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Liu Y, Huang S, Liu WQ, Ba F, Liu Y, Ling S, Li J. An In Vitro Hybrid Biocatalytic System Enabled by a Combination of Surface-Displayed, Purified, and Cell-Free Expressed Enzymes. ACS Synth Biol 2024; 13:1434-1441. [PMID: 38695987 DOI: 10.1021/acssynbio.4c00201] [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: 05/18/2024]
Abstract
Enzymatic cascades have become a green and sustainable approach for the synthesis of valuable chemicals and pharmaceuticals. Using sequential enzymes to construct a multienzyme complex is an effective way to enhance the overall performance of biosynthetic routes. Here we report the design of an efficient in vitro hybrid biocatalytic system by assembling three enzymes that can convert styrene to (S)-1-phenyl-1,2-ethanediol. Specifically, we prepared the three enzymes in different ways, which were cell surface-displayed, purified, and cell-free expressed. To assemble them, we fused two orthogonal peptide-protein pairs (i.e., SpyTag/SpyCatcher and SnoopTag/SnoopCatcher) to the three enzymes, allowing their spatial organization by covalent assembly. By doing this, we constructed a multienzyme complex, which could enhance the production of (S)-1-phenyl-1,2-ethanediol by 3 times compared to the free-floating enzyme system without assembly. After optimization of the reaction system, the final product yield reached 234.6 μM with a substrate conversion rate of 46.9% (based on 0.5 mM styrene). Taken together, our strategy integrates the merits of advanced biochemical engineering techniques, including cellular surface display, spatial enzyme organization, and cell-free expression, which offers a new solution for chemical biosynthesis by enzymatic cascade biotransformation. We, therefore, anticipate that our approach will hold great potential for designing and constructing highly efficient systems to synthesize chemicals of agricultural, industrial, and pharmaceutical significance.
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Affiliation(s)
- Ying Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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2
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Babot M, Boulard Y, Agouda S, Pieri L, Fieulaine S, Bressanelli S, Gervais V. Oligomeric assembly of the C-terminal and transmembrane region of SARS-CoV-2 nsp3. J Virol 2024; 98:e0157523. [PMID: 38483167 PMCID: PMC11019948 DOI: 10.1128/jvi.01575-23] [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: 10/16/2023] [Accepted: 02/22/2024] [Indexed: 04/17/2024] Open
Abstract
As for all single-stranded, positive-sense RNA (+RNA) viruses, intracellular RNA synthesis relies on extensive remodeling of host cell membranes that leads to the formation of specialized structures. In the case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus causing COVID-19, endoplasmic reticulum membranes are modified, resulting in the formation of double-membrane vesicles (DMVs), which contain the viral dsRNA intermediate and constitute membrane-bound replication organelles. The non-structural and transmembrane protein nsp3 is a key player in the biogenesis of DMVs and, therefore, represents an interesting antiviral target. However, as an integral transmembrane protein, it is challenging to express for structural biology. The C-terminus of nsp3 encompasses all the membrane-spanning, -interacting, and -remodeling elements. By using a cell-free expression system, we successfully produced the C-terminal region of nsp3 (nsp3C) and reconstituted purified nsp3C into phospholipid nanodiscs, opening the way for structural studies. Negative-stain transmission electron microscopy revealed the presence of nsp3C oligomers very similar to the region abutting and spanning the membrane on the cytosolic side of DMVs in a recent subtomogram average of the SARS-CoV-2 nsp3-4 pore (1). AlphaFold-predicted structural models fit particularly well with our experimental data and support a pore-forming hexameric assembly. Altogether, our data give unprecedented clues to understand the structural organization of nsp3, the principal component that shapes the molecular pore that spans the DMVs and is required for the export of RNA in vivo. IMPORTANCE Membrane remodeling is at the heart of intracellular replication for single-stranded, positive-sense RNA viruses. In the case of coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this leads to the formation of a network of double-membrane vesicles (DMVs). Targeting DMV biogenesis offers promising prospects for antiviral therapies. This requires a better understanding of the molecular mechanisms and proteins involved. Three non-structural proteins (nsp3, nsp4, and nsp6) direct the intracellular membrane rearrangements upon SARS-CoV-2 infection. All of them contain transmembrane helices. The nsp3 component, the largest and multi-functional protein of the virus, plays an essential role in this process. Aiming to understand its structural organization, we used a cell-free protein synthesis assay to produce and reconstitute the C-terminal part of nsp3 (nsp3C) including transmembrane domains into phospholipid nanodiscs. Our work reveals the oligomeric organization of one key player in the biogenesis of SARS-CoV-2 DMVs, providing basis for the design of future antiviral strategies.
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Affiliation(s)
- Marion Babot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Samira Agouda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Laura Pieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Virginie Gervais
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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3
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Robinson AO, Lee J, Cameron A, Keating CD, Adamala KP. Cell-Free Expressed Membraneless Organelles Inhibit Translation in Synthetic Cells. ACS Biomater Sci Eng 2024; 10:773-781. [PMID: 38226971 DOI: 10.1021/acsbiomaterials.3c01052] [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: 01/17/2024]
Abstract
Compartments within living cells create specialized microenvironments, allowing multiple reactions to be carried out simultaneously and efficiently. While some organelles are bound by a lipid bilayer, others are formed by liquid-liquid phase separation such as P-granules and nucleoli. Synthetic minimal cells are widely used to study many natural processes, including organelle formation. In this work, synthetic cells expressing artificial membrane-less organelles that inhibit translation are described. RGG-GFP-RGG, a phase-separating protein derived from Caenorhabditis elegans P-granules, is expressed by cell-free transcription and translation, forming artificial membraneless organelles that can sequester RNA and reduce protein expression in synthetic cells. The introduction of artificial membrane-less organelles creates complex microenvironments within the synthetic cell cytoplasm and functions as a tool to inhibit protein expression in synthetic cells. The engineering of compartments within synthetic cells furthers the understanding of the evolution and function of natural organelles and facilitates the creation of more complex and multifaceted synthetic lifelike systems.
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Affiliation(s)
- Abbey O Robinson
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
| | - Jessica Lee
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Anders Cameron
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
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Momoh EO, Ghag SK, White J, Mudeppa DG, Rathod PK. Multiplex Assays for Analysis of Antibody Responses to South Asian Plasmodium falciparum and Plasmodium vivax Malaria Infections. Vaccines (Basel) 2023; 12:1. [PMID: 38276660 PMCID: PMC10818873 DOI: 10.3390/vaccines12010001] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Malaria remains a major global health challenge, causing over 0.6 million yearly deaths. To understand naturally acquired immunity in adult human populations in malaria-prevalent regions, improved serological tools are needed, particularly where multiple malaria parasite species co-exist. Slide-based and bead-based multiplex approaches can help characterize antibodies in malaria patients from endemic regions, but these require pure, well-defined antigens. To efficiently bypass purification steps, codon-optimized malaria antigen genes with N-terminal FLAG-tag and C-terminal Ctag sequences were expressed in a wheat germ cell-free system and adsorbed on functionalized BioPlex beads. In a pilot study, 15 P. falciparum antigens, 8 P. vivax antigens, and a negative control (GFP) were adsorbed individually on functionalized bead types through their Ctag. To validate the multiplexing powers of this platform, 10 P. falciparum-infected patient sera from a US NIH MESA-ICEMR study site in Goa, India, were tested against all 23 parasite antigens. Serial dilution of patient sera revealed variations in potency and breadth of antibodies to various parasite antigens. Individual patients revealed informative variations in immunity to P. falciparum versus P. vivax. This multiplex approach to malaria serology captures varying immunity to different human malaria parasite species and different parasite antigens. This approach can be scaled to track the dynamics of antibody production during one or more human malaria infections.
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Affiliation(s)
| | | | | | - Devaraja G. Mudeppa
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; (E.O.M.); (S.K.G.); (J.W.)
| | - Pradipsinh K. Rathod
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; (E.O.M.); (S.K.G.); (J.W.)
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5
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Cho S, Lee H, Han YH, Park TS, Seo SW, Park TH. Design of an effective small expression tag to enhance GPCR production in E. coli-based cell-free and whole cell expression systems. Protein Sci 2023; 32:e4839. [PMID: 37967042 PMCID: PMC10682694 DOI: 10.1002/pro.4839] [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: 08/29/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/17/2023]
Abstract
G protein-coupled receptors (GPCRs) play crucial roles in sensory, immune, and tumor metastasis processes, making them valuable targets for pharmacological and sensing applications in various industries. However, most GPCRs have low production yields in Escherichia coli (E. coli) expression systems. To overcome this limitation, we introduced AT10 tag, an effective fusion tag that could significantly enhance expression levels of various GPCRs in E. coli and its derived cell-free protein synthesis (CFPS) system. This AT10 tag consisted of an A/T-rich gene sequence designed via optimization of translation initiation rate. It is translated into a short peptide sequence of 10 amino acids at the N-terminus of GPCRs. Additionally, effector proteins could be utilized to suppress cytotoxicity caused by membrane protein expression, further boosting GPCR production in E. coli. Enhanced expression of various GPCRs using this AT10 tag is a promising approach for large-scale production of functional GPCRs in E. coli-based CFPS and whole cell systems, enabling their potential utilization across a wide range of industrial applications.
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Affiliation(s)
- Seongyeon Cho
- School of Chemical and Biological Engineering, Institute of Chemical ProcessSeoul National UniversitySeoulRepublic of Korea
| | - Haein Lee
- School of Chemical and Biological Engineering, Institute of Chemical ProcessSeoul National UniversitySeoulRepublic of Korea
| | - Yong Hee Han
- Interdisciplinary Program in BioengineeringSeoul National UniversitySeoulRepublic of Korea
| | - Tae Shin Park
- Receptech Research Institute, Receptech Inc.SiheungRepublic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical ProcessSeoul National UniversitySeoulRepublic of Korea
- Interdisciplinary Program in BioengineeringSeoul National UniversitySeoulRepublic of Korea
| | - Tai Hyun Park
- School of Chemical and Biological Engineering, Institute of Chemical ProcessSeoul National UniversitySeoulRepublic of Korea
- Interdisciplinary Program in BioengineeringSeoul National UniversitySeoulRepublic of Korea
- Department of Nutritional Science and Food ManagementEwha Womans UniversitySeoulRepublic of Korea
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6
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Peruzzi JA, Vu TQ, Gunnels TF, Kamat NP. Rapid Generation of Therapeutic Nanoparticles Using Cell-Free Expression Systems. Small Methods 2023; 7:e2201718. [PMID: 37116099 PMCID: PMC10611898 DOI: 10.1002/smtd.202201718] [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] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/06/2023] [Indexed: 05/05/2023]
Abstract
The surface modification of membrane-based nanoparticles, such as liposomes, polymersomes, and lipid nanoparticles, with targeting molecules, such as binding proteins, is an important step in the design of therapeutic materials. However, this modification can be costly and time-consuming, requiring cellular hosts for protein expression and lengthy purification and conjugation steps to attach proteins to the surface of nanocarriers, which ultimately limits the development of effective protein-conjugated nanocarriers. Here, the use of cell-free protein synthesis systems to rapidly create protein-conjugated membrane-based nanocarriers is demonstrated. Using this approach, multiple types of functional binding proteins, including affibodies, computationally designed proteins, and scFvs, can be cell-free expressed and conjugated to liposomes in one-pot. The technique can be expanded further to other nanoparticles, including polymersomes and lipid nanoparticles, and is amenable to multiple conjugation strategies, including surface attachment to and integration into nanoparticle membranes. Leveraging these methods, rapid design of bispecific artificial antigen presenting cells and enhanced delivery of lipid nanoparticle cargo in vitro is demonstrated. It is envisioned that this workflow will enable the rapid generation of membrane-based delivery systems and bolster our ability to create cell-mimetic therapeutics.
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Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Timothy Q. Vu
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Taylor F. Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Neha P. Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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7
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Goh MWS, Tozawa Y, Tero R. Assembly of Cell-Free Synthesized Ion Channel Molecules in Artificial Lipid Bilayer Observed by Atomic Force Microscopy. Membranes (Basel) 2023; 13:854. [PMID: 37999340 PMCID: PMC10673230 DOI: 10.3390/membranes13110854] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
Artificial lipid bilayer systems, such as vesicles, black membranes, and supported lipid bilayers (SLBs), are valuable platforms for studying ion channels at the molecular level. The reconstitution of the ion channels in an active form is a crucial process in studies using artificial lipid bilayer systems. In this study, we investigated the assembly of the human ether-a-go-go-related gene (hERG) channel prepared in a cell-free synthesis system. AFM topographies revealed the presence of protrusions with a uniform size in the entire SLB that was prepared with the proteoliposomes (PLs) incorporating the cell-free-synthesized hERG channel. We attributed the protrusions to hERG channel monomers, taking into consideration the AFM tip size, and identified assembled structures of the monomer that exhibited dimeric, trimeric, and tetrameric-like arrangements. We observed molecular images of the functional hERG channel reconstituted in a lipid bilayer membrane using AFM and quantitatively evaluated the association state of the cell-free synthesized hERG channel.
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Affiliation(s)
- Melvin Wei Shern Goh
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi 441-8580, Japan
| | - Yuzuru Tozawa
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan;
| | - Ryugo Tero
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi 441-8580, Japan
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8
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Brookwell AW, Gonzalez JL, Martinez AW, Oza JP. Development of Solid-State Storage for Cell-Free Expression Systems. ACS Synth Biol 2023; 12:2561-2577. [PMID: 37490644 DOI: 10.1021/acssynbio.3c00111] [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: 07/27/2023]
Abstract
The fragility of biological systems during storage, transport, and utilization necessitates reliable cold-chain infrastructure and limits the potential of biotechnological applications. In order to unlock the broad applications of existing and emerging biological technologies, we report the development of a novel solid-state storage platform for complex biologics. The resulting solid-state biologics (SSB) platform meets four key requirements: facile rehydration of solid materials, activation of biochemical activity, ability to support complex downstream applications and functionalities, and compatibility for deployment in a variety of reaction formats and environments. As a model system of biochemical complexity, we utilized crudeEscherichia colicell extracts that retain active cellular metabolism and support robust levels of in vitro transcription and translation. We demonstrate broad versatility and utility of SSB through proof-of-concepts for on-demand in vitro biomanufacturing of proteins at a milliliter scale, the activation of downstream CRISPR activity, as well as deployment on paper-based devices. SSBs unlock a breadth of applications in biomanufacturing, discovery, diagnostics, and education in resource-limited environments on Earth and in space.
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Affiliation(s)
- August W Brookwell
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Jorge L Gonzalez
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Andres W Martinez
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Javin P Oza
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
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9
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Mezhyrova J, Martin J, Börnsen C, Dötsch V, Frangakis AS, Morgner N, Bernhard F. In vitro characterization of the phage lysis protein MS2-L. Microbiome Res Rep 2023; 2:28. [PMID: 38045926 PMCID: PMC10688784 DOI: 10.20517/mrr.2023.28] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 12/05/2023]
Abstract
Background: The peptide MS2-L represents toxins of the ssRNA Leviviridae phage family and consists of a predicted N-terminal soluble domain followed by a transmembrane domain. MS2-L mediates bacterial cell lysis through the formation of large lesions in the cell envelope, but further details of this mechanism as a prerequisite for applied bioengineering studies are lacking. The chaperone DnaJ is proposed to modulate MS2-L activity, whereas other cellular targets of MS2-L are unknown. Methods: Here, we provide a combined in vitro and in vivo overexpression approach to reveal molecular insights into MS2-L action and its interaction with DnaJ. Full-length MS2-L and truncated derivatives were synthesized cell-free and co-translationally inserted into nanodiscs or solubilized in detergent micelles. By native liquid bead ion desorption mass spectrometry, we demonstrate that MS2-L assembles into high oligomeric states after membrane insertion. Results: Oligomerization is directed by the transmembrane domain and is impaired in detergent environments. Studies with truncated MS2-L derivatives provide evidence that the soluble domain acts as a modulator of oligomer formation. DnaJ strongly interacts with MS2-L in membranes as well as in detergent environments. However, this interaction affects neither the MS2-L membrane insertion efficiency nor its oligomerization in nanodisc membranes. In accordance with the in vitro data, the assembly of MS2-L derivatives into large membrane located clusters was monitored by overexpression of corresponding fusions with fluorescent monitors in E. coli cells. Analysis by cryo-electron microscopy indicates that lesion formation is initiated in the outer membrane, followed by disruption of the peptidoglycan layer and disintegration of the inner membrane. Conclusion: MS2-L forms oligomeric complexes similar to the related phage toxin ΦX174-E. The oligomeric interface of both peptides is located within their transmembrane domains. We propose a potential function of the higher-order assembly of small phage toxins in membrane disintegration and cell lysis.
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Affiliation(s)
- Julija Mezhyrova
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main 60438, Germany
| | - Janosch Martin
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main 60438, Germany
| | - Clara Börnsen
- Buchmann Institute for Molecular Life Sciences & Institute of Biophysics, Goethe University, Frankfurt am Main 60438, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main 60438, Germany
| | - Achilleas Stefanos Frangakis
- Buchmann Institute for Molecular Life Sciences & Institute of Biophysics, Goethe University, Frankfurt am Main 60438, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main 60438, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main 60438, Germany
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10
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Godino E, Restrepo Sierra AM, Danelon C. Imaging Flow Cytometry for High-Throughput Phenotyping of Synthetic Cells. ACS Synth Biol 2023. [PMID: 37155828 PMCID: PMC10367129 DOI: 10.1021/acssynbio.3c00074] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The reconstitution of basic cellular functions in micrometer-sized liposomes has led to a surge of interest in the construction of synthetic cells. Microscopy and flow cytometry are powerful tools for characterizing biological processes in liposomes with fluorescence readouts. However, applying each method separately leads to a compromise between information-rich imaging by microscopy and statistical population analysis by flow cytometry. To address this shortcoming, we here introduce imaging flow cytometry (IFC) for high-throughput, microscopy-based screening of gene-expressing liposomes in laminar flow. We developed a comprehensive pipeline and analysis toolset based on a commercial IFC instrument and software. About 60 thousands of liposome events were collected per run starting from one microliter of the stock liposome solution. Robust population statistics from individual liposome images was performed based on fluorescence and morphological parameters. This allowed us to quantify complex phenotypes covering a wide range of liposomal states that are relevant for building a synthetic cell. The general applicability, current workflow limitations, and future prospects of IFC in synthetic cell research are finally discussed.
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Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Ana Maria Restrepo Sierra
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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11
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McSweeney MA, Zhang Y, Styczynski MP. Short Activators and Repressors of RNA Toehold Switches. ACS Synth Biol 2023; 12:681-688. [PMID: 36802167 PMCID: PMC10028691 DOI: 10.1021/acssynbio.2c00641] [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: 02/23/2023]
Abstract
RNA toehold switches are a widely used class of molecule to detect specific RNA "trigger" sequences, but their design, intended function, and characterization to date leave it unclear whether they can function properly with triggers shorter than 36 nucleotides. Here, we explore the feasibility of using standard toehold switches with 23-nucleotide truncated triggers. We assess the crosstalk of different triggers with significant homology and identify a highly sensitive trigger region where just one mutation from the consensus trigger sequence can reduce switch activation by 98.6%. However, we also find that triggers with as many as seven mutations outside of this region can still lead to 5-fold induction of the switch. We also present a new approach using 18- to 22-nucleotide triggers as translational repressors for toehold switches and assess the off-target regulation for this strategy as well. The development and characterization of these strategies could help enable applications like microRNA sensors, where well-characterized crosstalk between sensors and detection of short target sequences are critical.
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Affiliation(s)
- Megan A McSweeney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yan Zhang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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12
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Moghimianavval H, Patel C, Mohapatra S, Hwang SW, Kayikcioglu T, Bashirzadeh Y, Liu AP, Ha T. Engineering Functional Membrane-Membrane Interfaces by InterSpy. Small 2023; 19:e2202104. [PMID: 35618485 PMCID: PMC9789529 DOI: 10.1002/smll.202202104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/04/2022] [Revised: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Engineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane interfaces between apposing synthetic as well as cell membranes through the SpyTag/SpyCatcher interaction. The inclusion of split fluorescent protein fragments in InterSpy allows tracking of the formation of a membrane-membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. First, InterSpy is demonstrated by testing split protein designs using a mammalian cell-free expression (CFE) system. By utilizing co-translational helix insertion, cell-free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with the desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, InterSpy is demonstrated in mammalian cells by detecting fluorescence reconstitution of split protein at the membrane-membrane interface between two cells each expressing a component of InterSpy. InterSpy demonstrates the power of CFE systems in the functional reconstitution of synthetic membrane interfaces via proximity-inducing proteins. This technology may also prove useful where cell-cell contacts and communication are recreated in a controlled manner using minimal components.
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Affiliation(s)
- Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Chintan Patel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sonisilpa Mohapatra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tunc Kayikcioglu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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13
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Haueis L, Stech M, Schneider E, Lanz T, Hebel N, Zemella A, Kubick S. Rapid One-Step Capturing of Native, Cell-Free Synthesized and Membrane-Embedded GLP-1R. Int J Mol Sci 2023; 24:ijms24032808. [PMID: 36769142 PMCID: PMC9917595 DOI: 10.3390/ijms24032808] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are of outstanding pharmacological interest as they are abundant in cell membranes where they perform diverse functions that are closely related to the vitality of cells. The analysis of GPCRs in natural membranes is laborious, as established methods are almost exclusively cell culture-based and only a few methods for immobilization in a natural membrane outside the cell are known. Within this study, we present a one-step, fast and robust immobilization strategy of the GPCR glucagon-like peptide 1 receptor (GLP-1R). GLP-1R was synthesized in eukaryotic lysates harboring endogenous endoplasmic reticulum-derived microsomes enabling the embedment of GLP-1R in a natural membrane. Interestingly, we found that these microsomes spontaneously adsorbed to magnetic Neutravidin beads thus providing immobilized membrane protein preparations which required no additional manipulation of the target receptor or its supporting membrane. The accessibility of the extracellular domain of membrane-embedded and bead-immobilized GLP-1R was demonstrated by bead-based enzyme-linked immunosorbent assay (ELISA) using GLP-1R-specific monoclonal antibodies. In addition, ligand binding of immobilized GLP-1R was verified in a radioligand binding assay. In summary, we present an easy and straightforward synthesis and immobilization methodology of an active GPCR which can be beneficial for studying membrane proteins in general.
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Affiliation(s)
- Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Correspondence:
| | | | - Thorsten Lanz
- 3B Pharmaceuticals GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Nicole Hebel
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus–Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, 14476 Potsdam, Germany
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14
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Krebs SK, Stech M, Jorde F, Rakotoarinoro N, Ramm F, Marinoff S, Bahrke S, Danielczyk A, Wüstenhagen DA, Kubick S. Synthesis of an Anti-CD7 Recombinant Immunotoxin Based on PE24 in CHO and E. coli Cell-Free Systems. Int J Mol Sci 2022; 23:ijms232213697. [PMID: 36430170 PMCID: PMC9697001 DOI: 10.3390/ijms232213697] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Recombinant immunotoxins (RITs) are an effective class of agents for targeted therapy in cancer treatment. In this article, we demonstrate the straight-forward production and testing of an anti-CD7 RIT based on PE24 in a prokaryotic and a eukaryotic cell-free system. The prokaryotic cell-free system was derived from Escherichia coli BL21 StarTM (DE3) cells transformed with a plasmid encoding the chaperones groEL/groES. The eukaryotic cell-free system was prepared from Chinese hamster ovary (CHO) cells that leave intact endoplasmic reticulum-derived microsomes in the cell-free reaction mix from which the RIT was extracted. The investigated RIT was built by fusing an anti-CD7 single-chain variable fragment (scFv) with the toxin domain PE24, a shortened variant of Pseudomonas Exotoxin A. The RIT was produced in both cell-free systems and tested for antigen binding against CD7 and cell killing on CD7-positive Jurkat, HSB-2, and ALL-SIL cells. CD7-positive cells were effectively killed by the anti-CD7 scFv-PE24 RIT with an IC50 value of 15 pM to 40 pM for CHO and 42 pM to 156 pM for E. coli cell-free-produced RIT. CD7-negative Raji cells were unaffected by the RIT. Toxin and antibody domain alone did not show cytotoxic effects on either CD7-positive or CD7-negative cells. To our knowledge, this report describes the production of an active RIT in E. coli and CHO cell-free systems for the first time. We provide the proof-of-concept that cell-free protein synthesis allows for on-demand testing of antibody−toxin conjugate activity in a time-efficient workflow without cell lysis or purification required.
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Affiliation(s)
- Simon K. Krebs
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin, Ackerstrasse 76, 13355 Berlin, Germany
| | - Marlitt Stech
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Felix Jorde
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Nathanaël Rakotoarinoro
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
| | - Franziska Ramm
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Sophie Marinoff
- Glycotope GmbH, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Sven Bahrke
- Glycotope GmbH, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Antje Danielczyk
- Glycotope GmbH, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Doreen A. Wüstenhagen
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, 14476 Potsdam, Germany
- Correspondence:
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15
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Romantseva E, Alperovich N, Ross D, Lund SP, Strychalski EA. Effects of DNA template preparation on variability in cell-free protein production. Synth Biol (Oxf) 2022; 7:ysac015. [PMID: 36046152 PMCID: PMC9425043 DOI: 10.1093/synbio/ysac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/01/2022] [Accepted: 08/12/2022] [Indexed: 08/08/2023] Open
Abstract
DNA templates for protein production remain an unexplored source of variability in the performance of cell-free expression (CFE) systems. To characterize this variability, we investigated the effects of two common DNA extraction methodologies, a postprocessing step and manual versus automated preparation on protein production using CFE. We assess the concentration of the DNA template, the quality of the DNA template in terms of physical damage and the quality of the DNA solution in terms of purity resulting from eight DNA preparation workflows. We measure the variance in protein titer and rate of protein production in CFE reactions associated with the biological replicate of the DNA template, the technical replicate DNA solution prepared with the same workflow and the measurement replicate of nominally identical CFE reactions. We offer practical guidance for preparing and characterizing DNA templates to achieve acceptable variability in CFE performance.
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Affiliation(s)
| | - Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | - Steven P Lund
- National Institute of Standards and Technology, Gaithersburg, MD USA
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16
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Abstract
![]()
Engineering synthetic cells has a broad appeal, from
understanding
living cells to designing novel biomaterials for therapeutics, biosensing,
and hybrid interfaces. A key prerequisite to creating synthetic cells
is a three-dimensional container capable of orchestrating biochemical
reactions. In this study, we present an easy and effective technique
to make cell-sized porous containers, coined actinosomes, using the
interactions between biomolecular condensates and the actin cytoskeleton.
This approach uses polypeptide/nucleoside triphosphate condensates
and localizes actin monomers on their surface. By triggering actin
polymerization and using osmotic gradients, the condensates are transformed
into containers, with the boundary made up of actin filaments and
polylysine polymers. We show that the guanosine triphosphate (GTP)-to-adenosine
triphosphate (ATP) ratio is a crucial parameter for forming actinosomes:
insufficient ATP prevents condensate dissolution, while excess ATP
leads to undesired crumpling. Permeability studies reveal the porous
surface of actinosomes, allowing small molecules to pass through while
restricting bigger macromolecules within the interior. We show the
functionality of actinosomes as bioreactors by carrying out in vitro protein translation within them. Actinosomes are
a handy addition to the synthetic cell platform, with appealing properties
like ease of production, inherent encapsulation capacity, and a potentially
active surface to trigger signaling cascades and form multicellular
assemblies, conceivably useful for biotechnological applications.
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Affiliation(s)
- Ketan A Ganar
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Liza Leijten
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Siddharth Deshpande
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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17
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Rhea KA, McDonald ND, Cole SD, Noireaux V, Lux MW, Buckley PE. Variability in cell-free expression reactions can impact qualitative genetic circuit characterization. Synth Biol (Oxf) 2022; 7:ysac011. [PMID: 35966404 PMCID: PMC9365049 DOI: 10.1093/synbio/ysac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/24/2022] [Accepted: 08/01/2022] [Indexed: 09/21/2023] Open
Abstract
Cell-free expression systems provide a suite of tools that are used in applications from sensing to biomanufacturing. One of these applications is genetic circuit prototyping, where the lack of cloning is required and a high degree of control over reaction components and conditions enables rapid testing of design candidates. Many studies have shown utility in the approach for characterizing genetic regulation elements, simple genetic circuit motifs, protein variants or metabolic pathways. However, variability in cell-free expression systems is a known challenge, whether between individuals, laboratories, instruments, or batches of materials. While the issue of variability has begun to be quantified and explored, little effort has been put into understanding the implications of this variability. For genetic circuit prototyping, it is unclear when and how significantly variability in reaction activity will impact qualitative assessments of genetic components, e.g. relative activity between promoters. Here, we explore this question by assessing DNA titrations of seven genetic circuits of increasing complexity using reaction conditions that ostensibly follow the same protocol but vary by person, instrument and material batch. Although the raw activities vary widely between the conditions, by normalizing within each circuit across conditions, reasonably consistent qualitative performance emerges for the simpler circuits. For the most complex case involving expression of three proteins, we observe a departure from this qualitative consistency, offering a provisional cautionary line where normal variability may disrupt reliable reuse of prototyping results. Our results also suggest that a previously described closed loop controller circuit may help to mitigate such variability, encouraging further work to design systems that are robust to variability. Graphical Abstract.
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Affiliation(s)
- Katherine A Rhea
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Nathan D McDonald
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Stephanie D Cole
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Matthew W Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Patricia E Buckley
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, USA
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18
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Bruni R. High-Throughput Cell-Free Screening of Eukaryotic Membrane Proteins in Lipidic Mimetics. Curr Protoc 2022; 2:e510. [PMID: 35926131 DOI: 10.1002/cpz1.510] [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] [Indexed: 06/15/2023]
Abstract
Membrane proteins (MPs) carry out important functions in the metabolism of cells, such as the detection of extracellular activities and the transport of small molecules across the plasma and organelle membranes. Expression of MPs for biochemical, biophysical, and structural analysis is in most cases achieved by overexpression of the desired target in an appropriate host, such as a bacterium. However, overexpression of MPs is usually toxic to the host cells and can lead to aggregation of target protein and to resistance to detergent extraction. An alternative to cell-based MP expression is cell-free (CF), or in vitro, expression. CF expression of MPs has several advantages over cell-based methods, including lack of toxicity issues, no requirement for detergent extraction, and direct incorporation of target proteins in various lipidic mimetics. This article describes a high-throughput method for the expression and purification of eukaryotic membrane proteins used in the author's lab. Basic Protocol 1 describes the selection and cloning of target genes into appropriate vectors for CF expression. Basic Protocol 2 describes the assembly of CF reactions for high-throughput screening. Basic Protocol 3 outlines methods for purification and detection of target proteins. Support Protocols 1-6 describe various accessory procedures: amplification of target, treatment of vectors to prepare them for ligation-independent cloning, and the preparation of S30 extract, T7 RNA polymerase, liposomes, and nanodiscs. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Target selection, construct design, and cloning into pET-based expression vectors Support Protocol 1: Amplification of target DNA Support Protocol 2: Preparation of ligation-independent cloning (LIC)-compatible vectors Basic Protocol 2: Assembly of small-scale cell-free reactions for high-throughput screening Support Protocol 3: Preparation of Escherichia coli S30 extract Support Protocol 4: Preparation of T7 RNA polymerase Support Protocol 5: Preparation of liposomes Support Protocol 6: Preparation of nanodiscs Basic Protocol 3: Purification and detection of cell-free reaction products.
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Affiliation(s)
- Renato Bruni
- Center on Membrane Protein Production and Analysis (COMPPÅ), New York Structural Biology Center, New York, New York
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19
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Abstract
INTRODUCTION Antibody therapies have made huge strides in providing safe and efficacious drugs for autoimmune, cancer and infectious disease. These bispecific antibodies can be assembled from the basic building blocks of IgGs, resulting in dozens of formats. AREAS COVERED It is important to consider the manufacturability of these formats early in the antibody discovery phases. Broadly categorizing bispecific antibodies into IgG-like, fragment-based, appended and hybrid formats can help in looking at early manufacturability considerations. EXPERT OPINION Ideally, bispecific antibody manufacturing should contain a minimal number of steps, with processes that give high yields of protein with no contaminants. Many of these have been determined for the fragment-based bispecific blinatumomab and the IgG-like bispecifics from hybridomas. However, for new formats, these need to be considered early in the research and development pipeline. The hybrid formats offer an unusual alternative in generating high pure yields of bispecific molecules if the engineering challenges can be deciphered.
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Affiliation(s)
| | | | - Zahra Jawad
- Agenus inc., 3 Forbes Road, Lexington, MA, 02421-7305, United States.,Creasallis ltd, Babraham Research Campus, Babraham, Cambridgeshire, CB22 3AT, United Kingdom
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20
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Köck Z, Ermel U, Martin J, Morgner N, Achilleas Frangakis S, Dötsch V, Hilger D, Bernhard F. Biochemical characterization of cell-free synthesized human β 1 adrenergic receptor cotranslationally inserted into nanodiscs. J Mol Biol 2022; 434:167687. [PMID: 35717996 DOI: 10.1016/j.jmb.2022.167687] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022]
Abstract
Cell-free expression enables direct cotranslational insertion of G protein coupled receptors (GPCRs) and other membrane proteins into the defined membrane environments of nanodiscs. This technique avoids GPCR contacts with detergents and allows rapid identification of lipid effects on GPCR function as well as fast screening of receptor derivatives. Critical steps of conventional GPCR preparation from cellular membranes followed by detergent-based reconstitution into nanodisc membranes are thus eliminated. We report the efficient cotranslational insertion of full-length human β1-adrenergic receptor and of a truncated derivative into preformed nanodisc membranes. Their biochemical characterization revealed significant differences in lipid requirements, dimer formation and ligand binding activity. The truncated receptor showed a higher affinity to most tested ligands, in particular in presence of choline-containing lipids. However, introducing the naturally occurring G389R polymorphism in the full-length receptor resulted into an increased affinity to the antagonists alprenolol and carvedilol. Receptor quality was generally improved by coexpression with the agonist isoproterenol and the percentage of the ligand binding active fraction was twofold increased. Specific coupling of full-length and truncated human receptors in nanodisc membranes to Mini-Gαs protein as well as to purified Gs heterotrimer could be demonstrated and homogeneity of purified GPCR/Gs protein complexes in nanodiscs was demonstrated by negative stain single particle analysis.
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Affiliation(s)
- Zoe Köck
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main
| | - Utz Ermel
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University of Frankfurt/Main
| | - Janosch Martin
- Institute of Physical and Theoretical Chemistry, Goethe University of Frankfurt/Main
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University of Frankfurt/Main
| | - S Achilleas Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University of Frankfurt/Main
| | - Volker Dötsch
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main
| | - Daniel Hilger
- Department of Pharmaceutical Chemistry, Philipps-University Marburg
| | - Frank Bernhard
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main.
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21
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Bruni R, Laguerre A, Kaminska A, McSweeney S, Hendrickson WA, Liu Q. High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics. Protein Sci 2022; 31:639-651. [PMID: 34910339 PMCID: PMC8862427 DOI: 10.1002/pro.4259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/16/2022]
Abstract
Membrane proteins play essential roles in cellular function and metabolism. Nonetheless, biophysical and structural studies of membrane proteins are impeded by the difficulty of their expression in and purification from heterologous cell-based systems. As an alternative to these cell-based systems, cell-free protein synthesis has proven to be an exquisite method for screening membrane protein targets in a variety of lipidic mimetics. Here we report a high-throughput screening workflow and apply it to screen 61 eukaryotic membrane protein targets. For each target, we tested its expression in lipidic mimetics: two detergents, two liposomes, and two nanodiscs. We show that 35 membrane proteins (57%) can be expressed in a soluble fraction in at least one of the mimetics with the two detergents performing significantly better than nanodiscs and liposomes, in that order. Using the established cell-free workflow, we studied the production and biophysical assays for mitochondrial pyruvate carrier (MPC) complexes. Our studies show that the complexes produced in cell-free are functionally competent in complex formation and substrate binding. Our results highlight the utility of using cell-free systems for screening and production of eukaryotic membrane proteins.
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Affiliation(s)
- Renato Bruni
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA
| | - Aisha Laguerre
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Present address:
Roche DiagnosticsSanta ClaraCaliforniaUSA
| | - Anna‐Maria Kaminska
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Present address:
New York Blood CenterNew YorkNew YorkUSA
| | | | - Wayne A. Hendrickson
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Qun Liu
- NSLS‐II, Brookhaven National LaboratoryUptonNew YorkUSA,Biology DepartmentBrookhaven National LaboratoryUptonNew YorkUSA
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22
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Rashid MH. Full-length recombinant antibodies from Escherichia coli: production, characterization, effector function (Fc) engineering, and clinical evaluation. MAbs 2022; 14:2111748. [PMID: 36018829 PMCID: PMC9423848 DOI: 10.1080/19420862.2022.2111748] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Although several antibody fragments and antibody fragment-fusion proteins produced in Escherichia coli (E. coli) are approved as therapeutics for various human diseases, a full-length monoclonal or a bispecific antibody produced in E. coli has not yet been approved. The past decade witnessed substantial progress in expression of full-length antibodies in the E. coli cytoplasm and periplasm, as well as in cell-free expression systems. The equivalency of E. coli-produced aglycosylated antibodies and their mammalian cell-produced counterparts, with respect to biochemical and biophysical properties, including antigen binding, in vitro and in vivo serum stability, pharmacokinetics, and in vivo serum half-life, has been demonstrated. Extensive engineering of the Fc domain of aglycosylated antibodies enables recruitment of various effector functions, despite the lack of N-linked glycans. This review summarizes recent research, preclinical advancements, and clinical development of E. coli-produced aglycosylated therapeutic antibodies as monoclonal, bispecific, and antibody-drug conjugates for use in autoimmune, oncology, and immuno-oncology areas.Abbreviations: ADA Anti-drug antibody; ADCC Antibody-dependent cellular cytotoxicity; ADCP Antibody-dependent cellular phagocytosis; ADC Antibody-drug conjugate; aFc Aglycosylated Fc; AMD Age-related macular degeneration aTTP Acquired thrombotic thrombocytopenic purpura; BCMA B-cell maturation antigen; BLA Biologics license application; BsAb Bispecific antibody; C1q Complement protein C1q; CDC Complement-dependent cytotoxicity; CDCC Complement-dependent cellular cytotoxicity; CDCP Complement-dependent cellular phagocytosis; CEX Cation exchange chromatography; CFPS Cell-free protein expression; CHO Chinese Hamster Ovary; CH1-3 Constant heavy chain 1-3; CL Constant light chain; DLBCL Diffuse large B-cell lymphoma; DAR Drug antibody ratio; DC Dendritic cell; dsFv Disulfide-stabilized Fv; EU European Union; EGFR Epidermal growth factor receptor; E. coli Escherichia coli; EpCAM Epithelial cell adhesion molecule; Fab Fragment antigen binding; FACS Fluorescence activated cell sorting; Fc Fragment crystallizable; FcRn Neonatal Fc receptor; FcɣRs Fc gamma receptors; FDA Food and Drug Administration; FL-IgG Full-length immunoglobulin; Fv Fragment variable; FolRαa Folate receptor alpha; gFc Glycosylated Fc; GM-CSF Granulocyte macrophage-colony stimulating factor; GPx7 Human peroxidase 7; HCL Hairy cell leukemia; HIV Human immunodeficiency virusl; HER2 Human epidermal growth factor receptor 2; HGF Hepatocyte growth factor; HIC Hydrophobic interaction chromatography; HLA Human leukocyte antigen; IBs Inclusion bodies; IgG1-4 Immunoglobulin 1-4; IP Intraperitoneal; ITC Isothermal titration calorimetry; ITP Immune thrombocytopenia; IV Intravenous; kDa Kilodalton; KiH Knob-into-Hole; mAb Monoclonal antibody; MAC Membrane-attack complex; mCRC Metastatic colorectal cancer; MM Multipl myeloma; MOA Mechanism of action; MS Mass spectrometry; MUC1 Mucin 1; MG Myasthenia gravis; NB Nanobody; NK Natural killer; nsAA Nonstandard amino acid; NSCLC Non-small cell lung cancer; P. aeruginosa Pseudomonas aeruginosa; PD-1 Programmed cell death 1; PD-L1 Programmed cell death-ligand 1; PDI Protein disulfide isomerase; PECS Periplasmic expression cytometric screening; PK Pharmacokinetics; P. pastoris Pichia pastoris; PTM Post-translational modification; Rg Radius of gyration; RA Rheumatoid arthritis; RT-PCR Reverse transcription polymerase chain reaction; SAXS Small angle X-ray scattering; scF Single chain Fv; SCLC Small cell lung cancer; SDS-PAGE Sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SEC Size exclusion chromatography; SEED Strand-exchange engineered domain; sRNA Small regulatory RNA; SRP Signal recognition particle; T1/2 Half-life; Tagg Aggregation temperature; TCR T cell receptor; TDB T cell-dependent bispecific; TF Tissue factor; TIR Translation initiation region; Tm Melting temperature; TNBC Triple-negative breast cancer; TNF Tumor necrosis factor; TPO Thrombopoietin; VEGF Vascular endothelial growth factor; vH Variable heavy chain; vL Variable light chain; vWF von Willebrand factor; WT Wild type.
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23
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Tamiya-Ishitsuka H, Tsuruga M, Noda N, Yokota A. Conserved Amino Acid Moieties of Candidatus Desulforudis audaxviator MazF Determine Ribonuclease Activity and Specificity. Front Microbiol 2021; 12:748619. [PMID: 34867867 PMCID: PMC8634880 DOI: 10.3389/fmicb.2021.748619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
The toxin-antitoxin (TA) system, inherent to various prokaryotes, plays a critical role in survival and adaptation to diverse environmental stresses. The toxin MazF, belonging to the type II TA system, functions as a sequence-specific ribonuclease that recognizes 3 to 7 bases. In recent studies, crystallographic analysis of MazFs from several species have suggested the presence of amino acid sites important for MazF substrate RNA binding and for its catalytic activity. Herein, we characterized MazF obtained from Candidatus Desulforudis audaxviator (MazF-Da) and identified the amino acid residues necessary for its catalytic function. MazF-Da, expressed using a cell-free protein synthesis system, is a six-base-recognition-specific ribonuclease that preferentially cleaves UACAAA sequences and weakly cleaves UACGAA and UACUAA sequences. We found that MazF-Da exhibited the highest activity at around 60°C. Analysis using mutants with a single mutation at an amino acid residue site that is well conserved across various MazF toxins showed that G18, E20, R25, and P26 were important for the ribonuclease activity of MazF-Da. The recognition sequence of the N36A mutant differed from that of the wild type. This mutant cleaved UACAAG sequences in addition to UACAAA sequences, but did not cleave UACGAA or UACUAA sequences, suggesting that Asn36 affects the loosening and narrowing of MazF-Da cleavage sequence recognition. Our study posits UACAAA as the recognition sequence of MazF-Da and provides insight into the amino acid sites that are key to its unique enzymatic properties.
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Affiliation(s)
- Hiroko Tamiya-Ishitsuka
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masako Tsuruga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Naohiro Noda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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Beabout K, Bernhards CB, Thakur M, Turner KB, Cole SD, Walper SA, Chávez JL, Lux MW. Optimization of Heavy Metal Sensors Based on Transcription Factors and Cell-Free Expression Systems. ACS Synth Biol 2021; 10:3040-3054. [PMID: 34723503 DOI: 10.1021/acssynbio.1c00331] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Many bacterial mechanisms for highly specific and sensitive detection of heavy metals and other hazards have been reengineered to serve as sensors. In some cases, these sensors have been implemented in cell-free expression systems, enabling easier design optimization and deployment in low-resource settings through lyophilization. Here, we apply the advantages of cell-free expression systems to optimize sensors based on three separate bacterial response mechanisms for arsenic, cadmium, and mercury. We achieved detection limits below the World Health Organization-recommended levels for arsenic and mercury and below the short-term US Military Exposure Guideline levels for all three. The optimization of each sensor was approached differently, leading to observations useful for the development of future sensors: (1) there can be a strong dependence of specificity on the particular cell-free expression system used, (2) tuning of relative concentrations of the sensing and reporter elements improves sensitivity, and (3) sensor performance can vary significantly with linear vs plasmid DNA. In addition, we show that simply combining DNA for the three sensors into a single reaction enables detection of each target heavy metal without any further optimization. This combined approach could lead to sensors that detect a range of hazards at once, such as a panel of water contaminants or all known variants of a target virus. For low-resource settings, such "all-hazard" sensors in a cheap, easy-to-use format could have high utility.
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Affiliation(s)
- Kathryn Beabout
- UES, Inc., Dayton, Ohio 45432, United States
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Casey B. Bernhards
- Excet, Inc., 6225 Brandon Avenue #360, Springfield, Virginia 22150, United States
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Meghna Thakur
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Kendrick B. Turner
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Stephanie D. Cole
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Scott A. Walper
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Jorge L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Matthew W. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
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25
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Worst EG, Finkler M, Schenkelberger M, Kurt Ö, Helms V, Noireaux V, Ott A. A Methylation-Directed, Synthetic Pap Switch Based on Self-Complementary Regulatory DNA Reconstituted in an All E. coli Cell-Free Expression System. ACS Synth Biol 2021; 10:2725-2739. [PMID: 34550672 DOI: 10.1021/acssynbio.1c00326] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyelonephritis-associated pili (pap) enable migration of the uropathogenic Escherichia coli strain (UPEC) through the urinary tract. UPEC can switch between a stable 'ON phase' where the corresponding pap genes are expressed and a stable 'OFF phase' where their transcription is repressed. Hereditary DNA methylation of either one of two GATC motives within the regulatory region stabilizes the respective phase over many generations. The underlying molecular mechanism is only partly understood. Previous investigations suggest that in vivo phase-variation stability results from cooperative action of the transcriptional regulators Lrp and PapI. Here, we use an E. coli cell-free expression system to study molecular functions of the pap regulatory region based on a specially designed, synthetic construct flanked by two reporter genes encoding fluorescent proteins for simple readout. On the basis of our observations we suggest that besides Lrp, the conformation of the self-complementary regulatory DNA plays a strong role in the regulation of phase-variation. Our work not only contributes to better understand the phase variation mechanism, but it represents a successful start for mimicking stable, hereditary, and strong expression control based on methylation. The conformation of the regulatory DNA corresponds to a Holliday junction. Gene expression must be expected to respond if opposite arms of the junction are drawn outward.
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Affiliation(s)
- Emanuel G. Worst
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Marc Finkler
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Marc Schenkelberger
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Ömer Kurt
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Volkhard Helms
- Universität des Saarlandes, Center for Bioinformatics, Saarbrücken, 66041, Germany
| | - Vincent Noireaux
- University of Minnesota, School of Physics and Astronomy, Minneapolis, Minnesota 55455, United States
| | - Albrecht Ott
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
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26
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Lüddecke T, Paas A, Talmann L, Kirchhoff KN, von Reumont BM, Billion A, Timm T, Lochnit G, Vilcinskas A. A Spider Toxin Exemplifies the Promises and Pitfalls of Cell-Free Protein Production for Venom Biodiscovery. Toxins (Basel) 2021; 13:toxins13080575. [PMID: 34437446 PMCID: PMC8402385 DOI: 10.3390/toxins13080575] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Arthropod venoms offer a promising resource for the discovery of novel bioactive peptides and proteins, but the limited size of most species translates into minuscule venom yields. Bioactivity studies based on traditional fractionation are therefore challenging, so alternative strategies are needed. Cell-free synthesis based on synthetic gene fragments is one of the most promising emerging technologies, theoretically allowing the rapid, laboratory-scale production of specific venom components, but this approach has yet to be applied in venom biodiscovery. Here, we tested the ability of three commercially available cell-free protein expression systems to produce venom components from small arthropods, using U2-sicaritoxin-Sdo1a from the six-eyed sand spider Hexophtalma dolichocephala as a case study. We found that only one of the systems was able to produce an active product in low amounts, as demonstrated by SDS-PAGE, mass spectrometry, and bioactivity screening on murine neuroblasts. We discuss our findings in relation to the promises and limitations of cell-free synthesis for venom biodiscovery programs in smaller invertebrates.
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Affiliation(s)
- Tim Lüddecke
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; (A.P.); (K.N.K.); (A.B.); (A.V.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 30325 Frankfurt am Main, Germany;
- Correspondence:
| | - Anne Paas
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; (A.P.); (K.N.K.); (A.B.); (A.V.)
| | - Lea Talmann
- Syngenta Crop Protection, Werk Stein, Schaffhauserstrasse, CH4332 Stein, Switzerland;
| | - Kim N. Kirchhoff
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; (A.P.); (K.N.K.); (A.B.); (A.V.)
| | - Björn M. von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 30325 Frankfurt am Main, Germany;
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - André Billion
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; (A.P.); (K.N.K.); (A.B.); (A.V.)
| | - Thomas Timm
- Institute of Biochemistry, Justus Liebig University of Giessen, Friedrichstr. 24, 35392 Giessen, Germany; (T.T.); (G.L.)
| | - Günter Lochnit
- Institute of Biochemistry, Justus Liebig University of Giessen, Friedrichstr. 24, 35392 Giessen, Germany; (T.T.); (G.L.)
| | - Andreas Vilcinskas
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; (A.P.); (K.N.K.); (A.B.); (A.V.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 30325 Frankfurt am Main, Germany;
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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27
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Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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28
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Blum SM, Lee MS, Mgboji GE, Funk VL, Beabout K, Harbaugh SV, Roth PA, Liem AT, Miklos AE, Emanuel PA, Walper SA, Chávez JL, Lux MW. Impact of Porous Matrices and Concentration by Lyophilization on Cell-Free Expression. ACS Synth Biol 2021; 10:1116-1131. [PMID: 33843211 DOI: 10.1021/acssynbio.0c00634] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cell-free expression systems have drawn increasing attention as a tool to achieve complex biological functions outside of the cell. Several applications of the technology involve the delivery of functionality to challenging environments, such as field-forward diagnostics or point-of-need manufacturing of pharmaceuticals. To achieve these goals, cell-free reaction components are preserved using encapsulation or lyophilization methods, both of which often involve an embedding of components in porous matrices like paper or hydrogels. Previous work has shown a range of impacts of porous materials on cell-free expression reactions. Here, we explored a panel of 32 paperlike materials and 5 hydrogel materials for the impact on reaction performance. The screen included a tolerance to lyophilization for reaction systems based on both cell lysates and purified expression components. For paperlike materials, we found that (1) materials based on synthetic polymers were mostly incompatible with cell-free expression, (2) lysate-based reactions were largely insensitive to the matrix for cellulosic and microfiber materials, and (3) purified systems had an improved performance when lyophilized in cellulosic but not microfiber matrices. The impact of hydrogel materials ranged from completely inhibitory to a slight enhancement. The exploration of modulating the rehydration volume of lyophilized reactions yielded reaction speed increases using an enzymatic colorimetric reporter of up to twofold with an optimal ratio of 2:1 lyophilized reaction to rehydration volume for the lysate system and 1.5:1 for the purified system. The effect was independent of the matrices assessed. Testing with a fluorescent nonenzymatic reporter and no matrix showed similar improvements in both yields and reaction speeds for the lysate system and yields but not reaction speeds for the purified system. We finally used these observations to show an improved performance of two sensors that span reaction types, matrix, and reporters. In total, these results should enhance efforts to develop field-forward applications of cell-free expression systems.
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Affiliation(s)
- Steven M. Blum
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Marilyn S. Lee
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Glory E. Mgboji
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37830-6209, United States
| | - Vanessa L. Funk
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Kathryn Beabout
- UES, Inc., Dayton, Ohio 45432, United States
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Svetlana V. Harbaugh
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Pierce A. Roth
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- DCS Corporation, 4696 Millenium Drive, Suite 450, Belcamp, Maryland 21017, United States
| | - Alvin T. Liem
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- DCS Corporation, 4696 Millenium Drive, Suite 450, Belcamp, Maryland 21017, United States
| | - Aleksandr E. Miklos
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Peter A. Emanuel
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Scott A. Walper
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Jorge Luis Chávez
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Matthew W. Lux
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
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29
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Abstract
Cell-free gene expression systems with linear DNA expression templates (LDETs) have been widely applied in artificial cells, biochips, and high-throughput screening. However, due to the degradation caused by native nucleases in cell extracts, the transcription with linear DNA templates is weak, thereby resulting in low protein expression level, which greatly limits the development of cell-free systems using linear DNA templates. In this study, the protective sequences for stabilizing linear DNA and the transcribed mRNAs were rationally designed according to nucleases' action mechanism, whose effectiveness was evaluated through computer simulation and cell-free gene expression. The cell-free experiment results indicated that, with the combined protection of designed sequence and GamS protein, the protein expression of LDET-based cell-free systems could reach the same level as plasmid-based cell-free systems. This study would potentially promote the development of the LDET-based cell-free gene expression system for broader applications.
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Affiliation(s)
- Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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30
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Lindenburg L, Hollfelder F. "NAD-display": Ultrahigh-Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021; 60:9015-9021. [PMID: 33470025 PMCID: PMC8048591 DOI: 10.1002/anie.202013486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/21/2020] [Indexed: 12/25/2022]
Abstract
NAD(H)‐utiliing enzymes have been the subject of directed evolution campaigns to improve their function. To enable access to a larger swath of sequence space, we demonstrate the utility of a cell‐free, ultrahigh‐throughput directed evolution platform for dehydrogenases. Microbeads (1.5 million per sample) carrying both variant DNA and an immobilised analogue of NAD+ were compartmentalised in water‐in‐oil emulsion droplets, together with cell‐free expression mixture and enzyme substrate, resulting in the recording of the phenotype on each bead. The beads’ phenotype could be read out and sorted for on a flow cytometer by using a highly sensitive fluorescent protein‐based sensor of the NAD+:NADH ratio. Integration of this “NAD‐display” approach with our previously described Split & Mix (SpliMLiB) method for generating large site‐saturation libraries allowed straightforward screening of fully balanced site saturation libraries of formate dehydrogenase, with diversities of 2×104. Based on modular design principles of synthetic biology NAD‐display offers access to sophisticated in vitro selections, avoiding complex technology platforms.
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Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.,Current address: Genmab, Uppsalalaan 15, 3584 CT, Utrecht, The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
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31
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Pacull EM, Sendker F, Bernhard F, Scheidt HA, Schmidt P, Huster D, Krug U. Integration of Cell-Free Expression and Solid-State NMR to Investigate the Dynamic Properties of Different Sites of the Growth Hormone Secretagogue Receptor. Front Pharmacol 2020; 11:562113. [PMID: 33324203 PMCID: PMC7723455 DOI: 10.3389/fphar.2020.562113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023] Open
Abstract
Cell-free expression represents an attractive method to produce large quantities of selectively labeled protein for NMR applications. Here, cell-free expression was used to label specific regions of the growth hormone secretagogue receptor (GHSR) with NMR-active isotopes. The GHSR is a member of the class A family of G protein-coupled receptors. A cell-free expression system was established to produce the GHSR in the precipitated form. The solubilized receptor was refolded in vitro and reconstituted into DMPC lipid membranes. Methionines, arginines, and histidines were chosen for 13C-labeling as they are representative for the transmembrane domains, the loops and flanking regions of the transmembrane α-helices, and the C-terminus of the receptor, respectively. The dynamics of the isotopically labeled residues was characterized by solid-state NMR measuring motionally averaged 1H-13C dipolar couplings, which were converted into molecular order parameters. Separated local field DIPSHIFT experiments under magic-angle spinning conditions using either varying cross polarization contact times or direct excitation provided order parameters for these residues showing that the C-terminus was the segment with the highest motional amplitude. The loop regions and helix ends as well as the transmembrane regions of the GHSR represent relatively rigid segments in the overall very flexible receptor molecule. Although no site resolution could be achieved in the experiments, the previously reported highly dynamic character of the receptor concluded from uniformly 13C labeled receptor samples could be further specified by this segmental labeling approach, leading to a more diversified understanding of the receptor dynamics under equilibrium conditions.
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Affiliation(s)
- Emelyne M Pacull
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Franziska Sendker
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Peter Schmidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Ulrike Krug
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
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32
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Finkler M, Ott A. Bead-based assay for spatiotemporal gene expression control in cell-free transcription-translation systems. Biotechniques 2019; 66:29-33. [PMID: 30730208 DOI: 10.2144/btn-2018-0097] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cell-free gene expression has applications in synthetic biology, biotechnology and biomedicine. In this technique gene expression regulation plays an important role. Transcription factors do not completely suppress expression while other methods for expression control, for example CRISPR/Cas, often require important biochemical modifications. Here we use an all Escherichia coli-based cell-free expression system and present a bead-based method to instantly start and, at a later stage, completely stop gene expression. Magnetic beads coated with DNA of the gene of interest trigger gene expression. The expression stops if we remove the bead-bound DNA as well as transcribed mRNA by hybridization to bead-bound ssDNA. Our method is a simple way to control expression duration very accurately in time and space.
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Calmet P, Cullin C, Cortès S, Vang M, Caudy N, Baccouch R, Dessolin J, Maamar NT, Lecomte S, Tillier B, Alves ID. Cholesterol impacts chemokine CCR5 receptor ligand-binding activity. FEBS J 2019; 287:2367-2385. [PMID: 31738467 DOI: 10.1111/febs.15145] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/27/2019] [Accepted: 11/16/2019] [Indexed: 01/03/2023]
Abstract
The chemokine CCR5 receptor is target of maraviroc, a negative allosteric modulator of CCR5 that blocks the HIV protein gp120 from associating with the receptor, thereby inhibiting virus cellular entry. As noted with other G-protein-coupled receptor family members, the role of the lipid environment in CCR5 signaling remains obscure and very modestly investigated. Controversial literature on the impact of cholesterol (Chol) depletion in HIV infection and CCR5 signaling, including the hypothesis that Chol depletion could inhibit HIV infection, lead us to focus on the understanding of Chol impact in the first stages of receptor activation. To address this aim, the approach chosen was to employ reconstituted model lipid systems of controlled lipid composition containing CCR5 from two distinct expression systems: Pichia pastoris and cell-free expression. The characterization of receptor/ligand interaction in terms of total binding or competition binding assays was independently performed by plasmon waveguide resonance and fluorescence anisotropy, respectively. Maraviroc, a potent receptor antagonist, was the ligand investigated. Additionally, coarse-grained molecular dynamics simulation was employed to investigate Chol impact in the receptor-conformational flexibility and dynamics. Results obtained with receptor produced by different expression systems and using different biophysical approaches clearly demonstrate a considerable impact of Chol in the binding affinity of maraviroc to the receptor and receptor-conformational dynamics. Chol considerably decreases maraviroc binding affinity to the CCR5 receptor. The mechanisms by which this effect occurs seem to involve the adoption of distinct receptor-conformational states with restrained structural dynamics and helical motions in the presence of Chol.
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Affiliation(s)
- Pierre Calmet
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | | | | | - Maylou Vang
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | - Nada Caudy
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | - Rim Baccouch
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | - Jean Dessolin
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | | | - Sophie Lecomte
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | | | - Isabel D Alves
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
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34
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Souza SA, Kurohara DT, Dabalos CL, Ng HL. G Protein-Coupled Estrogen Receptor Production Using an Escherichia coli Cell-Free Expression System. ACTA ACUST UNITED AC 2019; 97:e88. [PMID: 31517450 DOI: 10.1002/cpps.88] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Heterologous expression of the G protein-coupled estrogen receptor (GPER) comes with a suite of challenges intrinsic to membrane proteins. This receptor's low expression levels and tendency to form insoluble aggregates in Escherichia coli and yeast make it a difficult receptor-target to study. In this unit, we detail steps to produce monomeric GPER using a precipitation-based cell-free system. We provide information on the DNA construct for expression, the pipetting scheme for the reaction supplements to generate a master mix, and the cell-free reaction setup. In the last portion of this unit, we outline steps for solubilization and purification, and we provide a viable method for qualitatively observing functionality by liquid chromatography-mass spectrometry detection. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Samson A Souza
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
| | - Dane T Kurohara
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Chester L Dabalos
- Department of Chemistry, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Ho Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
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Myshkin MY, Männikkö R, Krumkacheva OA, Kulbatskii DS, Chugunov AO, Berkut AA, Paramonov AS, Shulepko MA, Fedin MV, Hanna MG, Kullmann DM, Bagryanskaya EG, Arseniev AS, Kirpichnikov MP, Lyukmanova EN, Vassilevski AA, Shenkarev ZO. Cell-Free Expression of Sodium Channel Domains for Pharmacology Studies. Noncanonical Spider Toxin Binding Site in the Second Voltage-Sensing Domain of Human Na v1.4 Channel. Front Pharmacol 2019; 10:953. [PMID: 31555136 PMCID: PMC6737007 DOI: 10.3389/fphar.2019.00953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/26/2019] [Indexed: 01/06/2023] Open
Abstract
Voltage-gated sodium (NaV) channels are essential for the normal functioning of cardiovascular, muscular, and nervous systems. These channels have modular organization; the central pore domain allows current flow and provides ion selectivity, whereas four peripherally located voltage-sensing domains (VSDs-I/IV) are needed for voltage-dependent gating. Mutations in the S4 voltage-sensing segments of VSDs in the skeletal muscle channel NaV1.4 trigger leak (gating pore) currents and cause hypokalemic and normokalemic periodic paralyses. Previously, we have shown that the gating modifier toxin Hm-3 from the crab spider Heriaeus melloteei binds to the S3-S4 extracellular loop in VSD-I of NaV1.4 channel and inhibits gating pore currents through the channel with mutations in VSD-I. Here, we report that Hm-3 also inhibits gating pore currents through the same channel with the R675G mutation in VSD-II. To investigate the molecular basis of Hm-3 interaction with VSD-II, we produced the corresponding 554-696 fragment of NaV1.4 in a continuous exchange cell-free expression system based on the Escherichia coli S30 extract. We then performed a combined nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy study of isolated VSD-II in zwitterionic dodecylphosphocholine/lauryldimethylamine-N-oxide or dodecylphosphocholine micelles. To speed up the assignment of backbone resonances, five selectively 13C,15N-labeled VSD-II samples were produced in accordance with specially calculated combinatorial scheme. This labeling approach provides assignment for ∼50% of the backbone. Obtained NMR and electron paramagnetic resonance data revealed correct secondary structure, quasi-native VSD-II fold, and enhanced ps-ns timescale dynamics in the micelle-solubilized domain. We modeled the structure of the VSD-II/Hm-3 complex by protein-protein docking involving binding surfaces mapped by NMR. Hm-3 binds to VSDs I and II using different modes. In VSD-II, the protruding ß-hairpin of Hm-3 interacts with the S1-S2 extracellular loop, and the complex is stabilized by ionic interactions between the positively charged toxin residue K24 and the negatively charged channel residues E604 or D607. We suggest that Hm-3 binding to these charged groups inhibits voltage sensor transition to the activated state and blocks the depolarization-activated gating pore currents. Our results indicate that spider toxins represent a useful hit for periodic paralyses therapy development and may have multiple structurally different binding sites within one NaV molecule.
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Affiliation(s)
- Mikhail Yu Myshkin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Roope Männikkö
- MRC Centre for Neuromuscular Diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | | | - Dmitrii S Kulbatskii
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anton O Chugunov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia.,International Laboratory for Supercomputer Atomistic Modelling and Multi-scale Analysis, National Research University Higher School of Economics, Moscow, Russia
| | - Antonina A Berkut
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Paramonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail A Shulepko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Novosibirsk, Russia
| | - Michael G Hanna
- MRC Centre for Neuromuscular Diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - Dimitri M Kullmann
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, United Kingdom
| | - Elena G Bagryanskaya
- N.N.Voroztsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Alexander S Arseniev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina N Lyukmanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - Alexander A Vassilevski
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - Zakhar O Shenkarev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
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36
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Abstract
The assembly of channel proteins into vesicle membranes is a useful strategy to control activities of vesicle-based systems. Here, we developed a membrane AND gate that responds to both a fatty acid and a pore-forming channel protein to induce the release of encapsulated cargo. We explored how membrane composition affects the functional assembly of α-hemolysin into phospholipid vesicles as a function of oleic acid content and α-hemolysin concentration. We then showed that we could induce α-hemolysin assembly when we added oleic acid micelles to a specific composition of phospholipid vesicles. Finally, we demonstrated that our membrane AND gate could be coupled to a gene expression system. Our study provides a new method to control the temporal dynamics of vesicle permeability by controlling when the functional assembly of a channel protein into synthetic vesicles occurs. Furthermore, a membrane AND gate that utilizes membrane-associating biomolecules introduces a new way to implement Boolean logic that should complement genetic logic circuits and ultimately enhance the capabilities of artificial cellular systems.
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Abstract
Cell-free protein synthesis (CFPS) is a fast and convenient way to synthesize proteins for analytical studies and applications. CFPS, when equipped with a suitable orthogonal pair, allows for protein-site-directed labeling with desired functionalities such as fluorescent dyes or therapeutic groups that are needed to tailor proteins for analytical applications. In this context, chemoselective reactive pyrrolysine analogues (CR-OAs) are of particular value, as this class of unnatural amino acids, among other useful properties, covers a wide range of different chemoselective reactions. In this study, we present a flexible approach that facilitates incorporation of CR-OAs in CFPS systems. In particular, a fairly simple addition of two expression plasmids in our cell-free system, one encoding pyrrolysyl-tRNA synthetase and the other one the target protein, enabled ribosomal synthesis of proteins in the half-milligram range with the pre-installed orthogonal reactivity, easily modifiable by using mild, copper-free bioorthogonal chemistry. Our CFPS system allows rapid and highly customizable expression, as shown by several examples of successful site-directed fluorescence labeling. The feasibility of our CFPS system for protein analytics is further proved by demonstrating the functional integrity of a labeled protein by interaction measurements using microscale thermophoresis.
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Affiliation(s)
- Michael Gerrits
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
- biotechrabbit GmbH, 12489 Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
- Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, 144 Dysart Road, R3T 2N2 Winnipeg, MB, Canada
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Dong F, Rues RB, Kazemi S, Dötsch V, Bernhard F. Molecular Determinants for Ligand Selectivity of the Cell-Free Synthesized Human Endothelin B Receptor. J Mol Biol 2018; 430:5105-5119. [PMID: 30342934 DOI: 10.1016/j.jmb.2018.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/02/2018] [Accepted: 10/12/2018] [Indexed: 01/14/2023]
Abstract
Extracellular domains of G-protein-coupled receptors act as initial molecular selectivity filters for subtype specific ligands and drugs. Chimeras of the human endothelin-B receptor containing structural units from the extracellular domains of the endothelin-A receptor were analyzed after their co-translational insertion into preformed nanodiscs. A short β-strand and a linker region in the second extracellular loop as well as parts of the extracellular N-terminal domain were identified as molecular discrimination sites for the endothelin-B receptor-selective agonists IRL1620, sarafotoxin 6c, 4Ala-ET-1 and ET-3, but not for the non-selective agonist ET-1 recognized by both endothelin receptors. A proposed second disulfide bridge in the endothelin-B receptor tethering the N-terminal domain with the third extracellular loop was not essential for ET-1 recognition and binding, but increased the receptor thermostability. We further demonstrate an experimental approach with cell-free synthesized engineered agonists to analyze the differential discrimination of peptide ligand topologies by the two endothelin receptors. The study is based on the engineering and cell-free insertion of G-protein-coupled receptors into defined membranes and may become interesting also for other targets as an alternative platform to reveal molecular details of ligand selectivity and ligand binding mechanisms.
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Affiliation(s)
- Fang Dong
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Ralf B Rues
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Sina Kazemi
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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39
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Tang TYD, Cecchi D, Fracasso G, Accardi D, Coutable-Pennarun A, Mansy SS, Perriman AW, Anderson JLR, Mann S. Gene-Mediated Chemical Communication in Synthetic Protocell Communities. ACS Synth Biol 2018; 7:339-346. [PMID: 29091420 DOI: 10.1021/acssynbio.7b00306] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A gene-directed chemical communication pathway between synthetic protocell signaling transmitters (lipid vesicles) and receivers (proteinosomes) was designed, built and tested using a bottom-up modular approach comprising small molecule transcriptional control, cell-free gene expression, porin-directed efflux, substrate signaling, and enzyme cascade-mediated processing.
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Affiliation(s)
- T-Y. Dora Tang
- Max Planck Institute of Molecular Cell and Genetics, 01307 Dresden, Germany
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Dario Cecchi
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Giorgio Fracasso
- Max Planck Institute of Molecular Cell and Genetics, 01307 Dresden, Germany
| | - Davide Accardi
- Max Planck Institute of Molecular Cell and Genetics, 01307 Dresden, Germany
| | - Angelique Coutable-Pennarun
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Sheref S. Mansy
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Adam W. Perriman
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - J. L. Ross Anderson
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Stephen Mann
- Centre
for Protolife Research, School of Chemistry University, of Bristol, Bristol BS8 1TS United, Kingdom
- BrisSynBio
Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
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40
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Cleveland TE, He W, Evans AC, Fischer NO, Lau EY, Coleman MA, Butler P. Small-angle X-ray and neutron scattering demonstrates that cell-free expression produces properly formed disc-shaped nanolipoprotein particles. Protein Sci 2018; 27:780-789. [PMID: 29266475 DOI: 10.1002/pro.3365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 01/22/2023]
Abstract
Nanolipoprotein particles (NLPs), composed of membrane scaffold proteins and lipids, have been used to support membrane proteins in a native-like bilayer environment for biochemical and structural studies. Traditionally, these NLPs have been prepared by the controlled removal of detergent from a detergent-solubilized protein-lipid mixture. Recently, an alternative method has been developed using direct cell-free expression of the membrane scaffold protein in the presence of preformed lipid vesicles, which spontaneously produces NLPs without the need for detergent at any stage. Using SANS/SAXS, we show here that NLPs produced by this cell-free expression method are structurally indistinguishable from those produced using detergent removal methodologies. This further supports the utility of single step cell-free methods for the production of lipid binding proteins. In addition, detailed structural information describing these NLPs can be obtained by fitting a capped core-shell cylinder type model to all SANS/SAXS data simultaneously.
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Affiliation(s)
- Thomas E Cleveland
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland, 20899.,Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, Maryland, 20850
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, California, 94550
| | - Angela C Evans
- Lawrence Livermore National Laboratory, Livermore, California, 94550
| | | | - Edmond Y Lau
- Lawrence Livermore National Laboratory, Livermore, California, 94550
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, California, 94550
| | - Paul Butler
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland, 20899.,Department of Chemistry, University of Tennessee, Knoxville, Tennessee, 37996-1600
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41
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Wang P, Chang AY, Novosad V, Chupin VV, Schaller RD, Rozhkova EA. Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion. ACS Nano 2017; 11:6739-6745. [PMID: 28602073 DOI: 10.1021/acsnano.7b01142] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report on an entirely man-made nano-bio architecture fabricated through noncovalent assembly of a cell-free expressed transmembrane proton pump and TiO2 semiconductor nanoparticles as an efficient nanophotocatalyst for H2 evolution. The system produces hydrogen at a turnover of about 240 μmol of H2 (μmol protein)-1 h-1 and 17.74 mmol of H2 (μmol protein)-1 h-1 under monochromatic green and white light, respectively, at ambient conditions, in water at neutral pH and room temperature, with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allow for systemic manipulation at the nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.
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Affiliation(s)
- Peng Wang
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
- State Key Laboratory of Crystal Materials, Shandong University , Jinan, Shandong 250100, People's Republic of China
| | - Angela Y Chang
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Valentyn Novosad
- Materials Science Division, Argonne National Laboratory , Argonne, Illinois 60439-4855, United States
| | - Vladimir V Chupin
- Laboratory Chemistry and Physics of Lipids, Department of General and Applied Physics, Moscow Institute of Physics and Technology , Dolgoprudny, Moscow Region 141701, Russia
| | - Richard D Schaller
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Elena A Rozhkova
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
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42
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He W, Felderman M, Evans AC, Geng J, Homan D, Bourguet F, Fischer NO, Li Y, Lam KS, Noy A, Xing L, Cheng RH, Rasley A, Blanchette CD, Kamrud K, Wang N, Gouvis H, Peterson TC, Hubby B, Coleman MA. Cell-free production of a functional oligomeric form of a Chlamydia major outer-membrane protein (MOMP) for vaccine development. J Biol Chem 2017; 292:15121-15132. [PMID: 28739800 DOI: 10.1074/jbc.m117.784561] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/13/2017] [Indexed: 11/06/2022] Open
Abstract
Chlamydia is a prevalent sexually transmitted disease that infects more than 100 million people worldwide. Although most individuals infected with Chlamydia trachomatis are initially asymptomatic, symptoms can arise if left undiagnosed. Long-term infection can result in debilitating conditions such as pelvic inflammatory disease, infertility, and blindness. Chlamydia infection, therefore, constitutes a significant public health threat, underscoring the need for a Chlamydia-specific vaccine. Chlamydia strains express a major outer-membrane protein (MOMP) that has been shown to be an effective vaccine antigen. However, approaches to produce a functional recombinant MOMP protein for vaccine development are limited by poor solubility, low yield, and protein misfolding. Here, we used an Escherichia coli-based cell-free system to express a MOMP protein from the mouse-specific species Chlamydia muridarum (MoPn-MOMP or mMOMP). The codon-optimized mMOMP gene was co-translated with Δ49apolipoprotein A1 (Δ49ApoA1), a truncated version of mouse ApoA1 in which the N-terminal 49 amino acids were removed. This co-translation process produced mMOMP supported within a telodendrimer nanolipoprotein particle (mMOMP-tNLP). The cell-free expressed mMOMP-tNLPs contain mMOMP multimers similar to the native MOMP protein. This cell-free process produced on average 1.5 mg of purified, water-soluble mMOMP-tNLP complex in a 1-ml cell-free reaction. The mMOMP-tNLP particle also accommodated the co-localization of CpG oligodeoxynucleotide 1826, a single-stranded synthetic DNA adjuvant, eliciting an enhanced humoral immune response in vaccinated mice. Using our mMOMP-tNLP formulation, we demonstrate a unique approach to solubilizing and administering membrane-bound proteins for future vaccine development. This method can be applied to other previously difficult-to-obtain antigens while maintaining full functionality and immunogenicity.
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Affiliation(s)
- Wei He
- From the Lawrence Livermore National Laboratory, Livermore, California 94550
| | | | - Angela C Evans
- From the Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Jia Geng
- From the Lawrence Livermore National Laboratory, Livermore, California 94550.,School of Natural Sciences, University of California, Merced, California 95343
| | - David Homan
- From the Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Feliza Bourguet
- From the Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Nicholas O Fischer
- From the Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Yuanpei Li
- the Department of Biochemistry and Molecular Medicine and
| | - Kit S Lam
- the Department of Biochemistry and Molecular Medicine and
| | - Aleksandr Noy
- From the Lawrence Livermore National Laboratory, Livermore, California 94550.,School of Natural Sciences, University of California, Merced, California 95343
| | - Li Xing
- the Department of Molecular and Cellular Biology, University of California, Davis, California 95618
| | - R Holland Cheng
- the Department of Molecular and Cellular Biology, University of California, Davis, California 95618
| | - Amy Rasley
- From the Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Craig D Blanchette
- From the Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Kurt Kamrud
- Synthetic Genomics Vaccine Inc., La Jolla, California 92037
| | - Nathaniel Wang
- Synthetic Genomics Vaccine Inc., La Jolla, California 92037
| | - Heather Gouvis
- Synthetic Genomics Vaccine Inc., La Jolla, California 92037
| | | | - Bolyn Hubby
- Synthetic Genomics Vaccine Inc., La Jolla, California 92037
| | - Matthew A Coleman
- From the Lawrence Livermore National Laboratory, Livermore, California 94550, .,Radiation Oncology, School of Medicine, University of California Davis, Sacramento, California 95817, and
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43
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Hein C, Löhr F, Schwarz D, Dötsch V. Acceleration of protein backbone NMR assignment by combinatorial labeling: Application to a small molecule binding study. Biopolymers 2017; 107. [PMID: 28035667 DOI: 10.1002/bip.23013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 10/24/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022]
Abstract
Selective labeling with stable isotopes has long been recognized as a valuable tool in protein NMR to alleviate signal overlap and sensitivity limitations. In this study, combinatorial 15 N-, 13 Cα -, and 13 C'-selective labeling has been used during the backbone assignment of human cyclophilin D to explore binding of an inhibitor molecule. Using a cell-free expression system, a scheme that involves 15 N, 1-13 C, 2-13 C, fully 15 N/13 C, and unlabeled amino acids was optimized to gain a maximum of assignment information from three samples. This scheme was combined with time-shared triple-resonance NMR experiments, which allows a fast and efficient backbone assignment by giving the unambiguous assignment of unique amino acid pairs in the protein, the identity of ambiguous pairs and information about all 19 non-proline amino acid types. It is therefore well suited for binding studies where de novo assignments of amide 1 H and 15 N resonances need to be obtained, even in cases where sensitivity is the limiting factor.
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Affiliation(s)
- Christopher Hein
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
| | - Daniel Schwarz
- Merck KGaA, Discovery Pharmacology, Global Research and Development, Darmstadt, 64293, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
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44
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Kol M, Panatala R, Nordmann M, Swart L, van Suijlekom L, Cabukusta B, Hilderink A, Grabietz T, Mina JGM, Somerharju P, Korneev S, Tafesse FG, Holthuis JCM. Switching head group selectivity in mammalian sphingolipid biosynthesis by active-site-engineering of sphingomyelin synthases. J Lipid Res 2017; 58:962-973. [PMID: 28336574 DOI: 10.1194/jlr.m076133] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/07/2017] [Indexed: 12/17/2022] Open
Abstract
SM is a fundamental component of mammalian cell membranes that contributes to mechanical stability, signaling, and sorting. Its production involves the transfer of phosphocholine from phosphatidylcholine onto ceramide, a reaction catalyzed by SM synthase (SMS)1 in the Golgi and SMS2 at the plasma membrane. Mammalian cells also synthesize trace amounts of the SM analog, ceramide phosphoethanolamine (CPE), but the physiological relevance of CPE production is unclear. Previous work revealed that SMS2 is a bifunctional enzyme producing both SM and CPE, whereas a closely related enzyme, SMS-related protein (SMSr)/SAMD8, acts as a monofunctional CPE synthase in the endoplasmic reticulum. Using domain swapping and site-directed mutagenesis on enzymes expressed in defined lipid environments, we here identified structural determinants that mediate the head group selectivity of SMS family members. Notably, a single residue adjacent to the catalytic histidine in the third exoplasmic loop profoundly influenced enzyme specificity, with Glu permitting SMS-catalyzed CPE production and Asp confining the enzyme to produce SM. An exchange of exoplasmic residues with SMSr proved sufficient to convert SMS1 into a bulk CPE synthase. This allowed us to establish mammalian cells that produce CPE rather than SM as the principal phosphosphingolipid and provide a model of the molecular interactions that impart catalytic specificity among SMS enzymes.
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Affiliation(s)
- Matthijs Kol
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany .,Membrane Biochemistry and Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Radhakrishnan Panatala
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.,Membrane Biochemistry and Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Mirjana Nordmann
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Leoni Swart
- Membrane Biochemistry and Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Leonie van Suijlekom
- Membrane Biochemistry and Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Birol Cabukusta
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Angelika Hilderink
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Tanja Grabietz
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - John G M Mina
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Pentti Somerharju
- Medical Biochemistry, Institute of Biomedicine, University of Helsinki, Helsinki 00014, Finland
| | - Sergei Korneev
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Fikadu G Tafesse
- Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239
| | - Joost C M Holthuis
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany .,Membrane Biochemistry and Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
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45
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Kol M, Panatala R, Nordmann M, Swart L, van Suijlekom L, Cabukusta B, Hilderink A, Grabietz T, Mina JGM, Somerharju P, Korneev S, Tafesse FG, Holthuis JCM. Switching head group selectivity in mammalian sphingolipid biosynthesis by active-site engineering of sphingomyelin synthases. J Lipid Res 2016; 57:1273-85. [PMID: 27165857 DOI: 10.1194/jlr.m068692] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 01/23/2023] Open
Abstract
SM is a fundamental component of mammalian cell membranes that contributes to mechanical stability, signaling, and sorting. Its production involves the transfer of phosphocholine from phosphatidylcholine onto ceramide, a reaction catalyzed by SM synthase (SMS) 1 in the Golgi and SMS2 at the plasma membrane. Mammalian cells also synthesize trace amounts of the SM analog ceramide phosphoethanolamine (CPE), but the physiological relevance of CPE production is unclear. Previous work revealed that SMS2 is a bifunctional enzyme producing both SM and CPE, whereas a closely related enzyme, sphingomyelin synthase-related protein (SMSr)/SAMD8, acts as a monofunctional CPE synthase in the endoplasmatic reticulum. Using domain swapping and site-directed mutagenesis on enzymes expressed in defined lipid environments, we here identified structural determinants that mediate head group selectivity of SMS family members. Notably, a single residue adjacent to the catalytic histidine in the third exoplasmic loop profoundly influenced enzyme specificity, with glutamic acid permitting SMS-catalyzed CPE production and aspartic acid confining the enzyme to produce SM. An exchange of exoplasmic residues with SMSr proved sufficient to convert SMS1 into a bulk CPE synthase. This allowed us to establish mammalian cells that produce CPE rather than SM as the principal phosphosphingolipid and provide a model of the molecular interactions that impart catalytic specificity among SMS enzymes.
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Affiliation(s)
- Matthijs Kol
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Radhakrishnan Panatala
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Mirjana Nordmann
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Leoni Swart
- Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Leonie van Suijlekom
- Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Birol Cabukusta
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Angelika Hilderink
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Tanja Grabietz
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - John G M Mina
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Pentti Somerharju
- Medical Biochemistry, Institute of Biomedicine, University of Helsinki, Helsinki 00014, Finland
| | - Sergei Korneev
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Fikadu G Tafesse
- Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239
| | - Joost C M Holthuis
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
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46
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Henrich E, Ma Y, Engels I, Münch D, Otten C, Schneider T, Henrichfreise B, Sahl HG, Dötsch V, Bernhard F. Lipid Requirements for the Enzymatic Activity of MraY Translocases and in Vitro Reconstitution of the Lipid II Synthesis Pathway. J Biol Chem 2015; 291:2535-46. [PMID: 26620564 DOI: 10.1074/jbc.m115.664292] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 12/19/2022] Open
Abstract
Screening of new compounds directed against key protein targets must continually keep pace with emerging antibiotic resistances. Although periplasmic enzymes of bacterial cell wall biosynthesis have been among the first drug targets, compounds directed against the membrane-integrated catalysts are hardly available. A promising future target is the integral membrane protein MraY catalyzing the first membrane associated step within the cytoplasmic pathway of bacterial peptidoglycan biosynthesis. However, the expression of most MraY homologues in cellular expression systems is challenging and limits biochemical analysis. We report the efficient production of MraY homologues from various human pathogens by synthetic cell-free expression approaches and their subsequent characterization. MraY homologues originating from Bordetella pertussis, Helicobacter pylori, Chlamydia pneumoniae, Borrelia burgdorferi, and Escherichia coli as well as Bacillus subtilis were co-translationally solubilized using either detergent micelles or preformed nanodiscs assembled with defined membranes. All MraY enzymes originating from Gram-negative bacteria were sensitive to detergents and required nanodiscs containing negatively charged lipids for obtaining a stable and functionally folded conformation. In contrast, the Gram-positive B. subtilis MraY not only tolerates detergent but is also less specific for its lipid environment. The MraY·nanodisc complexes were able to reconstitute a complete in vitro lipid I and lipid II forming pipeline in combination with the cell-free expressed soluble enzymes MurA-F and with the membrane-associated protein MurG. As a proof of principle for future screening platforms, we demonstrate the inhibition of the in vitro lipid II biosynthesis with the specific inhibitors fosfomycin, feglymycin, and tunicamycin.
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Affiliation(s)
- Erik Henrich
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany
| | - Yi Ma
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany, the School of Bioscience and Bioengineering, South China University of Technology, 510006 Guangzhou, China,
| | - Ina Engels
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Daniela Münch
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Christian Otten
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Tanja Schneider
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Beate Henrichfreise
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Hans-Georg Sahl
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Volker Dötsch
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany
| | - Frank Bernhard
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany,
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47
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Abstract
The large-scale production of recombinant G protein-coupled receptors (GPCRs) is one of the major bottlenecks that hamper functional and structural studies of this important class of integral membrane proteins. Heterologous overexpression of GPCRs often results in low yields of active protein, usually due to a combination of several factors, such as low expression levels, protein insolubility, host cell toxicity, and the need to use harsh and often denaturing detergents (e.g., SDS, LDAO, OG, and DDM, among others) to extract the recombinant receptor from the host cell membrane. Many of these problematic issues are inherently linked to cell-based expression systems and can therefore be circumvented by the use of cell-free systems. In this unit, we provide a range of protocols for the production of GPCRs in a cell-free expression system. Using this system, we typically obtain GPCR expression levels of ∼1 mg per ml of reaction mixture in the continuous-exchange configuration. Although the protocols in this unit have been optimized for the cell-free expression of GPCRs, they should provide a good starting point for the production of other classes of membrane proteins, such as ion channels, aquaporins, carrier proteins, membrane-bound enzymes, and even large molecular complexes.
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Affiliation(s)
- Kenneth Segers
- VIB Center for the Biology of Disease, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.,Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
| | - Stefan Masure
- Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
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48
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He W, Luo J, Bourguet F, Xing L, Yi SK, Gao T, Blanchette C, Henderson PT, Kuhn E, Malfatti M, Murphy WJ, Cheng RH, Lam KS, Coleman MA. Controlling the diameter, monodispersity, and solubility of ApoA1 nanolipoprotein particles using telodendrimer chemistry. Protein Sci 2013; 22:1078-86. [PMID: 23754445 DOI: 10.1002/pro.2292] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 04/15/2013] [Accepted: 05/28/2013] [Indexed: 12/16/2022]
Abstract
Nanolipoprotein particles (NLPs) are nanometer-scale discoidal particles that feature a phospholipid bilayer confined within an apolipoprotein "scaffold," which are useful for solubilizing hydrophobic molecules such as drugs and membrane proteins. NLPs are synthesized either by mixing the purified apolipoprotein with phospholipids and other cofactors or by cell-free protein synthesis followed by self-assembly of the nanoparticles in the reaction mixture. Either method can be problematic regarding the production of homogeneous and monodispersed populations of NLPs, which also currently requires multiple synthesis and purification steps. Telodendrimers (TD) are branched polymers made up of a dendritic oligo-lysine core that is conjugated to linear polyethylene glycol (PEG) on one end, and the lysine "branches" are terminated with cholic acid moieties that enable the formation of nanomicelles in aqueous solution. We report herein that the addition of TD during cell-free synthesis of NLPs produces unique hybrid nanoparticles that have drastically reduced polydispersity as compared to NLPs made in the absence of TD. This finding was supported by dynamic light scattering, fluorescence correlation spectroscopy, and cryo transmission electron microscopy (Cryo-EM). These techniques demonstrate the ability of TDs to modulate both the NLP size (6-30 nm) and polydispersity. The telodendrimer NLPs (TD-NLPs) also showed 80% less aggregation as compared to NLPs alone. Furthermore, the versatility of these novel nanoparticles was shown through direct conjugation of small molecules such as fluorescent dyes directly to the TD as well as the insertion of a functional membrane protein.
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Affiliation(s)
- Wei He
- NSF Center for Biophotonics Science and Technology, Sacramento, California, 95817, USA
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49
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Löhr F, Reckel S, Karbyshev M, Connolly PJ, Abdul-Manan N, Bernhard F, Moore JM, Dötsch V. Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment. J Biomol NMR 2012; 52:197-210. [PMID: 22252484 PMCID: PMC3725308 DOI: 10.1007/s10858-012-9601-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [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: 12/20/2011] [Accepted: 12/28/2011] [Indexed: 05/03/2023]
Abstract
Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with (15)N-(1)H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three different species of amino acids in each sample, (15)N, 1-(13)C, and fully (13)C/(15)N labeled, permits identification of more amino acid types and sequential pairs than would be possible with previously published combinatorial methods. The new protocol involves recording of up to five 2D triple-resonance experiments to distinguish the various isotopomeric dipeptide species. The pattern of backbone NH cross peaks in this series of spectra adds a new dimension to the combinatorial grid, which otherwise mostly relies on comparison of [(15)N, (1)H]-HSQC and possibly 2D HN(CO) spectra of samples with different labeled amino acid compositions. Application to two α-helical membrane proteins shows that using no more than three samples information can be accumulated such that backbone assignments can be completed solely based on 3D HNCA/HN(CO)CA experiments. Alternatively, in the case of severe signal overlap in certain regions of the standard suite of triple-resonance spectra acquired on uniformly labeled protein, or missing signals due to a lack of efficiency of 3D experiments, the remaining gaps can be filled.
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Affiliation(s)
- Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Sina Reckel
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Mikhail Karbyshev
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | | | | | - Frank Bernhard
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | | | - Volker Dötsch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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50
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Reckel S, Gottstein D, Stehle J, Löhr F, Verhoefen MK, Takeda M, Silvers R, Kainosho M, Glaubitz C, Wachtveitl J, Bernhard F, Schwalbe H, Güntert P, Dötsch V. Solution NMR structure of proteorhodopsin. Angew Chem Int Ed Engl 2011; 50:11942-6. [PMID: 22034093 PMCID: PMC4234116 DOI: 10.1002/anie.201105648] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Sina Reckel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany, Fax: (+49)-69-798-29632
| | - Daniel Gottstein
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany, Fax: (+49)-69-798-29632
| | - Jochen Stehle
- Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7-9, 60438 Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany, Fax: (+49)-69-798-29632
| | - Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Mitsuhiro Takeda
- Structural Biology Research Center, Nagoya University, Furo‐cho, Chikusa-ku, 464-8601, Japan
| | - Robert Silvers
- Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7-9, 60438 Frankfurt, Germany
| | - Masatsune Kainosho
- Structural Biology Research Center, Nagoya University, Furo‐cho, Chikusa-ku, 464-8601, Japan; Center for Priority Areas, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany, Fax: (+49)-69-798-29632
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany, Fax: (+49)-69-798-29632
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7-9, 60438 Frankfurt, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany, Fax: (+49)-69-798-29632; Frankfurt Institute for Advanced Studies, Goethe University Frankfurt, Ruth-Moufang-Str.1, 60438 Frankfurt am Main, Germany; Center for Priority Areas, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany, Fax: (+49)-69-798-29632
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