Allaudin
- Institute of Biosciences, Universiti Putra, Serdang, Malaysia
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor 43400 UPM, Malaysia
| | - Mohd Azmi b Mohd Lila
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor 43400 UPM, Malaysia
| | | | | |
Collapse
|
40
|
Hung TJ, Chang WT, Tomiya N, Lee YC, Chang HT, Chen CJ, Kuo PH, Fan TC, Chang MDT. Basic amino acid residues of human eosinophil derived neurotoxin essential for glycosaminoglycan binding. Int J Mol Sci 2013; 14:19067-85. [PMID: 24065103 PMCID: PMC3794821 DOI: 10.3390/ijms140919067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/06/2013] [Accepted: 09/11/2013] [Indexed: 12/26/2022] Open
Abstract
Human eosinophil derived neurotoxin (EDN), a granule protein secreted by activated eosinophils, is a biomarker for asthma in children. EDN belongs to the human RNase A superfamily possessing both ribonucleolytic and antiviral activities. EDN interacts with heparin oligosaccharides and heparin sulfate proteoglycans on bronchial epithelial Beas-2B cells. In this study, we demonstrate that the binding of EDN to cells requires cell surface glycosaminoglycans (GAGs), and the binding strength between EDN and GAGs depends on the sulfation levels of GAGs. Furthermore, in silico computer modeling and in vitro binding assays suggest critical roles for the following basic amino acids located within heparin binding regions (HBRs) of EDN 34QRRCKN39 (HBR1), 65NKTRKN70 (HBR2), and 113NRDQRRD119 (HBR3) and in particular Arg35, Arg36, and Arg38 within HBR1, and Arg114 and Arg117 within HBR3. Our data suggest that sulfated GAGs play a major role in EDN binding, which in turn may be related to the cellular effects of EDN.
Collapse
Affiliation(s)
- Ta-Jen Hung
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
| | - Wei-Tang Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
| | - Noboru Tomiya
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; E-Mail:
| | - Yuan-Chuan Lee
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; E-Mail:
| | - Hao-Teng Chang
- Graduate Institute of Basic Medical Science, China Medical University, Taichung 404, Taiwan; E-Mail:
| | - Chien-Jung Chen
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
| | - Ping-Hsueh Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
| | - Tan-chi Fan
- Stem Cell and Translational Cancer Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan; E-Mail:
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
- Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +886-3-574-2463; Fax: +886-3-571-5934
| |
Collapse
|
41
|
Boeneman K, Delehanty JB, Blanco-Canosa JB, Susumu K, Stewart MH, Oh E, Huston AL, Dawson G, Ingale S, Walters R, Domowicz M, Deschamps JR, Algar WR, DiMaggio S, Manono J, Spillmann CM, Thompson D, Jennings TL, Dawson PE, Medintz IL. Selecting improved peptidyl motifs for cytosolic delivery of disparate protein and nanoparticle materials. ACS Nano 2013; 7:3778-96. [PMID: 23710591 PMCID: PMC3880025 DOI: 10.1021/nn400702r] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cell penetrating peptides facilitate efficient intracellular uptake of diverse materials ranging from small contrast agents to larger proteins and nanoparticles. However, a significant impediment remains in the subsequent compartmentalization/endosomal sequestration of most of these cargoes. Previous functional screening suggested that a modular peptide originally designed to deliver palmitoyl-protein thioesterase inhibitors to neurons could mediate endosomal escape in cultured cells. Here, we detail properties relevant to this peptide's ability to mediate cytosolic delivery of quantum dots (QDs) to a wide range of cell-types, brain tissue culture and a developing chick embryo in a remarkably nontoxic manner. The peptide further facilitated efficient endosomal escape of large proteins, dendrimers and other nanoparticle materials. We undertook an iterative structure-activity relationship analysis of the peptide by discretely modifying key components including length, charge, fatty acid content and their order using a comparative, semiquantitative assay. This approach allowed us to define the key motifs required for endosomal escape, to select more efficient escape sequences, along with unexpectedly identifying a sequence modified by one methylene group that specifically targeted QDs to cellular membranes. We interpret our results within a model of peptide function and highlight implications for in vivo labeling and nanoparticle-mediated drug delivery by using different peptides to co-deliver cargoes to cells and engage in multifunctional labeling.
Collapse
Affiliation(s)
- Kelly Boeneman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - James B. Delehanty
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - Juan B. Blanco-Canosa
- Departments of Cell Biology & Chemistry, The Scripps Research Institute, La Jolla, CA 92037 U.S.A
- Institute for Research in Biomedicine (IRB Barcelona), Chemistry and Molecular Pharmacology Programme, Barcelona 08028 Spain
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
- Sotera Defense Solutions, Annapolis Junction, MD 20701 U.S.A
| | - Michael H. Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - Eunkeu Oh
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
- Sotera Defense Solutions, Annapolis Junction, MD 20701 U.S.A
| | - Alan L. Huston
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - Glyn Dawson
- Departments of Pediatrics, Biochemistry, Committee on Neurobiology, University of Chicago, Chicago, IL 60637 U.S.A
| | - Sampat Ingale
- Departments of Cell Biology & Chemistry, The Scripps Research Institute, La Jolla, CA 92037 U.S.A
| | - Ryan Walters
- Departments of Pediatrics, Biochemistry, Committee on Neurobiology, University of Chicago, Chicago, IL 60637 U.S.A
- Institute for Research in Biomedicine (IRB Barcelona), Chemistry and Molecular Pharmacology Programme, Barcelona 08028 Spain
| | - Miriam Domowicz
- Departments of Pediatrics, Biochemistry, Committee on Neurobiology, University of Chicago, Chicago, IL 60637 U.S.A
| | - Jeffrey R. Deschamps
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - W. Russ Algar
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
- College of Science, George Mason University, Fairfax, VA 22030 U.S.A
| | - Stassi DiMaggio
- Department of Chemistry, Xavier University of Louisiana, New Orleans LA 70125 U.S.A
| | - Janet Manono
- Department of Chemistry, Xavier University of Louisiana, New Orleans LA 70125 U.S.A
| | - Christopher M. Spillmann
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - Darren Thompson
- Departments of Cell Biology & Chemistry, The Scripps Research Institute, La Jolla, CA 92037 U.S.A
| | - Travis L. Jennings
- eBioscience, Inc., 10255 Science Center Drive, San Diego, CA 92121 U.S.A
| | - Philip E. Dawson
- Departments of Cell Biology & Chemistry, The Scripps Research Institute, La Jolla, CA 92037 U.S.A
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| |
Collapse
|
42
|
Bae JY, Koo BK, Ryu HB, Song JA, Nguyen MT, Vu TTT, Son YJ, Lee HK, Choe H. Cu/Zn incorporation during purification of soluble human EC-SOD from E. coli stabilizes proper disulfide bond formation. Appl Biochem Biotechnol 2013; 169:1633-47. [PMID: 23329142 DOI: 10.1007/s12010-012-0025-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/05/2012] [Indexed: 01/05/2023]
Abstract
Extracellular superoxide dismutase (EC-SOD) is the only enzyme that removes superoxide radical in the extracellular space. The reduction of EC-SOD is linked to many diseases, suggesting that the protein may have therapeutic value. EC-SOD is reported to be insoluble and to make inclusion bodies when overexpressed in the cytoplasm of Escherichia coli. The refolding process has the advantage of high yield, but has the disadvantage of frequent aggregation or misfolding during purification. For the first time, this study shows that fusion with maltose-binding protein (MBP), N-utilization substance protein A, and protein disulfide isomerase enabled the soluble overexpression of EC-SOD in the cytoplasm of E. coli. MBP-tagged human EC-SOD (hEC-SOD) was purified by MBP affinity and anion exchange chromatography, and its identity was confirmed by MALDI-TOF MS analysis. The purified protein showed good enzyme activity in vitro; however, there was a difference in metal binding. When copper and zinc were incorporated into hEC-SOD before MBP tag cleavage, the enzymatic activity was higher than when the metal ions were bound to the purified protein after MBP tag cleavage. Therefore, the enzymatic activity of hEC-SOD is associated with metal incorporation and protein folding via disulfide bond.
Collapse
Affiliation(s)
- Ji-Young Bae
- Department of Physiology and Bio-Medical Institute of Technology, University of Ulsan College of Medicine, 86 Asanbyeongwon-gil, Seoul 138-736, South Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Raran-Kurussi S, Waugh DS. The ability to enhance the solubility of its fusion partners is an intrinsic property of maltose-binding protein but their folding is either spontaneous or chaperone-mediated. PLoS One 2012; 7:e49589. [PMID: 23166722 PMCID: PMC3500312 DOI: 10.1371/journal.pone.0049589] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli maltose binding protein (MBP) is commonly used to promote the solubility of its fusion partners. To investigate the mechanism of solubility enhancement by MBP, we compared the properties of MBP fusion proteins refolded in vitro with those of the corresponding fusion proteins purified under native conditions. We fused five aggregation-prone passenger proteins to 3 different N-terminal tags: His6-MBP, His6-GST and His6. After purifying the 15 fusion proteins under denaturing conditions and refolding them by rapid dilution, we recovered far more of the soluble MBP fusion proteins than their GST- or His-tagged counterparts. Hence, we can reproduce the solubilizing activity of MBP in a simple in vitro system, indicating that no additional factors are required to mediate this effect. We assayed both the soluble fusion proteins and their TEV protease digestion products (i.e., with the N-terminal tag removed) for biological activity. Little or no activity was detected for some fusion proteins whereas others were quite active. When the MBP fusions proteins were purified from E. coli under native conditions they were all substantially active. These results indicate that the ability of MBP to promote the solubility of its fusion partners in vitro sometimes, but not always, results in their proper folding. We show that the folding of some passenger proteins is mediated by endogenous chaperones in vivo. Hence, MBP serves as a passive participant in the folding process; passenger proteins either fold spontaneously or with the assistance of chaperones.
Collapse
Affiliation(s)
- Sreejith Raran-Kurussi
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David S. Waugh
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail:
| |
Collapse
|
44
|
Minde DP, Maurice MM, Rüdiger SGD. Determining biophysical protein stability in lysates by a fast proteolysis assay, FASTpp. PLoS One 2012; 7:e46147. [PMID: 23056252 PMCID: PMC3463568 DOI: 10.1371/journal.pone.0046147] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 08/27/2012] [Indexed: 11/26/2022] Open
Abstract
The biophysical stability is an important parameter for protein activity both in vivo and in vitro. Here we propose a method to analyse thermal melting of protein domains in lysates: Fast parallel proteolysis (FASTpp). Combining unfolding by a temperature gradient in a thermal cycler with simultaneous proteolytic cleavage of the unfolded state, we probed stability of single domains in lysates. We validated FASTpp on proteins from 10 kDa to 240 kDa and monitored stabilisation and coupled folding and binding upon interaction with small-molecule ligands. Within a total reaction time of approximately 1 min, we probed subtle stability differences of point mutations with high sensitivity and in agreement with data obtained by intrinsic protein fluorescence. We anticipate a wide range of applications of FASTpp in biomedicine and protein engineering as it requires only standard laboratory equipment.
Collapse
Affiliation(s)
- David P. Minde
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Madelon M. Maurice
- Department of Cell Biology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- * E-mail: (SGDR); (MMM)
| | - Stefan G. D. Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- * E-mail: (SGDR); (MMM)
| |
Collapse
|
45
|
Sauge-Merle S, Lecomte-Pradines C, Carrier P, Cuiné S, Dubow M. Heavy metal accumulation by recombinant mammalian metallothionein within Escherichia coli protects against elevated metal exposure. Chemosphere 2012; 88:918-924. [PMID: 22560974 DOI: 10.1016/j.chemosphere.2012.04.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/23/2012] [Accepted: 04/04/2012] [Indexed: 05/31/2023]
Abstract
Metallothioneins (MTs) are ubiquitous metal-binding, cysteine-rich, small proteins known to provide protection against toxic heavy metals such as cadmium. In an attempt to increase the ability of bacterial cells to accumulate heavy metals, sheep MTII was produced in fusion with the maltose binding protein (MBP) and localized to the cytoplasmic or periplasmic compartments of Escherichia coli. For all metals tested, higher levels of bioaccumulation were measured with strains over-expressing MBP-MT in comparison with control strains. A marked bioaccumulation of Cd, As, Hg and Zn was observed in the strain over-expressing MBP-MT in the cytoplasm, whereas Cu was accumulated to higher levels when MBP-MT was over-expressed in the periplasm. Metal export systems may also play a role in this bioaccumulation. To illustrate this, we over-expressed MBP-MT in the cytoplasm of two mutant strains of E. coli affected in metal export. The first, deficient in the transporter ZntA described to export numerous divalent metal ions, showed increasing quantities of Zn, Cd, Hg and Pb being bioaccumulated. The second, strain LF20012, deficient in As export, showed that As was bioaccumulated in the form of arsenite. Furthermore, high quantities of accumulated metals, chelated by MBP-MT in the cytoplasm, conferred greater metal resistance levels to the cells in the presence of added toxic metals, such as Cd or Hg, while other metals showed toxic effects when the export systems were deficient. The strain over-expressing MBP-MT in the cytoplasm, in combination, with disruption of metal export systems, could be used to develop strategies for bioremediation.
Collapse
Affiliation(s)
- Sandrine Sauge-Merle
- CEA, DSV, IBEB, Lab Interact Protein Metal, Saint-Paul-lez-Durance F-13108, France.
| | | | | | | | | |
Collapse
|
46
|
Ahmad N, Michoux F, McCarthy J, Nixon PJ. Expression of the affinity tags, glutathione-S-transferase and maltose-binding protein, in tobacco chloroplasts. Planta 2012; 235:863-71. [PMID: 22237946 DOI: 10.1007/s00425-011-1584-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 12/16/2011] [Indexed: 05/10/2023]
Abstract
Chloroplast transformation offers an exciting platform for the safe, inexpensive and large-scale production of recombinant proteins in plants. An important advantage for the isolation of proteins produced in the chloroplast would be the use of affinity tags for rapid purification by affinity chromatography. To date, only His-tags have been used. In this study, we have tested the feasibility of expressing two additional affinity tags: glutathione-S-transferase (GST) and a His-tagged derivative of the maltose-binding protein (His₆-MBP). By using the chloroplast 16S rRNA promoter and 5' untranslated region of phage T7 gene 10, GST and His₆-MBP were expressed in homoplastomic tobacco plants at approximately 7% and 37% of total soluble protein, respectively. GST could be purified by one-step-affinity purification using a glutathione column. Much better recoveries were obtained for His₆-MBP by using a twin-affinity purification procedure involving first immobilised nickel followed by binding to amylose. Interestingly, expression of GST led to cytoplasmic male sterility. Overall, our work expands the tools available for purifying recombinant proteins from the chloroplast.
Collapse
Affiliation(s)
- Niaz Ahmad
- Division of Molecular Biosciences, Wolfson Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | | | | |
Collapse
|
47
|
Hnilova M, Liu X, Yuca E, Jia C, Wilson B, Karatas AY, Gresswell C, Ohuchi F, Kitamura K, Tamerler C. Multifunctional protein-enabled patterning on arrayed ferroelectric materials. ACS Appl Mater Interfaces 2012; 4:1865-71. [PMID: 22458431 DOI: 10.1021/am300177t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This study demonstrates a biological route to programming well-defined protein-inorganic interfaces with an arrayed geometry via modular peptide tag technology. To illustrate this concept, we designed a model multifunctional fusion protein, which simultaneously displays a maltose-binding protein (MBP), a green fluorescence protein (GFPuv) and an inorganic-binding peptide (AgBP2C). The fused combinatorially selected AgBP2C tag controls and site-directs the multifunctional fusion protein to immobilize on silver nanoparticle arrays that are fabricated on specific domain surfaces of ferroelectric LiNbO(3) via photochemical deposition and in situ synthesis. Our combined peptide-assisted biological and ferroelectric lithography approach offers modular design and versatility in tailoring surface reactivity for fabrication of nanoscale devices in environmentally benign conditions.
Collapse
|
48
|
Sakai S, Hiro A, Kondo M, Mizuno T, Tanaka T, Dewa T, Nango M. Overexpression of Rhodobacter sphaeroides PufX-bearing maltose-binding protein and its effect on the stability of reconstituted light-harvesting core antenna complex. Photosynth Res 2012; 111:63-69. [PMID: 21809113 DOI: 10.1007/s11120-011-9673-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 07/12/2011] [Indexed: 05/31/2023]
Abstract
The PufX protein, encoded by the pufX gene of Rhodobacter sphaeroides, plays a key role in the organization and function of the core antenna (LH1)-reaction centre (RC) complex, which collects photons and triggers primary photochemical reactions. We synthesized a PufX/maltose-binding protein (MBP) fusion protein to study the effect of the PufX protein on the reconstitution of B820 subunit-type and LH1-type complexes. The fusion protein was synthesized using an Escherichia coli expression system and purified by affinity chromatography. Reconstitution experiments demonstrated that the MBP-PufX protein destabilizes the subunit-type complex (20°C), consistent with previous reports. Interestingly, however, the preformed LH1-type complex was stable in the presence of MBP-PufX. The MBP-PufX protein did not influence the preformed LH1-type complexes (4°C). The LH1-type complex containing MBP-PufX showed a unique temperature-dependent structural transformation that was irreversible. The predominant form of the complex at 4°C was the LH1-type. When shifted to 20°C, subunit-type complexes became predominant. Upon subsequent cooling back to 4°C, instead of re-forming the LH1-type complexes, the predominant form remained the subunit-type complexes. In contrast, reversible transformation of LH1 (4°C) and subunit-type complexes (20°C) occurs in the absence of PufX. These results are consistent with the suggestion that MBP-PufX interacts with the LH1α- polypeptide in the subunit (α/β)-type complex (at 20°C), preventing oligomerization of the subunit to form LH1-type complexes.
Collapse
Affiliation(s)
- Shunnsuke Sakai
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, 466-8555, Japan
| | | | | | | | | | | | | |
Collapse
|
49
|
Abstract
Membrane proteins function as receptors, channels, transporters, and enzymes. These proteins are generally difficult to express and purify in a functional form due to the hydrophobic nature of their membrane spanning sequences. Studies on membrane proteins with a single membrane spanning helix have been particularly challenging. Single-pass membrane proteins will often form dimers or higher order oligomers in cell membranes as a result of sequence motifs that mediate specific transmembrane helix interactions. Understanding the structural basis for helix association provides insights into how these proteins function. Nevertheless, nonspecific association or aggregation of hydrophobic membrane spanning sequences can occur when isolated transmembrane domains are reconstituted into membrane bilayers or solubilized into detergent micelles for structural studies by solid-state or solution NMR spectroscopy. Here, we outline the methods used to synthesize, purify, and characterize single transmembrane segments for structural studies. Two synthetic strategies are discussed. The first strategy is to express hydrophobic peptides as protein chimera attached to the maltose binding protein. The second strategy is by direct chemical synthesis. Purification is carried out by several complementary chromatography methods. The peptides are solubilized in detergent for solution NMR studies or reconstituted into model membranes for solid-state NMR studies. We describe the methods used to characterize the reconstitution of these systems prior to NMR structural studies to establish if there is nonspecific aggregation.
Collapse
Affiliation(s)
- Miki Itaya
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | | | | |
Collapse
|
50
|
Heins RA, Choi JH, Sohka T, Ostermeier M. In vitro recombination of non-homologous genes can result in gene fusions that confer a switching phenotype to cells. PLoS One 2011; 6:e27302. [PMID: 22096548 PMCID: PMC3214044 DOI: 10.1371/journal.pone.0027302] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/13/2011] [Indexed: 11/18/2022] Open
Abstract
Regulation of protein activity is central to the complexity of life. The ability to regulate protein activity through exogenously added molecules has biotechnological/biomedical applications and offers tools for basic science. Such regulation can be achieved by establishing a means to modulate the specific activity of the protein (i.e. allostery). An alternative strategy for intracellular regulation of protein activity is to control the amount of protein through effects on its production, accumulation, and degradation. We have previously demonstrated that the non-homologous recombination of the genes encoding maltose binding protein (MBP) and TEM1 β-lactamase (BLA) can result in fusion proteins in which β-lactamase enzyme activity is allosterically regulated by maltose. Here, through use of a two-tiered genetic selection scheme, we demonstrate that such recombination can result in genes that confer maltose-dependent resistance to β-lactam even though they do not encode allosteric enzymes. These ‘phenotypic switch’ genes encode fusion proteins whose accumulation is a result of a specific interaction with maltose. Phenotypic switches represent an important class of proteins for basic science and biotechnological applications in vivo.
Collapse
Affiliation(s)
- Richard A. Heins
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jay H. Choi
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Takayuki Sohka
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Marc Ostermeier
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|