1
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Moser C, Muhle-Goll C. Cell-free protein production of a gamma secretase homolog. Protein Expr Purif 2024; 215:106407. [PMID: 38000778 DOI: 10.1016/j.pep.2023.106407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
Cleavage of the transmembrane domain (TMD) of amyloid-β precursor protein (APP) by γ-secretase, an intramembrane aspartyl protease, generates Aβ peptides of various lengths that form plaques in the brains of Alzheimer's disease patients. Although the debate has not been finally resolved whether these plaques trigger the onset of Alzheimer's or are side products, disease-related mutations suggest their implication in the etiology of the dementia. These occur both in presenilin, the catalytic subunit of γ-secretase, and in the TMD of APP. Despite two seminal cryo-electron microscopy structures that show the complex of γ-secretase with its substrates APP and Notch, the mechanism of γ-secretase is not yet fully understood. Especially on which basis it selects its substrates is still an enigma. The presenilin homolog PSH from the archaeon Methanoculleus marisnigri JR1 (MCMJR1) is catalytically active without accessory proteins in contrast to γ-secretase making it an excellent model for studies of the basic cleavage process. We here focused on the cell-free expression of PSH screening a range of conditions. Cleavage assays to verify the activity show that not only the yield, but mainly the activity of the protease depends on the careful selection of expression conditions. Optimal results were found for a cell-free expression at relatively low temperature, 20 °C, employing cell lysates prepared from E. coli Rosetta cells. To speed up protein preparation for immediate functional assays, a crude purification protocol was developed. This allows to produce ready-made PSH in a fast and efficient manner in less than two days.
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Affiliation(s)
- Celine Moser
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein- Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein- Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.
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2
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Laurence MJ, Carpenter TS, Laurence TA, Coleman MA, Shelby M, Liu C. Biophysical Characterization of Membrane Proteins Embedded in Nanodiscs Using Fluorescence Correlation Spectroscopy. MEMBRANES 2022; 12:membranes12040392. [PMID: 35448362 PMCID: PMC9028781 DOI: 10.3390/membranes12040392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023]
Abstract
Proteins embedded in biological membranes perform essential functions in all organisms, serving as receptors, transporters, channels, cell adhesion molecules, and other supporting cellular roles. These membrane proteins comprise ~30% of all human proteins and are the targets of ~60% of FDA-approved drugs, yet their extensive characterization using established biochemical and biophysical methods has continued to be elusive due to challenges associated with the purification of these insoluble proteins. In response, the development of nanodisc techniques, such as nanolipoprotein particles (NLPs) and styrene maleic acid polymers (SMALPs), allowed membrane proteins to be expressed and isolated in solution as part of lipid bilayer rafts with defined, consistent nanometer sizes and compositions, thus enabling solution-based measurements. Fluorescence correlation spectroscopy (FCS) is a relatively simple yet powerful optical microscopy-based technique that yields quantitative biophysical information, such as diffusion kinetics and concentrations, about individual or interacting species in solution. Here, we first summarize current nanodisc techniques and FCS fundamentals. We then provide a focused review of studies that employed FCS in combination with nanodisc technology to investigate a handful of membrane proteins, including bacteriorhodopsin, bacterial division protein ZipA, bacterial membrane insertases SecYEG and YidC, Yersinia pestis type III secretion protein YopB, yeast cell wall stress sensor Wsc1, epidermal growth factor receptor (EGFR), ABC transporters, and several G protein-coupled receptors (GPCRs).
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Affiliation(s)
- Matthew J. Laurence
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
| | - Timothy S. Carpenter
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
| | - Ted A. Laurence
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Matthew A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Department of Radiation Oncology, University of California Davis, Sacramento, CA 95616, USA
| | - Megan Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Correspondence: (M.S.); (C.L.)
| | - Chao Liu
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Correspondence: (M.S.); (C.L.)
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3
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Blackholly LR, Harris NJ, Findlay HE, Booth PJ. Cell-Free Expression to Probe Co-Translational Insertion of an Alpha Helical Membrane Protein. Front Mol Biosci 2022; 9:795212. [PMID: 35187078 PMCID: PMC8847741 DOI: 10.3389/fmolb.2022.795212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/11/2022] [Indexed: 01/23/2023] Open
Abstract
The majority of alpha helical membrane proteins fold co-translationally during their synthesis on the ribosome. In contrast, most mechanistic folding studies address refolding of full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation of membrane proteins is emerging as a useful tool to address folding during translation by a ribosome. We summarise the benefits of this approach and show how it can be successfully extended to a membrane protein with a complex topology. The bacterial leucine transporter, LeuT can be synthesised and inserted into lipid membranes using a variety of in vitro transcription translation systems. Unlike major facilitator superfamily transporters, where changes in lipids can optimise the amount of correctly inserted protein, LeuT insertion yields are much less dependent on the lipid composition. The presence of a bacterial translocon either in native membrane extracts or in reconstituted membranes also has little influence on the yield of LeuT incorporated into the lipid membrane, except at high reconstitution concentrations. LeuT is considered a paradigm for neurotransmitter transporters and possesses a knotted structure that is characteristic of this transporter family. This work provides a method in which to probe the formation of a protein as the polypeptide chain is being synthesised on a ribosome and inserting into lipids. We show that in comparison with the simpler major facilitator transporter structures, LeuT inserts less efficiently into membranes when synthesised cell-free, suggesting that more of the protein aggregates, likely as a result of the challenging formation of the knotted topology in the membrane.
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Affiliation(s)
| | | | | | - Paula J. Booth
- Department of Chemistry, King’s College London, London, United Kingdom
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4
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B Uribe K, Benito-Vicente A, Martin C, Blanco-Vaca F, Rotllan N. (r)HDL in theranostics: how do we apply HDL's biology for precision medicine in atherosclerosis management? Biomater Sci 2021; 9:3185-3208. [PMID: 33949389 DOI: 10.1039/d0bm01838d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
High-density lipoproteins (HDL) are key players in cholesterol metabolism homeostasis since they are responsible for transporting excess cholesterol from peripheral tissues to the liver. Imbalance in this process, due to either excessive accumulation or impaired clearance, results in net cholesterol accumulation and increases the risk of cardiovascular disease (CVD). Therefore, significant effort has been focused on the development of therapeutic tools capable of either directly or indirectly enhancing HDL-guided reverse cholesterol transport (RCT). More recently, in light of the emergence of precision nanomedicine, there has been renewed research interest in attempting to take advantage of the development of advanced recombinant HDL (rHDL) for both therapeutic and diagnostic purposes. In this review, we provide an update on the different approaches that have been developed using rHDL, focusing on the rHDL production methodology and rHDL applications in theranostics. We also compile a series of examples highlighting potential future perspectives in the field.
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Affiliation(s)
- Kepa B Uribe
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain.
| | - Asier Benito-Vicente
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo.644, 48080 Bilbao, Spain.
| | - Cesar Martin
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo.644, 48080 Bilbao, Spain.
| | - Francisco Blanco-Vaca
- Servei de Bioquímica, Hospital Santa Creu i Sant Pau-Institut d'Investigacions Biomèdiques (IIB) Sant Pau, 08041 Barcelona, Spain. and CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain and Departament de Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Spain and Institut de Recerca de l'Hospital Santa Creu i Sant Pau-Institut d'Investigacions Biomèdiques (IIB) Sant Pau, 08025 Barcelona, Spain.
| | - Noemi Rotllan
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain and Institut de Recerca de l'Hospital Santa Creu i Sant Pau-Institut d'Investigacions Biomèdiques (IIB) Sant Pau, 08025 Barcelona, Spain.
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5
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Darwish M, Shatz W, Leonard B, Loyet K, Barrett K, Wong JL, Li H, Abraham R, Lin M, Franke Y, Tam C, Mortara K, Zilberleyb I, Blanchette C. Nanolipoprotein Particles as a Delivery Platform for Fab Based Therapeutics. Bioconjug Chem 2020; 31:1995-2007. [DOI: 10.1021/acs.bioconjchem.0c00349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Martine Darwish
- Genentech, South San Francisco, California 94088, United States
| | - Whitney Shatz
- Genentech, South San Francisco, California 94088, United States
| | - Brandon Leonard
- Genentech, South San Francisco, California 94088, United States
| | - Kelly Loyet
- Genentech, South San Francisco, California 94088, United States
| | - Kathy Barrett
- Genentech, South San Francisco, California 94088, United States
| | - Janice L. Wong
- Genentech, South San Francisco, California 94088, United States
| | - Hong Li
- Genentech, South San Francisco, California 94088, United States
| | - Ryan Abraham
- Genentech, South San Francisco, California 94088, United States
| | - May Lin
- Genentech, South San Francisco, California 94088, United States
| | - Yvonne Franke
- Genentech, South San Francisco, California 94088, United States
| | - Christine Tam
- Genentech, South San Francisco, California 94088, United States
| | - Kyle Mortara
- Genentech, South San Francisco, California 94088, United States
| | - Inna Zilberleyb
- Genentech, South San Francisco, California 94088, United States
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6
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Shelby ML, He W, Dang AT, Kuhl TL, Coleman MA. Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins. Front Pharmacol 2019; 10:744. [PMID: 31333463 PMCID: PMC6616253 DOI: 10.3389/fphar.2019.00744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
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Affiliation(s)
- Megan L Shelby
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amanda T Dang
- University of California at Davis, Davis, CA, United States
| | - Tonya L Kuhl
- University of California at Davis, Davis, CA, United States
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States.,University of California at Davis, Davis, CA, United States
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7
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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] [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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8
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Minkoff BB, Makino SI, Haruta M, Beebe ET, Wrobel RL, Fox BG, Sussman MR. A cell-free method for expressing and reconstituting membrane proteins enables functional characterization of the plant receptor-like protein kinase FERONIA. J Biol Chem 2017; 292:5932-5942. [PMID: 28235802 DOI: 10.1074/jbc.m116.761981] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/09/2017] [Indexed: 01/17/2023] Open
Abstract
There are more than 600 receptor-like kinases (RLKs) in Arabidopsis, but due to challenges associated with the characterization of membrane proteins, only a few have known biological functions. The plant RLK FERONIA is a peptide receptor and has been implicated in plant growth regulation, but little is known about its molecular mechanism of action. To investigate the properties of this enzyme, we used a cell-free wheat germ-based expression system in which mRNA encoding FERONIA was co-expressed with mRNA encoding the membrane scaffold protein variant MSP1D1. With the addition of the lipid cardiolipin, assembly of these proteins into nanodiscs was initiated. FERONIA protein kinase activity in nanodiscs was higher than that of soluble protein and comparable with other heterologously expressed protein kinases. Truncation experiments revealed that the cytoplasmic juxtamembrane domain is necessary for maximal FERONIA activity, whereas the transmembrane domain is inhibitory. An ATP analogue that reacts with lysine residues inhibited catalytic activity and labeled four lysines; mutagenesis demonstrated that two of these, Lys-565 and Lys-663, coordinate ATP in the active site. Mass spectrometric phosphoproteomic measurements further identified phosphorylation sites that were examined using phosphomimetic mutagenesis. The results of these experiments are consistent with a model in which kinase-mediated phosphorylation within the C-terminal region is inhibitory and regulates catalytic activity. These data represent a step further toward understanding the molecular basis for the protein kinase catalytic activity of FERONIA and show promise for future characterization of eukaryotic membrane proteins.
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Affiliation(s)
- Benjamin B Minkoff
- From the Department of Biochemistry and.,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | | | - Miyoshi Haruta
- From the Department of Biochemistry and.,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | | | | | | | - Michael R Sussman
- From the Department of Biochemistry and .,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
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9
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Gilmore SF, Blanchette CD, Scharadin TM, Hura GL, Rasley A, Corzett M, Pan CX, Fischer NO, Henderson PT. Lipid Cross-Linking of Nanolipoprotein Particles Substantially Enhances Serum Stability and Cellular Uptake. ACS APPLIED MATERIALS & INTERFACES 2016; 8:20549-20557. [PMID: 27411034 DOI: 10.1021/acsami.6b04609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanolipoprotein particles (NLPs) consist of a discoidal phospholipid lipid bilayer confined by an apolipoprotein belt. NLPs are a promising platform for a variety of biomedical applications due to their biocompatibility, size, definable composition, and amphipathic characteristics. However, poor serum stability hampers the use of NLPs for in vivo applications such as drug formulation. In this study, NLP stability was enhanced upon the incorporation and subsequent UV-mediated intermolecular cross-linking of photoactive DiynePC phospholipids in the lipid bilayer, forming cross-linked nanoparticles (X-NLPs). Both the concentration of DiynePC in the bilayer and UV exposure time significantly affected the resulting X-NLP stability in 100% serum, as assessed by size exclusion chromatography (SEC) of fluorescently labeled particles. Cross-linking did not significantly impact the size of X-NLPs as determined by dynamic light scattering and SEC. X-NLPs had essentially no degradation over 48 h in 100% serum, which is a drastic improvement compared to non-cross-linked NLPs (50% degradation by ∼10 min). X-NLPs had greater uptake into the human ATCC 5637 bladder cancer cell line compared to non-cross-linked particles, indicating their potential utility for targeted drug delivery. X-NLPs also exhibited enhanced stability following intravenous administration in mice. These results collectively support the potential utility of X-NLPs for a variety of in vivo applications.
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Affiliation(s)
- Sean F Gilmore
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory , Livermore, California 94551, United States
| | - Craig D Blanchette
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory , Livermore, California 94551, United States
| | - Tiffany M Scharadin
- Department of Internal Medicine, Division of Hematology and Oncology, University of California-Davis (UC Davis) and UC Davis Comprehensive Cancer Center , 4501 X Street, Room 3016, Sacramento, California 95817, United States
| | - Greg L Hura
- Life Science Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Chemistry and Biochemistry, University of California-Santa Cruz , Santa Cruz, California 95064, United States
| | - Amy Rasley
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory , Livermore, California 94551, United States
| | - Michele Corzett
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory , Livermore, California 94551, United States
| | - Chong-Xian Pan
- Department of Internal Medicine, Division of Hematology and Oncology, University of California-Davis (UC Davis) and UC Davis Comprehensive Cancer Center , 4501 X Street, Room 3016, Sacramento, California 95817, United States
| | - Nicholas O Fischer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory , Livermore, California 94551, United States
| | - Paul T Henderson
- Department of Internal Medicine, Division of Hematology and Oncology, University of California-Davis (UC Davis) and UC Davis Comprehensive Cancer Center , 4501 X Street, Room 3016, Sacramento, California 95817, United States
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10
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Huang R, Kiss MM, Batonick M, Weiner MP, Kay BK. Generating Recombinant Antibodies to Membrane Proteins through Phage Display. Antibodies (Basel) 2016; 5:antib5020011. [PMID: 31557992 PMCID: PMC6698964 DOI: 10.3390/antib5020011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 01/03/2023] Open
Abstract
One of the most important classes of proteins in terms of drug targets is cell surface membrane proteins, and yet it is a challenging set of proteins for generating high-quality affinity reagents. In this review, we focus on the use of phage libraries, which display antibody fragments, for generating recombinant antibodies to membrane proteins. Such affinity reagents generally have high specificity and affinity for their targets. They have been used for cell staining, for promoting protein crystallization to solve three-dimensional structures, for diagnostics, and for treating diseases as therapeutics. We cover publications on this topic from the past 10 years, with a focus on the various formats of membrane proteins for affinity selection and the diverse affinity selection strategies used. Lastly, we discuss the challenges faced in this field and provide possible directions for future efforts.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
| | - Margaret M Kiss
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Melissa Batonick
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Michael P Weiner
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
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11
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Coleman MA, Cappuccio JA, Blanchette CD, Gao T, Arroyo ES, Hinz AK, Bourguet FA, Segelke B, Hoeprich PD, Huser T, Laurence TA, Motin VL, Chromy BA. Expression and Association of the Yersinia pestis Translocon Proteins, YopB and YopD, Are Facilitated by Nanolipoprotein Particles. PLoS One 2016; 11:e0150166. [PMID: 27015536 PMCID: PMC4807764 DOI: 10.1371/journal.pone.0150166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 02/10/2016] [Indexed: 12/18/2022] Open
Abstract
Yersinia pestis enters host cells and evades host defenses, in part, through interactions between Yersinia pestis proteins and host membranes. One such interaction is through the type III secretion system, which uses a highly conserved and ordered complex for Yersinia pestis outer membrane effector protein translocation called the injectisome. The portion of the injectisome that interacts directly with host cell membranes is referred to as the translocon. The translocon is believed to form a pore allowing effector molecules to enter host cells. To facilitate mechanistic studies of the translocon, we have developed a cell-free approach for expressing translocon pore proteins as a complex supported in a bilayer membrane mimetic nano-scaffold known as a nanolipoprotein particle (NLP) Initial results show cell-free expression of Yersinia pestis outer membrane proteins YopB and YopD was enhanced in the presence of liposomes. However, these complexes tended to aggregate and precipitate. With the addition of co-expressed (NLP) forming components, the YopB and/or YopD complex was rendered soluble, increasing the yield of protein for biophysical studies. Biophysical methods such as Atomic Force Microscopy and Fluorescence Correlation Spectroscopy were used to confirm that the soluble YopB/D complex was associated with NLPs. An interaction between the YopB/D complex and NLP was validated by immunoprecipitation. The YopB/D translocon complex embedded in a NLP provides a platform for protein interaction studies between pathogen and host proteins. These studies will help elucidate the poorly understood mechanism which enables this pathogen to inject effector proteins into host cells, thus evading host defenses.
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Affiliation(s)
- Matthew A. Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America, 94550
- University of California Davis, NSF, Center for Biophotonics, Sacramento, CA, United States of America, 95817
- * E-mail: (MAC); (BAC)
| | - Jenny A. Cappuccio
- Humboldt State University, Department of Chemistry, Arcata, CA, United States of America, 95521
| | - Craig D. Blanchette
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America, 94550
| | - Tingjuan Gao
- University of California Davis, NSF, Center for Biophotonics, Sacramento, CA, United States of America, 95817
| | - Erin S. Arroyo
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America, 94550
| | - Angela K. Hinz
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America, 94550
| | - Feliza A. Bourguet
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America, 94550
| | - Brent Segelke
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America, 94550
| | - Paul D. Hoeprich
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America, 94550
| | - Thomas Huser
- University of California Davis, NSF, Center for Biophotonics, Sacramento, CA, United States of America, 95817
| | - Ted A. Laurence
- Lawrence Livermore National Laboratory, Livermore, CA, United States of America, 94550
| | - Vladimir L. Motin
- University of Texas Medical Branch, Galveston, TX, United States of America, 77555
| | - Brett A. Chromy
- University of California Davis, NSF, Center for Biophotonics, Sacramento, CA, United States of America, 95817
- * E-mail: (MAC); (BAC)
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12
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Fang RH, Luk BT, Hu CMJ, Zhang L. Engineered nanoparticles mimicking cell membranes for toxin neutralization. Adv Drug Deliv Rev 2015; 90:69-80. [PMID: 25868452 DOI: 10.1016/j.addr.2015.04.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/08/2015] [Accepted: 04/01/2015] [Indexed: 11/27/2022]
Abstract
Protein toxins secreted from pathogenic bacteria and venomous animals rely on multiple mechanisms to overcome the cell membrane barrier to inflict their virulence effect. A promising therapeutic concept toward developing a broadly applicable anti-toxin platform is to administer cell membrane mimics as decoys to sequester these virulence factors. As such, lipid membrane-based nanoparticulates are an ideal candidate given their structural similarity to cellular membranes. This article reviews the virulence mechanisms employed by toxins at the cell membrane interface and highlights the application of cell-membrane mimicking nanoparticles as toxin decoys for systemic detoxification. In addition, the implication of particle/toxin nanocomplexes in the development of toxoid vaccines is discussed.
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13
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Developing cell-free protein synthesis systems: a focus on mammalian cells. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Fischer NO, Weilhammer DR, Dunkle A, Thomas C, Hwang M, Corzett M, Lychak C, Mayer W, Urbin S, Collette N, Chiun Chang J, Loots GG, Rasley A, Blanchette CD. Evaluation of nanolipoprotein particles (NLPs) as an in vivo delivery platform. PLoS One 2014; 9:e93342. [PMID: 24675794 PMCID: PMC3968139 DOI: 10.1371/journal.pone.0093342] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 03/05/2014] [Indexed: 12/05/2022] Open
Abstract
Nanoparticles hold great promise for the delivery of therapeutics, yet limitations remain with regards to the use of these nanosystems for efficient long-lasting targeted delivery of therapeutics, including imparting functionality to the platform, in vivo stability, drug entrapment efficiency and toxicity. To begin to address these limitations, we evaluated the functionality, stability, cytotoxicity, toxicity, immunogenicity and in vivo biodistribution of nanolipoprotein particles (NLPs), which are mimetics of naturally occurring high-density lipoproteins (HDLs). We found that a wide range of molecules could be reliably conjugated to the NLP, including proteins, single-stranded DNA, and small molecules. The NLP was also found to be relatively stable in complex biological fluids and displayed no cytotoxicity in vitro at doses as high as 320 µg/ml. In addition, we observed that in vivo administration of the NLP daily for 14 consecutive days did not induce significant weight loss or result in lesions on excised organs. Furthermore, the NLPs did not display overt immunogenicity with respect to antibody generation. Finally, the biodistribution of the NLP in vivo was found to be highly dependent on the route of administration, where intranasal administration resulted in prolonged retention in the lung tissue. Although only a select number of NLP compositions were evaluated, the findings of this study suggest that the NLP platform holds promise for use as both a targeted and non-targeted in vivo delivery vehicle for a range of therapeutics.
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MESH Headings
- Administration, Intranasal
- Animals
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/genetics
- Antigens, Bacterial/metabolism
- Apolipoprotein E4/chemistry
- Apolipoprotein E4/genetics
- Apolipoprotein E4/metabolism
- Biomimetic Materials/chemical synthesis
- Biomimetic Materials/pharmacokinetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/metabolism
- DNA, Single-Stranded/metabolism
- Dimyristoylphosphatidylcholine/chemistry
- Dimyristoylphosphatidylcholine/metabolism
- Drug Carriers
- Drug Stability
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Female
- Fluorescent Dyes
- Lipoproteins, HDL/chemical synthesis
- Lipoproteins, HDL/pharmacokinetics
- Male
- Mice
- Mice, Inbred BALB C
- Nanoparticles/chemistry
- Nanoparticles/toxicity
- Particle Size
- Phosphatidylcholines/chemistry
- Phosphatidylcholines/metabolism
- Pore Forming Cytotoxic Proteins/chemistry
- Pore Forming Cytotoxic Proteins/genetics
- Pore Forming Cytotoxic Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Tissue Distribution
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Affiliation(s)
- Nicholas O. Fischer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Dina R. Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Alexis Dunkle
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Cynthia Thomas
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Mona Hwang
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Michele Corzett
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Cheri Lychak
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Wasima Mayer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Salustra Urbin
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Nicole Collette
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Jiun Chiun Chang
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Gabriela G. Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Amy Rasley
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
- * E-mail: (AR); (CB)
| | - Craig D. Blanchette
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
- * E-mail: (AR); (CB)
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15
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Cell-Free Systems: Functional Modules for Synthetic and Chemical Biology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:67-102. [DOI: 10.1007/10_2013_185] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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16
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Long AR, O'Brien CC, Alder NN. The cell-free integration of a polytopic mitochondrial membrane protein into liposomes occurs cotranslationally and in a lipid-dependent manner. PLoS One 2012; 7:e46332. [PMID: 23050015 PMCID: PMC3457961 DOI: 10.1371/journal.pone.0046332] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/31/2012] [Indexed: 01/19/2023] Open
Abstract
The ADP/ATP Carrier (AAC) is the most abundant transporter of the mitochondrial inner membrane. The central role that this transporter plays in cellular energy production highlights the importance of understanding its structure, function, and the basis of its pathologies. As a means of preparing proteoliposomes for the study of membrane proteins, several groups have explored the use of cell-free translation systems to facilitate membrane protein integration directly into preformed unilamellar vesicles without the use of surfactants. Using AAC as a model, we report for the first time the detergent-free reconstitution of a mitochondrial inner membrane protein into liposomes using a wheat germ-based in vitro translation system. Using a host of independent approaches, we demonstrate the efficient integration of AAC into vesicles with an inner membrane-mimetic lipid composition and, more importantly, that the integrated AAC is functionally active in transport. By adding liposomes at different stages of the translation reaction, we show that this direct integration is obligatorily cotranslational, and by synthesizing stable ribosome-bound nascent chain intermediates, we show that the nascent AAC polypeptide interacts with lipid vesicles while ribosome-bound. Finally, we show that the presence of the phospholipid cardiolipin in the liposomes specifically enhances AAC translation rate as well as the efficiency of vesicle association and integration. In light of these results, the possible mechanisms of liposome-assisted membrane protein integration during cell-free translation are discussed with respect to the mode of integration and the role of specific lipids.
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Affiliation(s)
- Ashley R. Long
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Catherine C. O'Brien
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
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17
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Fluorescent in situ folding control for rapid optimization of cell-free membrane protein synthesis. PLoS One 2012; 7:e42186. [PMID: 22848743 PMCID: PMC3407079 DOI: 10.1371/journal.pone.0042186] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/02/2012] [Indexed: 12/18/2022] Open
Abstract
Cell-free synthesis is an open and powerful tool for high-yield protein production in small reaction volumes predestined for high-throughput structural and functional analysis. Membrane proteins require addition of detergents for solubilization, liposomes, or nanodiscs. Hence, the number of parameters to be tested is significantly higher than with soluble proteins. Optimization is commonly done with respect to protein yield, yet without knowledge of the protein folding status. This approach contains a large inherent risk of ending up with non-functional protein. We show that fluorophore formation in C-terminal fusions with green fluorescent protein (GFP) indicates the folding state of a membrane protein in situ, i.e. within the cell-free reaction mixture, as confirmed by circular dichroism (CD), proteoliposome reconstitution and functional assays. Quantification of protein yield and in-gel fluorescence intensity imply suitability of the method for membrane proteins of bacterial, protozoan, plant, and mammalian origin, representing vacuolar and plasma membrane localization, as well as intra- and extracellular positioning of the C-terminus. We conclude that GFP-fusions provide an extension to cell-free protein synthesis systems eliminating the need for experimental folding control and, thus, enabling rapid optimization towards membrane protein quality.
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18
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Luo Z, Zhang S. Designer nanomaterials using chiral self-assembling peptide systems and their emerging benefit for society. Chem Soc Rev 2012; 41:4736-54. [DOI: 10.1039/c2cs15360b] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Cell-free protein synthesis: applications come of age. Biotechnol Adv 2011; 30:1185-94. [PMID: 22008973 DOI: 10.1016/j.biotechadv.2011.09.016] [Citation(s) in RCA: 465] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 09/30/2011] [Accepted: 09/30/2011] [Indexed: 12/17/2022]
Abstract
Cell-free protein synthesis has emerged as a powerful technology platform to help satisfy the growing demand for simple and efficient protein production. While used for decades as a foundational research tool for understanding transcription and translation, recent advances have made possible cost-effective microscale to manufacturing scale synthesis of complex proteins. Protein yields exceed grams protein produced per liter reaction volume, batch reactions last for multiple hours, costs have been reduced orders of magnitude, and reaction scale has reached the 100-liter milestone. These advances have inspired new applications in the synthesis of protein libraries for functional genomics and structural biology, the production of personalized medicines, and the expression of virus-like particles, among others. In the coming years, cell-free protein synthesis promises new industrial processes where short protein production timelines are crucial as well as innovative approaches to a wide range of applications.
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20
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Popot JL, Althoff T, Bagnard D, Banères JL, Bazzacco P, Billon-Denis E, Catoire LJ, Champeil P, Charvolin D, Cocco MJ, Crémel G, Dahmane T, de la Maza LM, Ebel C, Gabel F, Giusti F, Gohon Y, Goormaghtigh E, Guittet E, Kleinschmidt JH, Kühlbrandt W, Le Bon C, Martinez KL, Picard M, Pucci B, Sachs JN, Tribet C, van Heijenoort C, Wien F, Zito F, Zoonens M. Amphipols from A to Z. Annu Rev Biophys 2011; 40:379-408. [PMID: 21545287 DOI: 10.1146/annurev-biophys-042910-155219] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amphipols (APols) are short amphipathic polymers that can substitute for detergents to keep integral membrane proteins (MPs) water soluble. In this review, we discuss their structure and solution behavior; the way they associate with MPs; and the structure, dynamics, and solution properties of the resulting complexes. All MPs tested to date form water-soluble complexes with APols, and their biochemical stability is in general greatly improved compared with MPs in detergent solutions. The functionality and ligand-binding properties of APol-trapped MPs are reviewed, and the mechanisms by which APols stabilize MPs are discussed. Applications of APols include MP folding and cell-free synthesis, structural studies by NMR, electron microscopy and X-ray diffraction, APol-mediated immobilization of MPs onto solid supports, proteomics, delivery of MPs to preexisting membranes, and vaccine formulation.
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Affiliation(s)
- J-L Popot
- Institut de Biologie Physico-Chimique, CNRS/Université Paris-7 UMR 7099, Paris, France.
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21
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Babel I, Barderas R, Peláez-García A, Casal JI. Antibodies on demand: a fast method for the production of human scFvs with minimal amounts of antigen. BMC Biotechnol 2011; 11:61. [PMID: 21635725 PMCID: PMC3125328 DOI: 10.1186/1472-6750-11-61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 06/02/2011] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Antibodies constitute a powerful tool to study protein function, protein localization and protein-protein interactions, as well as for diagnostic and therapeutic purposes. High-throughput antibody development requires faster methodologies with lower antigen consumption. RESULTS Here, we describe a novel methodology to select human monoclonal recombinant antibodies by combining in vitro protein expression, phage display antibody libraries and antibody microarrays. The application of this combination of methodologies permitted us to generate human single-chain variable fragments (scFvs) against two proteins: green fluorescent protein (GFP) and thioredoxin (Trx) in a short time, using as low as 5 μg of purified protein. These scFvs showed specific reactivity against their respective targets and worked well by ELISA and western blot. The scFvs were able to recognise as low as 31 ng of protein of their respective targets by western blot. CONCLUSION This work describes a novel and miniaturized methodology to obtain human monoclonal recombinant antibodies against any target in a shorter time than other methodologies using only 5 μg of protein. The protocol could be easily adapted to a high-throughput procedure for antibody production.
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Affiliation(s)
- Ingrid Babel
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Rodrigo Barderas
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Alberto Peláez-García
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - J Ignacio Casal
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
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22
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Junge F, Haberstock S, Roos C, Stefer S, Proverbio D, Dötsch V, Bernhard F. Advances in cell-free protein synthesis for the functional and structural analysis of membrane proteins. N Biotechnol 2011; 28:262-71. [DOI: 10.1016/j.nbt.2010.07.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/28/2010] [Accepted: 07/04/2010] [Indexed: 11/25/2022]
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23
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Bricarello DA, Smilowitz JT, Zivkovic AM, German JB, Parikh AN. Reconstituted lipoprotein: a versatile class of biologically-inspired nanostructures. ACS NANO 2011; 5:42-57. [PMID: 21182259 DOI: 10.1021/nn103098m] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
One of biology's most pervasive nanostructures, the phospholipid membrane, represents an ideal scaffold for a host of nanotechnology applications. Whether engineering biomimetic technologies or designing therapies to interface with the cell, this adaptable membrane can provide the necessary molecular-level control of membrane-anchored proteins, glycopeptides, and glycolipids. If appropriately prepared, these components can replicate in vitro or influence in vivo essential living processes such as signal transduction, mass transport, and chemical or energy conversion. To satisfy these requirements, a lipid-based, synthetic nanoscale architecture with molecular-level tunability is needed. In this regard, discrete lipid particles, including reconstituted high density lipoprotein (HDL), have emerged as a versatile and elegant solution. Structurally diverse, native biological HDLs exist as discoidal lipid bilayers of 5-8 nm diameter and lipid monolayer-coated spheres 10-15 nm in diameter, all belted by a robust scaffolding protein. These supramolecular assemblies can be reconstituted using simple self-assembly methods to incorporate a broad range of amphipathic molecular constituents, natural or artificial, and provide a generic platform for stabilization and transport of amphipathic and hydrophobic elements capable of docking with targets at biological or inorganic surfaces. In conjunction with top-down or bottom-up engineering approaches, synthetic HDL can be designed, arrayed, and manipulated for a host of applications including biochemical analyses and fundamental studies of molecular structure. Also highly biocompatible, these assemblies are suitable for medical diagnostics and therapeutics. The collection of efforts reviewed here focuses on laboratory methods by which synthetic HDLs are produced, the advantages conferred by their nanoscopic dimension, and current and emerging applications.
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Affiliation(s)
- Daniel A Bricarello
- Department of Applied Science, University of California-Davis, Davis, California 95616, United States
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24
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Berrier C, Guilvout I, Bayan N, Park KH, Mesneau A, Chami M, Pugsley AP, Ghazi A. Coupled cell-free synthesis and lipid vesicle insertion of a functional oligomeric channel MscL. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:41-6. [DOI: 10.1016/j.bbamem.2010.09.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 09/22/2010] [Accepted: 09/23/2010] [Indexed: 10/19/2022]
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25
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Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. Nat Med 2010; 16:1439-43. [PMID: 21102461 DOI: 10.1038/nm.2245] [Citation(s) in RCA: 306] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 09/20/2010] [Indexed: 02/08/2023]
Abstract
Stroke is a major public health problem leading to high rates of death and disability in adults. Excessive stimulation of N-methyl-D-aspartate receptors (NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation are crucial for neuronal injury after stroke insult. However, directly inhibiting NMDARs or nNOS can cause severe side effects because they have key physiological functions in the CNS. Here we show that cerebral ischemia induces the interaction of nNOS with postsynaptic density protein-95 (PSD-95). Disrupting nNOS-PSD-95 interaction via overexpressing the N-terminal amino acid residues 1-133 of nNOS (nNOS-N(1-133)) prevented glutamate-induced excitotoxicity and cerebral ischemic damage. Given the mechanism of nNOS-PSD-95 interaction, we developed a series of compounds and discovered a small-molecular inhibitor of the nNOS-PSD-95 interaction, ZL006. This drug blocked the ischemia-induced nNOS-PSD-95 association selectively, had potent neuroprotective activity in vitro and ameliorated focal cerebral ischemic damage in mice and rats subjected to middle cerebral artery occlusion (MCAO) and reperfusion. Moreover, it readily crossed the blood-brain barrier, did not inhibit NMDAR function, catalytic activity of nNOS or spatial memory, and had no effect on aggressive behaviors. Thus, this new drug may serve as a treatment for stroke, perhaps without major side effects.
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26
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Khabibullina NF, Lyukmanova EN, Kopeina GS, Shenkarev ZO, Arsen’ev AS, Dolgikh DA, Kirpichnikov MP. Development and optimization of a coupled cell-free system for the synthesis of the transmembrane domain of the receptor tyrosine kinase ErbB3. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:654-60. [DOI: 10.1134/s1068162010050080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Park KH, Billon-Denis E, Dahmane T, Lebaupain F, Pucci B, Breyton C, Zito F. In the cauldron of cell-free synthesis of membrane proteins: playing with new surfactants. N Biotechnol 2010; 28:255-61. [PMID: 20800706 DOI: 10.1016/j.nbt.2010.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/22/2010] [Accepted: 08/18/2010] [Indexed: 02/06/2023]
Abstract
Cell-free protein synthesis is a well-known technique for the roles it has played in deciphering the genetic code and in the beginnings of signal sequence studies. Since then, many efforts have been made to optimise this technique and, recently, to adapt it to membrane protein production with yields compatible with structural investigations. The versatility of the method allows membrane proteins to be obtained directly stabilised in surfactant micelles or inserted in a lipidic environment (proteoliposome, bicelle, and nanodisc) at the end of synthesis. Among the surfactants used, non-detergent ones such as fluorinated surfactants proved to be a good alternative in terms of colloidal stability and preservation of the integrity of membrane proteins, as shown for Escherichia coli homo-pentameric channel, MscL (Park et al., Biochem. J., 403: 183-187). Here we report cell-free expression of Escherichia coli leader peptidase (a transmembrane protease), Halobacterium salinarium bacteriorhodopsin (a transmembrane protein binding a hydrophobic cofactor) and E. coli MscL in the presence of non-detergent surfactants, amphipols and fluorinated surfactants in comparison to their expression in classical detergents. The results confirm the potentialities of fluorinated surfactants and, although pointing to limitations in using the first generations amphipols, results are discussed in the light of membrane protein refolding, especially in the case of bacteriorhodopsin. Preliminary experiments using new generations of amphipols supports choices made in developing new molecules.
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Affiliation(s)
- Kyu-Ho Park
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS and Université Paris-7, Institut de Biologie Physico-Chimique, CNRS FRC 550, F-75005 Paris, France
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28
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Beebe ET, Makino SI, Nozawa A, Matsubara Y, Frederick RO, Primm JG, Goren MA, Fox BG. Robotic large-scale application of wheat cell-free translation to structural studies including membrane proteins. N Biotechnol 2010; 28:239-49. [PMID: 20637905 DOI: 10.1016/j.nbt.2010.07.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 07/03/2010] [Indexed: 10/19/2022]
Abstract
The use of the Protemist XE, an automated discontinuous-batch protein synthesis robot, in cell-free translation is reported. The soluble Galdieria sulphuraria protein DCN1 was obtained in greater than 2mg total synthesis yield per mL of reaction mixture from the Protemist XE, and the structure was subsequently solved by X-ray crystallography using material from one 10 mL synthesis (PDB ID: 3KEV). The Protemist XE was also capable of membrane protein translation. Thus human sigma-1 receptor was translated in the presence of unilamellar liposomes and bacteriorhodopsin was translated directly into detergent micelles in the presence of all-trans-retinal. The versatility, ease of use, and compact size of the Protemist XE robot demonstrate its suitability for large-scale synthesis of many classes of proteins.
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Affiliation(s)
- Emily T Beebe
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, 445 Henry Mall, Madison, WI 53706, USA
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29
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Popot JL. Amphipols, Nanodiscs, and Fluorinated Surfactants: Three Nonconventional Approaches to Studying Membrane Proteins in Aqueous Solutions. Annu Rev Biochem 2010; 79:737-75. [DOI: 10.1146/annurev.biochem.052208.114057] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jean-Luc Popot
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, Unité Mixte de Recherche 7099, Centre National de la Recherche Scientifique and Université Paris-7 Denis Diderot, Institut de Biologie Physico-Chimique, F-75005 Paris, France; e-mail:
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30
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Yoshiura C, Kofuku Y, Ueda T, Mase Y, Yokogawa M, Osawa M, Terashima Y, Matsushima K, Shimada I. NMR Analyses of the Interaction between CCR5 and Its Ligand Using Functional Reconstitution of CCR5 in Lipid Bilayers. J Am Chem Soc 2010; 132:6768-77. [DOI: 10.1021/ja100830f] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chie Yoshiura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Yoko Mase
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Yuya Terashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Kouji Matsushima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
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Koth CMM, Payandeh J. Strategies for the cloning and expression of membrane proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2009; 76:43-86. [PMID: 20663478 DOI: 10.1016/s1876-1623(08)76002-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Despite the determination of thousands of high-resolution structures of soluble proteins, many features of integral membrane proteins render them difficult targets for the structural biologist. Among these, the most important challenge is in expressing sufficient quantities of active protein to support downstream purification and structure determination efforts. Over 190 unique membrane protein structures have now been solved, and noticeable trends in successful expression strategies are beginning to emerge. A number of groups have also explored high-throughput (HTP) methods for membrane protein expression, with varying degrees of success. Here we review the current state of expressing membrane proteins for functional and structural studies. We first survey successful methods that have already yielded levels of membrane protein expression sufficient for structure determination. HTP methods are also examined since these aim to explore large numbers of targets and can predict reasonable starting points for many membrane proteins. Since HTP techniques may fail, particularly for certain classes of eukaryotic targets, detailed strategies for the expression of two prominent classes of eukaryotic protein families, G-protein-coupled receptors and ion channels, are also summarized.
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Affiliation(s)
- Christopher M M Koth
- Department of Structural Biology, Genentech, South San Francisco, California 94080, USA
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Abstract
Abstract
A major challenge in the research on membrane-anchored and integral membrane protein complexes is to obtain these in a functionally active, water-soluble, and monodisperse form. This requires the incorporation of the membrane proteins into a native-like membrane or detergent micelle that mimics the properties of the original biological membrane. However, solubilization in detergents or reconstitution in liposomes or supported monolayers sometimes suffers from loss of activity and problematic analyses due to heterogeneity and aggregation. A developing technology termed nanodiscs exploits discoidal phospholipid bilayers encircled by a stabilizing amphipatic helical membrane scaffold protein to reconstitute membranes with integral proteins. After reconstitution, the membrane nanodisc is soluble, stable, and monodisperse. In the present review, we outline the biological inspiration for nanodiscs as discoidal high-density lipoproteins, the assembly and handling of nanodiscs, and finally their diverse biochemical applications. In our view, major advantages of nanodisc technology for integral membrane proteins is homogeneity, control of oligomerization state, access to both sides of the membrane, and control of lipids in the local membrane environment of the integral protein.
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Katzen F, Peterson TC, Kudlicki W. Membrane protein expression: no cells required. Trends Biotechnol 2009; 27:455-60. [PMID: 19616329 DOI: 10.1016/j.tibtech.2009.05.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 05/02/2009] [Accepted: 05/06/2009] [Indexed: 01/10/2023]
Abstract
Structural and functional studies of membrane proteins have been severely hampered by difficulties in producing sufficient quantities of properly folded protein products. It is well established that cell-based expression of membrane proteins is generally problematic and frequently results in low yield, cell toxicity, protein aggregation and misfolding. Owing to its inherent open nature, cell-free protein expression has become a highly promising tool for the fast and efficient production of these difficult-to-express proteins. Here we review the most recent advances in this field, underscoring the potentials and weaknesses of the newly developed approaches and place specific emphasis on the use of nanolipoprotein particles (NLPs or nanodiscs).
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Affiliation(s)
- Federico Katzen
- Life Technologies, 5791 Van Allen Way, Carlsbad, CA 92008, USA
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