1
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc Reconstitution and Characterization of Amyloid-β Precursor Protein C99. Anal Chem 2024; 96:9362-9369. [PMID: 38826107 DOI: 10.1021/acs.analchem.3c05727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease (AD). Since the fragmentation of the membrane-bound APP that results in the production of amyloid-β peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable and suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in the native Escherichia. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
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2
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Widmalm G. Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy. JACS AU 2024; 4:20-39. [PMID: 38274261 PMCID: PMC10807006 DOI: 10.1021/jacsau.3c00639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.
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Affiliation(s)
- Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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3
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Zhao P, Zhao Z, Yu Z, Chen L, Jin Y, Wu J, Ren Z. Application of synthetic lipid droplets in metabolic diseases. Clin Transl Med 2023; 13:e1441. [PMID: 37997538 PMCID: PMC10668006 DOI: 10.1002/ctm2.1441] [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: 05/15/2023] [Revised: 09/16/2023] [Accepted: 10/01/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The study and synthesis of membrane organelles are becoming increasingly important, not only as simplified cellular models for corresponding molecular and metabolic studies but also for applications in synthetic biology of artificial cells and drug delivery vehicles. Lipid droplets (LDs) are central organelles in cellular lipid metabolism and are involved in almost all metabolic processes. Multiple studies have also demonstrated a high correlation between LDs and metabolic diseases. During these processes, LDs reveal a highly dynamic character, with their lipid fraction, protein composition and subcellular localisation constantly changing in response to metabolic demands. However, the molecular mechanisms underlying these functions have not been fully understood due to the limitations of cell biology approaches. Fortunately, developments in synthetic biology have provided a huge breakthrough for metabolism research, and methods for in vitro synthesis of LDs have been successfully established, with great advances in protein binding, lipid function, membrane dynamics and enzymatic reactions. AIMS AND METHODS In this review, we provide a comprehensive overview of the assembly and function of endogenous LDs, from the generation of lipid molecules to how they are assembled into LDs in the endoplasmic reticulum. In particular, we highlight two major classes of synthetic LD models for fabrication techniques and their recent advances in biology and explore their roles and challenges in achieving real applications of artificial LDs in the future.
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Affiliation(s)
- Pengxiang Zhao
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
- College of Animal Science and TechnologyShandong Agricultural UniversityTaianShandongP. R. China
| | - Zichen Zhao
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
| | - Ziwei Yu
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
| | - Lupeng Chen
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
| | - Yi Jin
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
| | - Jian Wu
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
- Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhanHubeiP. R. China
| | - Zhuqing Ren
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
- Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhanHubeiP. R. China
- Hubei Hongshan LaboratoryWuhanHubeiP. R. China
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4
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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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5
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Reichstein IS, König M, Wojtysiak N, Escher BI, Henneberger L, Behnisch P, Besselink H, Thalmann B, Colas J, Hörchner S, Hollert H, Schiwy A. Replacing animal-derived components in in vitro test guidelines OECD 455 and 487. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161454. [PMID: 36638987 DOI: 10.1016/j.scitotenv.2023.161454] [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: 10/25/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The evaluation of single substances or environmental samples for their genotoxic or estrogenic potential is highly relevant for human- and environment-related risk assessment. To examine the effects on a mechanism-specific level, standardized cell-based in vitro methods are widely applied. However, these methods include animal-derived components like fetal bovine serum (FBS) or rat-derived liver homogenate fractions (S9-mixes), which are a source of variability, reduced assay reproducibility and ethical concerns. In our study, we evaluated the adaptation of the cell-based in vitro OECD test guidelines TG 487 (assessment of genotoxicity) and TG 455 (detection of estrogenic activity) to an animal-component-free methodology. Firstly, the human cell lines A549 (for OECD TG 487), ERα-CALUX® and GeneBLAzer™ ERα-UAS-bla GripTite™ (for OECD TG 455) were investigated for growth in a chemically defined medium without the addition of FBS. Secondly, the biotechnological S9-mix ewoS9R was implemented in comparison to the induced rat liver S9 to simulate in vivo metabolism capacities in both OECD test guidelines. As a model compound, Benzo[a]pyrene was used due to its increased genotoxicity and endocrine activity after metabolization. The metabolization of Benzo[a]Pyrene by S9-mixes was examined via chemical analysis. All cell lines (A549, ERα-CALUX® and GeneBLAzer™ Erα-UAS-bla GripTite™) were successfully cultivated in chemically defined media without FBS. The micronucleus assay could not be conducted in chemically defined medium due to formation of cell clusters. The methods for endocrine activity assessment could be conducted in chemically defined media or reduced FBS content, but with decreased assay sensitivity. The biotechnological ewoS9R showed potential to replace rat liver S9 in the micronucleus in FBS-medium with A549 cells and in the ERα-CALUX® assay in FBS- and chemically defined medium. Our study showed promising steps towards an animal-component free toxicity testing. After further improvements, the new methodology could lead to more reproducible and reliable results for risk assessment.
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Affiliation(s)
- Inska S Reichstein
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria König
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Niklas Wojtysiak
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Beate I Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, Leipzig, Germany; Environmental Toxicology, Center for Applied Geosciences, Eberhard Karls University Tübingen, Germany
| | - Luise Henneberger
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | | | | | - Julien Colas
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sarah Hörchner
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Henner Hollert
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany; Department Environmental Media Related Ecotoxicology, Fraunhofer IME, Schmallenberg, Germany.
| | - Andreas Schiwy
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany; Department Environmental Media Related Ecotoxicology, Fraunhofer IME, Schmallenberg, Germany.
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6
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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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7
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Krishnarjuna B, Ravula T, Faison EM, Tonelli M, Zhang Q, Ramamoorthy A. Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids. Biomolecules 2022; 12:1628. [PMID: 36358983 PMCID: PMC9687133 DOI: 10.3390/biom12111628] [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: 09/29/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Residual dipolar couplings (RDCs) are increasingly used for high-throughput NMR-based structural studies and to provide long-range angular constraints to validate and refine structures of various molecules determined by X-ray crystallography and NMR spectroscopy. RDCs of a given molecule can be measured in an anisotropic environment that aligns in an external magnetic field. Here, we demonstrate the first application of polymer-based nanodiscs for the measurement of RDCs from nucleic acids. Polymer-based nanodiscs prepared using negatively charged SMA-EA polymer and zwitterionic DMPC lipids were characterized by size-exclusion chromatography, 1H NMR, dynamic light-scattering, and 2H NMR. The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a 13C/15N-labeled fluoride riboswitch aptamer using 2D ARTSY-HSQC NMR experiments. The results showed that the alignment of nanodiscs is stable for nucleic acids and nanodisc-induced RDCs fit well with the previously determined solution structure of the riboswitch. These results demonstrate that SMA-EA-based lipid-nanodiscs can be used as a stable alignment medium for high-resolution structural and dynamical studies of nucleic acids, and they can also be applicable to study various other biomolecules and small molecules in general.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Edgar M. Faison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
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8
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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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9
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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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10
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Krishnarjuna B, Ramamoorthy A. Detergent-Free Isolation of Membrane Proteins and Strategies to Study Them in a Near-Native Membrane Environment. Biomolecules 2022; 12:1076. [PMID: 36008970 PMCID: PMC9406181 DOI: 10.3390/biom12081076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important to fully understand their biological function and the roles played by them in the pathology of many diseases. However, the complexity of the cell membrane has severely limited the application of commonly used biophysical and biochemical techniques. Recent advancements in NMR spectroscopy and cryoEM approaches and the development of novel membrane mimetics have overcome some of the major challenges in this area. For example, the development of a variety of lipid-nanodiscs has enabled stable reconstitution and structural and functional studies of membrane proteins. In particular, the ability of synthetic amphipathic polymers to isolate membrane proteins directly from the cell membrane, along with the associated membrane components such as lipids, without the use of a detergent, has opened new avenues to study the structure and function of membrane proteins using a variety of biophysical and biological approaches. This review article is focused on covering the various polymers and approaches developed and their applications for the functional reconstitution and structural investigation of membrane proteins. The unique advantages and limitations of the use of synthetic polymers are also discussed.
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Affiliation(s)
- Bankala Krishnarjuna
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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11
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Iqbal T, Das D. Biochemical Investigation of Membrane-Bound Cytochrome b5 and the Catalytic Domain of Cytochrome b5 Reductase from Arabidopsis thaliana. Biochemistry 2022; 61:909-921. [PMID: 35475372 DOI: 10.1021/acs.biochem.2c00002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The endoplasmic reticulum (ER) membrane of plant cells contains several enzymes responsible for the biosynthesis of a diverse range of molecules essential for plant growth and holds potential for industrial applications. Many of these enzymes are dependent on electron transfer proteins to sustain their catalytic cycles. In plants, two crucial ER-bound electron transfer proteins are cytochrome b5 and cytochrome b5 reductase, which catalyze the stepwise transfer of electrons from NADH to redox enzymes such as fatty acid desaturases, cytochrome P450s, and plant aldehyde decarbonylase. Despite the high significance of plant cytochrome b5 and cytochrome b5 reductase, they have eluded detailed characterization to date. Here, we overexpressed the full-length membrane-bound cytochrome b5 isoform B from the model plant Arabidopsis thaliana in Escherichia coli, purified the protein employing detergents as well as styrene-maleic acid (SMA) copolymers, and biochemically characterized the protein. The SMA-encapsulated cytochrome b5 exhibits a discoidal shape and the characteristic features of the active heme-bound state. We also overexpressed and purified the soluble domain of cytochrome b5 reductase from A. thaliana, establishing its activity, stability, and kinetic parameters. Further, we demonstrated that the plant cytochrome b5, purified in detergents and styrene maleic acid lipid particles (SMALPs), readily accepts electrons from the cognate plant cytochrome b5 reductase and distant electron mediators such as plant NADPH-cytochrome P450 oxidoreductase and cyanobacterial NADPH-ferredoxin reductase. We also measured the kinetic parameters of cytochrome b5 reductase for cytochrome b5. Our studies are the first to report the purification and detailed biochemical characterization of the plant cytochrome b5 and cytochrome b5 reductase from the bacterial overexpression system.
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Affiliation(s)
- Tabish Iqbal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Debasis Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
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12
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Takagi Y, Uchida N, Anraku Y, Muraoka T. Stabilization of bicelles using metal-binding peptide for extended blood circulation. Chem Commun (Camb) 2022; 58:5164-5167. [PMID: 35388392 DOI: 10.1039/d2cc01058e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A metal-binding peptide appending cholic acid, Chol-MBP, formed bicelles by mixing with 1,2-dipalmitoyl-sn-glycero-3-phosphorylcholine (DPPC). Coordination of Chol-MBP with Cu2+ stabilized DPPC bicelles against dilution and contamination of serum proteins, enabling extended blood circulation. This study demonstrates an effective supramolecular design of phospholipid bicelles with enhanced stability useful for membrane-based biomaterials.
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Affiliation(s)
- Yuichiro Takagi
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yasutaka Anraku
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14, Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. .,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu-Shi, Tokyo 183-8538, Japan.,Kanagawa Institute of Industrial Science and Technology (KISTEC), 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan
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13
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Krishnarjuna B, Ravula T, Ramamoorthy A. Detergent-free isolation of CYP450-reductase's FMN-binding domain in E. coli lipid-nanodiscs using a charge-free polymer. Chem Commun (Camb) 2022; 58:4913-4916. [PMID: 35356954 PMCID: PMC9578324 DOI: 10.1039/d1cc07193a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The membrane-anchored flavin mononucleotide binding domain (FBD) of CYP450 reductase was extracted in E. coli lipid-nanodiscs using charge-free pentyl-inulin polymer. FBD in nanodiscs was found to be conformationally homogenous and enabled high-resolution NMR probing. 31P NMR revealed the polymer's lack of preference for any specific E. coli lipids and identified the lipid-types in nanodiscs.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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14
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Silicon Nitride-Based Micro-Apertures Coated with Parylene for the Investigation of Pore Proteins Fused in Free-Standing Lipid Bilayers. MEMBRANES 2022; 12:membranes12030309. [PMID: 35323784 PMCID: PMC8954132 DOI: 10.3390/membranes12030309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 12/21/2022]
Abstract
In this work, we present a microsystem setup for performing sensitive biological membrane translocation measurements. Thin free-standing synthetic bilayer lipid membranes (BLM) were constructed in microfabricated silicon nitride apertures (<100 µm in diameter), conformal coated with Parylene (Parylene-C or Parylene-AF4). Within these BLMs, electrophysiological measurements were conducted to monitor the behavior of different pore proteins. Two approaches to integrate pore-forming proteins into the membrane were applied: direct reconstitution and reconstitution via outer membrane vesicles (OMVs) released from Gram-negative bacteria. The advantage of utilizing OMVs is that the pore proteins remain in their native lipid and lipopolysaccharide (LPS) environment, representing a more natural state compared to the usage of fused purified pore proteins. Multiple aperture chips can be easily assembled in the 3d-printed holder to conduct parallel membrane transport investigations. Moreover, well defined microfabricated apertures are achievable with very high reproducibility. The presented microsystem allows the investigation of fast gating events (down to 1 ms), pore blocking by an antibiotic, and gating events of small pores (amplitude of approx. 3 pA).
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15
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Sahoo BR, Souders CL, Watanabe-Nakayama T, Deng Z, Linton H, Suladze S, Ivanova MI, Reif B, Ando T, Martyniuk CJ, Ramamoorthy A. Conformational Tuning of Amylin by Charged Styrene-Maleic-Acid Copolymers. J Mol Biol 2022; 434:167385. [PMID: 34883118 PMCID: PMC8752516 DOI: 10.1016/j.jmb.2021.167385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 02/01/2023]
Abstract
Human amylin forms structurally heterogeneous amyloids that have been linked to type-2 diabetes. Thus, understanding the molecular interactions governing amylin aggregation can provide mechanistic insights in its pathogenic formation. Here, we demonstrate that fibril formation of amylin is altered by synthetic amphipathic copolymer derivatives of the styrene-maleic-acid (SMAQA and SMAEA). High-speed AFM is used to follow the real-time aggregation of amylin by observing the rapid formation of de novo globular oligomers and arrestment of fibrillation by the positively-charged SMAQA. We also observed an accelerated fibril formation in the presence of the negatively-charged SMAEA. These findings were further validated by fluorescence, SOFAST-HMQC, DOSY and STD NMR experiments. Conformational analysis by CD and FT-IR revealed that the SMA copolymers modulate the conformation of amylin aggregates. While the species formed with SMAQA are α-helical, the ones formed with SMAEA are rich in β-sheet structure. The interacting interfaces between SMAEA or SMAQA and amylin are mapped by NMR and microseconds all-atom MD simulation. SMAEA displayed π-π interaction with Phe23, electrostatic π-cation interaction with His18 and hydrophobic packing with Ala13 and Val17; whereas SMAQA showed a selective interaction with amylin's C terminus (residues 31-37) that belongs to one of the two β-sheet regions (residues 14-19 and 31-36) involved in amylin fibrillation. Toxicity analysis showed both SMA copolymers to be non-toxic in vitro and the amylin species formed with the copolymers showed minimal deformity to zebrafish embryos. Together, this study demonstrates that chemical tools, such as copolymers, can be used to modulate amylin aggregation, alter the conformation of species.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, The University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | - Zhou Deng
- Biophysics Program, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Hunter Linton
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Saba Suladze
- Department of Chemistry, Technische Universität München, Garching 85748, Germany
| | - Magdalena I Ivanova
- Biophysics Program, The University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Bernd Reif
- Department of Chemistry, Technische Universität München, Garching 85748, Germany
| | - Toshio Ando
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 9201192, Japan
| | - Christopher J Martyniuk
- Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, The University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Flores SS, Clop PD, Barra JL, Argaraña CE, Perillo MA, Nolan V, Sánchez JM. His-tag β-galactosidase supramolecular performance. Biophys Chem 2021; 281:106739. [PMID: 34923392 DOI: 10.1016/j.bpc.2021.106739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/05/2021] [Accepted: 12/05/2021] [Indexed: 11/02/2022]
Abstract
β-Galactosidase is an important biotechnological enzyme used in the dairy industry, pharmacology and in molecular biology. In our laboratory we have overexpressed a recombinant β-galactosidase in Escherichia coli (E. coli). This enzyme differs from its native version (β-GalWT) in that 6 histidine residues have been added to the carboxyl terminus in the primary sequence (β-GalHis), which allows its purification by immobilized metal affinity chromatography (IMAC). In this work we compared the functionality and structure of both proteins and evaluated their catalytic behavior on the kinetics of lactose hydrolysis. We observed a significant reduction in the enzymatic activity of β-GalHis with respect to β-GalWT. Although, both enzymes showed a similar catalytic profile as a function of temperature, β-GalHis presented a higher resistance to the thermal inactivation compared to β-GalWT. At room temperature, β-GalHis showed a fluorescence spectrum compatible with a partially unstructured protein, however, it exhibited a lower tendency to the thermal-induced unfolding with respect to β-GalWT. The distinctively supramolecular arranges of the proteins would explain the effect of the presence of His-tag on the enzymatic activity and thermal stability.
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Affiliation(s)
- Sandra S Flores
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Pedro D Clop
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - José L Barra
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica "Ranwel Caputto", Av. Haya de la Torre s/N° Ciudad Universitaria CP, X5000HUA Córdoba, Argentina; CONICET, Centro de Investigaciones en Química Biológicas de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Carlos E Argaraña
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica "Ranwel Caputto", Av. Haya de la Torre s/N° Ciudad Universitaria CP, X5000HUA Córdoba, Argentina; CONICET, Centro de Investigaciones en Química Biológicas de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - María A Perillo
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Verónica Nolan
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina.
| | - Julieta M Sánchez
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina.
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17
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Farrelly MD, Martin LL, Thang SH. Polymer Nanodiscs and Their Bioanalytical Potential. Chemistry 2021; 27:12922-12939. [PMID: 34180107 DOI: 10.1002/chem.202101572] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/21/2022]
Abstract
Membrane proteins (MPs) play a pivotal role in cellular function and are therefore predominant pharmaceutical targets. Although detailed understanding of MP structure and mechanistic activity is invaluable for rational drug design, challenges are associated with the purification and study of MPs. This review delves into the historical developments that became the prelude to currently available membrane mimetic technologies before shining a spotlight on polymer nanodiscs. These are soluble nanosized particles capable of encompassing MPs embedded in a phospholipid ring. The expanding range of reported amphipathic polymer nanodisc materials is presented and discussed in terms of their tolerance to different solution conditions and their nanodisc properties. Finally, the analytical scope of polymer nanodiscs is considered in both the demonstration of basic nanodisc parameters as well as in the elucidation of structures, lipid-protein interactions, and the functional mechanisms of reconstituted membrane proteins. The final emphasis is given to the unique benefits and applications demonstrated for native nanodiscs accessed through a detergent free process.
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Affiliation(s)
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, 3800, Vic, Australia
| | - San H Thang
- School of Chemistry, Monash University, Clayton, 3800, Vic, Australia
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18
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CryoEM reconstructions of membrane proteins solved in several amphipathic solvents, nanodisc, amphipol and detergents, yield amphipathic belts of similar sizes corresponding to a common ordered solvent layer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183693. [PMID: 34271006 DOI: 10.1016/j.bbamem.2021.183693] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/31/2022]
Abstract
To maintain membrane proteins soluble in aqueous solution, amphipathic compounds are used to shield the hydrophobic patch of their membrane insertion, which forms a belt around the protein. This amphipathic belt is seldom looked at due to the difficulty to visualize it. Cryo-EM is now offering this possibility, where belts are visible in 3D reconstructions. We investigated membrane proteins solved in nanodiscs, amphipols or detergents to analyze whether the nature of the amphipathic compound influences the belt size in 3D reconstructions. We identified belt boundaries in map-density distributions and measured distances for every reconstruction. We showed that all the belts create on average similar reconstructions, whether they originate from the same protein, or from protein from different shapes and structures. There is no difference among detergents or types of nanodisc used. These observations illustrate that the belt observed in 3D reconstructions corresponds to the minimum ordered layer around membrane proteins.
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19
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Pereira RFS, de Carvalho CCCR. Optimization of Multiparameters for Increased Yields of Cytochrome B5 in Bioreactors. Molecules 2021; 26:4148. [PMID: 34299423 PMCID: PMC8306036 DOI: 10.3390/molecules26144148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/26/2022] Open
Abstract
The production of recombinant proteins is gaining increasing importance as the market requests high quality proteins for several applications. However, several process parameters affect both the growth of cells and product yields. This study uses high throughput systems and statistical methods to assess the influence of fermentation conditions in lab-scale bioreactors. Using this methodology, it was possible to find the best conditions to produce cytochrome b5 with recombinant cells of Escherichia coli. Using partial least squares, the height-to-diameter ratio of the bioreactor, aeration rate, and PID controller parameters were found to contribute significantly to the final biomass and cytochrome concentrations. Hence, we could use this information to fine-tune the process parameters, which increased cytochrome production and yield several-fold. Using aeration of 1 vvm, a bioreactor with a height-to-ratio of 2.4 and tuned PID parameters, a production of 72.72 mg/L of cytochrome b5 in the culture media, and a maximum of product to biomass yield of 24.97 mg/g could be achieved.
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Affiliation(s)
- Ricardo F. S. Pereira
- Department of Bioengineering, iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Carla C. C. R. de Carvalho
- Department of Bioengineering, iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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20
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Ravula T, Dai X, Ramamoorthy A. Solid-State NMR Study to Probe the Effects of Divalent Metal Ions (Ca 2+ and Mg 2+) on the Magnetic Alignment of Polymer-Based Lipid Nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7780-7788. [PMID: 34129342 PMCID: PMC8587631 DOI: 10.1021/acs.langmuir.1c01018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Divalent cations, especially Ca2+ and Mg2+, play a vital role in the function of biomolecules and making them important to be constituents in samples for in vitro biophysical and biochemical characterizations. Although lipid nanodiscs are becoming valuable tools for structural biology studies on membrane proteins and for drug delivery, most types of nanodiscs used in these studies are unstable in the presence of divalent metal ions. To avoid the interaction of divalent metal ions with the belt of the nanodiscs, synthetic polymers have been designed and demonstrated to form stable lipid nanodiscs under such unstable conditions. Such polymer-based nanodiscs have been shown to provide an ideal platform for structural studies using both solid-state and solution NMR spectroscopies because of the near-native cell-membrane environment they provide and the unique magnetic-alignment behavior of large-size nanodiscs. In this study, we report an investigation probing the effects of Ca2+ and Mg2+ ions on the formation of polymer-based lipid nanodiscs and the magnetic-alignment properties using a synthetic polymer, styrene maleimide quaternary ammonium (SMA-QA), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids. Phosphorus-31 NMR experiments were used to evaluate the stability of the magnetic-alignment behavior of the nanodiscs for varying concentrations of Ca2+ or Mg2+ at different temperatures. It is remarkable that the interaction of divalent cations with lipid headgroups promotes the stacking up of nanodiscs that results in the enhanced magnetic alignment of nanodiscs. Interestingly, the reported results show that both the temperature and the concentration of divalent metal ions can be optimized to achieve the optimal alignment of nanodiscs in the presence of an applied magnetic field. We expect the reported results to be useful in the design of nanodisc-based nanoparticles for various applications in addition to atomic-resolution structural and dynamics studies using NMR and other biophysical techniques.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Xiaofeng Dai
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
- Xiaofeng Dai was a visiting student from the College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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21
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Krishnarjuna B, Yamazaki T, Anantharamaiah GM, Ramamoorthy A. Nanodisc reconstitution of flavin mononucleotide binding domain of cytochrome-P450-reductase enables high-resolution NMR probing. Chem Commun (Camb) 2021; 57:4819-4822. [PMID: 33982687 PMCID: PMC8136615 DOI: 10.1039/d1cc01018b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cytochrome-P450-reductase transfers electrons to cytochrome-P450 through its flavin mononucleotide binding domain (FBD). Despite the importance of membrane-anchoring for FBD function, studies have focused on its soluble domain lacking the transmembrane-domain. Here we demonstrate that the reconstitution of FBD in nanodiscs enables high-resolution NMR measurements and renders a stable conformation.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Arbor, MI 48109, USA.
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22
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Di Mauro GM, La Rosa C, Condorelli M, Ramamoorthy A. Benchmarks of SMA-Copolymer Derivatives and Nanodisc Integrity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3113-3121. [PMID: 33645999 DOI: 10.1021/acs.langmuir.0c03554] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Poly(styrene-co-maleic acid) or SMA and its derivatives, a family of synthetic amphipathic copolymers, are increasingly used to directly solubilize cell membranes to functionally reconstitute membrane proteins in native-like copolymer-lipid nanodiscs. Although these copolymers act, de facto, like a "macromolecular detergent", the polymer-based lipid-nanodiscs has been demonstrated to be an excellent membrane mimetic for structural and functional studies of membrane proteins and their complexes by a variety of biophysical and biochemical approaches. In many studies reported in the literature, the choice of the right SMA formulation can depend on a number of factors, and the experimental conditions are typically developed according to a trial-and-error process since each studied system requires adapted protocols. While increasing number of nanodisc-forming copolymers are reported to be useful and they provide flexibilities in optimizing the sample preparation conditions, it is important to develop a systematic protocol that can be used for various applications. In this context, there is a vital necessity of benchmarking the performances of existing copolymer formulations, assessing crucial parameters for the successful extraction, isolation, and stabilization of membrane proteins. In this study, we compare both copolymers and copolymer-lipid nanodiscs obtained by SMA-EA with a set of anionic XIRAN copolymer formulations commercially available under the names of SL25010 P, SL30010 P, and SL40005 P. The reported results show how the critical micellar concentration (c.m.c.) of each copolymer is significantly altered in the presence of lipids and confirms the existence of an equilibrium between nanodisc-bound and "free" or "micellar" copolymer chains in the solution. We believe that these findings can be exploited to optimize studies that involve the necessity of special copolymers, which would not only simplify the applications but also broaden the scope of polymer-based nanodiscs.
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Affiliation(s)
- Giacomo M Di Mauro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Carmelo La Rosa
- Department of Chemistry, University of Catania, Catania 95125, Italy
| | | | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Biophysics and Chemistry Department, Macromolecular Science and Engineering, and Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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23
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Functional Assembly of Caenorhabditis elegans Cytochrome b-2 (Cecytb-2) into Phospholipid Bilayer Nanodisc with Enhanced Iron Reductase Activity. Biomolecules 2021; 11:biom11010096. [PMID: 33451048 PMCID: PMC7828500 DOI: 10.3390/biom11010096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
Among seven homologs of cytochrome b561 in a model organism C. elegans, Cecytb-2 was confirmed to be expressed in digestive organs and was considered as a homolog of human Dcytb functioning as a ferric reductase. Cecytb-2 protein was expressed in Pichia pastoris cells, purified, and reconstituted into a phospholipid bilayer nanodisc. The reconstituted Cecytb-2 in nanodisc environments was extremely stable and more reducible with ascorbate than in a detergent-micelle state. We confirmed the ferric reductase activity of Cecytb-2 by analyzing the oxidation of ferrous heme upon addition of ferric substrate under anaerobic conditions, where clear and saturable dependencies on the substrate concentrations following the Michaelis–Menten equation were observed. Further, we confirmed that the ferric substrate was converted to a ferrous state by using a nitroso-PSAP assay. Importantly, we observed that the ferric reductase activity of Cecytb-2 became enhanced in the phospholipid bilayer nanodisc.
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Investigating the Mechanisms of AquaporinZ Reconstitution through Polymeric Vesicle Composition for a Biomimetic Membrane. Polymers (Basel) 2020; 12:polym12091944. [PMID: 32872107 PMCID: PMC7565422 DOI: 10.3390/polym12091944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/06/2020] [Accepted: 08/12/2020] [Indexed: 11/17/2022] Open
Abstract
Aquaporin-Z (AqpZ) are water channel proteins with excellent water permeability and solute rejection properties. AqpZ can be reconstituted into vesicles utilizing cell-like bilayer membranes assembled from amphiphilic block copolymers, for the preparation of high-performance biomimetic membranes. However, only a few copolymers have been found suitable to act as the membrane matrix for protein reconstitution. Hence, this work analyzes the mechanism of protein reconstitution based on a composition-reconstitution relationship. The vesicle formation and AqpZ reconstitution processes in various amphiphilic block copolymers were investigated in terms of size, morphology, stability, polymeric bilayer membrane rigidity, and thermal behavior. Overall, this study contributes to the understanding of the composition-reconstitution relationship of biomimetic membranes based on AqpZ-reconstituted polymeric vesicles.
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