1
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Baskakova KO, Kuzmichev PK, Karbyshev MS. Advanced applications of Nanodiscs-based platforms for antibodies discovery. Biophys Chem 2024; 313:107290. [PMID: 39002246 DOI: 10.1016/j.bpc.2024.107290] [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: 03/31/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
Due to their fundamental biological importance, membrane proteins (MPs) are attractive targets for drug discovery, with cell surface receptors, transporters, ion channels, and membrane-bound enzymes being of particular interest. However, due to numerous challenges, these proteins present underutilized opportunities for discovering biotherapeutics. Antibodies hold the promise of exquisite specificity and adaptability, making them the ideal candidates for targeting complex membrane proteins. They can target specific conformations of a particular membrane protein and can be engineered into various formats. Generating specific and effective antibodies targeting these proteins is no easy task due to several factors. The antigen's design, antibody-generation strategies, lead optimization technologies, and antibody modalities can be modified to tackle these challenges. The rational employment of cutting-edge lipid nanoparticle systems for retrieving the membrane antigen has been successfully implemented to simplify the mechanism-based therapeutic antibody discovery approach. Despite the highlighted MP production challenges, this review unequivocally underscores the advantages of targeting complex membrane proteins with antibodies and designing membrane protein antigens. Selected examples of lipid nanoparticle success have been illustrated, emphasizing the potential of therapeutic antibody discovery in this regard. With further research and development, we can overcome these challenges and unlock the full potential of therapeutic antibodies directed to target complex MPs.
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Affiliation(s)
- Kristina O Baskakova
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation
| | - Pavel K Kuzmichev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudniy, Russian Federation
| | - Mikhail S Karbyshev
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation; Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, Moscow, Russian Federation.
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2
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Dadsena S, Cuevas Arenas R, Vieira G, Brodesser S, Melo MN, García-Sáez AJ. Lipid unsaturation promotes BAX and BAK pore activity during apoptosis. Nat Commun 2024; 15:4700. [PMID: 38830851 PMCID: PMC11148036 DOI: 10.1038/s41467-024-49067-6] [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: 07/07/2023] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
BAX and BAK are proapoptotic members of the BCL2 family that directly mediate mitochondrial outer membrane permeabilition (MOMP), a central step in apoptosis execution. However, the molecular architecture of the mitochondrial apoptotic pore remains a key open question and especially little is known about the contribution of lipids to MOMP. By performing a comparative lipidomics analysis of the proximal membrane environment of BAK isolated in lipid nanodiscs, we find a significant enrichment of unsaturated species nearby BAK and BAX in apoptotic conditions. We then demonstrate that unsaturated lipids promote BAX pore activity in model membranes, isolated mitochondria and cellular systems, which is further supported by molecular dynamics simulations. Accordingly, the fatty acid desaturase FADS2 not only enhances apoptosis sensitivity, but also the activation of the cGAS/STING pathway downstream mtDNA release. The correlation of FADS2 levels with the sensitization to apoptosis of different lung and kidney cancer cell lines by co-treatment with unsaturated fatty acids supports the relevance of our findings. Altogether, our work provides an insight on how local lipid environment affects BAX and BAK function during apoptosis.
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Affiliation(s)
- Shashank Dadsena
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Rodrigo Cuevas Arenas
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CG, Utrecht, The Netherlands
| | - Gonçalo Vieira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susanne Brodesser
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana J García-Sáez
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne, Germany.
- Department of Membrane Dynamics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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3
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Umar AW, Ahmad N, Xu M. Reviving Natural Rubber Synthesis via Native/Large Nanodiscs. Polymers (Basel) 2024; 16:1468. [PMID: 38891415 PMCID: PMC11174458 DOI: 10.3390/polym16111468] [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: 03/24/2024] [Revised: 04/28/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Natural rubber (NR) is utilized in more than 40,000 products, and the demand for NR is projected to reach $68.5 billion by 2026. The primary commercial source of NR is the latex of Hevea brasiliensis. NR is produced by the sequential cis-condensation of isopentenyl diphosphate (IPP) through a complex known as the rubber transferase (RTase) complex. This complex is associated with rubber particles, specialized organelles for NR synthesis. Despite numerous attempts to isolate, characterize, and study the RTase complex, definitive results have not yet been achieved. This review proposes an innovative approach to overcome this longstanding challenge. The suggested method involves isolating the RTase complex without using detergents, instead utilizing the native membrane lipids, referred to as "natural nanodiscs", and subsequently reconstituting the complex on liposomes. Additionally, we recommend the adaptation of large nanodiscs for the incorporation and reconstitution of the RTase complex, whether it is in vitro transcribed or present within the natural nanodiscs. These techniques show promise as a viable solution to the current obstacles. Based on our experimental experience and insights from published literature, we believe these refined methodologies can significantly enhance our understanding of the RTase complex and its role in in vitro NR synthesis.
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Affiliation(s)
- Abdul Wakeel Umar
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai 519087, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Ming Xu
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai 519087, China
- Guangdong-Hong Kong Joint Laboratory for Carbon Neutrality, Jiangmen Laboratory of Carbon Science and Technology, Jiangmen 529199, China
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4
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Iannotta D, A A, Lai A, Nair S, Koifman N, Lappas M, Salomon C, Wolfram J. Chemically-Induced Lipoprotein Breakdown for Improved Extracellular Vesicle Purification. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307240. [PMID: 38100284 DOI: 10.1002/smll.202307240] [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: 08/21/2023] [Revised: 11/08/2023] [Indexed: 12/17/2023]
Abstract
Extracellular vesicles (EVs) are nanosized biomolecular packages involved in intercellular communication. EVs are released by all cells, making them broadly applicable as therapeutic, diagnostic, and mechanistic components in (patho)physiology. Sample purity is critical for correctly attributing observed effects to EVs and for maximizing therapeutic and diagnostic performance. Lipoprotein contaminants represent a major challenge for sample purity. Lipoproteins are approximately six orders of magnitude more abundant in the blood circulation and overlap in size, shape, and density with EVs. This study represents the first example of an EV purification method based on the chemically-induced breakdown of lipoproteins. Specifically, a styrene-maleic acid (SMA) copolymer is used to selectively breakdown lipoproteins, enabling subsequent size-based separation of the breakdown products from plasma EVs. The use of the polymer followed by tangential flow filtration or size-exclusion chromatography results in improved EV yield, preservation of EV morphology, increased EV markers, and reduced contaminant markers. SMA-based EV purification enables improved fluorescent labeling, reduces interactions with macrophages, and enhances accuracy, sensitivity, and specificity to detect EV biomarkers, indicating benefits for various downstream applications. In conclusion, SMA is a simple and effective method to improve the purity and yield of plasma-derived EVs, which favorably impacts downstream applications.
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Affiliation(s)
- Dalila Iannotta
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Amruta A
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Andrew Lai
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, Faculty of Medicine, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, QLD, 4029, Australia
| | - Soumyalekshmi Nair
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, Faculty of Medicine, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, QLD, 4029, Australia
| | - Na'ama Koifman
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Martha Lappas
- University of Melbourne, Department of Obstetrics and Gynaecology, Australia, and Mercy Hospital for Women, 163 Studley Road, Heidelberg, Victoria, 3084, Australia
| | - Carlos Salomon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, Faculty of Medicine, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, QLD, 4029, Australia
| | - Joy Wolfram
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, 77030, USA
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5
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Renart ML, Giudici AM, González-Ros JM, Poveda JA. Steady-state and time-resolved fluorescent methodologies to characterize the conformational landscape of the selectivity filter of K + channels. Methods 2024; 225:89-99. [PMID: 38508347 DOI: 10.1016/j.ymeth.2024.02.010] [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: 10/13/2023] [Revised: 02/02/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
A variety of equilibrium and non-equilibrium methods have been used in a multidisciplinary approach to study the conformational landscape associated with the binding of different cations to the pore of potassium channels. These binding processes, and the conformational changes resulting therefrom, modulate the functional properties of such integral membrane properties, revealing these permeant and blocking cations as true effectors of such integral membrane proteins. KcsA, a prototypic K+ channel from Streptomyces lividans, has been extensively characterized in this regard. Here, we revise several fluorescence-based approaches to monitor cation binding under different experimental conditions in diluted samples, analyzing the advantages and disadvantages of each approach. These studies have contributed to explain the selectivity, conduction, and inactivation properties of K+ channels at the molecular level, together with the allosteric communication between the two gates that control the ion channel flux, and how they are modulated by lipids.
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Affiliation(s)
- María Lourdes Renart
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - Ana Marcela Giudici
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - José M González-Ros
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - José A Poveda
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
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6
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Young JW, Pfitzner E, van Wee R, Kirschbaum C, Kukura P, Robinson CV. Characterization of membrane protein interactions by peptidisc-mediated mass photometry. iScience 2024; 27:108785. [PMID: 38303728 PMCID: PMC10831248 DOI: 10.1016/j.isci.2024.108785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Membrane proteins perform numerous critical functions in the cell, making many of them primary drug targets. However, their preference for a lipid environment makes them challenging to study using established solution-based methods. Here, we show that peptidiscs, a recently developed membrane mimetic, provide an ideal platform to study membrane proteins and their interactions with mass photometry (MP) in detergent-free conditions. The mass resolution for membrane protein complexes is similar to that achievable with soluble proteins owing to the low carrier heterogeneity. Using the ABC transporter BtuCD, we show that MP can quantify interactions between peptidisc-reconstituted membrane protein receptors and their soluble protein binding partners. Using the BAM complex, we further show that MP reveals interactions between a membrane protein receptor and a bactericidal antibody. Our results highlight the utility of peptidiscs for membrane protein characterization in detergent-free solution and provide a rapid and powerful platform for quantifying membrane protein interactions.
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Affiliation(s)
- John William Young
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Emanuel Pfitzner
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Raman van Wee
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Carla Kirschbaum
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Philipp Kukura
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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7
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Krishnarjuna B, Sharma G, Ravula T, Ramamoorthy A. Factors influencing the detergent-free membrane protein isolation using synthetic nanodisc-forming polymers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184240. [PMID: 37866688 DOI: 10.1016/j.bbamem.2023.184240] [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: 05/12/2023] [Revised: 10/08/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
The detergent-free isolation of membrane proteins using synthetic polymers is becoming the desired approach for functional and structural studies of membrane proteins. Since the expression levels for many membrane proteins are low and a high yield of functionalized reconstituted membrane proteins is essential for in vitro studies, it is crucial to optimize the experimental conditions for a given polymer to solubilize target membranes/proteins effectively. The factors that affect membrane solubilization and subsequently the isolation of a target membrane protein include polymer concentration, polymer charge, temperature, pH, and concentration of divalent metal ions. Therefore, it is important to have knowledge about the efficacy of different types of polymers in solubilizing cell membranes. In this study, we evaluate the efficacy of inulin-based non-ionic polymers in solubilizing E. coli membranes enriched with rat flavin mononucleotide binding-domain (FBD) of cytochrome-P450-reductase (CPR) and rabbit cytochrome-b5 (Cyt-b5) under various solubilization conditions. Our results show that a 1:1 (w/w) membrane:polymer ratio, low temperature, high pH and sub-millimolar concentration of metal ions favor the solubilization of E. coli membranes enriched with FBD or Cyt-b5. Conversely, the presence of excess divalent metal ions affected the final protein levels in the polymer-solubilized samples. We believe that the results from this study provide knowledge to assess and plan the use of non-ionic polymers in membrane protein studies.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Gaurav Sharma
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayyalusamy Ramamoorthy
- National High Magnetic Field Laboratory, Department of Chemical and Biomedical Engineering, Florida State University, Tallahassee, FL 32310, USA.
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8
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Workman CE, Bag P, Cawthon B, Ali FH, Brady NG, Bruce BD, Long BK. Alternatives to Styrene- and Diisobutylene-Based Copolymers for Membrane Protein Solubilization via Nanodisc Formation. Angew Chem Int Ed Engl 2023; 62:e202306572. [PMID: 37682083 PMCID: PMC10591821 DOI: 10.1002/anie.202306572] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/09/2023]
Abstract
Styrene-maleic acid copolymers (SMAs), and related amphiphilic copolymers, are promising tools for isolating and studying integral membrane proteins in a native-like state. However, they do not exhibit this ability universally, as several reports have found that SMAs and related amphiphilic copolymers show little to no efficiency when extracting specific membrane proteins. Recently, it was discovered that esterified SMAs could enhance the selective extraction of trimeric Photosystem I from the thylakoid membranes of thermophilic cyanobacteria; however, these polymers are susceptible to saponification that can result from harsh preparation or storage conditions. To address this concern, we herein describe the development of α-olefin-maleic acid copolymers (αMAs) that can extract trimeric PSI from cyanobacterial membranes with the highest extraction efficiencies observed when using any amphiphilic copolymers, including diisobutylene-co-maleic acid (DIBMA) and functionalized SMA samples. Furthermore, we will show that αMAs facilitate the formation of photosystem I-containing nanodiscs that retain an annulus of native lipids and a native-like activity. We also highlight how αMAs provide an agile, tailorable synthetic platform that enables fine-tuning hydrophobicity, controllable molar mass, and consistent monomer incorporation while overcoming shortcomings of prior amphiphilic copolymers.
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Affiliation(s)
| | - Pushan Bag
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Bridgie Cawthon
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Fidaa H Ali
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Nathan G Brady
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Barry D Bruce
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, USA
| | - Brian K Long
- Department of Chemistry, University of Tennessee, Knoxville, USA
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9
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Rainsford P, Rylandsholm FG, Jakubec M, Silk M, Juskewitz E, Ericson JU, Svendsen JS, Engh RA, Isaksson J. Label-free measurement of antimicrobial peptide interactions with lipid vesicles and nanodiscs using microscale thermophoresis. Sci Rep 2023; 13:12619. [PMID: 37537266 PMCID: PMC10400562 DOI: 10.1038/s41598-023-39785-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023] Open
Abstract
One strategy to combat antimicrobial resistance is the discovery of new classes of antibiotics. Most antibiotics will at some point interact with the bacterial membrane to either interfere with its integrity or to cross it. Reliable and efficient tools for determining the dissociation constant for membrane binding (KD) and the partitioning coefficient between the aqueous- and membrane phases (KP) are therefore important tools for discovering and optimizing antimicrobial hits. Here we demonstrate that microscale thermophoresis (MST) can be used for label-free measurement of KD by utilising the intrinsic fluorescence of tryptophan and thereby removing the need for chromophore labelling. As proof of principle, we have used the method to measure the binding of a set of small cyclic AMPs to large unilamellar vesicles (LUVs) and two types of lipid nanodiscs assembled by styrene maleic acid (SMA) and quaternary ammonium SMA (SMA-QA). The measured KD values correlate well with the corresponding measurements using surface plasmon resonance (SPR), also broadly reflecting the tested AMPs' minimal inhibition concentration (MIC) towards S. aureus and E. coli. We conclude that MST is a promising method for fast and cost-efficient detection of peptide-lipid interactions or mapping of sample conditions in preparation for more advanced studies that rely on expensive sample preparation, labelling and/or instrument time.
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Affiliation(s)
- Philip Rainsford
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Fredrik G Rylandsholm
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Martin Jakubec
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Mitchell Silk
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Eric Juskewitz
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Johanna U Ericson
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - John-Sigurd Svendsen
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Richard A Engh
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway.
- Natural Products and Medicinal Chemistry, Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway.
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10
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Pettersen JM, Yang Y, Robinson AS. Advances in nanodisc platforms for membrane protein purification. Trends Biotechnol 2023; 41:1041-1054. [PMID: 36935323 DOI: 10.1016/j.tibtech.2023.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 03/19/2023]
Abstract
Membrane scaffold protein nanodiscs (MSPNDs) are an invaluable tool for improving purified membrane protein (MP) stability and activity compared to traditional micellar methods, thus enabling an increase in high-resolution MP structures, particularly in concert with cryogenic electron microscopy (cryo-EM) approaches. In this review we highlight recent advances and breakthroughs in MSPND methodology and applications. We also introduce and discuss saposin-lipoprotein nanoparticles (salipros) and copolymer nanodiscs which have recently emerged as authentic MSPND alternatives. We compare the advantages and disadvantages of MSPNDs, salipros, and copolymer nanodisc technologies to highlight potential opportunities for using each platform for MP purification and characterization.
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Affiliation(s)
- John M Pettersen
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yaxin Yang
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Anne S Robinson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
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11
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Trinh TKH, Cabezas AJ, Joshi S, Catalano C, Siddique AB, Qiu W, Deshmukh S, des Georges A, Guo Y. pH-tunable membrane-active polymers, NCMNP2a- x, and their potential membrane protein applications. Chem Sci 2023; 14:7310-7326. [PMID: 37416719 PMCID: PMC10321531 DOI: 10.1039/d3sc01890c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Accurate 3D structures of membrane proteins are essential for comprehending their mechanisms of action and designing specific ligands to modulate their activities. However, these structures are still uncommon due to the involvement of detergents in the sample preparation. Recently, membrane-active polymers have emerged as an alternative to detergents, but their incompatibility with low pH and divalent cations has hindered their efficacy. Herein, we describe the design, synthesis, characterization, and application of a new class of pH-tunable membrane-active polymers, NCMNP2a-x. The results demonstrated that NCMNP2a-x could be used for high-resolution single-particle cryo-EM structural analysis of AcrB in various pH conditions and can effectively solubilize BcTSPO with the function preserved. Molecular dynamic simulation is consistent with experimental data that shed great insights into the working mechanism of this class of polymers. These results demonstrated that NCMNP2a-x might have broad applications in membrane protein research.
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Affiliation(s)
- Thi Kim Hoang Trinh
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Andres Jorge Cabezas
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York New York New York 10017 USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York New York New York 10017 USA
| | - Soumil Joshi
- Department of Chemical Engineering, Virginia Tech Blacksburg VA2 4060 USA
| | - Claudio Catalano
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Abu Bakkar Siddique
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Sanket Deshmukh
- Department of Chemical Engineering, Virginia Tech Blacksburg VA2 4060 USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York New York New York 10017 USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York New York New York 10017 USA
- Department of Chemistry & Biochemistry, City College of New York New York New York 10017 USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
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12
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Real Hernandez LM, Levental I. Lipid packing is disrupted in copolymeric nanodiscs compared with intact membranes. Biophys J 2023; 122:2256-2266. [PMID: 36641625 PMCID: PMC10257115 DOI: 10.1016/j.bpj.2023.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/02/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Discoidal lipid-protein nanoparticles known as nanodiscs are widely used tools in structural and membrane biology. Amphipathic, synthetic copolymers have recently become an attractive alternative to membrane scaffold proteins for the formation of nanodiscs. Such copolymers can directly intercalate into, and form nanodiscs from, intact membranes without detergents. Although these copolymer nanodiscs can extract native membrane lipids, it remains unclear whether native membrane properties are also retained. To determine the extent to which bilayer lipid packing is retained in nanodiscs, we measured the behavior of packing-sensitive fluorescent dyes in various nanodisc preparations compared with intact lipid bilayers. We analyzed styrene-maleic acid (SMA), diisobutylene-maleic acid (DIBMA), and polymethacrylate (PMA) as nanodisc scaffolds at various copolymer-to-lipid ratios and temperatures. Measurements of Laurdan spectral shifts revealed that dimyristoyl-phosphatidylcholine (DMPC) nanodiscs had increased lipid headgroup packing compared with large unilamellar vesicles (LUVs) above the lipid melting temperature for all three copolymers. Similar effects were observed for DMPC nanodiscs stabilized by membrane scaffolding protein MSP1E1. Increased lipid headgroup packing was also observed when comparing nanodiscs with intact membranes composed of binary mixtures of 1-palmitoyl-2-oleoyl-phosphocholine (POPC) and di-palmitoyl-phosphocholine (DPPC), which show fluid-gel-phase coexistence. Similarly, Laurdan reported increased headgroup packing in nanodiscs for biomimetic mixtures containing cholesterol, most notable for relatively disordered membranes. The magnitudes of these ordering effects were not identical for the various copolymers, with SMA being the most and DIBMA being the least perturbing. Finally, nanodiscs derived from mammalian cell membranes showed similarly increased lipid headgroup packing. We conclude that nanodiscs generally do not completely retain the physical properties of intact membranes.
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Affiliation(s)
- Luis M Real Hernandez
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia.
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13
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Scherhag A, Räschle M, Unbehend N, Venn B, Glueck D, Mühlhaus T, Keller S, Pérez Patallo E, Zehner S, Frankenberg-Dinkel N. Characterization of a soluble library of the Pseudomonas aeruginosa PAO1 membrane proteome with emphasis on c-di-GMP turnover enzymes. MICROLIFE 2023; 4:uqad028. [PMID: 37441524 PMCID: PMC10335732 DOI: 10.1093/femsml/uqad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/30/2023] [Indexed: 07/15/2023]
Abstract
Studies of protein-protein interactions in membranes are very important to fully understand the biological function of a cell. The extraction of proteins from the native membrane environment is a critical step in the preparation of membrane proteins that might affect the stability of protein complexes. In this work, we used the amphiphilic diisobutylene/maleic acid copolymer to extract the membrane proteome of the opportunistic pathogen Pseudomonas aeruginosa, thereby creating a soluble membrane-protein library within a native-like lipid-bilayer environment. Size fractionation of nanodisc-embedded proteins and subsequent mass spectrometry enabled the identification of 3358 proteins. The native membrane-protein library showed a very good overall coverage compared to previous proteome data. The pattern of size fractionation indicated that protein complexes were preserved in the library. More than 20 previously described complexes, e.g. the SecYEG and Pili complexes, were identified and analyzed for coelution. Although the mass-spectrometric dataset alone did not reveal new protein complexes, combining pulldown assays with mass spectrometry was successful in identifying new protein interactions in the native membrane-protein library. Thus, we identified several candidate proteins for interactions with the membrane phosphodiesterase NbdA, a member of the c-di-GMP network. We confirmed the candidate proteins CzcR, PA4200, SadC, and PilB as novel interaction partners of NbdA using the bacterial adenylate cyclase two-hybrid assay. Taken together, this work demonstrates the usefulness of the native membrane-protein library of P. aeruginosa for the investigation of protein interactions and membrane-protein complexes. Data are available via ProteomeXchange with identifiers PXD039702 and PXD039700.
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Affiliation(s)
- Anna Scherhag
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Markus Räschle
- Department of Molecular Genetics, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Niklas Unbehend
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Benedikt Venn
- Department of Computational Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - David Glueck
- Department of Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Department of Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Timo Mühlhaus
- Department of Computational Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Sandro Keller
- Department of Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Department of Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Eugenio Pérez Patallo
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | | | - Nicole Frankenberg-Dinkel
- Corresponding author. RPTU Kaiserslautern-Landau, Microbiology, Kaiserslautern 67655, Germany. E-mail:
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14
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Zhou Y, Syed JH, Semchonok DA, Wright E, Kyrilis FL, Hamdi F, Kastritis PL, Bruce BD, Reynolds TB. Solubilization, purification, and characterization of the hexameric form of phosphatidylserine synthase from Candida albicans. J Biol Chem 2023:104756. [PMID: 37116705 DOI: 10.1016/j.jbc.2023.104756] [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: 12/16/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023] Open
Abstract
Phosphatidylserine (PS) synthase from Candida albicans, encoded by the CHO1 gene, has been identified as a potential drug target for new antifungals against systemic candidiasis. Rational drug design or small molecule screening are effective ways to identify specific inhibitors of Cho1, but both will be facilitated by protein purification. Due to the transmembrane nature of Cho1, methods were needed to solubilize and purify the native form of Cho1. Here, we used six non-ionic detergents and three styrene maleic acids (SMAs) to solubilize an HA-tagged Cho1 protein from the total microsomal fractions. Blue native PAGE (BN-PAGE) and immunoblot analysis revealed a single band corresponding to Cho1 in all detergent-solubilized fractions, while two bands were present in the SMA2000-solubilized fraction. Our enzymatic assay suggests that digitonin- or DDM-solubilized enzyme has the most PS synthase activity. Pull-downs of HA-tagged Cho1 in the digitonin-solubilized fraction reveal an apparent MW of Cho1 consistent with a hexamer. Furthermore, negative-staining electron microscopy analysis and AlphaFold2 structure prediction modeling suggest the hexamer is composed of a trimer of dimers. We purified Cho1 protein to near-homogeneity as a hexamer using affinity chromatography and TEV protease treatment, and optimized Cho1 enzyme activity for manganese and detergent concentrations, temperature (24°C), and pH (8.0). The purified Cho1 has a Km for its substrate CDP-diacylglycerol of 72.20 μM with a Vmax of 0.079 nmol/(μg*min) while exhibiting a sigmoidal kinetic curve for its other substrate serine, indicating cooperative binding. Purified hexameric Cho1 can potentially be used in downstream structure determination and small drug screening.
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Affiliation(s)
- Yue Zhou
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States
| | - Jawhar H Syed
- Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Edward Wright
- Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Barry D Bruce
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States; Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States
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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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Kamilar E, Bariwal J, Zheng W, Ma H, Liang H. SMALPs Are Not Simply Nanodiscs: The Polymer-to-Lipid Ratios of Fractionated SMALPs Underline Their Heterogeneous Nature. Biomacromolecules 2023; 24:1819-1838. [PMID: 36947865 DOI: 10.1021/acs.biomac.3c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Amphipathic styrene-maleic acid (SMA) copolymers directly solubilize biomembranes into SMA-lipid particles, or SMALPs, that are often regarded as nanodiscs and hailed as a native membrane platform. The promising outlook of SMALPs inspires the discovery of many SMA-like copolymers that also solubilize biomembranes into putative nanodiscs, but a fundamental question remains on how much the SMALPs or SMALP analogues truly resemble the bilayer structure of nanodiscs. This unfortunate ambiguity undermines the utility of SMA or SMA-like copolymers in membrane biology because the structure and function of many membrane proteins depend critically on their surrounding matrices. Here, we report the structural heterogeneity of SMALPs revealed through fractionating SMALPs comprised of lipids and well-defined SMAs via size-exclusion chromatography followed by quantitative determination of the polymer-to-lipid (P/L) stoichiometric ratios in individual fractions. Through the lens of P/L stoichiometric ratios, different self-assembled polymer-lipid nanostructures are inferred, such as polymer-remodeled liposomes, polymer-encased nanodiscs, polymer-lipid mixed micelles, and lipid-doped polymer micellar aggregates. We attribute the structural heterogeneity of SMALPs to the microstructure variations amongst individual polymer chains that give rise to their polydisperse detergency. As an example, we demonstrate that SMAs with a similar S/MA ratio but different chain sizes participate preferentially in different polymer-lipid nanostructures. We further demonstrate that proteorhodopsin, a light-driven proton pump solubilized within the same SMALPs is distributed amongst different self-assembled nanostructures to display different photocycle kinetics. Our discovery challenges the native nanodisc notion of SMALPs or SMALP analogues and highlights the necessity to separate and identify the structurally dissimilar polymer-lipid particles in membrane biology studies.
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Affiliation(s)
- Elizabeth Kamilar
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Jitender Bariwal
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Wan Zheng
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hairong Ma
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hongjun Liang
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
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17
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Eggenreich L, Vargas C, Kolar C, Keller S. Lipid exchange among electroneutral Sulfo-DIBMA nanodiscs is independent of ion concentration. Biol Chem 2023:hsz-2022-0319. [PMID: 36921292 DOI: 10.1515/hsz-2022-0319] [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: 10/31/2022] [Accepted: 02/21/2023] [Indexed: 03/17/2023]
Abstract
Polymer-encapsulated nanodiscs enable membrane proteins to be investigated within a native-like lipid-bilayer environment. Unlike other bilayer-based membrane mimetics, these nanodiscs are equilibrium structures that permit lipid exchange on experimentally relevant timescales. Therefore, examining the kinetics and mechanisms of lipid exchange is of great interest. Since the high charge densities of existing anionic polymers can interfere with protein-protein and protein-lipid interactions as well as charge-sensitive analysis techniques, electroneutral nanodisc-forming polymers have been recently introduced. However, it has remained unclear how the electroneutrality of these polymers affects the lipid-exchange behavior of the nanodiscs. Here, we use time-resolved Förster resonance energy transfer to study the kinetics and the mechanisms of lipid exchange among nanodiscs formed by the electroneutral polymer Sulfo-DIBMA. We also examine the role of coulombic repulsion and specific counterion association in lipid exchange. Our results show that Sulfo-DIBMA nanodiscs exchange lipids on a similar timescale as DIBMA nanodiscs. In contrast with nanodiscs made from polyanionic DIBMA, however, the presence of mono- and divalent cations does not influence lipid exchange among Sulfo-DIBMA nanodiscs, as expected from their electroneutrality. The robustness of Sulfo-DIBMA nanodiscs against varying ion concentrations opens new possibilities for investigating charge-sensitive processes involving membrane proteins.
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Affiliation(s)
- Loretta Eggenreich
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, A-8010 Graz, Austria.,Field of Excellence BioHealth, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Carolyn Vargas
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, A-8010 Graz, Austria.,Field of Excellence BioHealth, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Cenek Kolar
- Glycon Biochemicals GmbH, Im Biotechnologiepark TGZ 1, D-14943 Luckenwalde, Germany
| | - Sandro Keller
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, A-8010 Graz, Austria.,Field of Excellence BioHealth, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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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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Bérczi A, Márton Z, Laskay K, Tóth A, Rákhely G, Duzs Á, Sebők-Nagy K, Páli T, Zimányi L. Spectral and Redox Properties of a Recombinant Mouse Cytochrome b561 Protein Suggest Transmembrane Electron Transfer Function. Molecules 2023; 28:molecules28052261. [PMID: 36903505 PMCID: PMC10005133 DOI: 10.3390/molecules28052261] [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: 02/02/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Cytochrome b561 proteins (CYB561s) are integral membrane proteins with six trans-membrane domains, two heme-b redox centers, one on each side of the host membrane. The major characteristics of these proteins are their ascorbate reducibility and trans-membrane electron transferring capability. More than one CYB561 can be found in a wide range of animal and plant phyla and they are localized in membranes different from the membranes participating in bioenergization. Two homologous proteins, both in humans and rodents, are thought to participate-via yet unidentified way-in cancer pathology. The recombinant forms of the human tumor suppressor 101F6 protein (Hs_CYB561D2) and its mouse ortholog (Mm_CYB561D2) have already been studied in some detail. However, nothing has yet been published about the physical-chemical properties of their homologues (Hs_CYB561D1 in humans and Mm_CYB561D1 in mice). In this paper we present optical, redox and structural properties of the recombinant Mm_CYB561D1, obtained based on various spectroscopic methods and homology modeling. The results are discussed in comparison to similar properties of the other members of the CYB561 protein family.
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Affiliation(s)
- Alajos Bérczi
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Zsuzsanna Márton
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Krisztina Laskay
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - András Tóth
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Gábor Rákhely
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Ágnes Duzs
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Correspondence:
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20
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [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: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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21
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Levental I, Lyman E. Regulation of membrane protein structure and function by their lipid nano-environment. Nat Rev Mol Cell Biol 2023; 24:107-122. [PMID: 36056103 PMCID: PMC9892264 DOI: 10.1038/s41580-022-00524-4] [Citation(s) in RCA: 150] [Impact Index Per Article: 150.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 02/04/2023]
Abstract
Transmembrane proteins comprise ~30% of the mammalian proteome, mediating metabolism, signalling, transport and many other functions required for cellular life. The microenvironment of integral membrane proteins (IMPs) is intrinsically different from that of cytoplasmic proteins, with IMPs solvated by a compositionally and biophysically complex lipid matrix. These solvating lipids affect protein structure and function in a variety of ways, from stereospecific, high-affinity protein-lipid interactions to modulation by bulk membrane properties. Specific examples of functional modulation of IMPs by their solvating membranes have been reported for various transporters, channels and signal receptors; however, generalizable mechanistic principles governing IMP regulation by lipid environments are neither widely appreciated nor completely understood. Here, we review recent insights into the inter-relationships between complex lipidomes of mammalian membranes, the membrane physicochemical properties resulting from such lipid collectives, and the regulation of IMPs by either or both. The recent proliferation of high-resolution methods to study such lipid-protein interactions has led to generalizable insights, which we synthesize into a general framework termed the 'functional paralipidome' to understand the mutual regulation between membrane proteins and their surrounding lipid microenvironments.
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Affiliation(s)
- Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Molecular and Cell Physiology, University of Virginia, Charlottesville, VA, USA.
| | - Ed Lyman
- Department of Physics and Astronomy, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
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22
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Sinha S, Kumar S, Singh K, Umam F, Agrawal V, Aggarwal A, Imperiali B. Immunochemical characterisation of styrene maleic acid lipid particles prepared from Mycobacterium tuberculosis plasma membrane. PLoS One 2023; 18:e0280074. [PMID: 36608027 PMCID: PMC9821473 DOI: 10.1371/journal.pone.0280074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
Membrane proteins of Mycobacterium tuberculosis (Mtb) can be targeted for the development of therapeutic and prophylactic interventions against tuberculosis. We have utilized the unique membrane-solubilising properties of the styrene maleic acid copolymer <styrene:maleic acid::2:1> (SMA) to prepare and characterise 'styrene maleic acid lipid particles' from the native membrane of Mtb (MtM-SMALPs). When resolved by SDS-PAGE and visualised with coomassie blue, the molecular weights of Mtb membrane (MtM) proteins solubilised by SMA were mostly in the range of 40-70 kDa. When visualised by transmission electron microscopy, MtM-SMALPs appeared as nanoparticles of discrete shapes and sizes. The discoid nanoparticles exhibited a range of diameters of ~10-90 nm, with largest portion (~61%) ranging from 20-40 nm. MtM proteins of a molecular weight-range overlapping with that of MtM-SMALPs were also amenable to chemical cross-linking, revealing protein complex formation. Characterisation using monoclonal antibodies against seven MtM-associated antigens confirmed the incorporation of the inner membrane protein PRA, membrane-associated proteins PstS1, LpqH and Ag85, and the lipoglycan LAM into MtM-SMALPs. Conversely, the peripheral membrane proteins Acr and PspA were nearly completely excluded. Furthermore, although MtM showed an abundance of Con A-binding glycoproteins, MtM-SMALPs appeared devoid of these species. Immune responses of healthcare workers harbouring 'latent TB infection' provided additional insights. While MtM-SMALPs and MtM induced comparable levels of the cytokine IFN-γ, only MtM-SMALPs could induce the production of TNF-α. Antibodies present in the donor sera showed significantly higher binding to MtM than to MtM-SMALPs. These results have implications for the development of MtM-based immunoprophylaxis against tuberculosis.
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Affiliation(s)
- Sudhir Sinha
- Department of Clinical Immunology & Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
- * E-mail:
| | - Shashikant Kumar
- Department of Clinical Immunology & Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Komal Singh
- Department of Clinical Immunology & Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Fareha Umam
- Department of Clinical Immunology & Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Vinita Agrawal
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Amita Aggarwal
- Department of Clinical Immunology & Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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23
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Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022; 41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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24
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Krishnarjuna B, Im SC, Ravula T, Marte J, Auchus RJ, Ramamoorthy A. Non-Ionic Inulin-Based Polymer Nanodiscs Enable Functional Reconstitution of a Redox Complex Composed of Oppositely Charged CYP450 and CPR in a Lipid Bilayer Membrane. Anal Chem 2022; 94:11908-11915. [PMID: 35977417 PMCID: PMC10851674 DOI: 10.1021/acs.analchem.2c02489] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Although polymer-based lipid nanodiscs are increasingly used in the structural studies of membrane proteins, the charge of the belt-forming polymer is a major limitation for functional reconstitution of membrane proteins possessing an opposite net charge to that of the polymer. This limitation also rules out the reconstitution of a protein-protein complex composed of oppositely charged membrane proteins. In this study, we report the first successful functional reconstitution of a membrane-bound redox complex constituting a cationic cytochrome P450 (CYP450) and an anionic cytochrome P450 reductase (CPR) in non-ionic inulin-based lipid nanodiscs. The gel-to-liquid-crystalline phase-transition temperature (Tm) of DMPC:DMPG (7:3 w/w) lipids in polymer nanodiscs was determined by differential scanning calorimetry (DSC) and 31P NMR experiments. The CYP450-CPR redox complex reconstitution in polymer nanodiscs was characterized by size-exclusion chromatography (SEC), and the electron transfer kinetics was carried out using the stopped-flow technique under anaerobic conditions. The Tm of DMPC:DMPG (7:3 w/w) in polymer nanodiscs measured from 31P NMR agrees with that obtained from DSC and was found to be higher than that for liposomes due to the decreased cooperativity of lipids present in the nanodiscs. The stopped-flow measurements revealed the CYP450-CPR redox complex reconstituted in nanodiscs to be functional, and the electron transfer kinetics was found to be temperature-dependent. Based on the successful demonstration of the use of non-ionic inulin-based polymer nanodiscs reported in this study, we expect them to be useful in studying the function and structures of a variety of membrane proteins/complexes irrespective of the charge of the molecular components. Since the polymer nanodiscs were shown to align in an externally applied magnetic field, they can also be used to measure residual dipolar couplings (RDCs) and residual quadrupolar couplings (RQCs) for various molecules ranging from small molecules to soluble proteins and nucleic acids.
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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
| | - Sang-Choul Im
- Department of Pharmacology and Internal Medicine, Division of Metabolism, Endocrinology, & Diabetes, University of Michigan, Ann Arbor, MI 48109
| | - 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
| | - 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
| | - Richard J. Auchus
- Department of Pharmacology and Internal Medicine, Division of Metabolism, Endocrinology, & Diabetes, University of Michigan, Ann Arbor, MI 48109
| | - 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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25
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van Walree CA. Intramolecular Hydrogen Bonding in DIBMA Model Compounds. MACROMOL THEOR SIMUL 2022. [DOI: 10.1002/mats.202200042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Cornelis A. van Walree
- Membrane Biochemistry and Biophysics Utrecht University Padualaan 8 Utrecht 3584 CH Netherlands
- University College Utrecht Campusplein 1 Utrecht 3584 ED the Netherlands
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26
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Punyamoonwongsa P. Lipid nanodiscs of poly(styrene- alt-maleic acid) to enhance plant antioxidant extraction. E-POLYMERS 2022. [DOI: 10.1515/epoly-2022-0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Plant antioxidants can be applied in the management of various human diseases. Despite these, extraction of these compounds still suffers from residual solvent impurities, low recovery yields, and the risks of undesirable chemical changes. Inspired by the protein–lipid interactions in the cell membranes, we proposed using poly(styrene-alt-maleic acid) (PSMA) to destabilize and associate with the bilayer lipids into the membrane-like nanodiscs. Such nanostructures could serve as protective reservoirs for the active compounds to reside with preserved bioactivities. This concept was demonstrated in the antioxidant extraction from robusta coffee leaves. Results indicated that aqueous PSMA extraction (no buffer agent) yielded products with the highest contents of phenolic acids (11.6 mg GAE·g−1) and flavonoids (9.6 mg CE·g−1). They also showed the highest antioxidant activity (IC50 = 3.7 µg·mL−1) compared to those obtained by typical sodium dodecyl sulfate and water extraction. This biomimetic approach could be considered for developing environmentally friendly extraction protocols in the future.
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27
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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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28
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The function of BK channels extracted and purified within SMALPs. Biochem J 2022; 479:1609-1619. [PMID: 35851603 PMCID: PMC9444072 DOI: 10.1042/bcj20210628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]
Abstract
Human BK channels are large voltage and Ca2+-activated K+ channels, involved in several important functions within the body. The core channel is a tetramer of α subunits, and its function is modulated by the presence of β and γ accessory subunits. BK channels composed of α subunits, as well as BK channels composed of α and β1 subunits, were successfully solubilised from HEK cells with styrene maleic acid (SMA) polymer and purified by nickel affinity chromatography. Native SMA–PAGE analysis of the purified proteins showed the α subunits were extracted as a tetramer. In the presence of β1 subunits, they were co-extracted with the α subunits as a heteromeric complex. Purified SMA lipid particles (SMALPs) containing BK channel could be inserted into planar lipid bilayers (PLB) and single channel currents recorded, showing a high conductance (≈260 pS), as expected. The open probability was increased in the presence of co-purified β1 subunits. However, voltage-dependent gating of the channel was restricted. In conclusion, we have demonstrated that SMA can be used to effectively extract and purify large, complex, human ion channels, from low expressing sources. That these large channels can be incorporated into PLB from SMALPs and display voltage-dependent channel activity. However, the SMA appears to reduce the voltage dependent gating of the channels.
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29
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Mouhib M, Chi CN. Solution nuclear magnetic resonance spectroscopy of bacterial outer membrane proteins in natively excreted vesicles using engineered Escherichia coli. Microbiologyopen 2022; 11:e1302. [PMID: 35765189 PMCID: PMC9234478 DOI: 10.1002/mbo3.1302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/30/2022] [Indexed: 11/12/2022] Open
Abstract
Gaining structural information on membrane proteins in their native lipid environment is a long-standing challenge in molecular biology. Instead, it is common to employ membrane mimetics, which has been shown to affect protein structure, dynamics, and function severely. Here, we describe the incorporation of a bacterial outer membrane protein (OmpW) into natively excreted membrane vesicles for solution nuclear magnetic resonance (NMR) spectroscopy using a mutant Escherichia coli strain with a high outer membrane vesicle (OMV) production rate. We collected NMR spectra from both vesicles containing overexpressed OmpW and vesicles from a control strain to account for the presence of physiologically relevant outer membrane proteins in vesicles and observed distinct resonance signals from OmpW. Due to the increased production of OMVs and the use of non-uniform sampling techniques we were able to obtain high-resolution 2D (HSQC) and 3D (HNCO) NMR spectra of our target protein inside its native lipid environment. While this workflow is not yet sufficient to achieve in situ structure determination, our results pave the way for further research on vesicle-based solution NMR spectroscopy.
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Affiliation(s)
- Mohammed Mouhib
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Institute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Celestine N. Chi
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
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30
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Nishimura T, Hatatani Y, Ando M, Sasaki Y, Akiyoshi K. Single-component nanodiscs via the thermal folding of amphiphilic graft copolymers with the adjusted flexibility of the main chain. Chem Sci 2022; 13:5243-5251. [PMID: 35655565 PMCID: PMC9093194 DOI: 10.1039/d2sc01674e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 12/26/2022] Open
Abstract
Nanodiscs have attracted considerable attention as structural scaffolds for membrane-protein research and as biomaterials in e.g. drug-delivery systems. However, conventional disc-fabrication methods are usually laborious, and disc fabrication via the self-assembly of amphiphiles is difficult. Herein, we report the formation of polymer nanodiscs based on the self-assembly of amphiphilic graft copolymers by adjusting the persistence length of the main chain. Amphiphilic graft copolymers with a series of different main-chain persistence lengths were prepared and these formed, depending on the persistence length, either rods, discs, or vesicles. Notably, polymer nanodiscs were formed upon heating a chilled polymer solution without the need for any additives, and the thus obtained nanodiscs were used to solubilize a membrane protein during cell-free protein synthesis. Given the simplicity of this disc-fabrication method and the ability of these discs to solubilize membrane proteins, this study considerably expands the fundamental and practical scope of graft-copolymer nanodiscs and demonstrates their utility as tools for studying the structure and function of membrane proteins.
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Affiliation(s)
- Tomoki Nishimura
- Department of Chemistry and Materials, Faculty of Textile Science and Technology, Shinshu University 3-15-1, Tokida Ueda Nagano 386-8567 Japan
| | - Yusuke Hatatani
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Mitsuru Ando
- Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University Shogoin Kawahara-cho, Sakyo-ku Kyoto 606-8507 Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
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31
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Zhu L, Zhao H, Wang Y, Yu C, Liu J, Li L, Li Z, Zhang J, Dai H, Wang J, Zhu L. Solubilization, purification, and ligand binding characterization of G protein-coupled receptor SMO in native membrane bilayer using styrene maleic acid copolymer. PeerJ 2022; 10:e13381. [PMID: 35529497 PMCID: PMC9074879 DOI: 10.7717/peerj.13381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 01/13/2023] Open
Abstract
Smoothened (SMO) protein is a member of the G protein-coupled receptor (GPCR) family that is involved in the Hedgehog (Hh) signaling pathway. It is a putative target for treating various cancers, including medulloblastoma and basal cell carcinoma (BCC). Characterizing membrane proteins such as SMO in their native state is highly beneficial for the development of effective pharmaceutical drugs, as their structures and functions are retained to the highest extent in this state. Therefore, although SMO protein is conventionally solubilized in detergent micelles, incorporating the protein in a lipid-based membrane mimic is still required. In this study, we used styrene maleic acid (SMA) copolymer that directly extracted membrane protein and surrounding lipids as well as formed the so-called polymer nanodiscs, to solubilize and purify the SMO transmembrane domain encapsulated by SMA-nanodiscs. The obtained SMA-nanodiscs showed high homogeneity and maintained the physiological activity of SMO protein, thereby enabling the measurement of the dissociation constant (Kd) for SMO ligands SMO-ligands Shh Signaling Antagonist V (SANT-1) and Smoothened Agonist (SAG) using ligand-based solution nuclear magnetic resonance spectroscopy. This work paves the way for investigating the structure, function, and drug development of SMO proteins in a native-like lipid environment.
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Affiliation(s)
- Lina Zhu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China,High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hongxin Zhao
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Yizhuo Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Chuandi Yu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Juanjuan Liu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Ling Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Zehua Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Han Dai
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Junfeng Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China,High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Lei Zhu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
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32
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Wang C, Sani ES, Gao W. Wearable Bioelectronics for Chronic Wound Management. ADVANCED FUNCTIONAL MATERIALS 2022; 32:2111022. [PMID: 36186921 PMCID: PMC9518812 DOI: 10.1002/adfm.202111022] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 05/05/2023]
Abstract
Chronic wounds are a major healthcare issue and can adversely affect the lives of millions of patients around the world. The current wound management strategies have limited clinical efficacy due to labor-intensive lab analysis requirements, need for clinicians' experiences, long-term and frequent interventions, limiting therapeutic efficiency and applicability. The growing field of flexible bioelectronics enables a great potential for personalized wound care owing to its advantages such as wearability, low-cost, and rapid and simple application. Herein, recent advances in the development of wearable bioelectronics for monitoring and management of chronic wounds are comprehensively reviewed. First, the design principles and the key features of bioelectronics that can adapt to the unique wound milieu features are introduced. Next, the current state of wound biosensors and on-demand therapeutic systems are summarized and highlighted. Furthermore, we discuss the design criteria of the integrated closed loop devices. Finally, the future perspectives and challenges in wearable bioelectronics for wound care are discussed.
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Affiliation(s)
- Canran Wang
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ehsan Shirzaei Sani
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wei Gao
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
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33
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Catania R, Machin J, Rappolt M, Muench SP, Beales PA, Jeuken LJC. Detergent-Free Functionalization of Hybrid Vesicles with Membrane Proteins Using SMALPs. Macromolecules 2022; 55:3415-3422. [PMID: 35571225 PMCID: PMC9097535 DOI: 10.1021/acs.macromol.2c00326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/08/2022] [Indexed: 11/28/2022]
Abstract
![]()
Hybrid
vesicles (HVs) that consist of mixtures of block copolymers
and lipids are robust biomimetics of liposomes, providing a valuable
building block in bionanotechnology, catalysis, and synthetic biology.
However, functionalization of HVs with membrane proteins remains laborious
and expensive, creating a significant current challenge in the field.
Here, using a new approach of extraction with styrene-maleic acid
(SMA), we show that a membrane protein (cytochrome bo3) directly transfers into HVs with an efficiency of 73.9
± 13.5% without the requirement of detergent, long incubation
times, or mechanical disruption. Direct transfer of membrane proteins
using this approach was not possible into liposomes, suggesting that
HVs are more amenable than liposomes to membrane protein incorporation
from a SMA lipid particle system. Finally, we show that this transfer
method is not limited to cytochrome bo3 and can also be performed with complex membrane protein mixtures.
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Affiliation(s)
- Rosa Catania
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Jonathan Machin
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Michael Rappolt
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, U.K
| | - Stephen P. Muench
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Paul A. Beales
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| | - Lars J. C. Jeuken
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Leiden Institute of Chemistry, University Leiden, Leiden 2300RA, The Netherlands
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34
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Krishnarjuna B, Ravula T, Ramamoorthy A. Detergent-free isolation of CYP450-reductase's FMN-binding domain in E. coli lipid-nanodiscs using a charge-free polymer. Chem Commun (Camb) 2022; 58:4913-4916. [PMID: 35356954 PMCID: PMC9578324 DOI: 10.1039/d1cc07193a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The membrane-anchored flavin mononucleotide binding domain (FBD) of CYP450 reductase was extracted in E. coli lipid-nanodiscs using charge-free pentyl-inulin polymer. FBD in nanodiscs was found to be conformationally homogenous and enabled high-resolution NMR probing. 31P NMR revealed the polymer's lack of preference for any specific E. coli lipids and identified the lipid-types in nanodiscs.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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35
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Laurence MJ, Carpenter TS, Laurence TA, Coleman MA, Shelby M, Liu C. Biophysical Characterization of Membrane Proteins Embedded in Nanodiscs Using Fluorescence Correlation Spectroscopy. MEMBRANES 2022; 12:membranes12040392. [PMID: 35448362 PMCID: PMC9028781 DOI: 10.3390/membranes12040392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023]
Abstract
Proteins embedded in biological membranes perform essential functions in all organisms, serving as receptors, transporters, channels, cell adhesion molecules, and other supporting cellular roles. These membrane proteins comprise ~30% of all human proteins and are the targets of ~60% of FDA-approved drugs, yet their extensive characterization using established biochemical and biophysical methods has continued to be elusive due to challenges associated with the purification of these insoluble proteins. In response, the development of nanodisc techniques, such as nanolipoprotein particles (NLPs) and styrene maleic acid polymers (SMALPs), allowed membrane proteins to be expressed and isolated in solution as part of lipid bilayer rafts with defined, consistent nanometer sizes and compositions, thus enabling solution-based measurements. Fluorescence correlation spectroscopy (FCS) is a relatively simple yet powerful optical microscopy-based technique that yields quantitative biophysical information, such as diffusion kinetics and concentrations, about individual or interacting species in solution. Here, we first summarize current nanodisc techniques and FCS fundamentals. We then provide a focused review of studies that employed FCS in combination with nanodisc technology to investigate a handful of membrane proteins, including bacteriorhodopsin, bacterial division protein ZipA, bacterial membrane insertases SecYEG and YidC, Yersinia pestis type III secretion protein YopB, yeast cell wall stress sensor Wsc1, epidermal growth factor receptor (EGFR), ABC transporters, and several G protein-coupled receptors (GPCRs).
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Affiliation(s)
- Matthew J. Laurence
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
| | - Timothy S. Carpenter
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
| | - Ted A. Laurence
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Matthew A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Department of Radiation Oncology, University of California Davis, Sacramento, CA 95616, USA
| | - Megan Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Correspondence: (M.S.); (C.L.)
| | - Chao Liu
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Correspondence: (M.S.); (C.L.)
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36
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Kojima K, Sudo Y. Expression of microbial rhodopsins in Escherichia coli and their extraction and purification using styrene-maleic acid copolymers. STAR Protoc 2022; 3:101046. [PMID: 34984357 PMCID: PMC8693275 DOI: 10.1016/j.xpro.2021.101046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Microbial rhodopsins are photoreceptive membrane proteins showing various light-dependent biological activities. Styrene-maleic acid (SMA) copolymers spontaneously form nanoscale lipid particles containing membrane proteins and associated lipids without detergent, and can be used to characterize membrane molecules. Here, we provide a protocol to functionally express a thermally stable rhodopsin, Rubrobacter xylanophilus rhodopsin, and an unstable rhodopsin, Halobacterium salinarum sensory rhodopsin I, in Escherichia coli. We then describe the preparation of SMA and the extraction and purification of rhodopsin molecules using SMA. For complete details on the use and execution of this protocol, please refer to Ueta et al. (2020). Functional expression of microbial rhodopsins in Escherichia coli cells Preparation of styrene-maleic acid (SMA) copolymer Extraction and purification of microbial rhodopsins using SMA Applicability of SMA for biophysical analysis of microbial rhodopsins in membrane
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Affiliation(s)
- Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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37
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Morrison KA, Wood L, Edler KJ, Doutch J, Price GJ, Koumanov F, Whitley P. Membrane extraction with styrene-maleic acid copolymer results in insulin receptor autophosphorylation in the absence of ligand. Sci Rep 2022; 12:3532. [PMID: 35241773 PMCID: PMC8894449 DOI: 10.1038/s41598-022-07606-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
Extraction of integral membrane proteins with poly(styrene-co-maleic acid) provides a promising alternative to detergent extraction. A major advantage of extraction using copolymers rather than detergent is the retention of the lipid bilayer around the proteins. Here we report the first functional investigation of the mammalian insulin receptor which was extracted from cell membranes using poly(styrene-co-maleic acid). We found that the copolymer efficiently extracted the insulin receptor from 3T3L1 fibroblast membranes. Surprisingly, activation of the insulin receptor and proximal downstream signalling was detected upon copolymer extraction even in the absence of insulin stimulation. Insulin receptor and IRS1 phosphorylations were above levels measured in the control extracts made with detergents. However, more distal signalling events in the insulin signalling cascade, such as the phosphorylation of Akt were not observed. Following copolymer extraction, in vitro addition of insulin had no further effect on insulin receptor or IRS1 phosphorylation. Therefore, under our experimental conditions, the insulin receptor is not functionally responsive to insulin. This study is the first to investigate receptor tyrosine kinases extracted from mammalian cells using a styrene-maleic acid copolymer and highlights the importance of thorough functional characterisation when using this method of protein extraction.
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Affiliation(s)
- Kerrie A Morrison
- Department of Biology and Biochemistry, University of Bath, Bath, UK.,Department of Chemistry, University of Bath, Bath, UK.,Centre for Sustainable Circular Technologies, University of Bath, Bath, UK
| | - Laura Wood
- Department of Biology and Biochemistry, University of Bath, Bath, UK.,Department for Health, Centre for Nutrition, Exercise and Metabolism, University of Bath, Bath, UK
| | - Karen J Edler
- Department of Chemistry, University of Bath, Bath, UK
| | - James Doutch
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Gareth J Price
- Department of Chemistry, University of Bath, Bath, UK.,Department of Chemistry, Khalifa University, Abu Dhabi, UAE
| | - Francoise Koumanov
- Department for Health, Centre for Nutrition, Exercise and Metabolism, University of Bath, Bath, UK.
| | - Paul Whitley
- Department of Biology and Biochemistry, University of Bath, Bath, UK.
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38
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Cao Y, Fang J, Shi Y, Wang H, Chen X, Liu Y, Zhu Z, Cao Y, Hong Z, Chai Y. Screening potential P-glycoprotein inhibitors by combination of a detergent-free membrane protein extraction with surface plasmon resonance biosensor. Acta Pharm Sin B 2022; 12:3113-3123. [PMID: 35865104 PMCID: PMC9293711 DOI: 10.1016/j.apsb.2022.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 01/13/2023] Open
Affiliation(s)
- Yuhong Cao
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
- Zhejiang Institute for Food and Drug Control, Hangzhou 310057, China
| | - Jiahao Fang
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
| | - Yiwei Shi
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
| | - Hui Wang
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
| | - Xiaofei Chen
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
| | - Yue Liu
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
| | - Zhenyu Zhu
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
| | - Yan Cao
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
- Corresponding authors. Tel.: +86 21 81871269 (Zhanying Hong), Tel/fax: +86 21 81871331 (Yan Cao).
| | - Zhanying Hong
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
- Corresponding authors. Tel.: +86 21 81871269 (Zhanying Hong), Tel/fax: +86 21 81871331 (Yan Cao).
| | - Yifeng Chai
- School of Pharmacy, Second Military Medical University, Shanghai Key Laboratory for Pharmaceutical Metabolites Research, Shanghai 200433, China
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Danielczak B, Rasche M, Lenz J, Pérez Patallo E, Weyrauch S, Mahler F, Agbadaola MT, Meister A, Babalola JO, Vargas C, Kolar C, Keller S. A bioinspired glycopolymer for capturing membrane proteins in native-like lipid-bilayer nanodiscs. NANOSCALE 2022; 14:1855-1867. [PMID: 35040850 DOI: 10.1039/d1nr03811g] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amphiphilic copolymers that directly extract membrane proteins and lipids from cellular membranes to form nanodiscs combine the advantages of harsher membrane mimics with those of a native-like membrane environment. Among the few commercial polymers that are capable of forming nanodiscs, alternating diisobutylene/maleic acid (DIBMA) copolymers have gained considerable popularity as gentle and UV-transparent alternatives to aromatic polymers. However, their moderate hydrophobicities and high electric charge densities render all existing aliphatic copolymers rather inefficient under near-physiological conditions. Here, we introduce Glyco-DIBMA, a bioinspired glycopolymer that possesses increased hydrophobicity and reduced charge density but nevertheless retains excellent solubility in aqueous solutions. Glyco-DIBMA outperforms established aliphatic copolymers in that it solubilizes lipid vesicles of various compositions much more efficiently, thereby furnishing smaller, more narrowly distributed nanodiscs that preserve a bilayer architecture and exhibit rapid lipid exchange. We demonstrate the superior performance of Glyco-DIBMA in preparative and analytical applications by extracting a broad range of integral membrane proteins from cellular membranes and further by purifying a membrane-embedded voltage-gated K+ channel, which was fluorescently labeled and analyzed with the aid of microfluidic diffusional sizing (MDS) directly within native-like lipid-bilayer nanodiscs.
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Affiliation(s)
- Bartholomäus Danielczak
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Marie Rasche
- Glycon Biochemicals GmbH, Im Biotechnologiepark TGZ 1, 14943 Luckenwalde, Germany
| | - Julia Lenz
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Eugenio Pérez Patallo
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Sophie Weyrauch
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Michael Tope Agbadaola
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- Department of Chemistry, University of Ibadan, 200284, Ibadan, Nigeria
| | - Annette Meister
- Institute of Biochemistry and Biotechnology, and ZIK HALOmem, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | | | - Carolyn Vargas
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Cenek Kolar
- Glycon Biochemicals GmbH, Im Biotechnologiepark TGZ 1, 14943 Luckenwalde, Germany
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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40
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Cheng WWL, Arcario MJ, Petroff JT. Druggable Lipid Binding Sites in Pentameric Ligand-Gated Ion Channels and Transient Receptor Potential Channels. Front Physiol 2022; 12:798102. [PMID: 35069257 PMCID: PMC8777383 DOI: 10.3389/fphys.2021.798102] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Lipids modulate the function of many ion channels, possibly through direct lipid-protein interactions. The recent outpouring of ion channel structures by cryo-EM has revealed many lipid binding sites. Whether these sites mediate lipid modulation of ion channel function is not firmly established in most cases. However, it is intriguing that many of these lipid binding sites are also known sites for other allosteric modulators or drugs, supporting the notion that lipids act as endogenous allosteric modulators through these sites. Here, we review such lipid-drug binding sites, focusing on pentameric ligand-gated ion channels and transient receptor potential channels. Notable examples include sites for phospholipids and sterols that are shared by anesthetics and vanilloids. We discuss some implications of lipid binding at these sites including the possibility that lipids can alter drug potency or that understanding protein-lipid interactions can guide drug design. Structures are only the first step toward understanding the mechanism of lipid modulation at these sites. Looking forward, we identify knowledge gaps in the field and approaches to address them. These include defining the effects of lipids on channel function in reconstituted systems using asymmetric membranes and measuring lipid binding affinities at specific sites using native mass spectrometry, fluorescence binding assays, and computational approaches.
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Affiliation(s)
- Wayland W L Cheng
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
| | - Mark J Arcario
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
| | - John T Petroff
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
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41
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Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene-maleic acid (SMA), diisobutylene-maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
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Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
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42
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Ravula T, Ramamoorthy A. Measurement of Residual Dipolar Couplings Using Magnetically Aligned and Flipped Nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:244-252. [PMID: 34965145 PMCID: PMC9575995 DOI: 10.1021/acs.langmuir.1c02449] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent developments in lipid nanodisc technology have successfully overcome the major challenges in the structural and functional studies of membrane proteins and drug delivery. Among the different types of nanodiscs, the use of synthetic amphiphilic polymers created new directions including the applications of solution and solid-state NMR spectroscopy. The ability to magnetically align large-size (>20 nm diameter) polymer nanodiscs and flip them using paramagnetic lanthanide ions has enabled high-resolution studies on membrane proteins using solid-state NMR techniques. The use of polymer-based macro-nanodiscs (>20 nm diameter) as an alignment medium to measure residual dipolar couplings (RDCs) and residual quadrupole couplings by NMR experiments has also been demonstrated. In this study, we demonstrate the use of magnetically aligned and 90°-flipped polymer nanodiscs as alignment media for structural studies on proteins by solution NMR spectroscopy. These macro-nanodiscs, composed of negatively charged SMA-EA polymers and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids, were used to measure residual 1H-15N dipolar couplings (RDCs) from the water-soluble ∼21 kDa uniformly 15N-labeled flavin mononucleotide binding domain (FBD) of cytochrome-P450 reductase. The experimentally measured 1H-15N RDC values are compared with the values calculated from the crystal structures of cytochrome-P450 reductase that lacks the transmembrane domain. The N-H RDCs measured using aligned and 90°-flipped nanodiscs show a modulation by the function (3 cos2 θ - 1), where θ is the angle between the N-H bond vector and the applied magnetic field direction. This successful demonstration of the use of two orthogonally oriented alignment media should enable structural studies on a variety of systems including small molecules, DNA, and RNA.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
- Corresponding author’s
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43
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Kopf AH, Lijding O, Elenbaas BOW, Koorengevel MC, Dobruchowska JM, van Walree CA, Killian JA. Synthesis and Evaluation of a Library of Alternating Amphipathic Copolymers to Solubilize and Study Membrane Proteins. Biomacromolecules 2022; 23:743-759. [PMID: 34994549 PMCID: PMC8924871 DOI: 10.1021/acs.biomac.1c01166] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Amphipathic copolymers
such as poly(styrene-maleic acid) (SMA)
are promising tools for the facile extraction of membrane proteins
(MPs) into native nanodiscs. Here, we designed and synthesized a library
of well-defined alternating copolymers of SMA analogues in order to
elucidate polymer properties that are important for MP solubilization
and stability. MP extraction efficiency was determined using KcsA
from E. coli membranes, and general solubilization
efficiency was investigated via turbidimetry experiments on membranes
of E. coli, yeast mitochondria, and synthetic
lipids. Remarkably, halogenation of SMA copolymers dramatically improved
solubilization efficiency in all systems, while substituents on the
copolymer backbone improved resistance to Ca2+. Relevant
polymer properties were found to include hydrophobic balance, size
and positioning of substituents, rigidity, and electronic effects.
The library thus contributes to the rational design of copolymers
for the study of MPs.
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Affiliation(s)
- Adrian H Kopf
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Odette Lijding
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Barend O W Elenbaas
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Justyna M Dobruchowska
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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44
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Broadbent L, Depping P, Lodé A, Vaitsopoulou A, Hardy D, Ayub H, Mitchell-White J, Kerr ID, Goddard AD, Bill RM, Rothnie AJ. Detergent-Free Membrane Protein Purification Using SMA Polymer. Methods Mol Biol 2022; 2507:389-404. [PMID: 35773594 DOI: 10.1007/978-1-0716-2368-8_21] [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
One of the big challenges for the study of structure and function of membrane proteins is the need to extract them from the membrane. Traditionally this was achieved using detergents which disrupt the membrane and form a micelle around the protein, but this can cause issues with protein function and/or stability. In 2009 an alternative approach was reported, using styrene maleic acid (SMA) copolymer to extract small discs of lipid bilayer encapsulated by the polymer and termed SMALPs (SMA lipid particles). Since then this approach has been shown to work for a range of different proteins from many different expression systems. It allows the extraction and purification of a target protein while maintaining a lipid bilayer environment. Recently this has led to several new high-resolution structures and novel insights to function. As with any method there are some limitations and issues to be aware of. Here we describe a standard protocol for preparation of the polymer and its use for membrane protein purification, and also include details of typical challenges that may be encountered and possible ways to address those.
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Affiliation(s)
- Luke Broadbent
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | - Peer Depping
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | - Alexis Lodé
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | | | - David Hardy
- College of Health & Life Sciences, Aston University, Birmingham, UK
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Hoor Ayub
- College of Health & Life Sciences, Aston University, Birmingham, UK
- Faculty of Health & Life Sciences, Coventry University, Coventry, UK
| | - James Mitchell-White
- School of Life Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham, UK
| | - Ian D Kerr
- School of Life Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham, UK
| | - Alan D Goddard
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | - Roslyn M Bill
- College of Health & Life Sciences, Aston University, Birmingham, UK
| | - Alice J Rothnie
- College of Health & Life Sciences, Aston University, Birmingham, UK.
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45
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Dimitrova VS, Song S, Karagiaridi A, Marand A, Pinkett HW. Detergent Alternatives: Membrane Protein Purification Using Synthetic Nanodisc Polymers. Methods Mol Biol 2022; 2507:375-387. [PMID: 35773593 PMCID: PMC9361707 DOI: 10.1007/978-1-0716-2368-8_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA) copolymers provides an alternative to traditional detergent extraction of integral membrane proteins. By inserting into the membrane, these polymers can extract membrane proteins along with lipids in the form of native nanodiscs made by poly(styrene co-maleic anhydride) derivatives. Unlike detergent solubilization, where membrane proteins may lose annular lipids necessary for proper folding and stability, native nanodiscs allow for proteins to reside in the natural lipid environment. In addition, polymer-based nanodiscs can be purified using common chromatography methods similar to protocols established with detergent solubilization purification. Here we describe the solubilization screening and purification of an integral membrane protein using several commercial copolymers.
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Affiliation(s)
| | - Saemee Song
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Department of Infectious Diseases Research, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | | | - Anika Marand
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Heather W Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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46
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Harwood CR, Sykes DA, Hoare BL, Heydenreich FM, Uddin R, Poyner DR, Briddon SJ, Veprintsev DB. Functional solubilization of the β 2-adrenoceptor using diisobutylene maleic acid. iScience 2021; 24:103362. [PMID: 34825145 PMCID: PMC8605084 DOI: 10.1016/j.isci.2021.103362] [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: 07/21/2020] [Revised: 07/16/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
The β2-adrenoceptor (β2AR) is a well-established target in asthma and a prototypical G protein-coupled receptor for biophysical studies. Solubilization of membrane proteins has classically involved the use of detergents. However, the detergent environment differs from the native membrane environment and often destabilizes membrane proteins. Use of amphiphilic copolymers is a promising strategy to solubilize membrane proteins within their native lipid environment in the complete absence of detergents. Here we show the isolation of the β2AR in the polymer diisobutylene maleic acid (DIBMA). We demonstrate that β2AR remains functional in the DIBMA lipid particle and shows improved thermal stability compared with the n-dodecyl-β-D-maltopyranoside detergent-solubilized β2AR. This unique method of extracting β2AR offers significant advantages over previous methods routinely employed such as the introduction of thermostabilizing mutations and the use of detergents, particularly for functional biophysical studies.
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Affiliation(s)
- Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Bradley L Hoare
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Franziska M Heydenreich
- Laboratory of Biomolecular Research, Paul Scherrer Institute, PSI, 5232 Villigen, Switzerland.,Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Romez Uddin
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,School of Life and Health Sciences, Aston University, Birmingham B47ET, UK
| | - David R Poyner
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,School of Life and Health Sciences, Aston University, Birmingham B47ET, UK
| | - Stephen J Briddon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - D B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
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47
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Hawkins OP, Jahromi CPT, Gulamhussein AA, Nestorow S, Bahra T, Shelton C, Owusu-Mensah QK, Mohiddin N, O'Rourke H, Ajmal M, Byrnes K, Khan M, Nahar NN, Lim A, Harris C, Healy H, Hasan SW, Ahmed A, Evans L, Vaitsopoulou A, Akram A, Williams C, Binding J, Thandi RK, Joby A, Guest A, Tariq MZ, Rasool F, Cavanagh L, Kang S, Asparuhov B, Jestin A, Dafforn TR, Simms J, Bill RM, Goddard AD, Rothnie AJ. Membrane protein extraction and purification using partially-esterified SMA polymers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183758. [PMID: 34480878 PMCID: PMC8484863 DOI: 10.1016/j.bbamem.2021.183758] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/16/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022]
Abstract
Styrene maleic acid (SMA) polymers have proven to be very successful for the extraction of membrane proteins, forming SMA lipid particles (SMALPs), which maintain a lipid bilayer around the membrane protein. SMALP-encapsulated membrane proteins can be used for functional and structural studies. The SMALP approach allows retention of important protein-annular lipid interactions, exerts lateral pressure, and offers greater stability than traditional detergent solubilisation. However, SMA polymer does have some limitations, including a sensitivity to divalent cations and low pH, an absorbance spectrum that overlaps with many proteins, and possible restrictions on protein conformational change. Various modified polymers have been developed to try to overcome these challenges, but no clear solution has been found. A series of partially-esterified variants of SMA (SMA 2625, SMA 1440 and SMA 17352) has previously been shown to be highly effective for solubilisation of plant and cyanobacterial thylakoid membranes. It was hypothesised that the partial esterification of maleic acid groups would increase tolerance to divalent cations. Therefore, these partially-esterified polymers were tested for the solubilisation of lipids and membrane proteins, and their tolerance to magnesium ions. It was found that all partially esterified polymers were capable of solubilising and purifying a range of membrane proteins, but the yield of protein was lower with SMA 1440, and the degree of purity was lower for both SMA 1440 and SMA 17352. SMA 2625 performed comparably to SMA 2000. SMA 1440 also showed an increased sensitivity to divalent cations. Thus, it appears the interactions between SMA and divalent cations are more complex than proposed and require further investigation.
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Affiliation(s)
- Olivia P Hawkins
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | | | - Aiman A Gulamhussein
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephanie Nestorow
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Taranpreet Bahra
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Christian Shelton
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Quincy K Owusu-Mensah
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Naadiya Mohiddin
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Hannah O'Rourke
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Mariam Ajmal
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Kara Byrnes
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Madiha Khan
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Nila N Nahar
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Arcella Lim
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Cassandra Harris
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Hannah Healy
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Syeda W Hasan
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Asma Ahmed
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Lora Evans
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Afroditi Vaitsopoulou
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aneel Akram
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Chris Williams
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Johanna Binding
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Rumandeep K Thandi
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aswathy Joby
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Ashley Guest
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Mohammad Z Tariq
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Farah Rasool
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Luke Cavanagh
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Simran Kang
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Biser Asparuhov
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aleksandr Jestin
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - John Simms
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alan D Goddard
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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48
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Biophysical characterisation of SMALPs. Biochem Soc Trans 2021; 49:2037-2050. [PMID: 34643233 DOI: 10.1042/bst20201088] [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: 08/02/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022]
Abstract
Membrane proteins such as receptors, ion channels and transport proteins are important drug targets. The structure-based study of membrane proteins is challenging, especially when the target protein contains both soluble and insoluble domains. Most membrane proteins are insoluble in aqueous solvent and embedded in the plasma membrane lipid bilayer, which significantly complicates biophysical studies. Poly(styrene-co-maleic acid) (SMA) and other polymer derivatives are increasingly common solubilisation agents, used to isolate membrane proteins stabilised in their native lipid environment in the total absence of detergent. Since the initial report of SMA-mediated solubilisation, and the formation of SMA lipid particles (SMALPs), this technique can directly isolate therapeutic targets from biological membranes, including G-protein coupled receptors (GPCRs). SMA now allows biophysical and structural analyses of membrane proteins in solution that was not previously possible. Here, we critically review several existing biophysical techniques compatible with SMALPs, with a focus on hydrodynamic analysis, microcalorimetric analysis and optical spectroscopic techniques.
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49
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Baeta T, Giandoreggio-Barranco K, Ayala I, Moura ECCM, Sperandeo P, Polissi A, Simorre JP, Laguri C. The lipopolysaccharide-transporter complex LptB 2FG also displays adenylate kinase activity in vitro dependent on the binding partners LptC/LptA. J Biol Chem 2021; 297:101313. [PMID: 34673027 PMCID: PMC8633020 DOI: 10.1016/j.jbc.2021.101313] [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: 07/09/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 02/02/2023] Open
Abstract
Lipopolysaccharide (LPS) is an essential glycolipid that covers the surface of gram-negative bacteria. The transport of LPS involves a dedicated seven-protein transporter system called the lipopolysaccharide transport system (Lpt) machinery that physically spans the entire cell envelope. The LptB2FG complex is an ABC transporter that hydrolyzes ATP to extract LPS from the inner membrane for transport to the outer membrane. Here, we extracted LptB2FG directly from the inner membrane with its original lipid environment using styrene-maleic acid polymers. We found that styrene-maleic acid polymers–LptB2FG in nanodiscs display not only ATPase activity but also a previously uncharacterized adenylate kinase (AK) activity, as it catalyzed phosphotransfer between two ADP molecules to generate ATP and AMP. The ATPase and AK activities of LptB2FG were both stimulated by the interaction on the periplasmic side with the periplasmic LPS transport proteins LptC and LptA and inhibited by the presence of the LptC transmembrane helix. We determined that the isolated ATPase module (LptB) had weak AK activity in the absence of transmembrane proteins LptF and LptG, and one mutation in LptB that weakens its affinity for ADP led to AK activity similar to that of fully assembled complex. Thus, we conclude that LptB2FG is capable of producing ATP from ADP, depending on the assembly of the Lpt bridge, and that this AK activity might be important to ensure efficient LPS transport in the fully assembled Lpt system.
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Affiliation(s)
- Tiago Baeta
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Isabel Ayala
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Elisabete C C M Moura
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | | | - Cedric Laguri
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.
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50
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Kacher YG, Karlova MG, Glukhov GS, Zhang H, Zaklyazminskaya EV, Loussouarn G, Sokolova OS. The Integrative Approach to Study of the Structure and Functions of Cardiac Voltage-Dependent Ion Channels. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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