1
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Facchetti D, Dang Y, Seif-Eddine M, Geoghegan BL, Roessler MM. Film-electrochemical EPR spectroscopy to investigate electron transfer in membrane proteins in their native environment. Chem Commun (Camb) 2024. [PMID: 39348210 DOI: 10.1039/d4cc04013a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
Abstract
Film-electrochemical electron paramagnetic resonance spectroscopy (FE-EPR) enables simultaneous electrochemical and spectroscopic characterisation of paramagnetic electron-transfer centres, including in soluble proteins. We now report a modified set-up FE-EPR with tuneable macroporous working electrodes and demonstrate the feasibility to investigate electron transfer in membrane proteins in their native membrane environment.
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Affiliation(s)
- Davide Facchetti
- Department of Chemistry and Centre for Pulse EPR Spectroscopy (PEPR), Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Yunfei Dang
- Department of Chemistry and Centre for Pulse EPR Spectroscopy (PEPR), Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Maryam Seif-Eddine
- Department of Chemistry and Centre for Pulse EPR Spectroscopy (PEPR), Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
- CNRS: Marseille, Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13009, Marseille, France.
| | - Blaise L Geoghegan
- Department of Chemistry and Centre for Pulse EPR Spectroscopy (PEPR), Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Maxie M Roessler
- Department of Chemistry and Centre for Pulse EPR Spectroscopy (PEPR), Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
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2
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Hotiana HA, Nordlin KP, Gotfryd K, Pedersen PA, Gourdon P. Isolation of Functional Human MCT Transporters in Saccharomyces cerevisiae. Cells 2024; 13:1585. [PMID: 39329766 PMCID: PMC11430032 DOI: 10.3390/cells13181585] [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] [Received: 08/14/2024] [Revised: 09/05/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
Human monocarboxylate transporters (hMCTs) belong to the solute carrier 16 (SLC16) family of proteins and are responsible for the bi-directional transport of various metabolites, including monocarboxylates, hormones, and aromatic amino acids. Hence, the metabolic role of hMCTs is undisputable, as they are directly involved in providing nutrients for oxidation and gluconeogenesis as well as participate in circulation of iodothyronines. However, due to the difficulty in obtaining suitable amounts of stable hMCT samples, the structural information available for these transporters is limited, hindering the development of effective therapeutics. Here we provide a straightforward, cost-effective strategy for the overproduction of hMCTs using a whole-cell Saccharomyces cerevisiae-based system. Our results indicate that this platform is able to provide three hMCTs, i.e., hMCT1 and hMCT4 (monocarboxylate transporters), and hMCT10 (an aromatic amino acid transporter). hMCT1 and hMCT10 are recovered in the quantity and quality required for downstream structural and functional characterization. Overall, our findings demonstrate the suitability of this platform to deliver physiologically relevant membrane proteins for biophysical studies.
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Affiliation(s)
- Hajira Ahmed Hotiana
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK-2200 Copenhagen N, Denmark
| | - Karl Patric Nordlin
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK-2200 Copenhagen N, Denmark
| | - Kamil Gotfryd
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK-2200 Copenhagen N, Denmark
| | - Per Amstrup Pedersen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen OE, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK-2200 Copenhagen N, Denmark
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, Sölvegatan 19, SE-221 84 Lund, Sweden
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3
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Zhu Q, Wang S, Fu G, Guo F, Huang W, Zhang T, Dong H, Jin Z, Zhang D. Highly flexible cell membranes are the key to efficient production of lipophilic compounds. J Lipid Res 2024; 65:100597. [PMID: 39029799 PMCID: PMC11367113 DOI: 10.1016/j.jlr.2024.100597] [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: 03/30/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
Lipophilic compounds have a variety of positive effects on human physiological functions and exhibit good effects in the prevention and treatment of clinical diseases. This has led to significant interest in the technical applications of synthetic biology for the production of lipophilic compounds. However, the strict selective permeability of the cell membrane and the hydrophobic nature of lipophilic compounds pose significant challenges to their production. During fermentation, lipophilic compounds tend to accumulate within cell membrane compartments rather than being secreted extracellularly. The toxic effects of excessive lipophilic compound accumulation can threaten cell viability, while the limited space within the cell membrane restricts further increases in production yield. Consequently, to achieve efficient production of lipophilic compounds, research is increasingly focused on constructing robust and multifunctional microbial cell factories. Utilizing membrane engineering techniques to construct highly flexible cell membranes is considered an effective strategy to break through the upper limit of lipophilic compound production. Currently, there are two main approaches to cell membrane modification: constructing artificial storage compartments for lipophilic compounds and engineering the cell membrane structure to facilitate product outflow. This review summarizes recent cell membrane engineering strategies applied in microbial cell factories for the production of liposoluble compounds, discussing the challenges and future prospects. These strategies enhance membrane flexibility and effectively promote the production of liposoluble compounds.
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Affiliation(s)
- Qiyao Zhu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Sijia Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Fengming Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Wei Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tengyue Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zhaoxia Jin
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
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4
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Li P, Mei C, Raza SHA, Cheng G, Ning Y, Zhang L, Zan L. Arginine (315) is required for the PLIN2-CGI-58 interface and plays a functional role in regulating nascent LDs formation in bovine adipocytes. Genomics 2024; 116:110817. [PMID: 38431031 DOI: 10.1016/j.ygeno.2024.110817] [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: 11/06/2023] [Revised: 02/02/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Perilipin-2 (PLIN2) can anchor to lipid droplets (LDs) and play a crucial role in regulating nascent LDs formation. Bimolecular fluorescence complementation (BiFC) and flow cytometry were examined to verify the PLIN2-CGI-58 interaction efficiency in bovine adipocytes. GST-Pulldown assay was used to detect the key site arginine315 function in PLIN2-CGI-58 interaction. Experiments were also examined to research these mutations function of PLIN2 in LDs formation during adipocytes differentiation, LDs were measured after staining by BODIPY, lipogenesis-related genes were also detected. Results showed that Leucine (L371A, L311A) and glycine (G369A, G376A) mutations reduced interaction efficiencies. Serine (S367A) mutations enhanced the interaction efficiency. Arginine (R315A) mutations resulted in loss of fluorescence in the cytoplasm and disrupted the interaction with CGI-58, as verified by pulldown assay. R315W mutations resulted in a significant increase in the number of LDs compared with wild-type (WT) PLIN2 or the R315A mutations. Lipogenesis-related genes were either up- or downregulated when mutated PLIN2 interacted with CGI-58. Arginine315 in PLIN2 is required for the PLIN2-CGI-58 interface and could regulate nascent LD formation and lipogenesis. This study is the first to study amino acids on the PLIN2 interface during interaction with CGI-58 in bovine and highlight the role played by PLIN2 in the regulation of bovine adipocyte lipogenesis.
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Affiliation(s)
- Peiwei Li
- Shaanxi Institute of Zoology, Xi'an, Shaanxi, 710032, China
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Sayed Haidar Abbas Raza
- Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China; College of Animal Science &Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gong Cheng
- College of Animal Science &Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yue Ning
- College of Animal Science &Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Le Zhang
- School of Physical Education, Yan'an University, Yan'an, Shaanxi, 716000, China
| | - Linsen Zan
- College of Animal Science &Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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5
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Vasilopoulos G, Heflik L, Czolkoss S, Heinrichs F, Kleetz J, Yesilyurt C, Tischler D, Westhoff P, Exterkate M, Aktas M, Narberhaus F. Characterization of multiple lysophosphatidic acid acyltransferases in the plant pathogen Xanthomonas campestris. FEBS J 2024; 291:705-721. [PMID: 37943159 DOI: 10.1111/febs.16996] [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] [Received: 02/20/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023]
Abstract
Phosphatidic acid (PA) is the precursor of most phospholipids like phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin. In bacteria, its biosynthesis begins with the acylation of glycerol-3-phosphate to lysophosphatidic acid (LPA), which is further acylated to PA by the PlsC enzyme. Some bacteria, like the plant pathogen Xanthomonas campestris, use a similar pathway to acylate lysophosphatidylcholine to phosphatidylcholine (PC). Previous studies assigned two acyltransferases to PC formation. Here, we set out to study their activity and found a second much more prominent function of these enzymes in LPA to PA conversion. This PlsC-like activity was supported by the functional complementation of a temperature-sensitive plsC-deficient Escherichia coli strain. Biocomputational analysis revealed two further PlsC homologs in X. campestris. The cellular levels of the four PlsC-like proteins varied with respect to growth phase and growth temperature. To address the question whether these enzymes have redundant or specific functions, we purified two recombinant, detergent-solubilized enzymes in their active form, which enabled the first direct biochemical comparison of PlsC isoenzymes from the same organism. Overlapping but not identical acyl acceptor and acyl donor preferences suggest redundant and specialized functions of the X. campestris PlsC enzymes. The altered fatty acid composition in plsC mutant strains further supports the functional differentiation of these enzymes.
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Affiliation(s)
- Georgios Vasilopoulos
- Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Germany
| | - Lukas Heflik
- Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Germany
| | - Simon Czolkoss
- Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Germany
| | - Florian Heinrichs
- Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Germany
| | - Julia Kleetz
- Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Germany
| | - Cansel Yesilyurt
- Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Germany
| | - Dirk Tischler
- Faculty of Biology and Biotechnology, Microbial Biotechnology, Ruhr University Bochum, Germany
| | - Philipp Westhoff
- Metabolomics and Metabolism Laboratory, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Germany
| | - Marten Exterkate
- Faculty of Mathematics and Natural Sciences, Membrane Biogenesis and Lipidomics, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Meriyem Aktas
- Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Germany
| | - Franz Narberhaus
- Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Germany
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6
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Saad A, Bechinger B. Solid-state NMR spectroscopy for structural studies of polypeptides and lipids in extended physiological membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184162. [PMID: 37949788 DOI: 10.1016/j.bbamem.2023.184162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 11/12/2023]
Abstract
Solid-state NMR is a quickly developing technique that allows one to obtain structural information at atomic resolution in extended lipid bilayers in a rather unique manner. Two approaches have been developed for membrane proteins and peptides namely magic angle sample spinning and the use of uniaxially oriented membrane samples. The state-of-the-art of both approaches will be introduced and the perspectives of solid-state NMR spectroscopy in the context of other structural biology techniques, pressing biomedical questions and membrane biophysics will be discussed.
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Affiliation(s)
- Ahmad Saad
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France; Institut Universitaire de France, 75005 Paris, France.
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7
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Knauer JF, Schulz C, Zemella A, Wüstenhagen DA, Walter RM, Küpper JH, Kubick S. Synthesis of mono Cytochrome P450 in a modified CHO-CPR cell-free protein production platform. Sci Rep 2024; 14:1271. [PMID: 38218994 PMCID: PMC10787779 DOI: 10.1038/s41598-024-51781-6] [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] [Received: 05/05/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
Cytochromes P450 (CYPs) are a group of monooxygenases that can be found in almost all kinds of organisms. For CYPs to receive electrons from co-substrate NADPH, the activity of NADPH-Cytochrome-P450-oxidoreductase (CPR) is required as well. In humans, CYPs are an integral part of liver-based phase-1 biotransformation, which is essential for the metabolization of multiple xenobiotics and drugs. Consequently, CYPs are important players during drug development and therefore these enzymes are implemented in diverse screening applications. For these applications it is usually advantageous to use mono CYP microsomes containing only the CYP of interest. The generation of mono-CYP containing mammalian cells and vesicles is difficult since endogenous CYPs are present in many cell types that contain the necessary co-factors. By obtaining translationally active lysates from a modified CHO-CPR cell line, it is now possible to generate mono CYPs in a cell-free protein synthesis process in a straightforward manner. As a proof of principle, the synthesis of active human CYPs from three different CYP450 gene families (CYP1A2, CYP2B6 and CYP3A4), which are of outstanding interest in industry and academia was demonstrated. Luciferase based activity assays confirm the activity of the produced CYPs and enable the individual adaptation of the synthesis process for efficient cell-free enzyme production. Furthermore, they allow for substrate and inhibitor screenings not only for wild-type CYPs but also for mutants and further CYP isoforms and variants. As an example, the turnover of selected CYP substrates by cell-free synthesized CYPs was demonstrated via an indirect luciferase assay-based screening setup.
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Affiliation(s)
- Jan Felix Knauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Berlin, Germany
| | - Christian Schulz
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Ruben Magnus Walter
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Jan-Heiner Küpper
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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8
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Shah A, Cui W, Harrahy J, Ivanov AR. Characterization of charge variants, including post-translational modifications and proteoforms, of bispecific antigen-binding protein by cation-exchange chromatography coupled to native mass spectrometry. Talanta 2024; 266:125062. [PMID: 37566926 PMCID: PMC10528315 DOI: 10.1016/j.talanta.2023.125062] [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] [Received: 05/09/2023] [Revised: 07/29/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Charge variant characterization of biologics is critical to ensure that product meets the required quality and regulatory requirements to ensure safety and efficacy of the biotherapeutic. Charge variants arise from post-translation modifications (PTMs) during upstream processing and due to enzymatic and non-enzymatic chemical reactions that occur during downstream processing and storage. Some of these modifications may impact therapeutic potency, efficacy, or immunogenicity of a biotherapeutic. The traditional workflow for characterizing charge variants that involves fraction enrichment is time-consuming and labor-intensive. This approach can be especially challenging if the product is manufactured at low concentrations (e.g., ≤2 mg/mL). Recent advances in pH-based elution for ion-exchange chromatography utilizing volatile buffers have enabled rapid native mass-spectrometry-based identification of PTMs and proteoforms associated with protein therapeutics. In this study, we develop a novel workflow to rapidly and unambiguously characterize modifications associated with a new class of biotherapeutics known as bispecific antigen-binding protein (BsABP), including low-level modifications. A cation-exchange separation was optimized using volatile buffers to provide online hyphenation for native mass spectrometry to profile modifications and proteoforms present at the native level of a biotherapeutic, such as deamidation, O-glycosylation, amino acid substitution, N-linked glycosylation and oxidation. Furthermore, a limited proteolysis method was developed to specifically inform about modifications in the different domains of the bispecific antibody. Using this approach, we could efficiently identify PTMs in unstressed, thermally and photo-stressed samples, and provide information about the impact of downstream purification in clearing out modified BsABP species. Furthermore, peptide mapping was performed to identify and confirm modifications at the amino acid residue level. The developed workflow is less time-consumable and reduces sample processing- and analysis-related artifacts compared to traditional approaches.
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Affiliation(s)
- Arnik Shah
- Amgen Inc, 360 Binney Street, Cambridge, MA, 02141, United States; Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, United States
| | - Weidong Cui
- Amgen Inc, 360 Binney Street, Cambridge, MA, 02141, United States
| | - John Harrahy
- Sanofi, 225 Second Avenue, Waltham, MA 02451, United States
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, United States.
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9
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Gao Y, Zhang X, Xu G, Zhang X, Li H, Shi J, Xu Z. Enhanced L-serine production by Corynebacterium glutamicum based on novel insights into L-serine exporters. Biotechnol J 2024; 19:e2300136. [PMID: 37971189 DOI: 10.1002/biot.202300136] [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] [Received: 03/25/2023] [Revised: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
The L-serine exporters ThrE and SerE play important roles in L-serine production by Corynebacterium glutamicum. Deletion of both thrE and serE decreased L-serine titer by 60%, suggesting the existence of other L-serine exporters. A comparative transcriptomics identified NCgl0254 and NCgl0255 as novel L-serine exporters. Further analysis of the contributions of ThrE, SerE, NCgl0254, and NCgl0255 found that SerE was the major L-serine exporter in C. glutamicum and these four L-serine exporters were responsible for 79.7% of L-serine export. Deletion of one L-serine exporter upregulated the transcription levels of the other three, which might be coursed by increased intracellular concentrations of L-serine. Overexpression of NCgl0254 and NCgl0255 increased L-serine titer by 20.8% in C. glutamicum A36, while overexpression of the four L-serine exporters increased L-serine production by 31.9% (41.1 g·L-1 ) in C. glutamicum A36. The identification of novel L-serine exporters in C. glutamicum will help to improve industrial production of L-serine.
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Affiliation(s)
- Yujie Gao
- Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Xiaomei Zhang
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, China
| | - Guoqiang Xu
- Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Xiaojuan Zhang
- Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Hui Li
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, China
| | - Jinsong Shi
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, China
| | - Zhenghong Xu
- Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
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10
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Zhang J, Kriebel CN, Wan Z, Shi M, Glaubitz C, He X. Automated Fragmentation Quantum Mechanical Calculation of 15N and 13C Chemical Shifts in a Membrane Protein. J Chem Theory Comput 2023; 19:7405-7422. [PMID: 37788419 DOI: 10.1021/acs.jctc.3c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
In this work, we developed an accurate and cost-effective automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method to calculate the chemical shifts of 15N and 13C of membrane proteins. The convergence of the AF-QM/MM method was tested using Krokinobacter eikastus rhodopsin 2 as a test case. When the distance threshold of the QM region is equal to or larger than 4.0 Å, the results of the AF-QM/MM calculations are close to convergence. In addition, the effects of selected density functionals, basis sets, and local chemical environment of target atoms on the chemical shift calculations were systematically investigated. Our results demonstrate that the predicted chemical shifts are more accurate when important environmental factors including cross-protomer interactions, lipid molecules, and solvent molecules are taken into consideration, especially for the 15N chemical shift prediction. Furthermore, with the presence of sodium ions in the environment, the chemical shift of residues, retinal, and retinal Schiff base are affected, which is consistent with the results of the solid-state nuclear magnetic resonance (NMR) experiment. Upon comparing the performance of various density functionals (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB95, and OPBE), the results show that mPW1PW91 is a suitable functional for the 15N and 13C chemical shift prediction of the membrane proteins. Meanwhile, we find that the improved accuracy of the 13Cβ chemical shift calculations can be achieved by the employment of the triple-ζ basis set. However, the employment of the triple-ζ basis set does not improve the accuracy of the 15N and 13Cα chemical shift calculations nor does the addition of a diffuse function improve the overall prediction accuracy of the chemical shifts. Our study also underscores that the AF-QM/MM method has significant advantages in predicting the chemical shifts of key ligands and nonstandard residues in membrane proteins than most widely used empirical models; therefore, it could be an accurate computational tool for chemical shift calculations on various types of biological systems.
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Affiliation(s)
- Jinhuan Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clara Nassrin Kriebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
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11
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Goncharuk MV, Vasileva EV, Ananiev EA, Gorokhovatsky AY, Bocharov EV, Mineev KS, Goncharuk SA. Facade-Based Bicelles as a New Tool for Production of Active Membrane Proteins in a Cell-Free System. Int J Mol Sci 2023; 24:14864. [PMID: 37834312 PMCID: PMC10573531 DOI: 10.3390/ijms241914864] [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] [Received: 08/26/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Integral membrane proteins are important components of a cell. Their structural and functional studies require production of milligram amounts of proteins, which nowadays is not a routine process. Cell-free protein synthesis is a prospective approach to resolve this task. However, there are few known membrane mimetics that can be used to synthesize active membrane proteins in high amounts. Here, we present the application of commercially available "Facade" detergents for the production of active rhodopsin. We show that the yield of active protein in lipid bicelles containing Facade-EM, Facade-TEM, and Facade-EPC is several times higher than in the case of conventional bicelles with CHAPS and DHPC and is comparable to the yield in the presence of lipid-protein nanodiscs. Moreover, the effects of the lipid-to-detergent ratio, concentration of detergent in the feeding mixture, and lipid composition of the bicelles on the total, soluble, and active protein yields are discussed. We show that Facade-based bicelles represent a prospective membrane mimetic, available for the production of membrane proteins in a cell-free system.
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Affiliation(s)
- Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Ekaterina V. Vasileva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Egor A. Ananiev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Andrey Y. Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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12
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Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
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Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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13
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Vénien-Bryan C, Fernandes CAH. Overview of Membrane Protein Sample Preparation for Single-Particle Cryo-Electron Microscopy Analysis. Int J Mol Sci 2023; 24:14785. [PMID: 37834233 PMCID: PMC10573263 DOI: 10.3390/ijms241914785] [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] [Received: 08/12/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB) has been observed. However, sample preparation remains a significant challenge in the field. Here, we evaluated the MPs solved using cryo-EM SPA deposited in the PDB in the last two years at a resolution below 3.0 Å. The most critical parameters for sample preparation are as follows: (i) the surfactant used for protein extraction from the membrane, (ii) the surfactant, amphiphiles, nanodiscs or other molecules present in the vitrification step, (iii) the vitrification method employed, and (iv) the type of grids used. The aim is not to provide a definitive answer on the optimal sample conditions for cryo-EM SPA of MPs but rather assess the current trends in the MP structural biology community towards obtaining high-resolution cryo-EM structures.
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Affiliation(s)
| | - Carlos A. H. Fernandes
- Unité Mixte de Recherche (UMR) 7590, Centre National de la Recherche Scientifique (CNRS), Muséum National d’Histoire Naturelle, Institut de Recherche pour le Développement (IRD), Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, 75005 Paris, France;
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14
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Zhang Y, Yuan W, Liu Y, Liu Y, Liang H, Xu Q, Liu Z, Weng X. Plasma membrane lipid composition and metabolomics analysis of Yorkshire boar sperms with high and low resistance to cryopreservation. Theriogenology 2023; 206:28-39. [PMID: 37178672 DOI: 10.1016/j.theriogenology.2023.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/01/2023] [Accepted: 04/15/2023] [Indexed: 05/15/2023]
Abstract
The resistance of sperm to freezing varies widely among boars. The semen ejaculate of different boars can be grouped into poor freezability ejaculate (PFE) and good freezability ejaculate (GFE). In this study, five Yorkshire boars each of the GFE and PFE were selected by comparing the changes in sperm motility before and after cryopreservation. Firstly, we found that the sperm plasma membrane of the PFE group showed weak integrity after PI and 6-CFDA staining. Then the electron microscopy results verified that the plasma membrane condition of all segments of GFE was better than that of PFE segments. Furthermore, the lipid composition of sperm plasma membranes in GPE and PFE sperm was analyzed by using mass spectrometry, and 15 lipids showed differences between the two groups. Among those lipids, only phosphatidylcholine (PC) (14:0/20:4) and phosphatidylethanolamine (PE) (14:0/20:4) were higher in PFE. The remaining lipid contents, including those of dihydroceramide (18:0/18:0), four hexosylceramides (18:1/20:1, 18:0/22:1, 18:1/16:0, 18:1/18:0), lactosylceramide (18:1/16:0), two hemolyzed phosphatidylethanolamines (18:2, 20:2), five phosphatidylcholines (16:1/18:2, 18:2/16:1, 14:0/20:4, 16:0/18:3, 18:1/20:2), and two phosphatidylethanolamines (14:0/20:4, 18:1/18:3), were all positively correlated with resistance to cryopreservation (p < 0.05, r > 0.6). Moreover, we analyzed the metabolic profile of sperm using untarget metabolomic. KEGG annotation analysis revealed that the altered metabolites were mainly involved in fatty acid biosynthesis. Finally, we determined that the contents of oleic acid, oleamideetc, N8-acetylspermidine etc., were different between GFE and PFE sperm. In summary, the different lipid metabolism levels and long-chain polyunsaturated fatty acids (PUFAs) in plasma membrane may be key factors contributing to differences in sperm resistance to cryopreservation among boars.
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Affiliation(s)
- Yuting Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Wenjing Yuan
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yuchen Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yan Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Hanlin Liang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Qianqian Xu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China; Engineering Research Center of Intelligent Breeding and Feeding of Pig in Northern Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China.
| | - Xiaogang Weng
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China; Engineering Research Center of Intelligent Breeding and Feeding of Pig in Northern Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China.
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15
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Dodge GJ, Bernstein HM, Imperiali B. A generalizable protocol for expression and purification of membrane-bound bacterial phosphoglycosyl transferases in liponanoparticles. Protein Expr Purif 2023; 207:106273. [PMID: 37068720 DOI: 10.1016/j.pep.2023.106273] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
Phosphoglycosyl transferases (PGTs) are among the first membrane-bound enzymes involved in the biosynthesis of bacterial glycoconjugates. Robust expression and purification protocols for an abundant subfamily of PGTs remains lacking. Recent advancements in detergent-free methods for membrane protein solubilization open the door for purification of difficult membrane proteins directly from cell membranes into native-like liponanoparticles. By leveraging autoinduction, in vivo SUMO tag cleavage, styrene maleic acid co-polymer liponanoparticles (SMALPs), and Strep-Tag purification, we have established a robust workflow for expression and purification of previously unobtainable PGTs. The material generated from this workflow is extremely pure and can be directly visualized by Cryogenic Electron Microscopy (CryoEM). The methods presented here promise to be generalizable to additional membrane proteins recombinantly expressed in E. coli and should be of interest to the greater membrane proteomics community.
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Affiliation(s)
- Greg J Dodge
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hannah M Bernstein
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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16
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Motov VV, Kot EF, Shabalkina AV, Goncharuk SA, Arseniev AS, Goncharuk MV, Mineev KS. Investigation of lipid/protein interactions in trifluoroethanol-water mixtures proposes the strategy for the refolding of helical transmembrane domains. JOURNAL OF BIOMOLECULAR NMR 2023; 77:15-24. [PMID: 36451032 DOI: 10.1007/s10858-022-00408-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/22/2022] [Indexed: 05/03/2023]
Abstract
Membrane proteins are one of the keystone objects in molecular biology, but their structural studies often require an extensive search for an appropriate membrane-like environment and an efficient refolding protocol for a recombinant protein. Isotropic bicelles are a convenient membrane mimetic used in structural studies of membrane proteins. Helical membrane domains are often transferred into bicelles from trifluoroethanol-water mixtures. However, the protocols for such a refolding are empirical and the process itself is still not understood in detail. In search of the optimal refolding approaches for helical membrane proteins, we studied here how membrane proteins, lipids, and detergents interact with each other at various trifluoroethanol-water ratios. Using high-resolution NMR spectroscopy and dynamic light scattering, we determined the key states of the listed compounds in the trifluoroethanol/water mixture, found the factors that could be critical for the efficiency of refolding, and proposed several most optimal protocols. These protocols were developed on the transmembrane domain of neurotrophin receptor TrkA and tested on two model helical membrane domains-transmembrane of Toll-like receptor TLR9 and voltage-sensing domain of a potassium channel KvAP.
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Affiliation(s)
- Vladislav V Motov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Erik F Kot
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997.
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Alexandra V Shabalkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
| | - Marina V Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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17
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Petrovskaya LE, Lukashev EP, Lyukmanova EN, Shulepko MA, Kryukova EA, Ziganshin RH, Dolgikh DA, Maksimov EG, Rubin AB, Kirpichnikov MP, Lanyi JK, Balashov SP. Expression of Xanthorhodopsin in Escherichia coli. Protein J 2023:10.1007/s10930-023-10109-5. [DOI: 10.1007/s10930-023-10109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
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18
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Krishnarjuna B, Marte J, Ravula T, Ramamoorthy A. Enhancing the stability and homogeneity of non-ionic polymer nanodiscs by tuning electrostatic interactions. J Colloid Interface Sci 2023; 634:887-896. [PMID: 36566634 PMCID: PMC10838601 DOI: 10.1016/j.jcis.2022.12.112] [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] [Received: 08/26/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The nanodisc technology is increasingly used for structural studies on membrane proteins and drug delivery. The development of synthetic polymer nanodiscs and the recent discovery of non-ionic inulin-based polymers have significantly broadened the scope of nanodiscs. While the lipid exchange and size flexibility properties of the self-assembled polymer-based nanodiscs are valuable for various applications, the non-ionic polymer nanodiscs are remarkably unique in that they enable the reconstitution of any protein, protein-protein complexes, or drugs irrespective of their charge. However, the non-ionic nature of the belt could influence the stability and size homogeneity of inulin-based polymer nanodiscs. In this study, we investigate the size stability and homogeneity of nanodiscs formed by non-ionic lipid-solubilizing polymers using different biophysical methods. Polymer nanodiscs containing zwitterionic DMPC and different ratios of DMPC:DMPG lipids were made using anionic SMA-EA or non-ionic pentyl-inulin polymers. Non-ionic polymer nanodiscs made using zwitterionic DMPC lipids produced a very broad elution profile on SEC due to their instability in the column, thus affecting sample monodispersity which was confirmed by DLS experiments that showed multiple peaks. However, the inclusion of anionic DMPG lipids improved the stability as observed from SEC and DLS profiles, which was further confirmed by TEM images. Whereas, anionic SMA-EA-based DMPC-nanodiscs showed excellent stability and size homogeneity when solubilizing zwitterionic lipids. The stability of DMPC:DMPG non-ionic polymer nanodiscs is attributed to the inter-nanodisc repulsion by the anionic-DMPG that prevents the uncontrolled collision and fusion of nanodiscs. Thus, the reported results demonstrate the use of electrostatic interactions to tune the solubility, stability, and size homogeneity of non-ionic polymer nanodiscs which are important features for enabling functional and atomic-resolution structural studies of membrane proteins, other lipid-binding molecules, and water-soluble biomolecules including cytosolic proteins, nucleic acids and metabolites.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Joseph Marte
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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19
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Zhu C, Liang X, Chen X, Liang M, Zheng J, Wan B, Luo S. Characterizing the Specific Recognition of Xanthurenic Acid by GEP1 and GEP1-GCα Interactions in cGMP Signaling Pathway in Gametogenesis of Malaria Parasites. Int J Mol Sci 2023; 24:ijms24032561. [PMID: 36768882 PMCID: PMC9916804 DOI: 10.3390/ijms24032561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Gametogenesis is an essential step for malaria parasite transmission and is activated in mosquito by signals including temperature drop, pH change, and mosquito-derived xanthurenic acid (XA). Recently, a membrane protein gametogenesis essential protein 1 (GEP1) was found to be responsible for sensing these signals and interacting with a giant guanylate cyclase α (GCα) to activate the cGMP-PKG-Ca2+ signaling pathway for malaria parasite gametogenesis. However, the molecular mechanisms for this process remain unclear. In this study, we used AlphaFold2 to predict the structure of GEP1 and found that it consists of a conserved N-terminal helical domain and a transmembrane domain that adopts a structure similar to that of cationic amino acid transporters. Molecular docking results showed that XA binds to GEP1 via a pocket similar to the ligand binding sites of known amino acid transporters. In addition, truncations of this N-terminal sequence significantly enhanced the expression, solubility, and stability of GEP1. In addition, we found that GEP1 interacts with GCα via its C-terminal region, which is interrupted by mutations of a few conserved residues. These findings provide further insights into the molecular mechanism for the XA recognition by GEP1 and the activation of the gametogenesis of malaria parasites through GEP1-GCα interaction.
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Affiliation(s)
- Cheng Zhu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Xiaoge Liang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Xu Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Miaomiao Liang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Jianting Zheng
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Bingbing Wan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Shukun Luo
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
- Correspondence:
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20
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Koo CW, Hershewe JM, Jewett MC, Rosenzweig AC. Cell-Free Protein Synthesis of Particulate Methane Monooxygenase into Nanodiscs. ACS Synth Biol 2022; 11:4009-4017. [PMID: 36417751 PMCID: PMC9910172 DOI: 10.1021/acssynbio.2c00366] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a multi-subunit membrane metalloenzyme used by methanotrophic bacteria to convert methane to methanol. A major hurdle to studying pMMO is the lack of a recombinant expression system, precluding investigation of individual residues by mutagenesis and hampering a complete understanding of its mechanism. Here, we developed an Escherichia coli lysate-based cell-free protein synthesis (CFPS) system that can be used to express pMMO in vitro in the presence of nanodiscs. We used a SUMO fusion construct to generate the native PmoB subunit and showed that the SUMO protease (Ulp1) cleaves the protein in the reaction mixture. Using an affinity tag to isolate the complete pMMO complex, we demonstrated that the complex forms without the need for exogenous translocon machinery or chaperones, confirmed by negative stain electron microscopy. This work demonstrates the potential for using CFPS to express multi-subunit membrane-bound metalloenzymes directly into lipid bilayers.
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Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jasmine M. Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and of Chemistry and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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21
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Isolation and characterization of human anti-CD20 single-chain variable fragment (scFv) from a Naive human scFv library. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:177. [PMID: 35999405 PMCID: PMC9398497 DOI: 10.1007/s12032-022-01757-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/30/2022] [Indexed: 12/03/2022]
Abstract
CD20 is a receptor expressed on B cells with anonymous functions. The receptor is the target of some food and drug administration (FDA) approved monoclonal antibodies (mAb), such as Rituximab and Obinutuzumab. Blocking CD20 using the aforementioned mAbs has improved Non-Hodgkin Lymphoma (NHL) therapy. All commercial mAbs on the market were raised in non-human animal models. Antibody humanization is inevitable to mitigate immune response. In order to keep the affinity of antibody intact, humanizations are only applied to frameworks which do not eliminate immune response to foreign CDRs sequences. To address this issue, human monoclonal antibody deemed imperative. Herein, we report the isolation and characterization of a fully human single-chain variable fragment (scFv) against the large loop of CD20 from naïve human antibody library. After three rounds of phage display, a library of enriched anti-CD20 scFv was obtained. The polyclonal phage ELISA demonstrated that after each round of phage display, the population of anti-CD20 scFv became dominant. The scFv, G7, with the most robust interaction with CD20 was selected for further characterization. The specificity of G7 scFv was evaluated by ELISA, western blot, and flow cytometry. Detecting CD20 in western blot showed that G7 binds to a linear epitope on CD20 large loop. Next, G7 scFv was also bound to Raji cell (CD20+) while no interaction was recorded with K562 cell line (CD20—). This data attested that the epitope recognized by G7 scFv is accessible on the cell membrane. The affinity of G7 scFv was estimated to be 63.41 ± 3.9 nM. Next, the sensitivity was evaluated to be 2 ng/ml. Finally, G7 scFv tertiary structure was modeled using Graylab software. The 3D structure illustrated two domains of variable heavy (VH) and variable light (VL) connected through a linker. Afterward, G7 scFv and CD20 were applied to in-silico docking using ClusPro to illustrate the interaction of G7 with the large loop of CD20. As the selected scFv from the human antibody library is devoid of interspecies immunogenic amino acids sequences, no humanization or any other modifications are required prior to clinical applications.
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22
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Krishnarjuna B, Ramamoorthy A. Detergent-Free Isolation of Membrane Proteins and Strategies to Study Them in a Near-Native Membrane Environment. Biomolecules 2022; 12:1076. [PMID: 36008970 PMCID: PMC9406181 DOI: 10.3390/biom12081076] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important to fully understand their biological function and the roles played by them in the pathology of many diseases. However, the complexity of the cell membrane has severely limited the application of commonly used biophysical and biochemical techniques. Recent advancements in NMR spectroscopy and cryoEM approaches and the development of novel membrane mimetics have overcome some of the major challenges in this area. For example, the development of a variety of lipid-nanodiscs has enabled stable reconstitution and structural and functional studies of membrane proteins. In particular, the ability of synthetic amphipathic polymers to isolate membrane proteins directly from the cell membrane, along with the associated membrane components such as lipids, without the use of a detergent, has opened new avenues to study the structure and function of membrane proteins using a variety of biophysical and biological approaches. This review article is focused on covering the various polymers and approaches developed and their applications for the functional reconstitution and structural investigation of membrane proteins. The unique advantages and limitations of the use of synthetic polymers are also discussed.
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Affiliation(s)
- Bankala Krishnarjuna
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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23
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Abstract
Membrane proteins, particularly those that are α-helical, such as transporters and G-protein-coupled receptors (GPCRs), have significant biological relevance. However, their expression and purification pose difficulties because of their poor water solubilities, which impedes progress in this field. The QTY method, a code-based protein-engineering approach, was recently developed to produce soluble transmembrane proteins. Here, we describe a comprehensive Web server built for QTY design and its relevance for in silico analyses. Typically, the simple design model is expected to require only 2 to 4 min of computer time, and the library design model requires 2 to 5 h, depending on the target protein size and the number of transmembrane helices. Detailed protocols for using the server with both the simple design and library design modules are provided. Methods for experiments following the QTY design are also included to facilitate the implementation of this approach. The design pipeline was further evaluated using microbial transmembrane proteins and structural alignment between the designed proteins and their origins by employing AlphaFold2. The results reveal that mutants generated by the developed pipeline were highly identical to their origins in terms of three-dimensional (3D) structures. In summary, the utilization of our Web server and associated protocols will enable QTY-based protein engineering to be implemented in a convenient, fast, accurate, and rational manner. The Protein Solubilizing Server (PSS) is publicly available at http://pss.sjtu.edu.cn. IMPORTANCE Water-soluble expression and purification are of considerable importance for protein identification and characterization. However, there has been a lack of an effective method for water-soluble expression of membrane proteins, which has severely hampered their studies. Here, an enabling comprehensive Web server, PSS, was developed for designing water-soluble mutants of α-helical membrane proteins, based on QTY design, a code-based protein-engineering approach. With microbial transmembrane proteins and GPCRs as examples, we systematically evaluated the server and demonstrated its successful performance. PSS is readily available for worldwide users as a Web-based tool, rendering QTY-based protein engineering convenient, efficient, accurate, and rational.
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24
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Depping P, Román Lara MM, Kesidis A, Bill RM, Rothnie AJ, Browning DF, Goddard AD. Heterologous Expression of Membrane Proteins in E. coli. Methods Mol Biol 2022; 2507:59-78. [PMID: 35773577 DOI: 10.1007/978-1-0716-2368-8_4] [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: 06/15/2023]
Abstract
Over the decades, the bacterium Escherichia coli (E. coli) has become the cornerstone of recombinant protein production, used for heterologous synthesis of a variety of membrane proteins. Due to its rapid growth to high densities in cheap media, and its ease of manipulation and handling, E. coli is an excellent host cell for a range of membrane protein targets. Furthermore, its genetic tractability allows for a variety of gene constructs to be screened for optimal expression conditions, resulting in relatively high yields of membrane protein in a short amount of time. Here, we describe the general workflow for the production of membrane proteins in E. coli. The protocols we provide show how the gene of interest is modified, transferred to an expression vector and host, and how membrane protein yields can be optimized and analyzed. The examples we illustrate are well suited for scientists who are starting their journey into the world of membrane protein production.
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Affiliation(s)
- Peer Depping
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | | | - Athanasios Kesidis
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | - Roslyn M Bill
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | - Alice J Rothnie
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | - Douglas F Browning
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham, UK.
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, UK.
| | - Alan D Goddard
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham, UK.
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25
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Barret L, Schubeis T, Kugler V, Guyot L, Pintacuda G, Wagner R. Production and Preparation of Isotopically Labeled Human Membrane Proteins in Pichia pastoris for Fast-MAS-NMR Analyses. Methods Mol Biol 2022; 2507:201-221. [PMID: 35773584 DOI: 10.1007/978-1-0716-2368-8_11] [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: 06/15/2023]
Abstract
Membrane proteins (MPs) comprise about one-third of the human proteome, playing critical roles in many physiological processes and associated disorders. Consistently, they represent one of the largest classes of targets for the pharmaceutical industry. Their study at the molecular level is however particularly challenging, resulting in a severe lack of structural and dynamic information that is hindering their detailed functional characterization and the identification of novel potent drug candidates.Magic Angle Spinning (MAS) NMR is a reliable and efficient method for the determination of protein structures and dynamics and for the identification of ligand binding sites and equilibria. MAS-NMR is particularly well suited for MPs since they can be directly analysed in a native-like lipid bilayer environment but used to require aggravating large amounts of isotope enriched material. The frequent toxicity of human MP overexpression in bacterial cultures poses an additional hurdle, resulting in the need for alternative (and often more costly) expression systems. The recent development of very fast (up to 150 kHz) MAS probes has revolutionized the field of biomolecular solid-state NMR enabling higher spectral resolution with significant reduction of the required sample, rendering eukaryotic expression systems cost-effective.Here is presented a set of accessible procedures validated for the production and preparation of eukaryotic MPs for Fast-MAS 1H-detected NMR analysis. The methodology is illustrated with the human copper uptake protein hCTR1 recombinantly produced and 13C-15N uniformly labeled with the versatile and affordable Pichia pastoris system. Subsequent purification procedures allow the recovery of mg amounts that are then reconstituted into liposome formulations compatible with solid-state NMR handling and analysis.
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Affiliation(s)
- Lina Barret
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Tobias Schubeis
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Valérie Kugler
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
| | - Lucile Guyot
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
- NovAliX, Illkirch, France
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Renaud Wagner
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France.
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26
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Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins. MEMBRANES 2021; 12:membranes12010050. [PMID: 35054576 PMCID: PMC8778870 DOI: 10.3390/membranes12010050] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/13/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022]
Abstract
The natural environment of proteins is the polar aquatic environment and the hydrophobic (amphipathic) environment of the membrane. The fuzzy oil drop model (FOD) used to characterize water-soluble proteins, as well as its modified version FOD-M, enables a mathematical description of the presence and influence of diverse environments on protein structure. The present work characterized the structures of membrane proteins, including those that act as channels, and a water-soluble protein for contrast. The purpose of the analysis was to verify the possibility that an external force field can be used in the simulation of the protein-folding process, taking into account the diverse nature of the environment that guarantees a structure showing biological activity.
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27
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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28
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Li D, Chu W, Sheng X, Li W. Optimization of Membrane Protein TmrA Purification Procedure Guided by Analytical Ultracentrifugation. MEMBRANES 2021; 11:membranes11100780. [PMID: 34677546 PMCID: PMC8537081 DOI: 10.3390/membranes11100780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022]
Abstract
Membrane proteins are involved in various cellular processes. However, purification of membrane proteins has long been a challenging task, as membrane protein stability in detergent is the bottleneck for purification and subsequent analyses. Therefore, the optimization of detergent conditions is critical for the preparation of membrane proteins. Here, we utilize analytical ultracentrifugation (AUC) to examine the effects of different detergents (OG, Triton X-100, DDM), detergent concentrations, and detergent supplementation on the behavior of membrane protein TmrA. Our results suggest that DDM is more suitable for the purification of TmrA compared with OG and TritonX-100; a high concentration of DDM yields a more homogeneous protein aggregation state; supplementing TmrA purified with a low DDM concentration with DDM maintains the protein homogeneity and aggregation state, and may serve as a practical and cost-effective strategy for membrane protein purification.
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Affiliation(s)
- Dongdong Li
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Wendan Chu
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Xinlei Sheng
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Correspondence: (X.S.); (W.L.); Tel.: +86-1062782031 (W.L.)
| | - Wenqi Li
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
- Correspondence: (X.S.); (W.L.); Tel.: +86-1062782031 (W.L.)
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29
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Barroca-Ferreira J, Cruz-Vicente P, Santos MFA, Rocha SM, Santos-Silva T, Maia CJ, Passarinha LA. Enhanced Stability of Detergent-Free Human Native STEAP1 Protein from Neoplastic Prostate Cancer Cells upon an Innovative Isolation Procedure. Int J Mol Sci 2021; 22:10012. [PMID: 34576175 PMCID: PMC8472055 DOI: 10.3390/ijms221810012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The STEAP1 is a cell-surface antigen over-expressed in prostate cancer, which contributes to tumor progression and aggressiveness. However, the molecular mechanisms underlying STEAP1 and its structural determinants remain elusive. METHODS The fraction capacity of Butyl- and Octyl-Sepharose matrices on LNCaP lysates was evaluated by manipulating the ionic strength of binding and elution phases, followed by a Co-Immunoprecipitation (Co-IP) polishing. Several potential stabilizing additives were assessed, and the melting temperature (Tm) values ranked the best/worst compounds. The secondary structure of STEAP1 was identified by circular dichroism. RESULTS The STEAP1 was not fully captured with 1.375 M (Butyl), in contrast with interfering heterologous proteins, which were strongly retained and mostly eluted with water. This single step demonstrated higher selectivity of Butyl-Sepharose for host impurities removal from injected crude samples. Co-IP allowed recovering a purified fraction of STEAP1 and contributed to unveil potential physiologically interacting counterparts with the target. A Tm of ~55 °C was determined, confirming STEAP1 stability in the purification buffer. A predominant α-helical structure was identified, ensuring the protein's structural stability. CONCLUSIONS A method for successfully isolating human STEAP1 from LNCaP cells was provided, avoiding the use of detergents to achieve stability, even outside a membrane-mimicking environment.
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Affiliation(s)
- Jorge Barroca-Ferreira
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Pedro Cruz-Vicente
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Marino F. A. Santos
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Sandra M. Rocha
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
| | - Teresa Santos-Silva
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Cláudio J. Maia
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
| | - Luís A. Passarinha
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Laboratório de Fármaco-Toxicologia-UBIMedical, University of Beira Interior, 6201-284 Covilhã, Portugal
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30
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Aggarwal S, Wachenfeldt CV, Fisher SZ, Oksanen E. A protocol for production of perdeuterated OmpF porin for neutron crystallography. Protein Expr Purif 2021; 188:105954. [PMID: 34416360 DOI: 10.1016/j.pep.2021.105954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/31/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
Hydrogen atoms are at the limit of visibility in X-ray structures even at high resolution. Neutron macromolecular crystallography (NMX) is an unambiguous method to locate hydrogens and study the significance of hydrogen bonding interactions in biological systems. Since NMX requires very large crystals, very few neutron structures of proteins have been determined yet. In addition, the most common hydrogen isotope 1H gives rise to significant background due to its large incoherent scattering cross-section. Therefore, it is advantageous to substitute as many hydrogens as possible with the heavier isotope 2H (deuterium) to reduce the sample volume requirement. While the solvent exchangeable hydrogens can be substituted by dissolving the protein in heavy water, complete deuterium labelling - perdeuteration - requires the protein to be expressed in heavy water with a deuterated carbon source. In this work, we developed an optimized method for large scale production of deuterium-labelled bacterial outer membrane protein F (OmpF) for NMX. OmpF was produced using deuterated media with different carbon sources. Mass spectrometry verified the integrity and level of deuteration of purified OmpF. Perdeuterated OmpF crystals diffracted X-rays to a resolution of 1.9 Å. This work lays the foundation for structural studies of membrane protein by neutron diffraction in future.
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Affiliation(s)
- Swati Aggarwal
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden; University Grenoble Alpes, CEA, CNRS, IBS, FR-380 00, Grenoble, France
| | | | - Suzanne Zoë Fisher
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden; Department of Biology, Lund University, Sölvegatan 35, Lund, SE-22 362, Sweden
| | - Esko Oksanen
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden.
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31
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Preisler SS, Hansen KM, Nurup CN, Beich-Frandsen M, Pedersen PA. Recombinant production of membrane proteins in yeast. Methods Enzymol 2021; 660:21-52. [PMID: 34742390 DOI: 10.1016/bs.mie.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biochemical pathways are compartmentalized in living cells. This permits each cell to maintain chemical compositions that differ between the cytosol, intracellular organelles and the external environment. Achieving this requires each compartment to be very selective in what is allowed to enter and leave. Nature has solved this by surrounding each cell and each organelle with a virtually solute impermeable lipid membrane, embedded with integral membrane proteins that mediate strictly controlled trans-membrane movement of matter and information. Access to pure and active integral membrane proteins is therefore required to comprehend membrane biology, ultimately through high-resolution structures of the membrane proteome and, therefore, also for our understanding of physiology. Unfortunately, apart from a few exceptions, membrane proteins cannot be purified from native tissue but need to be produced recombinantly, which is eminently challenging. This chapter shows how we have engineered yeast to provide high levels of prime quality membrane proteins of prokaryotic, archaeal or eukaryotic origin for structural biology.
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32
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Tailoring the evolution of BL21(DE3) uncovers a key role for RNA stability in gene expression toxicity. Commun Biol 2021; 4:963. [PMID: 34385596 PMCID: PMC8361080 DOI: 10.1038/s42003-021-02493-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Gene expression toxicity is an important biological phenomenon and a major bottleneck in biotechnology. Escherichia coli BL21(DE3) is the most popular choice for recombinant protein production, and various derivatives have been evolved or engineered to facilitate improved yield and tolerance to toxic genes. However, previous efforts to evolve BL21, such as the Walker strains C41 and C43, resulted only in decreased expression strength of the T7 system. This reveals little about the mechanisms at play and constitutes only marginal progress towards a generally higher producing cell factory. Here, we restrict the solution space for BL21(DE3) to evolve tolerance and isolate a mutant strain Evo21(DE3) with a truncation in the essential RNase E. This suggests that RNA stability plays a central role in gene expression toxicity. The evolved rne truncation is similar to a mutation previously engineered into the commercially available BL21Star(DE3), which challenges the existing assumption that this strain is unsuitable for expressing toxic proteins. We isolated another dominant mutation in a presumed substrate binding site of RNase E that improves protein production further when provided as an auxiliary plasmid. This makes it easy to improve other BL21 variants and points to RNases as prime targets for cell factory optimisation.
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33
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Incorporation of Membrane Proteins Into Bicontinuous Microemulsions Through
Winsor‐III System‐Based
Extraction. J SURFACTANTS DETERG 2021. [DOI: 10.1002/jsde.12500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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34
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Hybrid-Type SELEX for the Selection of Artificial Nucleic Acid Aptamers Exhibiting Cell Internalization Activity. Pharmaceutics 2021; 13:pharmaceutics13060888. [PMID: 34204006 PMCID: PMC8232673 DOI: 10.3390/pharmaceutics13060888] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers have attracted considerable attention as next-generation pharmaceutical agents and delivery vehicles for small molecule drugs and therapeutic oligonucleotides. Chemical modification is an effective approach for improving the functionality of aptamers. However, the process of selecting appropriately modified aptamers is laborious because of many possible modification patterns. Here, we describe a hybrid-type systematic evolution of ligands by exponential enrichment (SELEX) approach for the generation of the artificial nucleic acid aptamers effective against human TROP2, a cell surface protein identified by drug discovery as a promising target for cancer therapy. Capillary electrophoresis SELEX was used for the pre-screening of multiple modified nucleic acid libraries and enrichment of TROP2 binding aptamers in the first step, followed by functional screening using cell-SELEX in the second step for the generation of cell-internalizing aptamers. One representative aptamer, Tac-B1, had a nanomolar-level affinity to human TROP2 and exhibited elevated capacity for internalization by cells. Because of the growing interest in the application of aptamers for drug delivery, our hybrid selection approach has great potential for the generation of functional artificial nucleic acid aptamers with ideal modification patterns in vitro.
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35
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Therapeutic Antibodies Targeting Potassium Ion Channels. Handb Exp Pharmacol 2021; 267:507-545. [PMID: 33963460 DOI: 10.1007/164_2021_464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Monoclonal antibodies combine specificity and high affinity binding with excellent pharmacokinetic properties and are rapidly being developed for a wide range of drug targets including clinically important potassium ion channels. Nonetheless, while therapeutic antibodies come with great promise, K+ channels represent particularly difficult targets for biologics development for a variety of reasons that include their dynamic structures and relatively small extracellular loops, their high degree of sequence conservation (leading to immune tolerance), and their generally low-level expression in vivo. The process is made all the more difficult when large numbers of antibody candidates must be screened for a given target, or when lead candidates fail to cross-react with orthologous channels in animal disease models due to their highly selective binding properties. While the number of antibodies targeting potassium channels in preclinical or clinical development is still modest, significant advances in the areas of protein expression and antibody screening are converging to open the field to an avalanche of new drugs. Here, the opportunities and constraints associated with the discovery of antibodies against K+ channels are discussed, with an emphasis on novel technologies that are opening the field to exciting new possibilities for biologics development.
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36
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Phạm TTT, Rainey JK. On-cell nuclear magnetic resonance spectroscopy to probe cell surface interactions. Biochem Cell Biol 2021; 99:683-692. [PMID: 33945753 DOI: 10.1139/bcb-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy allows determination of atomic-level information about intermolecular interactions, molecular structure, and molecular dynamics in the cellular environment. This may be broadly divided into studies focused on obtaining detailed molecular information in the intracellular context ("in-cell") or those focused on characterizing molecules or events at the cell surface ("on-cell"). In this review, we outline some key NMR techniques applied for on-cell NMR studies through both solution-state and solid-state NMR and survey studies that have used these techniques to uncover key information. We particularly focus on application of on-cell NMR spectroscopy to characterize ligand interactions with cell surface membrane proteins such as G-protein coupled receptors (GPCRs), receptor tyrosine kinases, etc. These techniques allow for quantification of binding affinities, competitive binding assays, delineation of portions of ligands involved in binding, ligand bound-state conformational determination, evaluation of receptor structuring and dynamics, and inference of distance constraints characteristic of the ligand-receptor bound state. Excitingly, it is possible to avoid the barriers of production and purification of membrane proteins while obtaining directly physiologically-relevant information through on-cell NMR. We also provide a briefer survey of the applicability of on-cell NMR approaches to other classes of cell surface molecule.
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Affiliation(s)
- Trần Thanh Tâm Phạm
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Nova Scotia, Canada;
| | - Jan K Rainey
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Canada;
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37
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Roterman I, Stapor K, Fabian P, Konieczny L, Banach M. Model of Environmental Membrane Field for Transmembrane Proteins. Int J Mol Sci 2021; 22:ijms22073619. [PMID: 33807215 PMCID: PMC8036355 DOI: 10.3390/ijms22073619] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/20/2021] [Accepted: 03/27/2021] [Indexed: 11/16/2022] Open
Abstract
The water environment determines the activity of biological processes. The role of such an environment interpreted in the form of an external field expressed by the 3D Gaussian distribution in the fuzzy oil drop model directs the folding process towards the generation of a centrally located hydrophobic core with the simultaneous exposure of polar residues on the surface. In addition to proteins soluble in the water environment, there is a significant group of membrane proteins that act as receptors or channels, including ion channels in particular. The change of the polar (water) environment into a highly hydrophobic (membrane) environment is quite radical, resulting in a different hydrophobicity distribution within the membrane protein. Modification of the notation of the force field expressing the presence of the hydrophobic environment has been proposed in this work. A modified fuzzy oil drop model with its adaptation to membrane proteins was used to interpret the structure of membrane proteins–mechanosensitive channel. The modified model was also used to describe the so-called negative cases—i.e., for water-soluble proteins with a clear distribution consistent with the fuzzy oil drop model.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, 30-688 Kraków, Poland;
- Correspondence:
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University—Medical College, 31-034 Kraków, Poland;
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, 30-688 Kraków, Poland;
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Fluorescence-detection size-exclusion chromatography utilizing nanobody technology for expression screening of membrane proteins. Commun Biol 2021; 4:366. [PMID: 33742097 PMCID: PMC7979870 DOI: 10.1038/s42003-021-01891-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
GFP fusion-based fluorescence-detection size-exclusion chromatography (FSEC) has been widely employed for membrane protein expression screening. However, fused GFP itself may occasionally affect the expression and/or stability of the targeted membrane protein, leading to both false-positive and false-negative results in expression screening. Furthermore, GFP fusion technology is not well suited for some membrane proteins, depending on their membrane topology. Here, we developed an FSEC assay utilizing nanobody (Nb) technology, named FSEC-Nb, in which targeted membrane proteins are fused to a small peptide tag and recombinantly expressed. The whole-cell extracts are solubilized, mixed with anti-peptide Nb fused to GFP for FSEC analysis. FSEC-Nb enables the evaluation of the expression, monodispersity and thermostability of membrane proteins without the need for purification but does not require direct GFP fusion to targeted proteins. Our results show FSEC-Nb as a powerful tool for expression screening of membrane proteins for structural and functional studies.
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39
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Missel JW, Salustros N, Becares ER, Steffen JH, Laursen AG, Garcia AS, Garcia-Alai MM, Kolar Č, Gourdon P, Gotfryd K. Cyclohexyl-α maltoside as a highly efficient tool for membrane protein studies. Curr Res Struct Biol 2021; 3:85-94. [PMID: 34235488 PMCID: PMC8244287 DOI: 10.1016/j.crstbi.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/09/2021] [Accepted: 03/05/2021] [Indexed: 01/06/2023] Open
Abstract
Membrane proteins (MPs) constitute a large fraction of the proteome, but exhibit physicochemical characteristics that impose challenges for successful sample production crucial for subsequent biophysical studies. In particular, MPs have to be extracted from the membranes in a stable form. Reconstitution into detergent micelles represents the most common procedure in recovering MPs for subsequent analysis. n-dodecyl-β-D-maltoside (DDM) remains one of the most popular conventional detergents used in production of MPs. Here we characterize the novel DDM analogue 4-trans-(4-trans-propylcyclohexyl)-cyclohexyl α-maltoside (t-PCCαM), possessing a substantially lower critical micelle concentration (CMC) than the parental compound that represents an attractive feature when handling MPs. Using three different types of MPs of human and prokaryotic origin, i.e., a channel, a primary and a secondary active transporter, expressed in yeast and bacterial host systems, respectively, we investigate the performance of t-PCCαM in solubilization and affinity purification together with its capacity to preserve native fold and activity. Strikingly, t-PCCαM displays favorable behavior in extracting and stabilizing the three selected targets. Importantly, t-PCCαM promoted extraction of properly folded protein, enhanced thermostability and provided negatively-stained electron microscopy samples of promising quality. All-in-all, t-PCCαM emerges as competitive surfactant applicable to a broad portfolio of challenging MPs for downstream structure-function analysis.
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Affiliation(s)
- Julie Winkel Missel
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Nina Salustros
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Eva Ramos Becares
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Amalie Gerdt Laursen
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Maria M Garcia-Alai
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany.,Centre for Structural Systems Biology, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Čeněk Kolar
- Glycon Biochemicals GmbH, Im Biotechnologie Park TGZ 1, D-14943, Luckenwalde, Germany
| | - Pontus Gourdon
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark.,Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden
| | - Kamil Gotfryd
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
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40
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Errasti-Murugarren E, Bartoccioni P, Palacín M. Membrane Protein Stabilization Strategies for Structural and Functional Studies. MEMBRANES 2021; 11:membranes11020155. [PMID: 33671740 PMCID: PMC7926488 DOI: 10.3390/membranes11020155] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is a field experiencing significant growth as a result of the development of new strategies for structure determination. However, membrane protein preparation for structural studies continues to be a limiting step in many cases due to the inherent instability of these molecules in non-native membrane environments. This review describes the approaches that have been developed to improve membrane protein stability. Membrane protein mutagenesis, detergent selection, lipid membrane mimics, antibodies, and ligands are described in this review as approaches to facilitate the production of purified and stable membrane proteins of interest for structural and functional studies.
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Affiliation(s)
- Ekaitz Errasti-Murugarren
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
| | - Paola Bartoccioni
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
| | - Manuel Palacín
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
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41
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Sheshko V, Link M, Golovliov I, Balonova L, Stulik J. Utilization of a tetracycline-inducible system for high-level expression of recombinant proteins in Francisella tularensis LVS. Plasmid 2021; 115:102564. [PMID: 33610608 DOI: 10.1016/j.plasmid.2021.102564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/28/2022]
Abstract
Francisella tularensis is a Gram-negative intracellular pathogen causing tularemia. A number of its potential virulence factors have been identified, but their biology and functions are not precisely known. Understanding the biological and immunological functions of these proteins requires adequate genetic tools for homologous and heterologous expression of cloned genes, maintaining both original structure and post-translational modifications. Here, we report the construction of a new multipurpose shuttle plasmid - pEVbr - which can be used for high-level expression in F. tularensis. The pEVbr plasmid has been constructed by modifying the TetR-regulated expression vector pEDL17 (LoVullo, 2012) that includes (i) a strong F. tularensis bfr promoter, and (ii) two tet operator sequences cloned into the promoter. The cloned green fluorescent protein (GFP), used as a reporter, demonstrated almost undetectable basal expression level under uninduced conditions and a highly dynamic dose-dependent response to the inducer. The utility of the system was further confirmed by cloning the gapA and FTT_1676 genes into the pEVbr vector and quantifying proteins expression in F. tularensis LVS, as well as by studying post-translational modification of the cloned genes. This study demonstrates that high levels of recombinant native-like Francisella proteins can be produced in Francisella cells. Hence, this system may be beneficial for the analysis of protein function and the development of new treatments and vaccines.
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Affiliation(s)
- Valeria Sheshko
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic.
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - Igor Golovliov
- Department of Clinical Microbiology, Umeå University, SE-901 85 Umeå, Sweden
| | - Lucie Balonova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - Jiri Stulik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
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42
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Preisler SS, Wiuf AD, Friis M, Kjaergaard L, Hurd M, Becares ER, Nurup CN, Bjoerkskov FB, Szathmáry Z, Gourdon PE, Calloe K, Klaerke DA, Gotfryd K, Pedersen PA. Saccharomyces cerevisiae as a superior host for overproduction of prokaryotic integral membrane proteins. Curr Res Struct Biol 2021; 3:51-71. [PMID: 34235486 PMCID: PMC8244417 DOI: 10.1016/j.crstbi.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/02/2023] Open
Abstract
Integral membrane proteins (IMPs) constitute ~30% of all proteins encoded by the genome of any organism and Escherichia coli remains the first-choice host for recombinant production of prokaryotic IMPs. However, the expression levels of prokaryotic IMPs delivered by this bacterium are often low and overproduced targets often accumulate in inclusion bodies. The targets are therefore often discarded to avoid an additional and inconvenient refolding step in the purification protocol. Here we compared expression of five prokaryotic (bacterial and archaeal) IMP families in E. coli and Saccharomyces cerevisiae. We demonstrate that our S. cerevisiae-based production platform is superior in expression of four investigated IMPs, overall being able to deliver high quantities of active target proteins. Surprisingly, in case of the family of zinc transporters (Zrt/Irt-like proteins, ZIPs), S. cerevisiae rescued protein expression that was undetectable in E. coli. We also demonstrate the effect of localization of the fusion tag on expression yield and sample quality in detergent micelles. Lastly, we present a road map to achieve the most efficient expression of prokaryotic IMPs in our yeast platform. Our findings demonstrate the great potential of S. cerevisiae as host for high-throughput recombinant overproduction of bacterial and archaeal IMPs for downstream biophysical characterization. S. cerevisiae is superior to E. coli in expressing correctly folded and active IMPs. S. cerevisiae completely rescues the expression of the family of zinc transporters. Localization of the fusion tag affects expression yields and protein quality. We provide a roadmap to efficient expression of prokaryotic IMPs in S. cerevisiae.
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Affiliation(s)
- Sarah Spruce Preisler
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Anders Drabaek Wiuf
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Marc Friis
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Lasse Kjaergaard
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Molly Hurd
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Eva Ramos Becares
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Casper Normann Nurup
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | | | - Zsófia Szathmáry
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Pontus Emanuel Gourdon
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Kirstine Calloe
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Dan A Klaerke
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Kamil Gotfryd
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Per Amstrup Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
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43
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Membrane Protein Production and Purification from Escherichia coli and Sf9 Insect Cells. Methods Mol Biol 2021. [PMID: 33582985 DOI: 10.1007/978-1-0716-0724-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
A major obstacle to studying membrane proteins by biophysical techniques is the difficulty in producing sufficient amounts of materials for functional and structural studies. To overexpress the target membrane protein heterologously, especially an eukaryotic protein, a key step is to find the optimal host expression system and perform subsequent expression optimization. In this chapter, we describe protocols for screening membrane protein production using bacterial and insect cells, solubilization screening, large-scale production, and commonly used affinity chromatography purification methods. We discuss general optimization conditions, such as promoters and tags, and describe current techniques that can be used in any laboratory without specialized expensive equipment. Especially for insect cells, GFP fusions are particularly useful for localization and in-gel fluorescence detection of the proteins on SDS-PAGE. We give detailed protocols that can be used to screen the best expression and purification conditions for membrane protein study.
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44
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Cell-Free Expression of a Plant Membrane Protein BrPT2 From Boesenbergia Rotunda. Mol Biotechnol 2021; 63:316-326. [PMID: 33565047 DOI: 10.1007/s12033-021-00304-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
Prenylation of aromatic natural products by membrane-bound prenyltransferases (PTs) is an important biosynthesis step of many bioactive compounds. At present, only a few plant flavonoid-related PT genes have been functionally characterized, mainly due to the difficulties of expressing these membrane proteins. Rapid and effective methods to produce functional plant membrane proteins are thus indispensable. Here, we evaluated expression systems through cell-based and cell-free approaches to express Boesenbergia rotunda BrPT2 encoding a membrane-bound prenyltransferase. We attempted to express BrPT2 in Escherichia coli and tobacco plants but failed to detect this protein using the Western-blot technique, whereas an intact single band of 43 kDa was detected when BrPT2 was expressed using a cell-free protein synthesis system (PURE). Under in vitro enzymatic condition, the synthesized BrPT2 successfully catalyzed pinostrobin chalcone to pinostrobin. Molecular docking analysis showed that pinostrobin chalcone interacts with BrPT2 at two cavities: (1) the main binding site at the central cavity and (2) the allosteric binding site located away from the central cavity. Our findings suggest that cell-free protein synthesis could be an alternative for rapid production of valuable difficult-to-express membrane proteins.
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REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution. PLoS Comput Biol 2021; 17:e1008060. [PMID: 33524015 PMCID: PMC7877757 DOI: 10.1371/journal.pcbi.1008060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 02/11/2021] [Accepted: 01/05/2021] [Indexed: 01/10/2023] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the three primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by solution NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination from Residual Dipolar Couplings (RDCs) is relatively less well developed. Here, we describe the new features of the protein structure modeling program REDCRAFT and focus on the new Adaptive Decimation (AD) feature. The AD plays a critical role in improving the robustness of REDCRAFT to missing or noisy data, while allowing structure determination of larger proteins from less data. In this report we demonstrate the successful application of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data, and of larger proteins (145 to 573 residues) using simulated RDC data. In both cases, REDCRAFT uses only RDC data that can be collected from perdeuterated proteins. Finally, we compare the accuracy of structure determination from RDCs alone with traditional NOE-based methods for the structurally novel PF.2048.1 protein. The RDC-based structure of PF.2048.1 exhibited 1.0 Å BB-RMSD with respect to a high-quality NOE-based structure. Although optimal strategies would include using RDC data together with chemical shift, NOE, and other NMR data, these studies provide proof-of-principle for robust structure determination of largely-perdeuterated proteins from RDC data alone using REDCRAFT. Residual Dipolar Couplings have the potential to improve the accuracy and reduce the time needed to characterize protein structures. In addition, RDC data have been demonstrated to concurrently elucidate structure of proteins, provide assignment of resonances, and characterize the internal dynamics of proteins. Given all the advantages associated with the study of proteins from RDC data, based on the statistics provided by the Protein Databank (PDB), surprisingly only 124 proteins (out of nearly 150,000 proteins) have utilized RDCs as part of their structure determination. Even a smaller subset of these proteins (approximately 7) have utilized RDCs as the primary source of data for structure determination. One key factor in the use of RDCs is the challenging computational and analytical aspects of this source of data. In this report, we demonstrate the success of the REDCRAFT software package in structure determination of proteins using RDC data that can be collected from small and large proteins in a routine fashion. REDCRAFT accomplishes the challenging task of structure determination from RDCs by introducing a unique search and optimization technique that is both robust and computationally tractable. Structure determination from routinely collectable RDC data using REDCRAFT can complement existing methods to provide faster and more accurate studies of larger and more complex protein structures by NMR spectroscopy in solution state.
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46
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Gimenez D, Phelan A, Murphy CD, Cobb SL. 19F NMR as a tool in chemical biology. Beilstein J Org Chem 2021; 17:293-318. [PMID: 33564338 PMCID: PMC7849273 DOI: 10.3762/bjoc.17.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.
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Affiliation(s)
- Diana Gimenez
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
| | - Aoife Phelan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven L Cobb
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
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47
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Becares ER, Pedersen PA, Gourdon P, Gotfryd K. Overproduction of Human Zip (SLC39) Zinc Transporters in Saccharomyces cerevisiae for Biophysical Characterization. Cells 2021; 10:cells10020213. [PMID: 33494457 PMCID: PMC7911073 DOI: 10.3390/cells10020213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
Zinc constitutes the second most abundant transition metal in the human body, and it is implicated in numerous cellular processes, including cell division, DNA and protein synthesis as well as for the catalytic activity of many enzymes. Two major membrane protein families facilitate zinc homeostasis in the animal kingdom, i.e., Zrt/Irt-like proteins (ZIPs aka solute carrier 39, SLC39, family) and Zn transporters (ZnTs), essentially conducting zinc flux in the opposite directions. Human ZIPs (hZIPs) regulate import of extracellular zinc to the cytosol, being critical in preventing overaccumulation of this potentially toxic metal, and crucial for diverse physiological and pathological processes, including development of neurodegenerative disorders and several cancers. To date, our understanding of structure-function relationships governing hZIP-mediated zinc transport mechanism is scarce, mainly due to the notorious difficulty in overproduction of these proteins for biophysical characterization. Here we describe employment of a Saccharomyces cerevisiae-based platform for heterologous expression of hZIPs. We demonstrate that yeast is able to produce four full-length hZIP members belonging to three different subfamilies. One target (hZIP1) is purified in the high quantity and homogeneity required for the downstream biochemical analysis. Our work demonstrates the potential of the described production system for future structural and functional studies of hZIP transporters.
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Affiliation(s)
- Eva Ramos Becares
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK-2200 Copenhagen N, Denmark;
| | - Per Amstrup Pedersen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen OE, Denmark;
| | - Pontus Gourdon
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK-2200 Copenhagen N, Denmark;
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84 Lund, Sweden
- Correspondence: (P.G.); (K.G.); Tel.: +45-503-39990; (+45)-414-02869
| | - Kamil Gotfryd
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK-2200 Copenhagen N, Denmark;
- Correspondence: (P.G.); (K.G.); Tel.: +45-503-39990; (+45)-414-02869
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48
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ENDO Y. Development of a cell-free protein synthesis system for practical use. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:261-276. [PMID: 33980755 PMCID: PMC8141837 DOI: 10.2183/pjab.97.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Conventional cell-free protein synthesis systems had been the major platform to study the mechanism behind translating genetic information into proteins, as proven in the central dogma of molecular biology. Albeit being powerful research tools, most of the in vitro methods at the time failed to produce enough protein for practical use. Tremendous efforts were being made to overcome the limitations of in vitro translation systems, though mostly with limited success. While great knowledge was accumulated on the translation mechanism and ribosome structure, researchers rationalized that it may be impossible to fully reconstitute such a complex molecular process in a test tube. This review will examine how we have solved the difficulties holding back progress. Our newly developed cell-free protein synthesis system is based on wheat embryos and has many excellent characteristics, in addition to its high translation activity and robustness. Combined with other novel elementary technologies, we have established cell-free protein synthesis systems for practical use in research and applied sciences.
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Affiliation(s)
- Yaeta ENDO
- Ehime Prefectural University of Health Sciences, Tobe-cho, Iyo-gun, Ehime, Japan
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49
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Cole C, Parks C, Rachele J, Valafar H. Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package. BMC Bioinformatics 2020; 21:204. [PMID: 33272215 PMCID: PMC7712608 DOI: 10.1186/s12859-020-3522-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/29/2020] [Indexed: 02/08/2023] Open
Abstract
Background Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy is time consuming and expensive. Residual Dipolar Couplings (RDCs) have become an alternate approach for structure calculation by NMR spectroscopy. In previous works, the software package REDCRAFT has been presented as a means of harnessing the information containing in RDCs for structure calculation of proteins. However, to meet its full potential, several improvements to REDCRAFT must be made. Results In this work, we present improvements to REDCRAFT that include increased usability, better interoperability, and a more robust core algorithm. We have demonstrated the impact of the improved core algorithm in the successful folding of the protein 1A1Z with as high as ±4 Hz of added error. The REDCRAFT computed structure from the highly corrupted data exhibited less than 1.0 Å with respect to the X-ray structure. We have also demonstrated the interoperability of REDCRAFT in a few instances including with PDBMine to reduce the amount of required data in successful folding of proteins to unprecedented levels. Here we have demonstrated the successful folding of the protein 1D3Z (to within 2.4 Å of the X-ray structure) using only N-H RDCs from one alignment medium. Conclusions The additional GUI features of REDCRAFT combined with the NEF compliance have significantly increased the flexibility and usability of this software package. The improvements of the core algorithm have substantially improved the robustness of REDCRAFT in utilizing less experimental data both in quality and quantity.
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Affiliation(s)
- Casey Cole
- Department of Computer Science and Engineering, University of South Carolina, M. Bert Storey Engineering and Innovation Center, 550 Assembly St, Columbia, SC, 29201, USA
| | - Caleb Parks
- Department of Computer Science and Engineering, University of South Carolina, M. Bert Storey Engineering and Innovation Center, 550 Assembly St, Columbia, SC, 29201, USA
| | - Julian Rachele
- Department of Computer Science and Engineering, University of South Carolina, M. Bert Storey Engineering and Innovation Center, 550 Assembly St, Columbia, SC, 29201, USA
| | - Homayoun Valafar
- Department of Computer Science and Engineering, University of South Carolina, M. Bert Storey Engineering and Innovation Center, 550 Assembly St, Columbia, SC, 29201, USA.
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Mofradi M, Karimi H, Dashtian K, Ghaedi M. Corn derivative mesoporous carbon microspheres supported hydrophilic polydopamine for development of new membrane: Water treatment containing bovine serum albumin. CHEMOSPHERE 2020; 259:127440. [PMID: 32590178 DOI: 10.1016/j.chemosphere.2020.127440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 06/11/2023]
Abstract
A new mixed matrix membrane (MMM) was prepared by incorporating biological mesoporous carbon microspheres (mCMSs) from corn starch polysaccharide-supported hydrophilic polydopamine (PDA), as a mesoporous and large-surface area filler, selective modifier, and pore-forming agent, into polyvinylidene fluoride (PVDF) matrix in presence of polyethylene glycol (PEG) as a hydrophilic agent. The structural parameters of the prepared membranes were characterized via FE-SEM, BET/BJH, XRD, FT-IR, and AFM analyses, sorption experiments, water permeability assessments, porosimetry tests, flux recovery ratio (FRR) evaluations, and contact angle measurements, with the so-called central composite design (CCD) been successfully applied for optimization and investigation of the effects of the operational parameters. The results were then applied to treat double-distilled water containing bovine serum albumin (BSA) utilizing a cross-module set-up. Based on the findings, the content of the mCMS-PDA in the PVDF matrix significantly affected the contact angle, pure water flux (PWF), FRR, and BSA removal. In this respect, the PWF of the PVDF-PEG-mCMS-PDA increased from 10.25 to 27.78 L/m2 h with increasing the mCMS-PDA content, with the peak FRR (93.84%) of the PVDF-PEG-mCMS-PDA seen at maximum surface hydrophilicity of the membrane.
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Affiliation(s)
- Marziyeh Mofradi
- Chemical Engineering Department, Yasouj University, Yasouj, Iran
| | - Hajir Karimi
- Chemical Engineering Department, Yasouj University, Yasouj, Iran.
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