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Schütz A, Bernhard F, Berrow N, Buyel JF, Ferreira-da-Silva F, Haustraete J, van den Heuvel J, Hoffmann JE, de Marco A, Peleg Y, Suppmann S, Unger T, Vanhoucke M, Witt S, Remans K. A concise guide to choosing suitable gene expression systems for recombinant protein production. STAR Protoc 2023; 4:102572. [PMID: 37917580 PMCID: PMC10643540 DOI: 10.1016/j.xpro.2023.102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 11/04/2023] Open
Abstract
This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing a particular protein. By answering four key questions, readers can determine the most suitable gene expression system following a decision scheme. This guide addresses the most commonly used and accessible systems and provides brief descriptions of the main gene expression systems' key characteristics to assist decision making. Additionally, information has been included for selected less frequently used "exotic" gene expression systems.
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Affiliation(s)
- Anja Schütz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform for Protein Production & Characterization, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Goethe-University of Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Nick Berrow
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Johannes F Buyel
- Univeristy of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Muthgasse 18, 1190 Vienna, Austria
| | - Frederico Ferreira-da-Silva
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Jurgen Haustraete
- VIB, Center for Inflammation Research & Ugent, Department of Biomedical Molecular Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Joop van den Heuvel
- Helmholtz Centre for Infection Research (HZI), Department of Structure and Function of Proteins, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sabine Suppmann
- Protein Expression and Purification Core Facility, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tamar Unger
- Structural Proteomics Unit (SPU), Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martine Vanhoucke
- BCCM/GeneCorner Plasmid Collection, Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Gent, Belgium
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Notkestr. 85, 22607 Hamburg, Germany
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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2
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Manzer ZA, Selivanovitch E, Ostwalt AR, Daniel S. Membrane protein synthesis: no cells required. Trends Biochem Sci 2023; 48:642-654. [PMID: 37087310 DOI: 10.1016/j.tibs.2023.03.006] [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: 11/07/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/24/2023]
Abstract
Despite advances in membrane protein (MP) structural biology and a growing interest in their applications, these proteins remain challenging to study. Progress has been hindered by the complex nature of MPs and innovative methods will be required to circumvent technical hurdles. Cell-free protein synthesis (CFPS) is a burgeoning technique for synthesizing MPs directly into a membrane environment using reconstituted components of the cellular transcription and translation machinery in vitro. We provide an overview of CFPS and how this technique can be applied to the synthesis and study of MPs. We highlight numerous strategies including synthesis methods and folding environments, each with advantages and limitations, to provide a survey of how CFPS techniques can advance the study of MPs.
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Affiliation(s)
- Zachary A Manzer
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Ekaterina Selivanovitch
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Alexis R Ostwalt
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
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3
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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4
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Kai L, Sonal, Heermann T, Schwille P. Reconstitution of a Reversible Membrane Switch via Prenylation by One-Pot Cell-Free Expression. ACS Synth Biol 2022; 12:108-119. [PMID: 36445320 PMCID: PMC9872162 DOI: 10.1021/acssynbio.2c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reversible membrane targeting of proteins is one of the key regulators of cellular interaction networks, for example, for signaling and polarization. So-called "membrane switches" are thus highly attractive targets for the design of minimal cells but have so far been tricky to reconstitute in vitro. Here, we introduce cell-free prenylated protein synthesis (CFpPS), which enables the synthesis and membrane targeting of proteins in a single reaction mix including the prenylation machinery. CFpPS can confer membrane affinity to any protein via addition of a 4-peptide motif to its C-terminus and offers robust production of prenylated proteins not only in their soluble forms but also in the direct vicinity of biomimetic membranes. Thus, CFpPS enabled us to reconstitute the prenylated polarity hub Cdc42 and its regulatory protein in vitro, implementing a key membrane switch. We propose CFpPS to be a versatile and effective platform for engineering complex features, such as polarity induction, in synthetic cells.
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Affiliation(s)
- Lei Kai
- Department
of Cellular and Molecular Biophysics, Max
Planck Institute of Biochemistry, D-82152 Martinsried, Germany,School
of Life Sciences, Jiangsu Normal University, Shanghai Road 101, 221116 Xuzhou, P. R. China,. Phone: +86 15852001351
| | - Sonal
- Department
of Cellular and Molecular Biophysics, Max
Planck Institute of Biochemistry, D-82152 Martinsried, Germany,Biosciences
Division, University College London, Gower Street, WC1E 6BT London, U.K.
| | - Tamara Heermann
- Department
of Cellular and Molecular Biophysics, Max
Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Petra Schwille
- Department
of Cellular and Molecular Biophysics, Max
Planck Institute of Biochemistry, D-82152 Martinsried, Germany,. Phone: +49 89 8578 2900
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5
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Mezhyrova J, Mörs K, Glaubitz C, Dötsch V, Bernhard F. Applications of Cell-Free Synthesized Membrane Protein Precipitates. Methods Mol Biol 2022; 2406:245-266. [PMID: 35089562 DOI: 10.1007/978-1-0716-1859-2_15] [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] [Indexed: 06/14/2023]
Abstract
Cell-free protein expression systems are new core platforms for membrane protein synthesis. Expression in the presence of supplied artificial hydrophobic environments such as nanomembranes or micelles allows the co-translational solubilization and folding of membrane proteins. In the absence of hydrophobic compounds, the synthesized membrane proteins quantitatively precipitate, while frequently still retaining a significant part of folded structural elements. This so-called precipitate-forming cell-free (P-CF) expression mode is a very effective and reliable approach for numerous applications. Even from complex membrane proteins such as G-protein coupled receptors or large transporters, significant amounts of such precipitates can be synthesized within few hours. The precipitates can be solubilized in detergents or reconstituted into membranes for subsequent structural or functional analysis. Harsh denaturation and refolding procedures as known from the treatment of bacterial inclusion bodies are usually not required.This strategy is particularly interesting for applications requiring large amounts of membrane protein or fast access to a sample. It is further an excellent tool for the production of membrane protein antigens suitable for antibody generation. The purification of the precipitates in downstream processing is streamlined as only few proteins from the cell-free lysate may co-precipitate with the synthesized membrane protein. For most applications, a one-step affinity chromatography by taking advantage of small purification tags attached to the membrane protein target is sufficient. We give an overview on current applications of P-CF precipitates and describe the underlying techniques in detail. We furthermore provide protocols for the successful crystallization and NMR analysis of P-CF synthesized membrane proteins exemplified with the diacylglycerol kinase (DAGK). In addition, we describe the functional characterization of a P-CF synthesized large eukaryotic transporter.
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Affiliation(s)
- Julija Mezhyrova
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University , Frankfurt/Main, Germany
| | - Karsten Mörs
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University , Frankfurt/Main, Germany
| | - Clemens Glaubitz
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University , Frankfurt/Main, Germany
| | - Volker Dötsch
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University , Frankfurt/Main, Germany
| | - Frank Bernhard
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University , Frankfurt/Main, Germany.
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6
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Harris NJ, Reading E, Booth PJ. Cell-Free Synthesis Strategies to Probe Co-translational Folding of Proteins Within Lipid Membranes. Methods Mol Biol 2022; 2433:273-292. [PMID: 34985751 DOI: 10.1007/978-1-0716-1998-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In order to comprehend the molecular basis of transmembrane protein biogenesis, methods are required that are capable of investigating the co-translational folding of these hydrophobic proteins. Equally, in artificial cell studies, controllable methods are desirable for in situ synthesis of membrane proteins that then direct reactions in the synthetic cell membrane. Here we describe a method that exploits cell-free expression systems and tunable membrane mimetics to facilitate co-translational studies. Alteration of the lipid bilayer composition improves the efficiency of the folding system. The approach also enables membrane transport proteins to be made and inserted into artificial cell platforms such as droplet interface bilayers. Importantly, this gives a new facet to the droplet networks by enabling specific transport of molecules across the synthetic bilayer against a concentration gradient. This method also includes a protocol to pause and restart translation of membrane proteins at specified positions during their co-translational folding. This stop-start strategy provides an avenue to investigate whether the proteins fold in sequence order, or if the correct fold of N-terminal regions is reliant on the synthesis of downstream residues.
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Affiliation(s)
| | - Eamonn Reading
- Department of Chemistry, King's College London, London, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, London, UK.
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7
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Kögler LM, Stichel J, Beck-Sickinger AG. Structural investigations of cell-free expressed G protein-coupled receptors. Biol Chem 2020; 401:97-116. [PMID: 31539345 DOI: 10.1515/hsz-2019-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are of great pharmaceutical interest and about 35% of the commercial drugs target these proteins. Still there is huge potential left in finding molecules that target new GPCRs or that modulate GPCRs differentially. For a rational drug design, it is important to understand the structure, binding and activation of the protein of interest. Structural investigations of GPCRs remain challenging, although huge progress has been made in the last 20 years, especially in the generation of crystal structures of GPCRs. This is mostly caused by issues with the expression yield, purity or labeling. Cell-free protein synthesis (CFPS) is an efficient alternative for recombinant expression systems that can potentially address many of these problems. In this article the use of CFPS for structural investigations of GPCRs is reviewed. We compare different CFPS systems, including the cellular basis and reaction configurations, and strategies for an efficient solubilization. Next, we highlight recent advances in the structural investigation of cell-free expressed GPCRs, with special emphasis on the role of photo-crosslinking approaches to investigate ligand binding sites on GPCRs.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
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8
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Interfaces Between Alpha-helical Integral Membrane Proteins: Characterization, Prediction, and Docking. Comput Struct Biotechnol J 2019; 17:699-711. [PMID: 31303974 PMCID: PMC6603304 DOI: 10.1016/j.csbj.2019.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 11/28/2022] Open
Abstract
Protein-protein interaction (PPI) is an essential mechanism by which proteins perform their biological functions. For globular proteins, the molecular characteristics of such interactions have been well analyzed, and many computational tools are available for predicting PPI sites and constructing structural models of the complex. In contrast, little is known about the molecular features of the interaction between integral membrane proteins (IMPs) and few methods exist for constructing structural models of their complexes. Here, we analyze the interfaces from a non-redundant set of complexes of α-helical IMPs whose structures have been determined to a high resolution. We find that the interface is not significantly different from the rest of the surface in terms of average hydrophobicity. However, the interface is significantly better conserved and, on average, inter-subunit contacting residue pairs correlate more strongly than non-contacting pairs, especially in obligate complexes. We also develop a neural network-based method, with an area under the receiver operating characteristic curve of 0.75 and a Pearson correlation coefficient of 0.70, for predicting interface residues and their weighted contact numbers (WCNs). We further show that predicted interface residues and their WCNs can be used as restraints to reconstruct the structure α-helical IMP dimers through docking for fourteen out of a benchmark set of sixteen complexes. The RMSD100 values of the best-docked ligand subunit to its native structure are <2.5 Å for these fourteen cases. The structural analysis conducted in this work provides molecular details about the interface between α-helical IMPs and the WCN restraints represent an efficient means to score α-helical IMP docking candidates.
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Key Words
- AUC, Area under the ROC curve
- IMP, Integral membrane protein
- MAE, Mean absolute error
- MSA, Multiple sequence alignment
- Membrane protein docking
- Membrane protein interfaces
- Neural networks
- OPM, Orientations of proteins in membranes
- PCC, Pearson correlation coefficient
- PDB, Protein data bank
- PPI, Protein-protein interaction
- PPM, Positioning of proteins in membrane.
- PPV, Positive predictive value
- PSSM, Position-specific scoring matrix
- RMSD, Root-mean-square distance
- ROC, Receiver operating characteristic curve
- RSA, Relative solvent accessibility
- TNR, True negative rate
- TPR, True positive rate
- WCN, Weighted contact number
- Weighted contact numbers
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Peetz O, Hellwig N, Henrich E, Mezhyrova J, Dötsch V, Bernhard F, Morgner N. LILBID and nESI: Different Native Mass Spectrometry Techniques as Tools in Structural Biology. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:181-191. [PMID: 30225732 PMCID: PMC6318263 DOI: 10.1007/s13361-018-2061-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
Native mass spectrometry is applied for the investigation of proteins and protein complexes worldwide. The challenge in native mass spectrometry is maintaining the features of the proteins of interest, such as oligomeric state, bound ligands, or the conformation of the protein complex, during transfer from solution to gas phase. This is an essential prerequisite to allow conclusions about the solution state protein complex, based on the gas phase measurements. Therefore, soft ionization techniques are required. Widely used for the analysis of protein complexes are nanoelectro spray ionization (nESI) mass spectrometers. A newer ionization method is laser induced liquid bead ion desorption (LILBID), which is based on the release of protein complexes from solution phase via infrared (IR) laser desorption. We use both methods in our lab, depending on the requirements of the biological system we are interested in. Here we benchmark the performance of our LILBID mass spectrometer in comparison to a nESI instrument, regarding sample conditions, buffer and additive tolerances, dissociation mechanism and applicability towards soluble and membrane protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Oliver Peetz
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Nils Hellwig
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Julija Mezhyrova
- 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
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany.
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10
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Rues RB, Dong F, Dötsch V, Bernhard F. Systematic optimization of cell-free synthesized human endothelin B receptor folding. Methods 2018; 147:73-83. [DOI: 10.1016/j.ymeth.2018.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 12/16/2022] Open
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11
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Hoffmann B, Löhr F, Laguerre A, Bernhard F, Dötsch V. Protein labeling strategies for liquid-state NMR spectroscopy using cell-free synthesis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 105:1-22. [PMID: 29548364 DOI: 10.1016/j.pnmrs.2017.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 05/17/2023]
Abstract
Preparation of a protein sample for liquid-state nuclear magnetic resonance (NMR) spectroscopy analysis requires optimization of many parameters. This review describes labeling strategies for obtaining assignments of protein resonances. Particular emphasis is placed on the advantages of cell-free protein production, which enables exclusive labeling of the protein of interest, thereby simplifying downstream processing steps and increasing the availability of different labeling strategies for a target protein. Furthermore, proteins can be synthesized in milligram yields, and the open nature of the cell-free system allows the addition of stabilizers, scrambling inhibitors or hydrophobic solubilization environments directly during the protein synthesis, which is especially beneficial for membrane proteins. Selective amino acid labeling of the protein of interest, the possibility of addressing scrambling issues and avoiding the need for labile amino acid precursors have been key factors in enabling the introduction of new assignment strategies based on different labeling schemes as well as on new pulse sequences. Combinatorial selective labeling methods have been developed to reduce the number of protein samples necessary to achieve a complete backbone assignment. Furthermore, selective labeling helps to decrease spectral overlap and overcome size limitations for solution NMR analysis of larger complexes, oligomers, intrinsically disordered proteins and membrane proteins.
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Affiliation(s)
- Beate Hoffmann
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
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12
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Foshag D, Henrich E, Hiller E, Schäfer M, Kerger C, Burger-Kentischer A, Diaz-Moreno I, García-Mauriño SM, Dötsch V, Rupp S, Bernhard F. The E. coli S30 lysate proteome: A prototype for cell-free protein production. N Biotechnol 2017; 40:245-260. [PMID: 28943390 DOI: 10.1016/j.nbt.2017.09.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/28/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Protein production using processed cell lysates is a core technology in synthetic biology and these systems are excellent to produce difficult toxins or membrane proteins. However, the composition of the central lysate of cell-free systems is still a "black box". Escherichia coli lysates are most productive for cell-free expression, yielding several mgs of protein per ml of reaction. Their preparation implies proteome fractionation, resulting in strongly biased and yet unknown lysate compositions. Many metabolic pathways are expected to be truncated or completely removed. The lack of knowledge of basic cell-free lysate proteomes is a major bottleneck for directed lysate engineering approaches as well as for assay design using non-purified reaction mixtures. This study is starting to close this gap by providing a blueprint of the S30 lysate proteome derived from the commonly used E. coli strain A19. S30 lysates are frequently used for cell-free protein production and represent the basis of most commercial E. coli cell-free expression systems. A fraction of 821 proteins was identified as the core proteome in S30 lysates, representing approximately a quarter of the known E. coli proteome. Its classification into functional groups relevant for transcription/translation, folding, stability and metabolic processes will build the framework for tailored cell-free reactions. As an example, we show that SOS response induction during cultivation results in tuned S30 lysate with better folding capacity, and improved solubility and activity of synthesized proteins. The presented data and protocols can serve as a platform for the generation of customized cell-free systems and product analysis.
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Affiliation(s)
- Daniel Foshag
- Institute for Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Stuttgart, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Ekkehard Hiller
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Miriam Schäfer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Christian Kerger
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | | | - Irene Diaz-Moreno
- Instituto de Investigaciones Químicas (IIQ) - Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ) - Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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13
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The cubicon method for concentrating membrane proteins in the cubic mesophase. Nat Protoc 2017; 12:1745-1762. [DOI: 10.1038/nprot.2017.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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From Gene to Function: Cell-Free Electrophysiological and Optical Analysis of Ion Pumps in Nanodiscs. Biophys J 2017; 113:1331-1341. [PMID: 28450130 DOI: 10.1016/j.bpj.2017.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022] Open
Abstract
Nanodiscs that hold a lipid bilayer surrounded by a boundary of scaffold proteins have emerged as a powerful tool for membrane protein solubilization and analysis. By combining nanodiscs and cell-free expression technologies, even completely detergent-free membrane protein characterization protocols can be designed. Nanodiscs are compatible with various techniques, and due to their bilayer environment and increased stability, they are often superior to detergent micelles or liposomes for membrane protein solubilization. However, transport assays in nanodiscs have not been conducted so far, due to limitations of the two-dimensional nature of nanodisc membranes that offers no compartmentalization. Here, we study Krokinobacter eikastus rhodopsin-2 (KR2), a microbial light-driven sodium or proton pump, with noncovalent mass-spectrometric, electrophysiological, and flash photolysis measurements after its cotranslational insertion into nanodiscs. We demonstrate the feasibility of adsorbing nanodiscs containing KR2 to an artificial bilayer. This allows us to record light-induced capacitive currents that reflect KR2's ion transport activity. The solid-supported membrane assay with nanodisc samples provides reliable control over the ionic condition and information of the relative ion activity of this promiscuous pump. Our strategy is complemented with flash photolysis data, where the lifetimes of different photointermediates were determined at different ionic conditions. The advantage of using identical samples to three complementary approaches allows for a comprehensive comparability. The cell-free synthesis in combination with nanodiscs provides a defined hydrophobic lipid environment minimizing the detergent dependence often seen in assays with membrane proteins. KR2 is a promising tool for optogenetics, thus directed engineering to modify ion selectivity can be highly beneficial. Our approach, using the fast generation of functional ion pumps incorporated into nanodiscs and their subsequent analysis by several biophysical techniques, can serve as a versatile screening and engineering platform. This may open new avenues for the study of ion pumps and similar electrogenic targets.
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Shinoda T, Shinya N, Ito K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Hirata K, Kawano Y, Yamamoto M, Tomita T, Ishibashi Y, Hirabayashi Y, Kimura-Someya T, Shirouzu M, Yokoyama S. Cell-free methods to produce structurally intact mammalian membrane proteins. Sci Rep 2016; 6:30442. [PMID: 27465719 PMCID: PMC4964339 DOI: 10.1038/srep30442] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/04/2016] [Indexed: 01/19/2023] Open
Abstract
The crystal structures of four membrane proteins, from bacteria or a unicellular alga, have been solved with samples produced by cell-free protein synthesis. In this study, for mammalian membrane protein production, we established the precipitating and soluble membrane fragment methods: membrane proteins are synthesized with the Escherichia coli cell-free system in the presence of large and small membrane fragments, respectively, and are simultaneously integrated into the lipid environments. We applied the precipitating membrane fragment method to produce various mammalian membrane proteins, including human claudins, glucosylceramide synthase, and the γ-secretase subunits. These proteins were produced at levels of about 0.1–1.0 mg per ml cell-free reaction under the initial conditions, and were obtained as precipitates by ultracentrifugation. Larger amounts of membrane proteins were produced by the soluble membrane fragment method, collected in the ultracentrifugation supernatants, and purified directly by column chromatography. For several proteins, the conditions of the membrane fragment methods were further optimized, such as by the addition of specific lipids/detergents. The functional and structural integrities of the purified proteins were confirmed by analyses of their ligand binding activities, size-exclusion chromatography profiles, and/or thermal stabilities. We successfully obtained high-quality crystals of the complex of human claudin-4 with an enterotoxin.
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Affiliation(s)
- Takehiro Shinoda
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Naoko Shinya
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Kaori Ito
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Yoshiko Ishizuka-Katsura
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Noboru Ohsawa
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Takaho Terada
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama 230-0045, Japan
| | - Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yohei Ishibashi
- Laboratory for Molecular Membrane Neuroscience, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Yoshio Hirabayashi
- Laboratory for Molecular Membrane Neuroscience, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Tomomi Kimura-Someya
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama 230-0045, Japan
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16
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Holm-Bertelsen J, Bock S, Helmstetter F, Beitz E. High-level cell-free production of the malarial lactate transporter PfFNT as a basis for crystallization trials and directional transport studies. Protein Expr Purif 2016; 126:109-114. [PMID: 27345711 DOI: 10.1016/j.pep.2016.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 01/10/2023]
Abstract
The malaria parasite Plasmodium falciparum relies on the function of channel and transport proteins for the uptake of nutrients and the release of metabolic waste products. Inhibition of vital transport processes is an unexploited means for developing novel antimalarial drugs. The recently discovered plasmodial lactate transporter, PfFNT, represents a promising new drug target since the parasite's energy generation by anaerobic glycolysis depends on the rapid secretion of lactate. Yet, membrane proteins, in particular those of malaria parasites, are notoriously difficult to produce and purify in the native, functional form hampering crystallization and biophysical studies. Here, we show synthesis of milligram quantities of correctly folded PfFNT in a cell-free system. Solubilized PfFNT maintained its oligomeric, largely SDS-resistant quaternary structure and appears suitable for setting up crystallization trials. After reconstitution into proteoliposomes, PfFNT was functional as a transporter for formate, acetate, and lactate as determined by a light-scattering assay. Analysis of the accessibility of a protease cleavage site at the N-terminus revealed an even outside-in orientation of the total proteoliposomal PfFNT population that may be due to membrane curvature restrictions. Contrary to previous studies using heterologous expression in cell systems with oppositely oriented PfFNT, the proteoliposomes eventually allow for biophysical transport studies in the native, physiological direction.
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Affiliation(s)
- Julia Holm-Bertelsen
- Christian-Albrechts-University of Kiel, Department of Medicinal and Pharmaceutical Chemistry, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Sinja Bock
- Christian-Albrechts-University of Kiel, Department of Medicinal and Pharmaceutical Chemistry, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Folknand Helmstetter
- Christian-Albrechts-University of Kiel, Department of Medicinal and Pharmaceutical Chemistry, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Eric Beitz
- Christian-Albrechts-University of Kiel, Department of Medicinal and Pharmaceutical Chemistry, Gutenbergstraße 76, 24118 Kiel, Germany.
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17
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Cell-Free Synthesis of Macromolecular Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27165320 DOI: 10.1007/978-3-319-27216-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Cell-free protein synthesis based on E. coli cell extracts has been described for the first time more than 50 years ago. To date, cell-free synthesis is widely used for the preparation of toxic proteins, for studies of the translation process and its regulation as well as for the incorporation of artificial or labeled amino acids into a polypeptide chain. Many efforts have been directed towards establishing cell-free expression as a standard method for gene expression, with limited success. In this chapter we will describe the state-of-the-art of cell-free expression, extract preparation methods and recent examples for successful applications of cell-free synthesis of macromolecular complexes.
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18
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Vogeley L, El Arnaout T, Bailey J, Stansfeld PJ, Boland C, Caffrey M. Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin. Science 2016; 351:876-80. [PMID: 26912896 DOI: 10.1126/science.aad3747] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
With functions that range from cell envelope structure to signal transduction and transport, lipoproteins constitute 2 to 3% of bacterial genomes and play critical roles in bacterial physiology, pathogenicity, and antibiotic resistance. Lipoproteins are synthesized with a signal peptide securing them to the cytoplasmic membrane with the lipoprotein domain in the periplasm or outside the cell. Posttranslational processing requires a signal peptidase II (LspA) that removes the signal peptide. Here, we report the crystal structure of LspA from Pseudomonas aeruginosa complexed with the antimicrobial globomycin at 2.8 angstrom resolution. Mutagenesis studies identify LspA as an aspartyl peptidase. In an example of molecular mimicry, globomycin appears to inhibit by acting as a noncleavable peptide that sterically blocks the active site. This structure should inform rational antibiotic drug discovery.
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Affiliation(s)
- Lutz Vogeley
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Toufic El Arnaout
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Jonathan Bailey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Coilin Boland
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
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19
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Rues RB, Dötsch V, Bernhard F. Co-translational formation and pharmacological characterization of beta1-adrenergic receptor/nanodisc complexes with different lipid environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1306-16. [PMID: 26922884 DOI: 10.1016/j.bbamem.2016.02.031] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/17/2016] [Accepted: 02/24/2016] [Indexed: 12/24/2022]
Abstract
G protein-coupled receptors are of key significance for biomedical research. Streamlined approaches for their efficient recombinant production are of pivotal interest in order to explore their intrinsic conformational dynamics and complex ligand binding behavior. We have systematically optimized the co-translational association and folding of G protein-coupled receptors with defined membranes of nanodiscs by cell-free expression approaches. Each optimization step was quantified and the ligand binding active fraction of the receptor samples could drastically be improved. The strategy was exemplified with a stabilized and a non-stabilized derivative of the turkey beta1-adrenergic receptor. Systematic lipid screens with preformed nanodiscs revealed that generation of ligand binding active conformations of the analyzed beta1-adrenergic receptors strongly depends on lipid charge, flexibility and chain length. The lipid composition of the nanodisc membranes modulates the affinities to a variety of ligands of both receptor derivatives. In addition, the thermostabilization procedure had a significant impact on specific ligand affinities of the receptor and abolished or reduced the binding of certain antagonists. Both receptors were highly stable after purification with optimized nanodisc membranes. The procedure avoids any detergent contact of the receptors and sample production takes less than two days. Moreover, even non-stabilized receptors can be analyzed and their prior purification is not necessary for the formation of nanodisc complexes. The established process appears therefore to be suitable as a new platform for the functional or even structural characterization of recombinant G protein-coupled receptors associated with defined lipid environments.
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Affiliation(s)
- Ralf-Bernhardt Rues
- 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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20
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Rues RB, Henrich E, Boland C, Caffrey M, Bernhard F. Cell-Free Production of Membrane Proteins in Escherichia coli Lysates for Functional and Structural Studies. Methods Mol Biol 2016; 1432:1-21. [PMID: 27485326 DOI: 10.1007/978-1-4939-3637-3_1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The complexity of membrane protein synthesis is largely reduced in cell-free systems and it results into high success rates of target expression. Protocols for the preparation of bacterial lysates have been optimized in order to ensure reliable efficiencies in membrane protein production that are even sufficient for structural applications. The open accessibility of the semisynthetic cell-free expression reactions allows to adjust membrane protein solubilization conditions according to the optimal folding requirements of individual targets. Two basic strategies will be exemplified. The post-translational solubilization of membrane proteins in detergent micelles is most straightforward for crystallization approaches. The co-translational integration of membrane proteins into preformed nanodiscs will enable their functional characterization in a variety of natural lipid environments.
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Affiliation(s)
- Ralf-Bernhardt Rues
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Erik Henrich
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Coilin Boland
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Frank Bernhard
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany.
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21
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Ternary structure reveals mechanism of a membrane diacylglycerol kinase. Nat Commun 2015; 6:10140. [PMID: 26673816 PMCID: PMC4703834 DOI: 10.1038/ncomms10140] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 11/09/2015] [Indexed: 11/24/2022] Open
Abstract
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution. Diacylglycerol kinase is a small bacterial membrane-bound trimer that catalyses diacylglycerol conversion to phosphatidic acid. Here, the authors solve the crystal structure of the kinase bound to a lipid substrate and an ATP analogue, and show that the active site arose through convergent evolution.
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22
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23
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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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24
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LaGuerre A, Löhr F, Bernhard F, Dötsch V. Labeling of membrane proteins by cell-free expression. Methods Enzymol 2015; 565:367-88. [PMID: 26577739 DOI: 10.1016/bs.mie.2015.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The particular advantage of the cell-free reaction is that it allows a plethora of supplementation during protein expression and offers complete control over the available amino acid pool in view of concentration and composition. In combination with the fast and reliable production efficiencies of cell-free systems, the labeling and subsequent structural evaluation of very challenging targets, such as membrane proteins, comes into focus. We describe current methods for the isotopic labeling of cell-free synthesized membrane proteins and we review techniques available to the practitioner pursuing structural studies by nuclear magnetic resonance spectroscopy. Though isotopic labeling of individual amino acid types appears to be relatively straightforward, an ongoing critical issue in most labeling schemes for structural approaches is the selective substitution of deuterons for protons. While few options are available, the continuous refinement of labeling schemes in combination with improved pulse sequences and optimized instrumentation gives promising perspectives for extended applications in the structural evaluation of cell-free synthesized membrane.
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Affiliation(s)
- Aisha LaGuerre
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany.
| | - Frank Löhr
- 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
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
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25
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Henrich E, Hein C, Dötsch V, Bernhard F. Membrane protein production in Escherichia coli cell-free lysates. FEBS Lett 2015; 589:1713-22. [PMID: 25937121 DOI: 10.1016/j.febslet.2015.04.045] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/01/2023]
Abstract
Cell-free protein production has become a core technology in the rapidly spreading field of synthetic biology. In particular the synthesis of membrane proteins, highly problematic proteins in conventional cellular production systems, is an ideal application for cell-free expression. A large variety of artificial as well as natural environments for the optimal co-translational folding and stabilization of membrane proteins can rationally be designed. The high success rate of cell-free membrane protein production allows to focus on individually selected targets and to modulate their functional and structural properties with appropriate supplements. The efficiency and robustness of lysates from Escherichia coli strains allow a wide diversity of applications and we summarize current strategies for the successful production of high quality membrane protein samples.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Christopher Hein
- 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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26
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Henrich E, Dötsch V, Bernhard F. Screening for Lipid Requirements of Membrane Proteins by Combining Cell-Free Expression with Nanodiscs. Methods Enzymol 2015; 556:351-69. [DOI: 10.1016/bs.mie.2014.12.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Caffrey M. A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:3-18. [PMID: 25615961 PMCID: PMC4304740 DOI: 10.1107/s2053230x14026843] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/05/2014] [Indexed: 01/12/2023]
Abstract
A comprehensive and up-to-date review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes is reported. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach to crystallization. The possible involvement of the lamellar and inverted hexagonal phases in crystallogenesis and the application of the method to water-soluble, monotopic and lipid-anchored proteins are addressed. How to set up trials manually and automatically with a robot is introduced with reference to open-access online videos that provide a practical guide to all aspects of the method. These range from protein reconstitution to crystal harvesting from the hosting mesophase, which is noted for its viscosity and stickiness. The sponge phase, as an alternative medium in which to perform crystallization, is described. The compatibility of the method with additive lipids, detergents, precipitant-screen components and materials carried along with the protein such as denaturants and reducing agents is considered. The powerful host and additive lipid-screening strategies are described along with how samples that have low protein concentration and cell-free expressed protein can be used. Assaying the protein reconstituted in the bilayer of the cubic phase for function is an important element of quality control and is detailed. Host lipid design for crystallization at low temperatures and for large proteins and complexes is outlined. Experimental phasing by heavy-atom derivatization, soaking or co-crystallization is routine and the approaches that have been implemented to date are described. An overview and a breakdown by family and function of the close to 200 published structures that have been obtained using in meso-grown crystals are given. Recommendations for conducting the screening process to give a more productive outcome are summarized. The fact that the in meso method also works with soluble proteins should not be overlooked. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The review ends with a view to the future and to the bright prospects for the method, which continues to contribute to our understanding of the molecular mechanisms of some of nature’s most valued proteinaceous robots.
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Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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