1
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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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2
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Chang YC, Cao Z, Chen WT, Huang WC. Effects of stand-alone polar residue on membrane protein stability and structure. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184325. [PMID: 38653423 DOI: 10.1016/j.bbamem.2024.184325] [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: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Helical membrane proteins generally have a hydrophobic nature, with apolar side chains comprising the majority of the transmembrane (TM) helices. However, whenever polar side chains are present in the TM domain, they often exert a crucial role in structural interactions with other polar residues, such as TM helix associations and oligomerization. Moreover, polar residues in the TM region also often participate in protein functions, such as the Schiff base bonding between Lys residues and retinal in rhodopsin-like membrane proteins. Although many studies have focused on these functional polar residues, our understanding of stand-alone polar residues that are energetically unfavored in TM helixes is limited. Here, we adopted bacteriorhodopsin (bR) as a model system and systematically mutated 17 of its apolar Leu or Phe residues to polar Asn. Stability measurements of the resulting mutants revealed that all of these polar substitutions reduced bR stability to various extents, and the extent of destabilization of each mutant bR is also correlated to different structural factors, such as the relative accessible surface area and membrane depth of the mutation site. Structural analyses of these Asn residues revealed that they form sidechain-to-backbone hydrogen bonds that alleviate the unfavorable energetics in hydrophobic and apolar surroundings. Our results indicate that membrane proteins are able to accommodate certain stand-alone polar residues in the TM region without disrupting overall structures.
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Affiliation(s)
- Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan; International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Zheng Cao
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, United States of America
| | - Wai-Ting Chen
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chun Huang
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
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3
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Wilson S, Clarke CD, Carbajal MA, Buccafusca R, Fleck RA, Daskalakis V, Ruban AV. Hydrophobic Mismatch in the Thylakoid Membrane Regulates Photosynthetic Light Harvesting. J Am Chem Soc 2024; 146:14905-14914. [PMID: 38759103 PMCID: PMC11140739 DOI: 10.1021/jacs.4c05220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
The ability to harvest light effectively in a changing environment is necessary to ensure efficient photosynthesis and crop growth. One mechanism, known as qE, protects photosystem II (PSII) and regulates electron transfer through the harmless dissipation of excess absorbed photons as heat. This process involves reversible clustering of the major light-harvesting complexes of PSII (LHCII) in the thylakoid membrane and relies upon the ΔpH gradient and the allosteric modulator protein PsbS. To date, the exact role of PsbS in the qE mechanism has remained elusive. Here, we show that PsbS induces hydrophobic mismatch in the thylakoid membrane through dynamic rearrangement of lipids around LHCII leading to observed membrane thinning. We found that upon illumination, the thylakoid membrane reversibly shrinks from around 4.3 to 3.2 nm, without PsbS, this response is eliminated. Furthermore, we show that the lipid digalactosyldiacylglycerol (DGDG) is repelled from the LHCII-PsbS complex due to an increase in both the pKa of lumenal residues and in the dipole moment of LHCII, which allows for further conformational change and clustering in the membrane. Our results suggest a mechanistic role for PsbS as a facilitator of a hydrophobic mismatch-mediated phase transition between LHCII-PsbS and its environment. This could act as the driving force to sort LHCII into photoprotective nanodomains in the thylakoid membrane. This work shows an example of the key role of the hydrophobic mismatch process in regulating membrane protein function in plants.
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Affiliation(s)
- Sam Wilson
- Department
of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Charlea D. Clarke
- Department
of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - M. Alejandra Carbajal
- Centre
for Ultrastructural Imaging, King’s
College London, London SE1 1UL, United Kingdom
| | - Roberto Buccafusca
- Department
of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Roland A. Fleck
- Centre
for Ultrastructural Imaging, King’s
College London, London SE1 1UL, United Kingdom
| | - Vangelis Daskalakis
- Department
of Chemical Engineering, School of Engineering, University of Patras, Patras 26504, Greece
| | - Alexander V. Ruban
- Department
of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
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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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Hosokawa M, Inaba M, Tanaka M, Ogawara KI. Uptake Pathway of Styrene Maleic Acid Copolymer-Coated Lipid Emulsions Under Acidic Tumor Microenvironment. J Pharm Sci 2024; 113:1047-1053. [PMID: 37844758 DOI: 10.1016/j.xphs.2023.10.018] [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: 06/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
The purpose of this study was to elucidate and compare styrene maleic acid copolymer (SMA)-coated lipid emulsions (SMA emulsions) uptake pathway in vascular endothelial cells and surrounding cancer cells under not only neutral but also acidic pH, which is often observed in tumor microenvironment. DiI-labeled SMA emulsions were prepared using 1-palmitoyl-2-oleoyl-sn‑glycero-3-phosphocholine and triolein. In murine melanoma B16-BL6 (B16) cells and human umbilical vein endothelial cells (HUVEC), DiI-labeled SMA emulsions uptake under near-neutral (pH 7.4) and acidic (pH 6.0) conditions was determined by fluorescent analysis. SMA emulsions were taken up more efficiently into HUVEC than B16 cells under acidic condition in a temperature-dependent manner. Uptake study using endocytosis inhibitors showed that SMA emulsions were taken up by macropinocytosis and clathrin-mediated endocytosis in B16 cells. In HUVEC, however, they were taken up by clathrin- and caveolae-independent, but dynamin-dependent pathway. SMA emulsions would be internalized efficiently into vascular endothelial cells as well as cancer cells under acidic microenvironment via different endocytosis pathways. SMA emulsions could be a promising drug delivery carrier for anti-angiogenic drugs.
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Affiliation(s)
- Mika Hosokawa
- Laboratory of Pharmaceutics, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
| | - Moeka Inaba
- Laboratory of Pharmaceutics, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
| | - Masafumi Tanaka
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
| | - Ken-Ichi Ogawara
- Laboratory of Pharmaceutics, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan.
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6
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Hořejší V, Angelisová P, Pokorná J, Charnavets T, Benada O, Čajka T, Brdička T. Novel class of peptides disintegrating biological membranes to aid in the characterization of membrane proteins. J Biol Chem 2024; 300:107154. [PMID: 38479603 PMCID: PMC11002605 DOI: 10.1016/j.jbc.2024.107154] [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: 12/01/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 04/09/2024] Open
Abstract
Styrene-maleic acid (SMA) and similar amphiphilic copolymers are known to cut biological membranes into lipid nanoparticles/nanodiscs containing membrane proteins apparently in their relatively native membrane lipid environment. Our previous work demonstrated that membrane raft microdomains resist such disintegration by SMA. The use of SMA in studying membrane proteins is limited by its heterogeneity and the inability to prepare defined derivatives. In the present paper, we demonstrate that some amphiphilic peptides structurally mimicking SMA also similarly disintegrate cell membranes. In contrast to the previously used copolymers, the simple peptides are structurally homogeneous. We found that their membrane-disintegrating activity increases with their length (reaching optimum at 24 amino acids) and requires a basic primary structure, that is, (XXD)n, where X represents a hydrophobic amino acid (optimally phenylalanine), D aspartic acid, and n is the number of repeats of these triplets. These peptides may provide opportunities for various well-defined potentially useful modifications in the study of membrane protein biochemistry. Our present results confirm a specific character of membrane raft microdomains.
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Affiliation(s)
- Václav Hořejší
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Pavla Angelisová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Pokorná
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tatsiana Charnavets
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Čajka
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Brdička
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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7
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Wang X, Slater A, Lee SC, Harrison N, Pollock NL, Bakker SE, Navarro S, Nieswandt B, Dafforn TR, García Á, Watson SP, Tomlinson MG. Purification and characterisation of the platelet-activating GPVI/FcRγ complex in SMALPs. Arch Biochem Biophys 2024; 754:109944. [PMID: 38395124 DOI: 10.1016/j.abb.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The collagen/fibrin(ogen) receptor, glycoprotein VI (GPVI), is a platelet activating receptor and a promising anti-thrombotic drug target. However, while agonist-induced GPVI clustering on platelet membranes has been shown to be essential for its activation, it is unknown if GPVI dimerisation represents a unique conformation for ligand binding. Current GPVI structures all contain only the two immunoglobulin superfamily (IgSF) domains in the GPVI extracellular region, so lacking the mucin-like stalk, transmembrane, cytoplasmic tail of GPVI and its associated Fc receptor γ (FcRγ) homodimer signalling chain, and provide contradictory insights into the mechanisms of GPVI dimerisation. Here, we utilised styrene maleic-acid lipid particles (SMALPs) to extract GPVI in complex with its two associated FcRγ chains from transfected HEK-293T cells, together with the adjacent lipid bilayer, then purified and characterised the GPVI/FcRγ-containing SMALPs, to enable structural insights into the full-length GPVI/FcRγ complex. Using size exclusion chromatography followed by a native polyacrylamide gel electrophoresis (PAGE) method, SMA-PAGE, we revealed multiple sizes of the purified GPVI/FcRγ SMALPs, suggesting the potential existence of GPVI oligomers. Importantly, GPVI/FcRγ SMALPs were functional as they could bind collagen. Mono-dispersed GPVI/FcRγ SMALPs could be observed under negative stain electron microscopy. These results pave the way for the future investigation of GPVI stoichiometry and structure, while also validating SMALPs as a promising tool for the investigation of human membrane protein interactions, stoichiometry and structure.
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Affiliation(s)
- Xueqing Wang
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, and Instituto de Investigación Sanitaria de Santiago (IDIS), 15782 Santiago de Compostela, Spain.
| | - Alexandre Slater
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, UK
| | - Sarah C Lee
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Neale Harrison
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Naomi L Pollock
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Saskia E Bakker
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Stefano Navarro
- Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg Josef-Schneider-Straße 2, 97080 Wurzburg, Germany; Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Wurzburg, Germany
| | - Bernhard Nieswandt
- Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg Josef-Schneider-Straße 2, 97080 Wurzburg, Germany; Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Wurzburg, Germany
| | - Tim R Dafforn
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ángel García
- Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, and Instituto de Investigación Sanitaria de Santiago (IDIS), 15782 Santiago de Compostela, Spain
| | - Steve P Watson
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, UK
| | - Michael G Tomlinson
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, UK.
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8
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Mamatkulov K, Zavatski S, Arynbek Y, Esawii HA, Burko A, Bandarenka H, Arzumanyan G. Conformational analysis of lipid membrane mimetics modified with A β42 peptide by Raman spectroscopy and computer simulations. J Biomol Struct Dyn 2024:1-14. [PMID: 38520152 DOI: 10.1080/07391102.2024.2330706] [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: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024]
Abstract
Peptide-lipid interactions play an important role in maintaining the integrity and function of the cell membrane. Even slight changes in these interactions can induce the development of various diseases. Specifically, peptide misfolding and aggregation in the membrane is considered to be one of the triggers of Alzheimer's disease (AD), however its exact mechanism is still unclear. To this end, an increase of amyloid-beta (Aβ) peptide concentration in the human brain is widely accepted to gradually produce cytotoxic Aβ aggregates (plaques). These plaques initiate a sequence of pathogenic events ending up in observable symptoms of dementia. Understanding the mechanism of the Aβ interaction with cells is crucial for early detection and prevention of Alzheimer's disease. Hence, in this work, a comprehensive Raman analysis of the Aβ42 conformational dynamics in water and in liposomes and lipodiscs that mimic the membrane system is presented. The obtained results show that the secondary structure of Aβ42 in liposomes is dominated by the α-helix conformation, which remains stable over time. However, it comes as a surprise to reveal that the lipodisc environment induces the transformation of the Aβ42 secondary structure to a β-turn/random coil. Our Raman spectroscopy findings are supported with molecular dynamics (MD) and density functional theory (DFT) simulations, showing their good agreement.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kahramon Mamatkulov
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
| | - Siarhei Zavatski
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Yersultan Arynbek
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Faculty of Physics and Technology, al-Farabi, Kazakh National University, Almaty, Kazakhstan
| | - Heba A Esawii
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Biophysics Department, Faculty of Science, Cairo University, Egypt
| | - Aliaksandr Burko
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Hanna Bandarenka
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Grigory Arzumanyan
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
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9
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Lu J, Zhang C, Shi S, Li S, Liu J, Wu J, Huang C, Lei M. Stoichiometry and architecture of the platelet membrane complex glycoprotein Ib-IX-V. Biol Chem 2024; 405:91-104. [PMID: 36942505 DOI: 10.1515/hsz-2022-0227] [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: 07/12/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
Glycoprotein (GP) Ib-IX-V is the second most abundant platelet receptor for thrombin and other ligands crucial for hemostasis and thrombosis. Its activity is involved in platelet adhesion to vascular injury sites and thrombin-induced platelet aggregation. GPIb-IX-V is a heteromeric complex composed of four subunits, GPIbα, GPIbβ, GPV and GPIX, in a stoichiometric ratio that has been wildly debated. Despite its important physiological roles, the overall structure and molecular arrangement of GPIb-IX-V are not yet fully understood. Here, we purify stable and functional human GPIb-IX-V complex from reconstituted EXPi293F cells in high homogeneity, and perform biochemical and structural characterization of this complex. Single-particle cryo-electron microscopy structure of GPIb-IX-V is determined at ∼11 Å resolution, which unveils the architecture of GPIb-IX-V and its subunit organization. Size-exclusion chromatography-multi-angle static light scattering analysis reveals that GPIb-IX-V contains GPIb-IX and GPV at a 1:1 stoichiometric ratio and surface plasmon resonance assays show that association of GPV leads to slow kinetics of thrombin binding to GPIb-IX-V. Taken together, our results provide the first three-dimensional architecture of the intact GPIb-IX-V complex, which extends our understanding of the structure and functional mechanism of this complex in hemostasis and thrombosis.
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Affiliation(s)
- Juanjuan Lu
- Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Chunli Zhang
- Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Shaohua Shi
- Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Shaobai Li
- Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Junling Liu
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wu
- Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Chenhui Huang
- Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Ming Lei
- Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
- State Key laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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10
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Yoon S, Bae HE, Hariharan P, Nygaard A, Lan B, Woubshete M, Sadaf A, Liu X, Loland CJ, Byrne B, Guan L, Chae PS. Rational Approach to Improve Detergent Efficacy for Membrane Protein Stabilization. Bioconjug Chem 2024; 35:223-231. [PMID: 38215010 DOI: 10.1021/acs.bioconjchem.3c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Membrane protein structures are essential for the molecular understanding of diverse cellular processes and drug discovery. Detergents are not only widely used to extract membrane proteins from membranes but also utilized to preserve native protein structures in aqueous solution. However, micelles formed by conventional detergents are suboptimal for membrane protein stabilization, necessitating the development of novel amphiphilic molecules with enhanced protein stabilization efficacy. In this study, we prepared two sets of tandem malonate-derived glucoside (TMG) variants, both of which were designed to increase the alkyl chain density in micelle interiors. The alkyl chain density was modulated either by reducing the spacer length (TMG-Ms) or by introducing an additional alkyl chain between the two alkyl chains of the original TMGs (TMG-Ps). When evaluated with a few membrane proteins including a G protein-coupled receptor, TMG-P10,8 was found to be substantially more efficient at extracting membrane proteins and also effective at preserving protein integrity in the long term compared to the previously described TMG-A13. This result reveals that inserting an additional alkyl chain between the two existing alkyl chains is an effective way to optimize detergent properties for membrane protein study. This new biochemical tool and the design principle described have the potential to facilitate membrane protein structure determination.
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Affiliation(s)
- Soyoung Yoon
- Department of Bionano Engineering, Hanyang University ERICA, Ansan 155-88, South Korea
| | - Hyoung Eun Bae
- Department of Bionano Engineering, Hanyang University ERICA, Ansan 155-88, South Korea
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Andreas Nygaard
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Baoliang Lan
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Menebere Woubshete
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Aiman Sadaf
- Department of Bionano Engineering, Hanyang University ERICA, Ansan 155-88, South Korea
| | - Xiangyu Liu
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University ERICA, Ansan 155-88, South Korea
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11
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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12
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Mu Q, Deng H, An X, Liu G, Liu C. Designing nanodiscs as versatile platforms for on-demand therapy. NANOSCALE 2024; 16:2220-2234. [PMID: 38192208 DOI: 10.1039/d3nr05457h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Nowadays, there has been an increasing utilization of nanomedicines for disease treatment. Nanodiscs (NDs) have emerged as a novel platform technology that garners significant attention in biomedical research and drug discovery. NDs are nanoscale phospholipid bilayer discs capable of incorporating membrane proteins and lipids within a native-like environment. They are assembled using amphiphilic biomacromolecular materials, such as apolipoprotein A1 or membrane scaffold proteins (MSPs), peptides, and styrene-maleic acid polymers (SMAs). NDs possess well-defined sizes and shapes, offering a stable, homogeneous, and biologically relevant environment for studying membrane proteins and lipids. Their unique properties have made them highly desirable for diverse applications, including cancer immunotherapy, vaccine development, antibacterial and antiviral therapy, and treating Alzheimer's disease (AD) and diabetes-related conditions. This review discusses the classifications, advantages, and applications of NDs in disease therapy.
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Affiliation(s)
- Qianwen Mu
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Haolan Deng
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xiaoyu An
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Chao Liu
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
- Shenzhen Research Institute of Xiamen University, Shenzhen 518000, China
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13
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Ullrich J, Haueis L, Ohlhoff C, Zemella A, Kubick S, Stech M. Solubilization of Oligomeric Cell-Free Synthesized Proteins Using SMA Copolymers. Methods Mol Biol 2024; 2762:293-308. [PMID: 38315373 DOI: 10.1007/978-1-0716-3666-4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Although membrane proteins are abundant in nature, their investigation is limited due to bottlenecks in heterologous overexpression and consequently restricted accessibility for downstream applications. In this chapter, we address these challenges by presenting a fast and straightforward synthesis platform based on eukaryotic cell-free protein synthesis (CFPS) and an efficient solubilization strategy using styrene-maleic acid (SMA) copolymers. We demonstrate CFPS of TWIK-1, a dimeric ion channel, based on Sf21 (Spodoptera frugiperda) insect lysate showing homooligomerization and N-glycosylation enabled by endoplasmic reticulum-derived microsomes. Furthermore, we employ SMA copolymers for protein solubilization, which preserves the native-like microsomal environment. This approach not only retains the solubilized protein's suitability for downstream applications but also maintains the oligomerization and glycosylation of TWIK-1 post-solubilization. We validate the solubilization procedure using autoradiography, particle size analysis, and biomolecular fluorescence assay and confirm the very efficient, structurally intact solubilization of cell-free synthesized TWIK-1.
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Affiliation(s)
- Jessica Ullrich
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Carsten Ohlhoff
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.
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14
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Merklinger L, Morth JP. Phospholipid Preparations to Characterize Protein-Lipid Interactions In Vitro. Bio Protoc 2023; 22:e4887. [PMID: 38026763 PMCID: PMC10665634 DOI: 10.21769/bioprotoc.4887] [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] [Received: 02/10/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 12/01/2023] Open
Abstract
The lipid bilayers of the cell are composed of various lipid classes and species. These engage in cell signaling and regulation by recruiting cytosolic proteins to the membrane and interacting with membrane-embedded proteins to alternate their activity and stability. Like lipids, membrane proteins are amphipathic and are stabilized by the hydrophobic forces of the lipid bilayer. Membrane protein-lipid interactions are difficult to investigate since membrane proteins need to be reconstituted in a lipid-mimicking environment. A common and well-established approach is the detergent-based solubilization of the membrane proteins in detergent micelles. Nowadays, nanodiscs and liposomes are used to mimic the lipid bilayer and enable the work with membrane proteins in a more natural environment. However, these protocols need optimization and are labor intensive. The present protocol describes straightforward instructions on how the preparation of lipids is performed and how the lipid detergent mixture is integrated with the membrane protein MARCH5. The lipidation protocol was performed prior to an activity assay specific to membrane-bound E3 ubiquitin ligases and a stability assay that could be used for any membrane protein of choice.
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Affiliation(s)
- Lisa Merklinger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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15
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Neville GM, Morrison KA, Shilliday ER, Doutch J, Dalgliesh R, Price GJ, Edler KJ. The effect of polymer end-group on the formation of styrene - maleic acid lipid particles (SMALPs). SOFT MATTER 2023; 19:8507-8518. [PMID: 37889133 DOI: 10.1039/d3sm01180a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
A series of block copolymers comprising styrene and maleic acid (SMA) has been prepared using RAFT polymerisation. RAFT often results in a large hydrophobic alkylthiocarbonylthio end group and this work examines its effect on the solution behaviour of the copolymers. SMA variants with, and without, this end group were synthesised and their behaviour compared with a commercially-available random copolymer of similar molecular weight. Dynamic light scattering and surface tension measurements found the RAFT-copolymers preferentially self-assembled into higher-order aggregates in aqueous solution. Small angle neutron scattering using deuterated styrene varients add support to the accepted model that these agreggates comprise a solvent-protected styrenic core with an acid-rich shell. Replacing the hydrophobic RAFT end group with a more hydrophilic nitrile caused differences in the resulting surface activity, attributed to the ability of the adjoining styrene homoblock to drive aggregation. Each of the copolymers formed SMALP nanodiscs with DMPC lipids, which were found to encapsulate a model membrane protein, gramicidin. However, end group variation affected solubilisition of DPPC, a lipid with a higher phase transition temperature. When using RAFT-copolymers terminated with a hydrophobic group, swelling of the bilayer and greater penetration of the homoblock into the nanodisc core occurred with increasing homoblock length. Conversely, commercial and nitrile-terminated RAFT-copolymers produced nanodisc sizes that stayed constant, instead indicating interaction at the edge of the lipid patch. The results highlight how even minor changes to the copolymer can modify the amphiphilic balance between regions, knowledge useful towards optimising copolymer structure to enhance and control nanodisc formation.
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Affiliation(s)
- George M Neville
- Centre for Sustainable Chemical Technologies, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Kerrie A Morrison
- Centre for Sustainable Chemical Technologies, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Ella R Shilliday
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - James Doutch
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Robert Dalgliesh
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Gareth J Price
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Department of Chemistry, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Karen J Edler
- Centre for Sustainable Chemical Technologies, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
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16
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Hoang Trinh TK, Catalano C, Guo Y. Fabrication of membrane proteins in the form of native cell membrane nanoparticles using novel membrane active polymers. NANOSCALE ADVANCES 2023; 5:5932-5940. [PMID: 37881706 PMCID: PMC10597567 DOI: 10.1039/d3na00381g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Membrane proteins are a widespread class of bio-macromolecules responsible for numerous vital biological processes and serve as therapeutic targets for a vast array of contemporary medications. For membrane protein isolation and purification, detergents have historically been used. Despite this, detergents frequently result in protein instability. Consequently, their application was limited. Recent detergent-free approaches have been invented. Among these, styrene-maleic acid lipid particle (SMALP), diisobutylene-maleic acid lipid particle (DIBMALP), and native cell membrane nanoparticle (NCMN) systems are the most prevalent. The NCMN system intends to create a library of membrane-active polymers suitable for high-resolution structure determination of membrane protein. Design, synthesis, characterization, and comparative application evaluations of three novel classes of NCMN polymers, NCMNP13-x, NCMNP21-x, and NCMNP21b-x, are presented in this article. Although each NCMN polymer can solubilize distinct model membrane proteins and retain native lipids in NCMN particles, only the NCMNP21b-x family produces lipid-protein particles with ideal buffer compatibility and high homogeneity suitable for single-particle cryo-EM analysis. NCMNP21b-x polymers that generate high-quality NCMN particles are particularly desirable for membrane protein structural biology.
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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
| | - 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
| | - 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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17
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [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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18
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Janata M, Gupta S, Čadová E, Angelisová P, Krishnarjuna B, Ramamoorthy A, Hořejší V, Raus V. Sulfonated polystyrenes: pH and Mg 2+-insensitive amphiphilic copolymers for detergent-free membrane protein isolation. Eur Polym J 2023; 198:112412. [PMID: 37780808 PMCID: PMC10538444 DOI: 10.1016/j.eurpolymj.2023.112412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Amphiphilic polymers are increasingly applied in the detergent-free isolation and functional studies of membrane proteins. However, the carboxylate group present in the structure of many popular variants, such as styrene-maleic acid (SMA) copolymers, brings limitations in terms of polymer sensitivity to precipitation at acidic pH or in the presence of divalent metal cations. Herein, we addressed this problem by replacing carboxylate with the more acidic sulfonate groups. To this end, we synthesized a library of amphiphilic poly[styrene-co-(sodium 4-styrene sulfonate)] copolymers (termed SSS), differing in their molecular weight and overall polarity. Using model cell membranes (Jurkat), we identified two copolymer compositions (SSS-L30 and SSS-L36) that solubilized membranes to an extent similar to SMA. Interestingly, the density gradient ultracentrifugation/SDS-PAGE/Western blotting analysis of cell lysates revealed a distribution of studied membrane proteins in the gradient fractions that was different than for SMA-solubilized membranes. Importantly, unlike SMA, the SSS copolymers remained soluble at low pH and in the presence of Mg2+ ions. Additionally, the solubilization of DMPC liposomes by the lead materials was studied by turbidimetry, DLS, SEC, and high-resolution NMR, revealing, for SSS-L36, the formation of stable particles (nanodiscs), facilitated by the direct hydrophobic interaction of the copolymer phenyls with lipid acyl chains.
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Affiliation(s)
- Miroslav Janata
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czech Republic
| | - Sachin Gupta
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czech Republic
| | - Eva Čadová
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czech Republic
| | - Pavla Angelisová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - 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
| | - 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
| | - Václav Hořejší
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Vladimír Raus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czech Republic
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19
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Scheyer MW, Campbell C, William PL, Hussain M, Begum A, Fonseca SE, Asare IK, Dabney P, Dabney-Smith C, Lorigan GA, Sahu ID. Electron paramagnetic resonance spectroscopic characterization of the human KCNE3 protein in lipodisq nanoparticles for structural dynamics of membrane proteins. Biophys Chem 2023; 301:107080. [PMID: 37531799 DOI: 10.1016/j.bpc.2023.107080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
One of the major challenges in solubilization of membrane proteins is to find the optimal physiological environment for their biophysical studies. EPR spectroscopy is a powerful biophysical technique for studying the structural and dynamic properties of macromolecules. However, the challenges in the membrane protein sample preparation and flexible motion of the spin label limit the utilization of EPR spectroscopy to a majority of membrane protein systems in a physiological membrane-bound state. Recently, lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have emerged as a membrane mimetic system for investigating the structural studies of membrane proteins. However, its detail characterization for membrane protein studies is still poorly understood. Recently, we characterized the potassium channel membrane protein KCNQ1 voltage sensing domain (KCNQ1-VSD) and KCNE1 reconstituted into lipodisq nanoparticles using EPR spectroscopy. In this study, the potassium channel accessory protein KCNE3 containing flexible N- and C-termini was encapsulated into proteoliposomes and lipodisq nanoparticles and characterized for studying its structural and dynamic properties using nitroxide based site-directed spin labeling EPR spectroscopy. CW-EPR lineshape analysis data indicated an increase in spectral line broadenings with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated an enhanced quality of distance measurements with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles, when compared to proteoliposomes. These results agree with the solution NMR structural structure of the KCNE3 and EPR studies of other membrane proteins in lipodisq nanoparticles. This study along with our earlier studies will provide the reference characterization data that will provide benefit to the membrane protein researchers for studying structural dynamics of challenging membrane proteins.
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Affiliation(s)
- Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Conner Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Patrick L William
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Mustakim Hussain
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Afsana Begum
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | | | - Isaac K Asare
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Peyton Dabney
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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20
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Majumder A, Vuksanovic N, Ray LC, Bernstein HM, Allen KN, Imperiali B, Straub JE. Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble. J Biol Chem 2023; 299:105194. [PMID: 37633332 PMCID: PMC10519829 DOI: 10.1016/j.jbc.2023.105194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 08/28/2023] Open
Abstract
Complex glycans serve essential functions in all living systems. Many of these intricate and byzantine biomolecules are assembled employing biosynthetic pathways wherein the constituent enzymes are membrane-associated. A signature feature of the stepwise assembly processes is the essentiality of unusual linear long-chain polyprenol phosphate-linked substrates of specific isoprene unit geometry, such as undecaprenol phosphate (UndP) in bacteria. How these enzymes and substrates interact within a lipid bilayer needs further investigation. Here, we focus on a small enzyme, PglC from Campylobacter, structurally characterized for the first time in 2018 as a detergent-solubilized construct. PglC is a monotopic phosphoglycosyl transferase that embodies the functional core structure of the entire enzyme superfamily and catalyzes the first membrane-committed step in a glycoprotein assembly pathway. The size of the enzyme is significant as it enables high-level computation and relatively facile, for a membrane protein, experimental analysis. Our ensemble computational and experimental results provided a high-level view of the membrane-embedded PglC/UndP complex. The findings suggested that it is advantageous for the polyprenol phosphate to adopt a conformation in the same leaflet where the monotopic membrane protein resides as opposed to additionally disrupting the opposing leaflet of the bilayer. Further, the analysis showed that electrostatic steering acts as a major driving force contributing to the recognition and binding of both UndP and the soluble nucleotide sugar substrate. Iterative computational and experimental mutagenesis support a specific interaction of UndP with phosphoglycosyl transferase cationic residues and suggest a role for critical conformational transitions in substrate binding and specificity.
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Affiliation(s)
- Ayan Majumder
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | | | - Leah C Ray
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hannah M Bernstein
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts, USA; Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts, USA.
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA.
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21
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Vénien-Bryan C, Fernandes CAH. Overview of Membrane Protein Sample Preparation for Single-Particle Cryo-Electron Microscopy Analysis. Int J Mol Sci 2023; 24:14785. [PMID: 37834233 PMCID: PMC10573263 DOI: 10.3390/ijms241914785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB) has been observed. However, sample preparation remains a significant challenge in the field. Here, we evaluated the MPs solved using cryo-EM SPA deposited in the PDB in the last two years at a resolution below 3.0 Å. The most critical parameters for sample preparation are as follows: (i) the surfactant used for protein extraction from the membrane, (ii) the surfactant, amphiphiles, nanodiscs or other molecules present in the vitrification step, (iii) the vitrification method employed, and (iv) the type of grids used. The aim is not to provide a definitive answer on the optimal sample conditions for cryo-EM SPA of MPs but rather assess the current trends in the MP structural biology community towards obtaining high-resolution cryo-EM structures.
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Affiliation(s)
| | - Carlos A. H. Fernandes
- Unité Mixte de Recherche (UMR) 7590, Centre National de la Recherche Scientifique (CNRS), Muséum National d’Histoire Naturelle, Institut de Recherche pour le Développement (IRD), Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, 75005 Paris, France;
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22
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Odenkirk MT, Zhang G, Marty MT. Do Nanodisc Assembly Conditions Affect Natural Lipid Uptake? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2006-2015. [PMID: 37524089 PMCID: PMC10528108 DOI: 10.1021/jasms.3c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Lipids play critical roles in modulating membrane protein structure, interactions, and activity. Nanodiscs provide a tunable membrane mimetic that can model these endogenous protein-lipid interactions in a nanoscale lipid bilayer. However, most studies of membrane proteins with nanodiscs use simple synthetic lipids that lack the headgroup and fatty acyl diversity of natural extracts. Prior research has successfully used natural lipid extracts in nanodiscs that more accurately mimic natural environments, but it is not clear how nanodisc assembly may bias the incorporated lipid profiles. Here, we applied lipidomics to investigate how nanodisc assembly conditions affect the profile of natural lipids in nanodiscs. Specifically, we tested the effects of assembly temperature, nanodisc size, and lipidome extract complexity. Globally, our analysis demonstrates that the lipids profiles are largely unaffected by nanodisc assembly conditions. However, a few notable changes emerged within individual lipids and lipid classes, such as a differential incorporation of cardiolipin and phosphatidylglycerol lipids from the E. coli polar lipid extract at different temperatures. Conversely, some classes of brain lipids were affected by nanodisc size at higher temperatures. Collectively, these data enable the application of nanodiscs to study protein-lipid interactions in complex lipid environments.
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Affiliation(s)
- Melanie T. Odenkirk
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
- Bio5 Institute, University of Arizona, Tucson, AZ
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
- Bio5 Institute, University of Arizona, Tucson, AZ
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23
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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: 0] [Impact Index Per Article: 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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24
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Russell Lewis B, Uddin MR, Moniruzzaman M, Kuo KM, Higgins AJ, Shah LMN, Sobott F, Parks JM, Hammerschmid D, Gumbart JC, Zgurskaya HI, Reading E. Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein. Nat Commun 2023; 14:3900. [PMID: 37463890 PMCID: PMC10354078 DOI: 10.1038/s41467-023-39615-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Muhammad R Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Katie M Kuo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA
| | - Anna J Higgins
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Laila M N Shah
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Frank Sobott
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Jerry M Parks
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA.
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
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25
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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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26
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Olivas TJ, Wu Y, Yu S, Luan L, Choi P, Guinn ED, Nag S, De Camilli PV, Gupta K, Melia TJ. ATG9 vesicles comprise the seed membrane of mammalian autophagosomes. J Cell Biol 2023; 222:e202208088. [PMID: 37115958 PMCID: PMC10148236 DOI: 10.1083/jcb.202208088] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/20/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023] Open
Abstract
As the autophagosome forms, its membrane surface area expands rapidly, while its volume is kept low. Protein-mediated transfer of lipids from another organelle to the autophagosome likely drives this expansion, but as these lipids are only introduced into the cytoplasmic-facing leaflet of the organelle, full membrane growth also requires lipid scramblase activity. ATG9 harbors scramblase activity and is essential to autophagosome formation; however, whether ATG9 is integrated into mammalian autophagosomes remains unclear. Here we show that in the absence of lipid transport, ATG9 vesicles are already competent to collect proteins found on mature autophagosomes, including LC3-II. Further, we use styrene-maleic acid lipid particles to reveal the nanoscale organization of protein on LC3-II membranes; ATG9 and LC3-II are each fully integrated into expanding autophagosomes. The ratios of these two proteins at different stages of maturation demonstrate that ATG9 proteins are not continuously integrated, but rather are present on the seed vesicles only and become diluted in the expanding autophagosome membrane.
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Affiliation(s)
- Taryn J. Olivas
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, School of Medicine, Yale University, New Haven, CT, USA
- Program in Cellular Neuroscience Neurodegeneration and Repair, School of Medicine, Yale University, New Haven, CT, USA
| | - Shenliang Yu
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Lin Luan
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Peter Choi
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Emily D. Guinn
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Shanta Nag
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Pietro V. De Camilli
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, School of Medicine, Yale University, New Haven, CT, USA
- Program in Cellular Neuroscience Neurodegeneration and Repair, School of Medicine, Yale University, New Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Thomas J. Melia
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
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27
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Kojima K, Kawanishi S, Nishimura Y, Hasegawa M, Nakao S, Nagata Y, Yoshizawa S, Sudo Y. A blue-shifted anion channelrhodopsin from the Colpodellida alga Vitrella brassicaformis. Sci Rep 2023; 13:6974. [PMID: 37117398 PMCID: PMC10147648 DOI: 10.1038/s41598-023-34125-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/25/2023] [Indexed: 04/30/2023] Open
Abstract
Microbial rhodopsins, a family of photoreceptive membrane proteins containing the chromophore retinal, show a variety of light-dependent molecular functions. Channelrhodopsins work as light-gated ion channels and are widely utilized for optogenetics, which is a method for controlling neural activities by light. Since two cation channelrhodopsins were identified from the chlorophyte alga Chlamydomonas reinhardtii, recent advances in genomic research have revealed a wide variety of channelrhodopsins including anion channelrhodopsins (ACRs), describing their highly diversified molecular properties (e.g., spectral sensitivity, kinetics and ion selectivity). Here, we report two channelrhodopsin-like rhodopsins from the Colpodellida alga Vitrella brassicaformis, which are phylogenetically distinct from the known channelrhodopsins. Spectroscopic and electrophysiological analyses indicated that these rhodopsins are green- and blue-sensitive pigments (λmax = ~ 550 and ~ 440 nm) that exhibit light-dependent ion channeling activities. Detailed electrophysiological analysis revealed that one of them works as a monovalent anion (Cl-, Br- and NO3-) channel and we named it V. brassicaformis anion channelrhodopsin-2, VbACR2. Importantly, the absorption maximum of VbACR2 (~ 440 nm) is blue-shifted among the known ACRs. Thus, we identified the new blue-shifted ACR, which leads to the expansion of the molecular diversity of ACRs.
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Affiliation(s)
- Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
| | - Shiho Kawanishi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yosuke Nishimura
- Research Center for Bioscience and Nanoscience (CeBN), Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, 237-0061, Japan
| | - Masumi Hasegawa
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, 237-0061, Japan
| | - Shin Nakao
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yuya Nagata
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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28
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Ghani L, Zhang X, Munk CF, Hariharan P, Lan B, Yun HS, Byrne B, Guan L, Loland CJ, Liu X, Chae PS. Tris(hydroxymethyl)aminomethane Linker-Bearing Triazine-Based Triglucosides for Solubilization and Stabilization of Membrane Proteins. Bioconjug Chem 2023; 34:739-747. [PMID: 36919927 PMCID: PMC10145683 DOI: 10.1021/acs.bioconjchem.3c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/21/2023] [Indexed: 03/16/2023]
Abstract
High-resolution membrane protein structures are essential for a fundamental understanding of the molecular basis of diverse cellular processes and for drug discovery. Detergents are widely used to extract membrane-spanning proteins from membranes and maintain them in a functional state for downstream characterization. Due to limited long-term stability of membrane proteins encapsulated in conventional detergents, development of novel agents is required to facilitate membrane protein structural study. In the current study, we designed and synthesized tris(hydroxymethyl)aminomethane linker-bearing triazine-based triglucosides (TTGs) for solubilization and stabilization of membrane proteins. When these glucoside detergents were evaluated for four membrane proteins including two G protein-coupled receptors, a few TTGs including TTG-C10 and TTG-C11 displayed markedly enhanced behaviors toward membrane protein stability relative to two maltoside detergents [DDM (n-dodecyl-β-d-maltoside) and LMNG (lauryl maltose neopentyl glycol)]. This is a notable feature of the TTGs as glucoside detergents tend to be inferior to maltoside detergents at stabilizing membrane proteins. The favorable behavior of the TTGs for membrane protein stability is likely due to the high hydrophobicity of the lipophilic groups, an optimal range of hydrophilic-lipophilic balance, and the absence of cis-trans isomerism.
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Affiliation(s)
- Lubna Ghani
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
| | - Xiang Zhang
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Chastine F. Munk
- Department
of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Parameswaran Hariharan
- Department
of Cell Physiology and Molecular Biophysics, Center for Membrane Protein
Research, School of Medicine, Texas Tech
University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Baoliang Lan
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Hong Sik Yun
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
| | - Bernadette Byrne
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Lan Guan
- Department
of Cell Physiology and Molecular Biophysics, Center for Membrane Protein
Research, School of Medicine, Texas Tech
University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Claus J. Loland
- Department
of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Xiangyu Liu
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Pil Seok Chae
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
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29
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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: 0] [Impact Index Per Article: 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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30
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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: 0] [Impact Index Per Article: 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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31
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Harant K, Čajka T, Angelisová P, Pokorná J, Hořejší V. Composition of raft-like cell membrane microdomains resistant to styrene-maleic acid copolymer (SMA) solubilization. Biophys Chem 2023; 296:106989. [PMID: 36898346 DOI: 10.1016/j.bpc.2023.106989] [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: 09/07/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023]
Abstract
An advantageous alternative to the use of detergents in biochemical studies on membrane proteins are the recently developed styrene-maleic acid (SMA) amphipathic copolymers. In our recent study [1] we demonstrated that using this approach, most T cell membrane proteins were fully solubilized (presumably in small nanodiscs), while two types of raft proteins, GPI-anchored proteins and Src family kinases, were mostly present in much larger (>250 nm) membrane fragments markedly enriched in typical raft lipids, cholesterol and lipids containing saturated fatty acid residues. In the present study we demonstrate that disintegration of membranes of several other cell types by means of SMA copolymer follows a similar pattern and we provide a detailed proteomic and lipidomic characterization of these SMA-resistant membrane fragments (SRMs).
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Affiliation(s)
- Karel Harant
- Proteomics Core Facility, Faculty of Science, Charles University, BIOCEV, Prumyslova 595, Vestec CZ-25242, Czechia; Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 CZ-128 01, Czechia.
| | - Tomáš Čajka
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083 142 20 Praha 4, Czechia.
| | - Pavla Angelisová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská, 1083 142 20 Praha 4, Czechia
| | - Jana Pokorná
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská, 1083 142 20 Praha 4, Czechia
| | - Václav Hořejší
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská, 1083 142 20 Praha 4, Czechia.
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Maier R, Cuevas Arenas R, Zhang F, García-Sáez A, Schreiber F. Structural Insights into Polymer-Bounded Lipid Nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:2450-2459. [PMID: 36724350 DOI: 10.1021/acs.langmuir.2c03412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Membrane proteins are an essential part of signaling and transport processes and are targeted by multiple drugs. To isolate and investigate them in their native state, polymer-bounded nanodiscs have become valuable tools. In this study, we investigate the lipid model system dimyristoyl-phosphocholine (DMPC) with the nanodisc-forming copolymers styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA). Using small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS), we studied the influence of polymer concentration and temperature on the nanodisc structure. In Tris buffer, the size of nanodiscs formed with SMA is smaller compared to DIBMA at the same polymer ratio. In both cases, the size decreases monotonically with increasing polymer concentration, and this effect is more pronounced when using SMA. Measurements at temperatures (T) between 5 and 30 °C in phosphate buffer showed an incomplete solubilization at high T even at polymer/lipid ratios above that required for complete lipid solubilization. For DIBMA, the nanodiscs developed at lower temperatures are stable and the net repulsion increases, while for SMA, the individual nanodiscs possess smaller sizes and are less affected by T. However, using DLS, one can observe SMA agglomerates at low T. Interestingly, for both polymers, no drastic changes of the observable parameters (radius and bilayer thickness) are seen upon cooling, which would indicate a sharp (first-order) phase transition from liquid-crystalline to gel, but only gradual changes. Hence, we conclude that the transition from a gel toward a liquid-crystalline lipid phase proceeds over a broad T-range compared to a continuous lipid bilayer. These results can pave the way toward the development of better protocols for studying membrane proteins stabilized in this type of membrane mimics.
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Affiliation(s)
- Ralph Maier
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076Tübingen, Germany
| | - Rodrigo Cuevas Arenas
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076Tübingen, Germany
- Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584CGUtrecht, Netherlands
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076Tübingen, Germany
| | - Ana García-Sáez
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076Tübingen, Germany
- Institut für Genetik, Universität zu Köln, Joseph-Stelzmann-Strasse 26, 50931Köln, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076Tübingen, Germany
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Cooperative transitions involving hydrophobic polyelectrolytes. Proc Natl Acad Sci U S A 2023; 120:e2211088120. [PMID: 36716362 PMCID: PMC9963826 DOI: 10.1073/pnas.2211088120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Hydrophobic polyelectrolytes (HPEs) can solubilize bilayer membranes, form micelles, or can reversibly aggregate as a function of pH. The transitions are often remarkably sharp. We show that these cooperative transitions occur by a competition between two or more conformational states and can be explained within the framework of Monod-Wymann-Changeux (MWC) theory that was originally formulated for allosteric interactions. Here, we focus on the pH-dependent destabilization and permeation of bilayer membranes by HPEs. We formulate the general conditions that lead to sharp conformational transitions involving simple macromolecules mediated by concentration variations of molecular ligands. That opens up potential applications ranging from medicine to the development of switchable materials.
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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: 1] [Impact Index Per Article: 1.0] [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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Schachter I, Harries D. Capturing Lipid Nanodisc Shape and Properties Using a Continuum Elastic Theory. J Chem Theory Comput 2023; 19:1360-1369. [PMID: 36724052 PMCID: PMC9979604 DOI: 10.1021/acs.jctc.2c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Lipid nanodiscs are nanometric bilayer patches enveloped by confining structures, commonly composed of membrane scaffolding proteins (MSPs). To resolve the interplay between MSP geometry, lipid confinement, and membrane material properties on the nanodisc shape, we apply a continuum elastic theory accounting for lipid bending, tilting, and area deformations. The equilibrium nanodisc shape is then determined by minimizing the elastic free energy functional. Analytic expressions derived under simplifying assumptions demonstrate that the nanodisc shape is sensitive to its size, lipid density, and the lipid tilt and thickness imposed at the contact with the MSP. Under matching physical parameters, these expressions quantitatively reproduce the shape of nanodiscs seen in molecular dynamics simulations, but only if lipid tilt is explicitly considered. We further demonstrate how the bending rigidity can be extracted from the membrane shape profile by fitting the numerically minimized full elastic functional to the membrane shape found in simulations. This fitting procedure faithfully informs on the bending rigidity of nanodiscs larger than ca. 5 nm in radius. The fitted profiles accurately reproduce the increase in bending modulus found using real-space fluctuation analysis of simulated nanodiscs and, for large nanodiscs, also accurately resolve its spatial variations. Our study shows how deformations in lipid patches confined in nanodiscs can be well described by a continuum elastic theory and how this fit can be used to determine local material properties from shape analysis of nanodiscs in simulations. This methodology could potentially allow direct determination of lipid properties from experiments, for example cryo-electron microscopy images of lipid nanodiscs, thereby allowing to guide the development of future nanodisc formulations with desired properties.
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Affiliation(s)
- Itay Schachter
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000Prague 6, Czech Republic,Institute
of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger
Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem9190401, Israel
| | - Daniel Harries
- Institute
of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger
Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem9190401, Israel,E-mail:
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Martin J, Robert X, Gouet P, Falson P, Chaptal V. Specific Xray diffraction patterns of membrane proteins caused by secondary structure collinearity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184065. [PMID: 36206830 DOI: 10.1016/j.bbamem.2022.184065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
Diffraction anisotropy is a phenomenon that impacts more specifically membrane proteins, compared to soluble ones, but the reasons for this discrepancy remained unclear. Often, it is referred to a difference in resolution limits between highest and lowest diffraction limits as a signature for anisotropy. We show in this article that there is no single correlation between anisotropy and difference in resolution limits, with notably a substantial number of structures displaying various anisotropy with no difference in resolution limits. We further investigated diffraction intensity profiles, and observed a peak centred on 4.9 Å resolution more predominant in membrane proteins. Since this peak is in the region corresponding to secondary structures, we investigated the influence of secondary structure ratio. We showed that secondary structure content has little influence on this profile, while secondary structure collinearity in membrane proteins correlate with a stronger peak. Finally, we could further show that the presence of this peak is linked to higher diffraction anisotropy. These results bring to light a specific diffraction of membrane protein crystals, which calls for a specific handling by crystallographic software. It also brings an explanation for investigators struggling with their anisotropic data.
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Affiliation(s)
- Juliette Martin
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France.
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37
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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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38
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Russell Lewis B, Lawrence R, Hammerschmid D, Reading E. Structural mass spectrometry approaches to understand multidrug efflux systems. Essays Biochem 2022; 67:255-267. [PMID: 36504255 PMCID: PMC10070475 DOI: 10.1042/ebc20220190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Multidrug efflux pumps are ubiquitous across both eukaryotes and prokaryotes, and have major implications in antimicrobial and multidrug resistance. They reside within cellular membranes and have proven difficult to study owing to their hydrophobic character and relationship with their compositionally complex lipid environment. Advances in structural mass spectrometry (MS) techniques have made it possible to study these systems to elucidate critical information on their structure-function relationships. For example, MS techniques can report on protein structural dynamics, stoichiometry, connectivity, solvent accessibility, and binding interactions with ligands, lipids, and other proteins. This information proving powerful when used in conjunction with complementary structural biology methods and molecular dynamics (MD) simulations. In the present review, aimed at those not experts in MS techniques, we report on the current uses of MS in studying multidrug efflux systems, practical considerations to consider, and the future direction of the field. In the first section, we highlight the importance of studying multidrug efflux proteins, and introduce a range of different MS techniques and explain what information they yield. In the second section, we review recent studies that have utilised MS techniques to study and characterise a range of different multidrug efflux systems.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Ryan Lawrence
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
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39
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Janson K, Kyrilis FL, Tüting C, Alfes M, Das M, Träger TK, Schmidt C, Hamdi F, Vargas C, Keller S, Meister A, Kastritis PL. Cryo-Electron Microscopy Snapshots of Eukaryotic Membrane Proteins in Native Lipid-Bilayer Nanodiscs. Biomacromolecules 2022; 23:5084-5094. [PMID: 36399657 DOI: 10.1021/acs.biomac.2c00935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
New technologies for purifying membrane-bound protein complexes in combination with cryo-electron microscopy (EM) have recently allowed the exploration of such complexes under near-native conditions. In particular, polymer-encapsulated nanodiscs enable the study of membrane proteins at high resolution while retaining protein-protein and protein-lipid interactions within a lipid bilayer. However, this powerful technology has not been exploited to address the important question of how endogenous─as opposed to overexpressed─membrane proteins are organized within a lipid environment. In this work, we demonstrate that biochemical enrichment protocols for native membrane-protein complexes from Chaetomium thermophilum in combination with polymer-based lipid-bilayer nanodiscs provide a substantial improvement in the quality of recovered endogenous membrane-protein complexes. Mass spectrometry results revealed ∼1123 proteins, while multiple 2D class averages and two 3D reconstructions from cryo-EM data furnished prominent structural signatures. This integrated methodological approach to enriching endogenous membrane-protein complexes provides unprecedented opportunities for a deeper understanding of eukaryotic membrane proteomes.
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Affiliation(s)
- Kevin Janson
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany
| | - Marie Alfes
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
| | - Manabendra Das
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, Kaiserslautern 67663, Germany
| | - Toni K Träger
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany
| | - Carolyn Vargas
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, Kaiserslautern 67663, Germany.,Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria.,Field of Excellence BioHealth, University of Graz, Graz 8010, Austria.,BioTechMed-Graz, Graz 8010, Austria
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, Kaiserslautern 67663, Germany.,Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria.,Field of Excellence BioHealth, University of Graz, Graz 8010, Austria.,BioTechMed-Graz, Graz 8010, Austria
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
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40
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Masuda T, Takahashi S, Ochiai T, Yamada T, Shimada N, Maruyama A. Autonomous Vesicle/Sheet Transformation of Cell-Sized Lipid Bilayers by Hetero-Grafted Copolymers. ACS APPLIED MATERIALS & INTERFACES 2022; 14:53558-53566. [PMID: 36442490 DOI: 10.1021/acsami.2c17435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Lipid bilayer transformations are involved in biological phenomena including cell division, autophagy, virus infection, and vesicle transport. Artificial materials to manipulate membrane dynamics play a vital role in cellular engineering and drug delivery technology that accesses the membranes of cells or liposomes. Transformation from 3D lipid vesicles to 2D nanosheets is thermodynamically prohibited because the apolar/polar interfaces between the hydrophobic bilayer edges and water are energetically unfavorable. We recently reported that cell-sized lipid vesicles (or giant vesicles) can be thoroughly transformed to 2D nanosheets by the addition of the amphiphilic E5 peptide and a cationic graft copolymer. Here, to understand the mechanisms underlying the lipid nanosheet formation, we systematically investigated the structural effects of the cationic copolymers on nanosheet formation. We found that lipid nanosheet formation is controlled in an all-or-nothing manner when the graft content of the copolymer is increased from 5.7 mol % to 7.7 mol %. This finding prompted us to obtain autonomous 2D/3D transformation system. A newly designed hetero-grafted cationic copolymers with thermoresponsive poly(N-isopropylacrylamide) grafts enables spontaneous 3D vesicle/2D nanosheet transformation in response to temperature. These findings would enable us to obtain smart nanointerfaces that trigger cell-sized lipid membrane dynamics in response to diverse stimuli and to create 2D-3D convertible lipid-based biomaterials.
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Affiliation(s)
- Tsukuru Masuda
- School of Life Science and Technology, Tokyo Institute of Technology, B-57 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa226-8501, Japan
| | - Shutaro Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, B-57 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa226-8501, Japan
| | - Takuro Ochiai
- School of Life Science and Technology, Tokyo Institute of Technology, B-57 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa226-8501, Japan
| | - Takayoshi Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, B-57 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa226-8501, Japan
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, B-57 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa226-8501, Japan
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, B-57 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa226-8501, Japan
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41
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Characterization of heterogeneity in nanodisc samples using Feret signatures. J Struct Biol 2022; 214:107916. [PMID: 36332745 DOI: 10.1016/j.jsb.2022.107916] [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: 07/31/2022] [Revised: 10/15/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Nanodiscs have become a popular tool in structure determination of membrane proteins using cryogenic electron microscopy and single particle analysis. However, the structure determination of small membrane proteins remains challenging. When the embedded protein is in the same size range as the nanodisc, the nanodisc can significantly contribute to the alignment and classification during the structure determination process. In those cases, it is crucial to minimize the heterogeneity in the nanodisc preparations to assure maximum accuracy in the classification and alignment steps of single particle analysis. Here, we introduce a new in-silico method for the characterization of nanodisc samples that is based on analyzing the Feret diameter distribution of their particle projection as imaged in the electron microscope. We validated the method with comprehensive simulation studies and show that Feret signatures can detect subtle differences in nanodisc morphologies and composition that might otherwise go unnoticed. We used the method to identify a specific biochemical nanodisc preparation with low size variations, allowing us to obtain a structure of the 23-kDa single-span membrane protein Bcl-xL while embedded in a nanodisc. Feret signature analysis can steer experimental data collection strategies, allowing more efficient use of high-end data collection hardware, as well as image analysis investments in studies where nanodiscs significantly contribute to the total volume of the full molecular species.
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42
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Noh I, Guo Z, Zhou J, Gao W, Fang RH, Zhang L. Cellular Nanodiscs Made from Bacterial Outer Membrane as a Platform for Antibacterial Vaccination. ACS NANO 2022; 17:10.1021/acsnano.2c08360. [PMID: 36441916 PMCID: PMC10225015 DOI: 10.1021/acsnano.2c08360] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Vaccination has become an increasingly attractive strategy for protecting against antibiotic-resistant infections. Nanovaccines based on the outer membrane from Gram-negative bacteria are appealing due to their multiantigenic nature and inherent immunogenicity. Here, we develop cellular nanodiscs made of bacterial outer membrane (OM-NDs), as a platform for antibacterial vaccination. Using Pseudomonas aeruginosa as a model pathogen, the resulting OM-NDs can effectively interact with antigen-presenting cells, exhibiting accelerated uptake and an improved capacity for immune stimulation. With their small size, the OM-NDs are also capable of efficiently transporting to the lymph nodes after in vivo administration. As a result, the nanovaccine is effective at eliciting potent humoral and cellular immune responses against P. aeruginosa. In a murine model of pneumonia, immunization with OM-NDs confers strong protection against subsequent lung infection, resulting in improved survival, reduced bacterial loads, and alleviation of immune overactivation. Overall, this report illustrates the advantages of cellular nanodiscs, which can be readily generalized to other pathogens and may be applied toward other biomedical applications.
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Affiliation(s)
- Ilkoo Noh
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - Zhongyuan Guo
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - Jiarong Zhou
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - Weiwei Gao
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - Ronnie H. Fang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
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43
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Glueck D, Grethen A, Das M, Mmeka OP, Patallo EP, Meister A, Rajender R, Kins S, Räschle M, Victor J, Chu C, Etzkorn M, Köck Z, Bernhard F, Babalola JO, Vargas C, Keller S. Electroneutral Polymer Nanodiscs Enable Interference-Free Probing of Membrane Proteins in a Lipid-Bilayer Environment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202492. [PMID: 36228092 DOI: 10.1002/smll.202202492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Membrane proteins can be examined in near-native lipid-bilayer environments with the advent of polymer-encapsulated nanodiscs. These nanodiscs self-assemble directly from cellular membranes, allowing in vitro probing of membrane proteins with techniques that have previously been restricted to soluble or detergent-solubilized proteins. Often, however, the high charge densities of existing polymers obstruct bioanalytical and preparative techniques. Thus, the authors aim to fabricate electroneutral-yet water-soluble-polymer nanodiscs. By attaching a sulfobetaine group to the commercial polymers DIBMA and SMA(2:1), these polyanionic polymers are converted to the electroneutral maleimide derivatives, Sulfo-DIBMA and Sulfo-SMA(2:1). Sulfo-DIBMA and Sulfo-SMA(2:1) readily extract proteins and phospholipids from artificial and cellular membranes to form nanodiscs. Crucially, the electroneutral nanodiscs avert unspecific interactions, thereby enabling new insights into protein-lipid interactions through lab-on-a-chip detection and in vitro translation of membrane proteins. Finally, the authors create a library comprising thousands of human membrane proteins and use proteome profiling by mass spectrometry to show that protein complexes are preserved in electroneutral nanodiscs.
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Affiliation(s)
- David Glueck
- 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, Graz, 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Anne Grethen
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Manabendra Das
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Ogochukwu Patricia Mmeka
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
- Department of Chemistry, University of Ibadan, Ibadan, 200284, Nigeria
| | - Eugenio Pérez Patallo
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Annette Meister
- HALOmem and Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Ritu Rajender
- Human Biology, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Stefan Kins
- Human Biology, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, Technische Universität Kaiserslautern (TUK), Paul-Ehrlich-Str. 24, 67663, Kaiserslautern, Germany
| | - Julian Victor
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Ci Chu
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Zoe Köck
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University of Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Frank Bernhard
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University of Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | | | - 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, Graz, 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - 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, Graz, 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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44
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Workman CE, Cawthon B, Brady NG, Bruce BD, Long BK. Effects of Esterified Styrene-Maleic Acid Copolymer Degradation on Integral Membrane Protein Extraction. Biomacromolecules 2022; 23:4749-4755. [PMID: 36219772 DOI: 10.1021/acs.biomac.2c00928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The detergent-free extraction of integral membrane proteins using styrene-maleic acid copolymers (SMAs) has shown promise as a potentially effective technique to isolate proteins in a more native-like conformation. As the field continues to develop, the protein selectivity and extraction efficiency of many analogues of traditional SMAs are being investigated. Recently, we discovered that the monoesterification of SMAs with alkoxy ethoxylate sidechains drastically affects the bioactivity of these copolymers in the extraction of photosystem I from the cyanobacterium Thermosynechococcus elongatus. However, subsequent investigations also revealed that the conditions under which these esterified SMA polymer analogues are prepared, purified, and stored can alter the structure of the alkoxy ethoxylate-functionalized SMA and perturb the protein extraction process. Herein, we demonstrate that the basic conditions required to solubilize SMA analogues may lead to deleterious saponification side reactions, cleaving the sidechains of an esterified SMA and dramatically decreasing its efficacy for protein extraction. We found that this process is highly dependent on temperature, with polymer samples being prepared and stored at lower temperatures exhibiting significantly fewer saponification side reactions. Furthermore, the effects of small-molecule impurities and exposure to light were also investigated, both of which are shown to have significant effects on the polymer structure and/or protein extraction process.
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Affiliation(s)
- Cameron E Workman
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Bridgie Cawthon
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Nathan G Brady
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Barry D Bruce
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Brian K Long
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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45
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Bruggisser J, Iacovache I, Musson SC, Degiacomi MT, Posthaus H, Zuber B. Cryo-EM structure of the octameric pore of Clostridium perfringens β-toxin. EMBO Rep 2022; 23:e54856. [PMID: 36215680 PMCID: PMC9724662 DOI: 10.15252/embr.202254856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 12/12/2022] Open
Abstract
Clostridium perfringens is one of the most widely distributed and successful pathogens producing an impressive arsenal of toxins. One of the most potent toxins produced is the C. perfringens β-toxin (CPB). This toxin is the main virulence factor of type C strains. We describe the cryo-electron microscopy (EM) structure of CPB oligomer. We show that CPB forms homo-octameric pores like the hetero-oligomeric pores of the bi-component leukocidins, with important differences in the receptor binding region and the N-terminal latch domain. Intriguingly, the octameric CPB pore complex contains a second 16-stranded β-barrel protrusion atop of the cap domain that is formed by the N-termini of the eight protomers. We propose that CPB, together with the newly identified Epx toxins, is a member a new subclass of the hemolysin-like family. In addition, we show that the β-barrel protrusion domain can be modified without affecting the pore-forming ability, thus making the pore particularly attractive for macromolecule sensing and nanotechnology. The cryo-EM structure of the octameric pore of CPB will facilitate future developments in both nanotechnology and basic research.
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Affiliation(s)
- Julia Bruggisser
- Institute of Animal Pathology, Vetsuisse‐FacultyUniversity of BernBernSwitzerland
| | - Ioan Iacovache
- Institute of Anatomy, Medical FacultyUniversity of BernBernSwitzerland
| | | | | | - Horst Posthaus
- Institute of Animal Pathology, Vetsuisse‐FacultyUniversity of BernBernSwitzerland
| | - Benoît Zuber
- Institute of Anatomy, Medical FacultyUniversity of BernBernSwitzerland
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46
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Marconnet A, Michon B, Prost B, Solgadi A, Le Bon C, Giusti F, Tribet C, Zoonens M. Influence of Hydrophobic Groups Attached to Amphipathic Polymers on the Solubilization of Membrane Proteins along with Their Lipids. Anal Chem 2022; 94:14151-14158. [PMID: 36200347 DOI: 10.1021/acs.analchem.2c01746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the biggest challenges in membrane protein (MP) research is to secure physiologically relevant structural and functional information after extracting MPs from their native membrane. Amphipathic polymers represent attractive alternatives to detergents for stabilizing MPs in aqueous solutions. The predominant polymers used in MP biochemistry and biophysics are amphipols (APols), one class of which, styrene maleic acid (SMA) copolymers and their derivatives, has proven particularly efficient at MP extraction. In order to examine the relationship between the chemical structure of the polymers and their ability to extract MPs from membranes, we have developed two novel classes of APols bearing either cycloalkane or aryl (aromatic) rings, named CyclAPols and ArylAPols, respectively. The effect on solubilization of such parameters as the density of hydrophobic groups, the number of carbon atoms and their arrangement in the hydrophobic moieties, as well as the charge density of the polymers was evaluated. The membrane-solubilizing efficiency of the SMAs, CyclAPols, and ArylAPols was compared using as models (i) two MPs, BmrA and a GFP-fused version of LacY, overexpressed in the inner membrane of Escherichia coli, and (ii) bacteriorhodopsin, naturally expressed in the purple membrane of Halobacterium salinarum. This analysis shows that, as compared to SMAs, the novel APols feature an improved efficiency at extracting MPs while preserving native protein-lipid interactions.
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Affiliation(s)
- Anaïs Marconnet
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, Université Paris Cité, F-75005 Paris, France.,Fondation Edmond de Rothschild pour le développement de la recherche scientifique, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Baptiste Michon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, Université Paris Cité, F-75005 Paris, France.,Fondation Edmond de Rothschild pour le développement de la recherche scientifique, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Bastien Prost
- UMS-IPSIT SAMM, Inserm, CNRS, Ingénierie et Plateformes au Service de l'Innovation Thérapeutique, Université Paris-Saclay, F-92296 Châtenay-Malabry, France
| | - Audrey Solgadi
- UMS-IPSIT SAMM, Inserm, CNRS, Ingénierie et Plateformes au Service de l'Innovation Thérapeutique, Université Paris-Saclay, F-92296 Châtenay-Malabry, France
| | - Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, Université Paris Cité, F-75005 Paris, France.,Fondation Edmond de Rothschild pour le développement de la recherche scientifique, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Fabrice Giusti
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, Université Paris Cité, F-75005 Paris, France.,Fondation Edmond de Rothschild pour le développement de la recherche scientifique, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Christophe Tribet
- P.A.S.T.E.U.R., Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, F-75005 Paris, France
| | - Manuela Zoonens
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, Université Paris Cité, F-75005 Paris, France.,Fondation Edmond de Rothschild pour le développement de la recherche scientifique, Institut de Biologie Physico-Chimique, F-75005 Paris, France
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47
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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: 14] [Impact Index Per Article: 7.0] [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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48
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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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49
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Janata M, Čadová E, Angelisová P, Charnavets T, Hořejší V, Raus V. Tailoring Butyl Methacrylate/Methacrylic Acid Copolymers for the Solubilization of Membrane Proteins: The Influence of Composition and Molecular Weight. Macromol Biosci 2022; 22:e2200284. [PMID: 35964154 DOI: 10.1002/mabi.202200284] [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: 07/11/2022] [Revised: 08/02/2022] [Indexed: 11/11/2022]
Abstract
Low-molecular weight (MW) amphiphilic copolymers have been recently introduced as a powerful tool for the detergent-free isolation of cell membrane proteins. Herein, we use a screening approach to identify a new copolymer type for this application. Via a two-step ATRP/acidolysis procedure, we prepare a 3×3 matrix of well-defined poly[(butyl methacrylate)-co-(methacrylic acid)] copolymers (denoted BMAA) differing in their MW and ratio of hydrophobic (BMA) and hydrophilic (MAA) units. Subsequently, using the biologically relevant model (T-cell line Jurkat), we identify two compositions of BMAA copolymers that solubilize cell membranes to an extent comparable to the industry standard, styrene-maleic acid copolymer (SMA), while avoiding the potentially problematic phenyl groups. Surprisingly, while only the lowest-MW variant of the BMA/MAA 2:1 composition is effective, all the copolymers of the BMA/MAA 1:1 composition are found to solubilize the model membranes, including the high-MW variant (MW of 14 000). Importantly, the density gradient ultracentrifugation/SDS PAGE/Western blotting experiments reveal that the BMA/MAA 1:1 copolymers disintegrate the Jurkat membranes differently than SMA, as demonstrated by the different distribution patterns of two tested membrane protein markers. This makes the BMAA copolymers a useful tool for studies on membrane microdomains differing in their composition and resistance to membrane-disintegrating polymers. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Miroslav Janata
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, Prague 6, 162 06, Czech Republic
| | - Eva Čadová
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, Prague 6, 162 06, Czech Republic
| | - Pavla Angelisová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Czech Republic
| | - Tatsiana Charnavets
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Czech Republic.,T. Charnavets, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, CZ-25242, Czech Republic
| | - Václav Hořejší
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Czech Republic
| | - Vladimír Raus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, Prague 6, 162 06, Czech Republic
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50
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Shu S, Mi W. Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Nat Commun 2022; 13:4576. [PMID: 35931690 PMCID: PMC9356133 DOI: 10.1038/s41467-022-32277-1] [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: 02/16/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH-mediated degradation of LpxC, which catalyzes the first committed step in LPS synthesis. FtsH is a membrane-bound AAA+ protease, and its protease activity toward LpxC is regulated by essential membrane proteins LapB and YejM. However, the regulatory mechanisms are elusive. We establish an in vitro assay to analyze the kinetics of LpxC degradation and demonstrate that LapB is an adaptor protein that utilizes its transmembrane helix to interact with FtsH and its cytoplasmic domains to recruit LpxC. Our YejM/LapB complex structure reveals that YejM is an anti-adaptor protein, competing with FtsH for LapB to inhibit LpxC degradation. Structural analysis unravels that LapB and LPS have overlapping binding sites in YejM. Thus, LPS levels control formation of the YejM/LapB complex to determine LpxC protein levels.
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Affiliation(s)
- Sheng Shu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wei Mi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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