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Baskakova KO, Kuzmichev PK, Karbyshev MS. Advanced applications of Nanodiscs-based platforms for antibodies discovery. Biophys Chem 2024; 313:107290. [PMID: 39002246 DOI: 10.1016/j.bpc.2024.107290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
Due to their fundamental biological importance, membrane proteins (MPs) are attractive targets for drug discovery, with cell surface receptors, transporters, ion channels, and membrane-bound enzymes being of particular interest. However, due to numerous challenges, these proteins present underutilized opportunities for discovering biotherapeutics. Antibodies hold the promise of exquisite specificity and adaptability, making them the ideal candidates for targeting complex membrane proteins. They can target specific conformations of a particular membrane protein and can be engineered into various formats. Generating specific and effective antibodies targeting these proteins is no easy task due to several factors. The antigen's design, antibody-generation strategies, lead optimization technologies, and antibody modalities can be modified to tackle these challenges. The rational employment of cutting-edge lipid nanoparticle systems for retrieving the membrane antigen has been successfully implemented to simplify the mechanism-based therapeutic antibody discovery approach. Despite the highlighted MP production challenges, this review unequivocally underscores the advantages of targeting complex membrane proteins with antibodies and designing membrane protein antigens. Selected examples of lipid nanoparticle success have been illustrated, emphasizing the potential of therapeutic antibody discovery in this regard. With further research and development, we can overcome these challenges and unlock the full potential of therapeutic antibodies directed to target complex MPs.
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Affiliation(s)
- Kristina O Baskakova
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation
| | - Pavel K Kuzmichev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudniy, Russian Federation
| | - Mikhail S Karbyshev
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation; Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, Moscow, Russian Federation.
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2
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Brough Z, Zhao Z, Duong van Hoa F. From bottom-up to cell surface proteomics: detergents or no detergents, that is the question. Biochem Soc Trans 2024; 52:1253-1263. [PMID: 38666604 DOI: 10.1042/bst20231020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Measuring the expression levels of membrane proteins (MPs) is crucial for understanding cell differentiation and tissue specificity, defining disease characteristics, identifying biomarkers, and developing therapeutics. While bottom-up proteomics addresses the need for accurately surveying the membrane proteome, the lower abundance and hydrophobic nature of MPs pose challenges in sample preparation. As MPs normally reside in the lipid bilayer, conventional extraction methods rely on detergents, introducing here a paradox - detergents prevent aggregation and facilitate protein processing, but themselves become contaminants that interfere with downstream analytical applications. Various detergent removal methods exist to mitigate this issue, including filter-aided sample preparation, SP3, suspension trapping, and membrane mimetics. This review delves into the fundamentals of each strategy, applications, merits, and limitations, providing insights into their effectiveness in MP research.
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Affiliation(s)
- Zora Brough
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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3
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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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4
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Daniilidis M, Sperl LE, Müller BS, Babl A, Hagn F. Efficient Segmental Isotope Labeling of Integral Membrane Proteins for High-Resolution NMR Studies. J Am Chem Soc 2024; 146:15403-15410. [PMID: 38787792 PMCID: PMC11157531 DOI: 10.1021/jacs.4c03294] [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: 03/06/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
High-resolution structural NMR analyses of membrane proteins are challenging due to their large size, resulting in broad resonances and strong signal overlap. Among the isotope labeling methods that can remedy this situation, segmental isotope labeling is a suitable strategy to simplify NMR spectra and retain high-resolution structural information. However, protein ligation within integral membrane proteins is complicated since the hydrophobic protein fragments are insoluble, and the removal of ligation side-products is elaborate. Here, we show that a stabilized split-intein system can be used for rapid and high-yield protein trans-splicing of integral membrane proteins under denaturing conditions. This setup enables segmental isotope labeling experiments within folded protein domains for NMR studies. We show that high-quality NMR spectra of markedly reduced complexity can be obtained in detergent micelles and lipid nanodiscs. Of note, the nanodisc insertion step specifically selects for the ligated and correctly folded membrane protein and simultaneously removes ligation byproducts. Using this tailored workflow, we show that high-resolution NMR structure determination is strongly facilitated with just two segmentally isotope-labeled membrane protein samples. The presented method will be broadly applicable to structural and dynamical investigations of (membrane-) proteins and their complexes by solution and solid-state NMR but also other structural methods where segmental labeling is beneficial.
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Affiliation(s)
- Melina Daniilidis
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
| | - Laura E. Sperl
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
| | - Benedikt S. Müller
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
| | - Antonia Babl
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
- Institute
of Structural Biology, Helmholtz Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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5
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Thakur N, Ray AP, Jin B, Afsharian NP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane mimetic-dependence of GPCR energy landscapes. Structure 2024; 32:523-535.e5. [PMID: 38401537 PMCID: PMC11069452 DOI: 10.1016/j.str.2024.01.013] [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: 10/16/2023] [Revised: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
We leveraged variable-temperature 19F-NMR spectroscopy to compare the conformational equilibria of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), across a range of temperatures ranging from lower temperatures typically employed in 19F-NMR experiments to physiological temperature. A2AAR complexes with partial agonists and full agonists showed large increases in the population of a fully active conformation with increasing temperature. NMR data measured at physiological temperature were more in line with functional data. This was pronounced for complexes with partial agonists, where the population of active A2AAR was nearly undetectable at lower temperature but became evident at physiological temperature. Temperature-dependent behavior of complexes with either full or partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. Cellular signaling experiments correlated with the temperature-dependent conformational equilibria of A2AAR in lipid nanodiscs but not in some detergents, underscoring the importance of the membrane environment in studies of GPCR function.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Beining Jin
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | | | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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6
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.21.590446. [PMID: 38659865 PMCID: PMC11042261 DOI: 10.1101/2024.04.21.590446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta 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/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 native E. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, MI 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, MI 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32310, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States
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7
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Gu X, Zhang Y, Long D. Conserved allosteric perturbation of the GTPase domains by region 1 of Ras hypervariable regions. Biophys J 2024; 123:839-846. [PMID: 38419331 PMCID: PMC10995424 DOI: 10.1016/j.bpj.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Ras proteins are important intracellular signaling hubs that can interact with numerous downstream effectors and upstream regulators through their GTPase domains (G-domains) anchored to plasma membranes by the C-terminal hypervariable regions (HVRs). The biological functions of Ras were proposed to be regulated at multiple levels including the intramolecular G-domain-HVR interactions, of which the exact mechanism and specificity are still controversial. Here, we demonstrate that the HVRs, instead of having direct contacts, can weakly perturb the G-domains via an allosteric interaction that is restricted to a ∼20 Å range and highly conserved in the tested Ras isoforms (HRas and KRas4B) and nucleotide-bound states. The origin of this allosteric perturbation has been localized to a short segment (residues 167-171) coinciding with region 1 of HVRs, which exhibits moderate to weak α-helical propensities. A charge-reversal mutation (E168K) of KRas4B in region 1, previously described in the Catalog of Somatic Mutations in Cancer database, was found to induce similar chemical shift perturbations as truncation of the HVR does. Further membrane paramagnetic relaxation enhancement (mPRE) data show that this region 1 mutation alters the membrane orientations of KRas4B and moderately increases the relative population of the signaling-compatible state.
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Affiliation(s)
- Xue Gu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yalong Zhang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Dong Long
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, China; Department of Chemistry, University of Science and Technology of China, Hefei, China.
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8
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Fekri Kohan S, Nouhi Kararoudi A, Bazgosha M, Adelifar S, Hafezolghorani Esfahani A, Ghaderi Barmi F, Kouchakinejad R, Barzegari E, Shahriarinour M, Ranji N. Determining the potential targets of silybin by molecular docking and its antibacterial functions on efflux pumps and porins in uropathogenic E. coli. Int Microbiol 2024:10.1007/s10123-024-00488-9. [PMID: 38363383 DOI: 10.1007/s10123-024-00488-9] [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: 12/03/2023] [Revised: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND One of the causes of antibiotic resistance is the reduced accumulation of antibiotics in bacterial cells through pumping out the drugs. Silybin, a key component of the Silybum marianum plant, exhibits various beneficial properties, including anti-bacterial, anti-inflammatory, antioxidant, and hepatoprotective effects. METHODS AND RESULTS Clinical isolates of E. coli were procured from 17 Shahrivar Children's Hospital in Rasht, Guilan, located in northern Iran. Their susceptibility to six antibiotics was assessed using disc diffusion and broth dilution (MIC) methods. The antibacterial effects of silybin-loaded polymersome nanoparticles (SPNs) were investigated with broth dilution (MIC) and biofilm assays. Molecular docking was utilized to evaluate silybin's (the antibacterial component) binding affinity to efflux pumps, porins, and their regulatory elements. Additionally, qRT-PCR analysis explored the expression patterns of acrA, acrB, tolC, ompC, and ompF genes in both SPNs (sub-MIC) and ciprofloxacin (sub-MIC)-treated and untreated E. coli isolates. The combined use of SPNs and ciprofloxacin exhibited a notable reduction in bacterial growth and biofilm formation, in ciprofloxacin-resistant isolates. The study identified eight overlapping binding sites of the AcrABZ-TolC efflux pump in association with silybin, demonstrating a binding affinity ranging from -7.688 to -10.33 Kcal/mol. Furthermore, the qRT-PCR analysis showed that silybin upregulated AcrAB-TolC efflux pump genes and downregulated ompC and ompF porin genes in combination with ciprofloxacin in transcriptional level in uropathogenic E. coli. CONCLUSIONS Silybin, a safe herbal compound, exhibits potential in inhibiting antibiotic resistance within bacterial isolates, potentially through the regulation of gene expression and plausible binding to target proteins.
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Affiliation(s)
- Shirin Fekri Kohan
- Department of Biology, Faculty of Sciences, Rasht Branch, Islamic Azad University, P.O. Box: 41335-3516, Rasht, Iran
| | - Alireza Nouhi Kararoudi
- Department of Biology, Faculty of Sciences, Lahijan Branch, Islamic Azad University, Rasht, Iran
| | - Maryam Bazgosha
- Department of Biology, Faculty of Sciences, Rasht Branch, Islamic Azad University, P.O. Box: 41335-3516, Rasht, Iran
| | - Somayeh Adelifar
- Department of Biology, Faculty of Sciences, Rasht Branch, Islamic Azad University, P.O. Box: 41335-3516, Rasht, Iran
| | - Arman Hafezolghorani Esfahani
- Department of Biology, Faculty of Sciences, Rasht Branch, Islamic Azad University, P.O. Box: 41335-3516, Rasht, Iran
| | - Fatemeh Ghaderi Barmi
- Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
| | - Reyhaneh Kouchakinejad
- Department of Chemistry, Faculty of Sciences, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mahdi Shahriarinour
- Department of Biology, Faculty of Sciences, Rasht Branch, Islamic Azad University, P.O. Box: 41335-3516, Rasht, Iran.
| | - Najmeh Ranji
- Department of Biology, Faculty of Sciences, Rasht Branch, Islamic Azad University, P.O. Box: 41335-3516, Rasht, Iran.
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9
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Selvasingh JA, McDonald EF, Neufer PD, McKinney JR, Meiler J, Ledwitch KV. Dark nanodiscs for evaluating membrane protein thermostability by differential scanning fluorimetry. Biophys J 2024; 123:68-79. [PMID: 37978799 PMCID: PMC10808023 DOI: 10.1016/j.bpj.2023.11.019] [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: 05/24/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
Measuring protein thermostability provides valuable information on the biophysical rules that govern the structure-energy relationships of proteins. However, such measurements remain a challenge for membrane proteins. Here, we introduce a new experimental system to evaluate membrane protein thermostability. This system leverages a recently developed nonfluorescent membrane scaffold protein to reconstitute proteins into nanodiscs and is coupled with a nano-format of differential scanning fluorimetry (nanoDSF). This approach offers a label-free and direct measurement of the intrinsic tryptophan fluorescence of the membrane protein as it unfolds in solution without signal interference from the "dark" nanodisc. In this work, we demonstrate the application of this method using the disulfide bond formation protein B (DsbB) as a test membrane protein. NanoDSF measurements of DsbB reconstituted in dark nanodiscs loaded with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phosphorylglycerol (DMPG) lipids show a complex biphasic thermal unfolding pattern with a minor unfolding transition followed by a major transition. The inflection points of the thermal denaturation curve reveal two distinct unfolding midpoint melting temperatures (Tm) of 70.5°C and 77.5°C, consistent with a three-state unfolding model. Further, we show that the catalytically conserved disulfide bond between residues C41 and C130 drives the intermediate state of the unfolding pathway for DsbB in a DMPC and DMPG nanodisc. To extend the utility of this method, we evaluate and compare the thermostability of DsbB in different lipid environments. We introduce this method as a new tool that can be used to understand how compositionally and biophysically complex lipid environments drive membrane protein stability.
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Affiliation(s)
- Jazlyn A Selvasingh
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Eli F McDonald
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Preston D Neufer
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Jacob R McKinney
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, Leipzig, Germany.
| | - Kaitlyn V Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee.
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10
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Krishnarjuna B, Sharma G, Ravula T, Ramamoorthy A. Factors influencing the detergent-free membrane protein isolation using synthetic nanodisc-forming polymers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184240. [PMID: 37866688 DOI: 10.1016/j.bbamem.2023.184240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/08/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
The detergent-free isolation of membrane proteins using synthetic polymers is becoming the desired approach for functional and structural studies of membrane proteins. Since the expression levels for many membrane proteins are low and a high yield of functionalized reconstituted membrane proteins is essential for in vitro studies, it is crucial to optimize the experimental conditions for a given polymer to solubilize target membranes/proteins effectively. The factors that affect membrane solubilization and subsequently the isolation of a target membrane protein include polymer concentration, polymer charge, temperature, pH, and concentration of divalent metal ions. Therefore, it is important to have knowledge about the efficacy of different types of polymers in solubilizing cell membranes. In this study, we evaluate the efficacy of inulin-based non-ionic polymers in solubilizing E. coli membranes enriched with rat flavin mononucleotide binding-domain (FBD) of cytochrome-P450-reductase (CPR) and rabbit cytochrome-b5 (Cyt-b5) under various solubilization conditions. Our results show that a 1:1 (w/w) membrane:polymer ratio, low temperature, high pH and sub-millimolar concentration of metal ions favor the solubilization of E. coli membranes enriched with FBD or Cyt-b5. Conversely, the presence of excess divalent metal ions affected the final protein levels in the polymer-solubilized samples. We believe that the results from this study provide knowledge to assess and plan the use of non-ionic polymers in membrane protein studies.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Gaurav Sharma
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayyalusamy Ramamoorthy
- National High Magnetic Field Laboratory, Department of Chemical and Biomedical Engineering, Florida State University, Tallahassee, FL 32310, USA.
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11
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Kurakin S, Badreeva D, Dushanov E, Shutikov A, Efimov S, Timerova A, Mukhametzyanov T, Murugova T, Ivankov O, Mamatkulov K, Arzumanyan G, Klochkov V, Kučerka N. Arrangement of lipid vesicles and bicelle-like structures formed in the presence of Aβ(25-35) peptide. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184237. [PMID: 37820938 DOI: 10.1016/j.bbamem.2023.184237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/31/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Our complementary experimental data and molecular dynamics (MD) simulations results reveal the structure of previously observed lipid bicelle-like structures (BLSs) formed in the presence of amyloid-beta peptide Aβ(25-35) below the main phase transition temperature (Tm) of saturated phosphatidylcholine lipids and small unilamellar vesicles (SUVs) above this temperature. First, we show by using solid-state 31P nuclear magnetic resonance (NMR) spectroscopy that our BLSs being in the lipid gel phase demonstrate magnetic alignment along the magnetic field of NMR spectrometer and undergo a transition to SUVs in the lipid fluid phase when heated through the Tm. Secondly, thanks to the BLS alignment we present their lipid structure. Lipids are found located not only in the flat bilayered part but also around its perimeter, which is corroborated by the results of coarse-grained (CG) MD simulations. Finally, peptides appear to mix randomly with lipids in SUVs while assuming predominantly unordered secondary structures revealed by circular dichroism (CD), Raman spectroscopy, and all-atom MD simulations. Importantly, the former is changing little when the system undergoes morphological transitions between BLSs and SUVs. Our structural results then offer a platform for studying and understanding mechanisms of morphological transformations caused by the disruptive effect of amyloid-beta peptides on the lipid bilayer.
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Affiliation(s)
- Sergei Kurakin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia.
| | - Dina Badreeva
- Meshcheryakov Laboratory of Information Technologies, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Ermuhammad Dushanov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Artyom Shutikov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Sergey Efimov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Ayzira Timerova
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Timur Mukhametzyanov
- Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Tatiana Murugova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Oleksandr Ivankov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Kahramon Mamatkulov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Grigory Arzumanyan
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Vladimir Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Odbojárov 10, Bratislava 832 32, Slovakia.
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12
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Wei S, Pour NG, Tiruvadi-Krishnan S, Ray AP, Thakur N, Eddy MT, Lamichhane R. Single-molecule visualization of human A 2A adenosine receptor activation by a G protein and constitutively activating mutations. Commun Biol 2023; 6:1218. [PMID: 38036689 PMCID: PMC10689853 DOI: 10.1038/s42003-023-05603-6] [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: 06/22/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
Mutations that constitutively activate G protein-coupled receptors (GPCRs), known as constitutively activating mutations (CAMs), modify cell signaling and interfere with drugs, resulting in diseases with limited treatment options. We utilize fluorescence imaging at the single-molecule level to visualize the dynamic process of CAM-mediated activation of the human A2A adenosine receptor (A2AAR) in real time. We observe an active-state population for all CAMs without agonist stimulation. Importantly, activating mutations significantly increase the population of an intermediate state crucial for receptor activation, notably distinct from the addition of a partner G protein. Activation kinetics show that while CAMs increase the frequency of transitions to the intermediate state, mutations altering sodium sensitivity increase transitions away from it. These findings indicate changes in GPCR function caused by mutations may be predicted based on whether they favor or disfavor formation of an intermediate state, providing a framework for designing receptors with altered functions or therapies that target intermediate states.
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Affiliation(s)
- Shushu Wei
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Arka Prabha Ray
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Naveen Thakur
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA.
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA.
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13
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Zhang Y, Soubias O, Pant S, Heinrich F, Vogel A, Li J, Li Y, Clifton LA, Daum S, Bacia K, Huster D, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA. Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. Nat Commun 2023; 14:7570. [PMID: 37989735 PMCID: PMC10663523 DOI: 10.1038/s41467-023-43008-5] [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: 05/12/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
ADP-ribosylation factor 1 (Arf1) interacts with multiple cellular partners and membranes to regulate intracellular traffic, organelle structure and actin dynamics. Defining the dynamic conformational landscape of Arf1 in its active form, when bound to the membrane, is of high functional relevance and key to understanding how Arf1 can alter diverse cellular processes. Through concerted application of nuclear magnetic resonance (NMR), neutron reflectometry (NR) and molecular dynamics (MD) simulations, we show that, while Arf1 is anchored to the membrane through its N-terminal myristoylated amphipathic helix, the G domain explores a large conformational space, existing in a dynamic equilibrium between membrane-associated and membrane-distal conformations. These configurational dynamics expose different interfaces for interaction with effectors. Interaction with the Pleckstrin homology domain of ASAP1, an Arf-GTPase activating protein (ArfGAP), restricts motions of the G domain to lock it in what seems to be a conformation exposing functionally relevant regions.
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Affiliation(s)
- Yue Zhang
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Ring Therapeutics, Inc., Cambridge, MA, USA
| | - Olivier Soubias
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Loxo Oncology at Lilly, Louisville, CO, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- NIST Center for Neutron Research, Gaithersburg, MD, USA
| | - Alexander Vogel
- Institute of Medical Physics and Biophysics, University of Leipzig, 04107, Leipzig, Germany
| | - Jess Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Yifei Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Vonsun Pharmatech Co., Ltd., Suzhou, China
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK
| | - Sebastian Daum
- Institute for Chemistry, Department of Biophysical Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3A, 06120, Halle, Germany
| | - Kirsten Bacia
- Institute for Chemistry, Department of Biophysical Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3A, 06120, Halle, Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, 04107, Leipzig, Germany
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- NIST Center for Neutron Research, Gaithersburg, MD, USA
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - R Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA.
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14
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Thakur N, Ray AP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane Mimetic-Dependence of GPCR Energy Landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562552. [PMID: 37905159 PMCID: PMC10614885 DOI: 10.1101/2023.10.16.562552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Protein function strongly depends on temperature, which is related to temperature-dependent changes in the equilibria of protein conformational states. We leveraged variable-temperature 19F-NMR spectroscopy to interrogate the temperature dependence of the conformational landscape of the human A2A adenosine receptor (A2AAR), a class A GPCR. Temperature-induced changes in the conformational equilibria of A2AAR in lipid nanodiscs were markedly dependent on the efficacy of bound drugs. While antagonist complexes displayed only modest changes as the temperature rose, both full and partial agonist complexes exhibited substantial increases in the active state population. Importantly, the temperature-dependent response of complexes with both full and partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. In striking contrast to observations within lipid nanodiscs, in detergent micelles the active state population exhibited different behavior for A2AAR complexes with both full and partial agonists. This underscores the importance of the protein environment in understanding the thermodynamics of GPCR activation.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
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15
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Goncharuk MV, Vasileva EV, Ananiev EA, Gorokhovatsky AY, Bocharov EV, Mineev KS, Goncharuk SA. Facade-Based Bicelles as a New Tool for Production of Active Membrane Proteins in a Cell-Free System. Int J Mol Sci 2023; 24:14864. [PMID: 37834312 PMCID: PMC10573531 DOI: 10.3390/ijms241914864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Integral membrane proteins are important components of a cell. Their structural and functional studies require production of milligram amounts of proteins, which nowadays is not a routine process. Cell-free protein synthesis is a prospective approach to resolve this task. However, there are few known membrane mimetics that can be used to synthesize active membrane proteins in high amounts. Here, we present the application of commercially available "Facade" detergents for the production of active rhodopsin. We show that the yield of active protein in lipid bicelles containing Facade-EM, Facade-TEM, and Facade-EPC is several times higher than in the case of conventional bicelles with CHAPS and DHPC and is comparable to the yield in the presence of lipid-protein nanodiscs. Moreover, the effects of the lipid-to-detergent ratio, concentration of detergent in the feeding mixture, and lipid composition of the bicelles on the total, soluble, and active protein yields are discussed. We show that Facade-based bicelles represent a prospective membrane mimetic, available for the production of membrane proteins in a cell-free system.
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Affiliation(s)
- Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Ekaterina V. Vasileva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Egor A. Ananiev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Andrey Y. Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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16
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Morstein J, Shrestha R, Van QN, López CA, Arora N, Tonelli M, Liang H, Chen D, Zhou Y, Hancock JF, Stephen AG, Turbyville TJ, Shokat KM. Direct Modulators of K-Ras-Membrane Interactions. ACS Chem Biol 2023; 18:2082-2093. [PMID: 37579045 PMCID: PMC10510109 DOI: 10.1021/acschembio.3c00413] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Protein-membrane interactions (PMIs) are ubiquitous in cellular signaling. Initial steps of signal transduction cascades often rely on transient and dynamic interactions with the inner plasma membrane leaflet to populate and regulate signaling hotspots. Methods to target and modulate these interactions could yield attractive tool compounds and drug candidates. Here, we demonstrate that the conjugation of a medium-chain lipid tail to the covalent K-Ras(G12C) binder MRTX849 at a solvent-exposed site enables such direct modulation of PMIs. The conjugated lipid tail interacts with the tethered membrane and changes the relative membrane orientation and conformation of K-Ras(G12C), as shown by molecular dynamics (MD) simulation-supported NMR studies. In cells, this PMI modulation restricts the lateral mobility of K-Ras(G12C) and disrupts nanoclusters. The described strategy could be broadly applicable to selectively modulate transient PMIs.
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Affiliation(s)
- Johannes Morstein
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Rebika Shrestha
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N. Van
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - César A. López
- Theoretical
Biology and Biophysics Group, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Neha Arora
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Marco Tonelli
- National
Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Hong Liang
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - De Chen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Yong Zhou
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - John F. Hancock
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Andrew G. Stephen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J. Turbyville
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
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17
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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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18
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Guo C, Yang L, Liu Z, Liu D, Wüthrich K. Two-Dimensional NMR Spectroscopy of the G Protein-Coupled Receptor A 2AAR in Lipid Nanodiscs. Molecules 2023; 28:5419. [PMID: 37513291 PMCID: PMC10383251 DOI: 10.3390/molecules28145419] [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: 06/08/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Eight hundred and twenty-six human G protein-coupled receptors (GPCRs) mediate the actions of two-thirds of the human hormones and neurotransmitters and over one-third of clinically used drugs. Studying the structure and dynamics of human GPCRs in lipid bilayer environments resembling the native cell membrane milieu is of great interest as a basis for understanding structure-function relationships and thus benefits continued drug development. Here, we incorporate the human A2A adenosine receptor (A2AAR) into lipid nanodiscs, which represent a detergent-free environment for structural studies using nuclear magnetic resonance (NMR) in solution. The [15N,1H]-TROSY correlation spectra confirmed that the complex of [u-15N, ~70% 2H]-A2AAR with an inverse agonist adopts its global fold in lipid nanodiscs in solution at physiological temperature. The global assessment led to two observations of practical interest. First, A2AAR in nanodiscs can be stored for at least one month at 4 °C in an aqueous solvent. Second, LMNG/CHS micelles are a very close mimic of the environment of A2AAR in nanodiscs. The NMR signal of five individually assigned tryptophan indole 15N-1H moieties located in different regions of the receptor structure further enabled a detailed assessment of the impact of nanodiscs and LMNG/CHS micelles on the local structure and dynamics of A2AAR. As expected, the largest effects were observed near the lipid-water interface along the intra- and extracellular surfaces, indicating possible roles of tryptophan side chains in stabilizing GPCRs in lipid bilayer membranes.
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Affiliation(s)
- Canyong Guo
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lingyun Yang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Dongsheng Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
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19
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Lethcoe K, Fox CA, Hafiane A, Kiss RS, Ryan RO. Isolation of recombinant apolipoprotein E4 N-terminal domain by foam fractionation. Protein Expr Purif 2023; 210:106319. [PMID: 37290717 DOI: 10.1016/j.pep.2023.106319] [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: 05/17/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/10/2023]
Abstract
Apolipoprotein (apo) E functions in lipoprotein metabolism as a low density lipoprotein receptor ligand. ApoE is comprised of two structural domains, a 22 kDa N-terminal (NT) domain that adopts a helix bundle conformation and a 10 kDa C-terminal domain with strong lipid binding affinity. The NT domain is capable of transforming aqueous phospholipid dispersions into discoidal reconstituted high density lipoprotein (rHDL) particles. Given the utility of apoE-NT as a structural component of rHDL, expression studies were conducted. A plasmid construct encoding a pelB leader sequence fused to the N-terminus of human apoE4 (residues 1-183) was transformed into Escherichia coli. Upon expression, the fusion protein is directed to the periplasmic space where leader peptidase cleaves the pelB sequence, generating mature apoE4-NT. In shaker flask expression cultures, apoE4-NT escapes the bacteria and accumulates in the medium. In a bioreactor setting, however, apoE4-NT was found to combine with gas and liquid components in the culture medium to generate large quantities of foam. When this foam was collected in an external vessel and collapsed into a liquid foamate, analysis revealed that apoE4-NT was the sole major protein present. The product protein was further isolated by heparin affinity chromatography (60-80 mg/liter bacterial culture), shown to be active in rHDL formulation, and documented to serve as an acceptor of effluxed cellular cholesterol. Thus, foam fractionation provides a streamlined process to produce recombinant apoE4-NT for biotechnology applications.
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Affiliation(s)
- Kyle Lethcoe
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Colin A Fox
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Anouar Hafiane
- Department of Medicine, Division of Cardiology, McGill University, Montreal, QC, Canada
| | - Robert S Kiss
- Department of Medicine, Division of Cardiology, McGill University, Montreal, QC, Canada
| | - Robert O Ryan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA.
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20
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Mohamadi M, Goricanec D, Wagner G, Hagn F. NMR sample optimization and backbone assignment of a stabilized neurotensin receptor. J Struct Biol 2023; 215:107970. [PMID: 37142193 PMCID: PMC10242673 DOI: 10.1016/j.jsb.2023.107970] [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: 03/01/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 05/06/2023]
Abstract
G protein-coupled receptors (GPCRs) are involved in a multitude of cellular signaling cascades and consequently are a prominent target for pharmaceutical drugs. In the past decades, a growing number of high-resolution structures of GPCRs has been solved, providing unprecedented insights into their mode of action. However, knowledge on the dynamical nature of GPCRs is equally important for a better functional understanding, which can be obtained by NMR spectroscopy. Here, we employed a combination of size exclusion chromatography, thermal stability measurements and 2D-NMR experiments for the NMR sample optimization of the stabilized neurotensin receptor type 1 (NTR1) variant HTGH4 bound to the agonist neurotensin. We identified the short-chain lipid di-heptanoyl-glycero-phosphocholine (DH7PC) as a promising membrane mimetic for high resolution NMR experiments and obtained a partial NMR backbone resonance assignment. However, internal membrane-incorporated parts of the protein were not visible due to lacking amide proton back-exchange. Nevertheless, NMR and hydrogen deuterium exchange (HDX) mass spectrometry experiments could be used to probe structural changes at the orthosteric ligand binding site in the agonist and antagonist bound states. To enhance amide proton exchange we partially unfolded HTGH4 and observed additional NMR signals in the transmembrane region. However, this procedure led to a higher sample heterogeneity, suggesting that other strategies need to be applied to obtain high-quality NMR spectra of the entire protein. In summary, the herein reported NMR characterization is an essential step toward a more complete resonance assignment of NTR1 and for probing its structural and dynamical features in different functional states.
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Affiliation(s)
- Mariam Mohamadi
- Bavarian NMR Center (BNMRZ) and Structural Membrane Biochemistry, Dept. of Bioscience, TUM School of Natural Sciences, Technical University of Munich, 85748 Garching, Germany
| | - David Goricanec
- Bavarian NMR Center (BNMRZ) and Structural Membrane Biochemistry, Dept. of Bioscience, TUM School of Natural Sciences, Technical University of Munich, 85748 Garching, Germany
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) and Structural Membrane Biochemistry, Dept. of Bioscience, TUM School of Natural Sciences, Technical University of Munich, 85748 Garching, Germany; Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich 85764 Neuherberg, Germany.
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21
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Gu X, Liu D, Yu Y, Wang H, Long D. Quantitative Paramagnetic NMR-Based Analysis of Protein Orientational Dynamics on Membranes: Dissecting the KRas4B-Membrane Interactions. J Am Chem Soc 2023; 145:10295-10303. [PMID: 37116086 DOI: 10.1021/jacs.3c01597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Peripheral membrane proteins can adopt distinct orientations on the surfaces of lipid bilayers that are often short-lived and challenging to characterize by conventional experimental methods. Here we describe a robust approach for mapping protein orientational landscapes through quantitative interpretation of paramagnetic relaxation enhancement (PRE) data arising from membrane mimetics with spin-labeled lipids. Theoretical analysis, followed by experimental verification, reveals insights into the distinct properties of the PRE observables that are generally distorted in the case of stably membrane-anchored proteins. To suppress the artifacts, we demonstrate that undistorted Γ2 values can be obtained via transient membrane anchoring, based on which a computational framework is established for deriving accurate orientational ensembles obeying Boltzmann statistics. Application of the approach to KRas4B, a classical peripheral membrane protein whose orientations are critical for its functions and drug design, reveals four distinct orientational states that are close but not identical to those reported previously. Similar orientations are also found for a truncated KRas4B without the hypervariable region (HVR) that can sample a broader range of orientations, suggesting a confinement role of the HVR geometrically prohibiting severe tilting. Comparison of the KRas4B Γ2 rates measured using nanodiscs containing different types of anionic lipids reveals identical Γ2 patterns for the G-domain but different ones for the HVR, indicating only the latter is able to selectively interact with anionic lipids.
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Affiliation(s)
- Xue Gu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dan Liu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yongkui Yu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Hui Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dong Long
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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22
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Huang SK, Picard LP, Rahmatullah RSM, Pandey A, Van Eps N, Sunahara RK, Ernst OP, Sljoka A, Prosser RS. Mapping the conformational landscape of the stimulatory heterotrimeric G protein. Nat Struct Mol Biol 2023; 30:502-511. [PMID: 36997760 DOI: 10.1038/s41594-023-00957-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 02/24/2023] [Indexed: 04/01/2023]
Abstract
Heterotrimeric G proteins serve as membrane-associated signaling hubs, in concert with their cognate G-protein-coupled receptors. Fluorine nuclear magnetic resonance spectroscopy was employed to monitor the conformational equilibria of the human stimulatory G-protein α subunit (Gsα) alone, in the intact Gsαβ1γ2 heterotrimer or in complex with membrane-embedded human adenosine A2A receptor (A2AR). The results reveal a concerted equilibrium that is strongly affected by nucleotide and interactions with the βγ subunit, the lipid bilayer and A2AR. The α1 helix of Gsα exhibits significant intermediate timescale dynamics. The α4β6 loop and α5 helix undergo membrane/receptor interactions and order-disorder transitions respectively, associated with G-protein activation. The αN helix adopts a key functional state that serves as an allosteric conduit between the βγ subunit and receptor, while a significant fraction of the ensemble remains tethered to the membrane and receptor upon activation.
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Affiliation(s)
- Shuya Kate Huang
- Department of Chemistry, University of Toronto, UTM, Mississauga, Ontario, Canada
| | | | - Rima S M Rahmatullah
- Department of Chemistry, University of Toronto, UTM, Mississauga, Ontario, Canada
| | - Aditya Pandey
- Department of Chemistry, University of Toronto, UTM, Mississauga, Ontario, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Adnan Sljoka
- RIKEN Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan.
| | - R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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23
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Wang T, Lin X, Li Y, Lu Y. Artificial Lipid Biomembranes for Full-Length SARS-CoV-2 Receptor. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300575. [PMID: 36932971 DOI: 10.1002/adma.202300575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Indexed: 06/18/2023]
Abstract
The angiotensin-converting enzyme 2 (ACE2), as a functional receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is essential for assessing potential hosts and treatments. However, many studies are based on its truncated version but not full-length structure. Indeed, a single transmembrane (TM) helix presents in the full-length ACE2, influencing its interaction with SARS-CoV-2. Therefore, synthesis of the full-length ACE2 is an urgent requirement. Here, cell-free membrane protein synthesis systems (CFMPSs) are constructed for full-length membrane proteins. MscL is screened as a model among ten membrane proteins based on their expression and solubility. Next, CFMPSs are constructed and optimized based on natural vesicles, vesicles with four membrane proteins removed or two chaperonins added, and 37 types of nanodiscs. They all increase membrane protein solubility to over 50%. Finally, the full-length ACE2 of 21 species are successfully expressed with yields between 0.4 and 0.9 mg mL-1 . The definite functional differences from the truncated version suggest that the TM region affects ACE2's structure and function. CFMPSs can be extended to more membrane proteins, paving the way for further applications.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xiaomei Lin
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuting Li
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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24
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Lenz J, Larsen AH, Keller S, Luchini A. Effect of Cholesterol on the Structure and Composition of Glyco-DIBMA Lipid Particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:3569-3579. [PMID: 36854196 PMCID: PMC10018766 DOI: 10.1021/acs.langmuir.2c03019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Different amphiphilic co-polymers have been introduced to produce polymer-lipid particles with nanodisc structure composed of an inner lipid bilayer and polymer chains self-assembled as an outer belt. These particles can be used to stabilize membrane proteins in solution and enable their characterization by means of biophysical methods, including small-angle X-ray scattering (SAXS). Some of these co-polymers have also been used to directly extract membrane proteins together with their associated lipids from native membranes. Styrene/maleic acid and diisobutylene/maleic acid are among the most commonly used co-polymers for producing polymer-lipid particles, named SMALPs and DIBMALPs, respectively. Recently, a new co-polymer, named Glyco-DIBMA, was produced by partial amidation of DIBMA with the amino sugar N-methyl-d-glucosamine. Polymer-lipid particles produced with Glyco-DIBMA, named Glyco-DIBMALPs, exhibit improved structural properties and stability compared to those of SMALPs and DIBMALPs while retaining the capability of directly extracting membrane proteins from native membranes. Here, we characterize the structure and lipid composition of Glyco-DIBMALPs produced with either 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Glyco-DIBMALPs were also prepared with mixtures of either POPC or DMPC and cholesterol at different mole fractions. We estimated the lipid content in the Glyco-DIBMALPs and determined the particle structure and morphology by SAXS. We show that the Glyco-DIBMALPs are nanodisc-like particles whose size and shape depend on the polymer/lipid ratio. This is relevant for designing nanodisc particles with a tunable diameter according to the size of the membrane protein to be incorporated. We also report that the addition of >20 mol % cholesterol strongly perturbed the formation of Glyco-DIBMALPs. Altogether, we describe a detailed characterization of the Glyco-DIBMALPs, which provides relevant inputs for future application of these particles in the biophysical investigation of membrane proteins.
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Affiliation(s)
- Julia Lenz
- Molecular
Biophysics, Technische Universität
Kaiserslautern, Erwin-Schrödinger-Strasse
13, 67663 Kaiserslautern, Germany
| | | | - Sandro Keller
- Biophysics,
Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
- Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Alessandra Luchini
- European
Spallation Source - ERIC, Partikel Gatan, Lund 224
84, Sweden
- Department
of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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25
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Wang X, Neale C, Kim SK, Goddard WA, Ye L. Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery. Nat Commun 2023; 14:1325. [PMID: 36899002 PMCID: PMC10006191 DOI: 10.1038/s41467-023-36971-6] [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: 08/11/2022] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
Understanding the roles of intermediate states in signaling is pivotal to unraveling the activation processes of G protein-coupled receptors (GPCRs). However, the field is still struggling to define these conformational states with sufficient resolution to study their individual functions. Here, we demonstrate the feasibility of enriching the populations of discrete states via conformation-biased mutants. These mutants adopt distinct distributions among five states that lie along the activation pathway of adenosine A2A receptor (A2AR), a class A GPCR. Our study reveals a structurally conserved cation-π lock between transmembrane helix VI (TM6) and Helix8 that regulates cytoplasmic cavity opening as a "gatekeeper" for G protein penetration. A GPCR activation process based on the well-discerned conformational states is thus proposed, allosterically micro-modulated by the cation-π lock and a previously well-defined ionic interaction between TM3 and TM6. Intermediate-state-trapped mutants will also provide useful information in relation to receptor-G protein signal transduction.
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Affiliation(s)
- Xudong Wang
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, 91125, USA
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, 91125, USA
| | - Libin Ye
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.
- H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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26
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Jia X, Chin YKY, Zhang AH, Crawford T, Zhu Y, Fletcher NL, Zhou Z, Hamilton BR, Stroet M, Thurecht KJ, Mobli M. Self-cyclisation as a general and efficient platform for peptide and protein macrocyclisation. Commun Chem 2023; 6:48. [PMID: 36871076 PMCID: PMC9985607 DOI: 10.1038/s42004-023-00841-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Macrocyclisation of proteins and peptides results in a remarkable increase in structural stability, making cyclic peptides and proteins of great interest in drug discovery-either directly as drug leads or as in the case of cyclised nanodiscs (cNDs), as tools for studies of trans-membrane receptors and membrane-active peptides. Various biological methods have been developed that are capable of yielding head-to-tail macrocyclised products. Recent advances in enzyme-catalysed macrocyclisation include discovery of new enzymes or design of new engineered enzymes. Here, we describe the engineering of a self-cyclising "autocyclase" protein, capable of performing a controllable unimolecular reaction for generation of cyclic biomolecules in high yield. We characterise the self-cyclisation reaction mechanism, and demonstrate how the unimolecular reaction path provides alternative avenues for addressing existing challenges in enzymatic cyclisation. We use the method to produce several notable cyclic peptides and proteins, demonstrating how autocyclases offer a simple, alternative way to access a vast diversity of macrocyclic biomolecules.
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Affiliation(s)
- Xinying Jia
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Yanni K-Y Chin
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Alan H Zhang
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Theo Crawford
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Yifei Zhu
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Nicholas L Fletcher
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Zihan Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Brett R Hamilton
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Martin Stroet
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Kristofer J Thurecht
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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27
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Rosenberg EM, Jian X, Soubias O, Yoon HY, Yadav MP, Hammoudeh S, Pallikkuth S, Akpan I, Chen PW, Maity TK, Jenkins LM, Yohe ME, Byrd RA, Randazzo PA. The small molecule inhibitor NAV-2729 has a complex target profile including multiple ADP-ribosylation factor regulatory proteins. J Biol Chem 2023; 299:102992. [PMID: 36758799 PMCID: PMC10023970 DOI: 10.1016/j.jbc.2023.102992] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
The ADP-ribosylation factor (Arf) GTPases and their regulatory proteins are implicated in cancer progression. NAV-2729 was previously identified as a specific inhibitor of Arf6 that reduced progression of uveal melanoma in an orthotopic xenograft. Here, our goal was to assess the inhibitory effects of NAV-2729 on the proliferation of additional cell types. We found NAV-2729 inhibited proliferation of multiple cell lines, but Arf6 expression did not correlate with NAV-2729 sensitivity, and knockdown of Arf6 affected neither cell viability nor sensitivity to NAV-2729. Furthermore, binding to native Arf6 was not detected; however, we determined that NAV-2729 inhibited both Arf exchange factors and Arf GTPase-activating proteins. ASAP1, a GTPase-activating protein linked to cancer progression, was further investigated. We demonstrated that NAV-2729 bound to the PH domain of ASAP1 and changed ASAP1 cellular distribution. However, ASAP1 knockdown did not fully recapitulate the cytoskeletal effects of NAV-2729 nor affect cell proliferation. Finally, our screens identified 48 other possible targets of NAV-2729. These results illustrate the complexities of defining targets of small molecules and identify NAV-2729 as a model PH domain-binding inhibitor.
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Affiliation(s)
- Eric M Rosenberg
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Olivier Soubias
- Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Hye-Young Yoon
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Mukesh P Yadav
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sarah Hammoudeh
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Itoro Akpan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Tapan K Maity
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Marielle E Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA; Laboratory of Cell and Developmental Signaling, Center for Cancer Research, Frederick, Maryland, USA
| | - R Andrew Byrd
- Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
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28
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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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29
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Thakur N, Ray AP, Sharp L, Jin B, Duong A, Pour NG, Obeng S, Wijesekara AV, Gao ZG, McCurdy CR, Jacobson KA, Lyman E, Eddy MT. Anionic phospholipids control mechanisms of GPCR-G protein recognition. Nat Commun 2023; 14:794. [PMID: 36781870 PMCID: PMC9925817 DOI: 10.1038/s41467-023-36425-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we explore the impact of anionic lipids on the function-related conformational equilibria of the human A2A adenosine receptor (A2AAR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids prime the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeds through a less favorable induced fit mechanism. In computational models, anionic lipids mimic interactions between a G protein and positively charged residues in A2AAR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly alters the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Alexander Duong
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Anuradha V Wijesekara
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
- Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA.
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30
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Elbahnasawy MA, Nasr ML. DNA-nanostructure-templated assembly of planar and curved lipid-bilayer membranes. Front Chem 2023; 10:1047874. [PMID: 36844038 PMCID: PMC9944057 DOI: 10.3389/fchem.2022.1047874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/21/2022] [Indexed: 02/10/2023] Open
Abstract
Lipid-bilayer nanodiscs and liposomes have been developed to stabilize membrane proteins in order to study their structures and functions. Nanodiscs are detergent-free, water-soluble, and size-controlled planar phospholipid-bilayer platforms. On the other hand, liposomes are curved phospholipid-bilayer spheres with an aqueous core used as drug delivery systems and model membrane platforms for studying cellular activities. A long-standing challenge is the generation of a homogenous and monodispersed lipid-bilayer system with a very wide range of dimensions and curvatures (elongation, bending, and twisting). A DNA-origami template provides a way to control the shapes, sizes, and arrangements of lipid bilayers via enforcing the assembly of lipid bilayers within the cavities created by DNA nanostructures. Here, we provide a concise overview and discuss how to design planar and curved lipid-bilayer membranes by using DNA-origami nanostructures as templates. Finally, we will discuss the potential applications of DNA-origami nanostructures in the structural and functional studies of large membrane proteins and their complexes.
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Affiliation(s)
- Mostafa A. Elbahnasawy
- Immunology Laboratory, Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mahmoud L. Nasr
- Renal Division and Engineering in Medicine Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States,*Correspondence: Mahmoud L. Nasr,
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31
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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32
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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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33
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Thakur N, Ray AP, Sharp L, Jin B, Duong A, Pour NG, Obeng S, Wijesekara AV, Gao ZG, McCurdy CR, Jacobson KA, Lyman E, Eddy MT. Anionic Phospholipids Control Mechanisms of GPCR-G Protein Recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523010. [PMID: 36711594 PMCID: PMC9882065 DOI: 10.1101/2023.01.11.523010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we visualized the impact of anionic lipids on the function-related conformational equilibria of the human A 2A adenosine receptor (A 2A AR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids primed the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeded through a less favorable induced fit mechanism. In computational models, anionic lipids mimicked interactions between a G protein and positively charged residues in A 2A AR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly altered the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Alexander Duong
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Anuradha V Wijesekara
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
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34
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Xu D, Chen X, Li Y, Chen Z, Xu W, Wang X, Lv Y, Wang Z, Wu M, Liu G, Wang J. Reconfigurable Peptide Analogs of Apolipoprotein A-I Reveal Tunable Features of Nanodisc Assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1262-1276. [PMID: 36626237 DOI: 10.1021/acs.langmuir.2c03082] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nanodisc (ND)-forming membrane scaffold proteins or peptides developed from apolipoprotein A-I (apoA-I) have led to considerable promise in structural biology and therapeutic applications. However, the rationale and regularity characteristics in peptide sequence design remain inconclusive. Here, we proposed a consensus-based normalization approach through the reversed engineering of apoA-IΔ1-45 to design reconfigurable apoA-I peptide analogs (APAs) for tunable ND assembly. We present extensive morphological validations and computational simulation analyses on divergent APA-NDs that are generated by our method. Fifteen divergent APAs were generated accordingly to study the assembly machinery of NDs. We show that APA designs exhibit multifactorial influence in terms of varying APA tandem repeats, sequence composition, and lipid-to-APA ratio to form tunable diameters of NDs. There is a strong positive correlation between DMPC-to-APA ratios and ND diameters. Longer APA with more tandem repeats tends to yield higher particle size homogeneity. Our results also suggest proline is a dispensable residue for the APA-ND formation. Interestingly, proline-rich substitution not only provides an inward-bending effect in forming smaller NDs but also induces the cumulative chain flexibility that enables larger ND formation at higher lipid ratios. Additionally, proline-tryptophan residues in APAs play a dominant role in forming larger NDs. Molecular simulation shows that enriched basic and acidic residues in APAs evoke abundant hydrogen-bond and salt bridge networks to reinforce the structural stability of APA-NDs. Together, our findings provide a rational basis for understanding APA design. The proposed model could be extended to other apolipoproteins for desired ND engineering.
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Affiliation(s)
- Daiyun Xu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Yongxiao Li
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Zhidong Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Wanting Xu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Yonghui Lv
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen518033, China
| | - Meiying Wu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, 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, Xiamen361102, China
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
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35
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The Advanced Properties of Circularized MSP Nanodiscs Facilitate High-resolution NMR Studies of Membrane Proteins. J Mol Biol 2022; 434:167861. [PMID: 36273602 DOI: 10.1016/j.jmb.2022.167861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/12/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022]
Abstract
Membrane mimetics are essential for structural and functional studies of membrane proteins. A promising lipid-based system are phospholipid nanodiscs, where two copies of a so-called membrane scaffold protein (MSP) wrap around a patch of lipid bilayer. Consequently, the size of a nanodisc is determined by the length of the MSP. Furthermore, covalent MSP circularization was reported to improve nanodisc stability. However, a more detailed comparative analysis of the biophysical properties of circularized and linear MSP nanodiscs for their use in high-resolution NMR has not been conducted so far. Here, we analyze the membrane fluidity and temperature-dependent size variability of circularized and linear nanodiscs using a large set of analytical methods. We show that MSP circularization does not alter the membrane fluidity in nanodiscs. Further, we show that the phase transition temperature increases for circularized versions, while the cooperativity decreases. We demonstrate that circularized nanodiscs keep a constant size over a large temperature range, in contrast to their linear MSP counterparts. Due to this size stability, circularized nanodiscs are beneficial for high-resolution NMR studies of membrane proteins at elevated temperatures. Despite their slightly larger size as compared to linear nanodiscs, 3D NMR experiments of the voltage-dependent anion channel 1 (VDAC1) in circularized nanodiscs have a markedly improved spectral quality in comparison to VDAC1 incorporated into linear nanodiscs of a similar size. This study provides evidence that circularized MSP nanodiscs are a promising tool to facilitate high-resolution NMR studies of larger and challenging membrane proteins in a native lipid environment.
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36
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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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37
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Bimetallic nitrides Co3Mo3N nanosheets combined with phosphorus-doped carbon as superior Pt-based catalyst carriers for methanol electrooxidation reaction. J SOLID STATE CHEM 2022. [DOI: 10.1016/j.jssc.2022.123719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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38
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Korn P, Schwieger C, Gruhle K, Garamus VM, Meister A, Ihling C, Drescher S. Azide- and diazirine-modified membrane lipids: Physicochemistry and applicability to study peptide/lipid interactions via cross-linking/mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184004. [PMID: 35841926 DOI: 10.1016/j.bbamem.2022.184004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Although the incorporation of photo-activatable lipids into membranes potentially opens new avenues for studying interactions with peptides and proteins, the question of whether azide- or diazirine-modified lipids are suitable for such studies remains controversial. We have recently shown that diazirine-modified lipids can indeed form cross-links to membrane peptides after UV activation and that these cross-links can be precisely determined in their position by mass spectrometry (MS). However, we also observed an unexpected backfolding of the lipid's diazirine-containing stearoyl chain to the membrane interface challenging the potential application of this modified lipid for future cross-linking (XL)-MS studies of protein/lipid interactions. In this work, we compared an azide- (AzidoPC) and a diazirine-modified (DiazPC) membrane lipid regarding their self-assembly properties, their mixing behavior with saturated bilayer-forming phospholipids, and their reactivity upon UV activation using differential scanning calorimetry (DSC), dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and MS. Mixtures of both modified lipids with DMPC were further used for photo-chemically induced XL experiments with a transmembrane model peptide (KLAW23) to elucidate similarities and differences between the azide and the diazirine moiety. We showed that both photo-reactive lipids can be used to study lipid/peptide and lipid/protein interactions. The AzidoPC proved easier to handle, whereas the DiazPC had fewer degradation products and a higher cross-linking yield. However, the problem of backfolding occurs in both lipids; thus, it seems to be a general phenomenon.
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Affiliation(s)
- Patricia Korn
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Christian Schwieger
- Institute of Chemistry, MLU Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Kai Gruhle
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Vasil M Garamus
- Helmholtz-Zentrum Hereon, Max-Planck-Str. 1, 21502 Geesthacht, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, MLU Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Institute of Biochemistry and Biotechnology-Physical Biotechnology, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Christian Ihling
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Simon Drescher
- Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany; Phospholipid Research Center, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany.
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39
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Ye L, Wang X, McFarland A, Madsen JJ. 19F NMR: A promising tool for dynamic conformational studies of G protein-coupled receptors. Structure 2022; 30:1372-1384. [PMID: 36130592 DOI: 10.1016/j.str.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 07/31/2022] [Accepted: 08/23/2022] [Indexed: 10/14/2022]
Abstract
Advances in X-ray crystallography and cryoelectron microscopy enabled unprecedented insights into the activation processes of G protein-coupled receptors (GPCRs). However, these static receptor structures provide limited information about dynamics and conformational transitions that play pivotal roles in mediating signaling diversity through the multifaceted interactions between ligands, receptors, and transducers. Developing NMR approaches to probe the dynamics of conformational transitions will push the frontier of receptor science toward a more comprehensive understanding of these signaling processes. Although much progress has been made during the last decades, it remains challenging to delineate receptor conformational states and interrogate the functions of the individual states at a quantitative level. Here we cover the progress of 19F NMR applications in GPCR conformational and dynamic studies during the past 20 years. Current challenges and limitations of 19F NMR for studying GPCR dynamics are also discussed, along with experimental strategies that will drive this field forward.
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Affiliation(s)
- Libin Ye
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA.
| | - Xudong Wang
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Aidan McFarland
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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40
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You X, Thakur N, Ray AP, Eddy MT, Baiz CR. A comparative study of interfacial environments in lipid nanodiscs and vesicles. BIOPHYSICAL REPORTS 2022; 2. [PMID: 36176716 PMCID: PMC9518727 DOI: 10.1016/j.bpr.2022.100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane protein conformations and dynamics are driven by the protein-lipid interactions occurring within the local environment of the membrane. These environments remain challenging to accurately capture in structural and biophysical experiments using bilayers. Consequently, there is an increasing need for realistic cell-membrane mimetics for in vitro studies. Lipid nanodiscs provide certain advantages over vesicles for membrane protein studies. Nanodiscs are increasingly used for structural and spectroscopic characterization of membrane proteins. Despite the common use of nanodiscs, the interfacial environments of lipids confined to a ~10-nm diameter area have remained relatively underexplored. Here, we use ultrafast two-dimensional infrared spectroscopy and temperature-dependent infrared absorption measurements of the ester carbonyls to compare the interfacial hydrogen bond structure and dynamics in lipid nanodiscs of varying lipid compositions and sizes with ~100-nm vesicles. We examine the effects of lipid composition and nanodisc size. We found that nanodiscs and vesicles share largely similar lipid-water H-bond environments and interfacial dynamics. Differences in measured enthalpies of H-bonding suggest that H-bond dynamics in nanodiscs are modulated by the interaction between the annular lipids and the scaffold protein.
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41
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Wang Y, Wang J. PB1F2 from Influenza A Virus Regulates the Interaction between Cytochrome C and Cardiolipin. MEMBRANES 2022; 12:795. [PMID: 36005710 PMCID: PMC9414537 DOI: 10.3390/membranes12080795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
PB1F2 is a membrane associated protein encoded by the influenza virus gene in the host. Similar to endogenous pro-apoptotic proteins, it acts on the mitochondria of the host immune cells, inducing apoptosis of the cells. The PB1F2 protein has been demonstrated to facilitate the release of cytochrome c in addition to impairing the integrity of the inner mitochondrial membrane. This investigation focused on how the protein PB1F2 interacted with cardiolipin and cytochrome c. The regulation of PB1F2 on the binding of cytochrome c to cardiolipin in two kinds of in vitro membrane mimics was investigated by biophysical techniques. PB1F2 aids in the dissociation of cytochrome c-cardiolipin complexes in liposomes and nanodiscs. The results provide novel explanations and evidence for how PB1F2 functions as a viral virulence factor by inducing immune cell death.
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Affiliation(s)
- Yujuan Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
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42
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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: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important to fully understand their biological function and the roles played by them in the pathology of many diseases. However, the complexity of the cell membrane has severely limited the application of commonly used biophysical and biochemical techniques. Recent advancements in NMR spectroscopy and cryoEM approaches and the development of novel membrane mimetics have overcome some of the major challenges in this area. For example, the development of a variety of lipid-nanodiscs has enabled stable reconstitution and structural and functional studies of membrane proteins. In particular, the ability of synthetic amphipathic polymers to isolate membrane proteins directly from the cell membrane, along with the associated membrane components such as lipids, without the use of a detergent, has opened new avenues to study the structure and function of membrane proteins using a variety of biophysical and biological approaches. This review article is focused on covering the various polymers and approaches developed and their applications for the functional reconstitution and structural investigation of membrane proteins. The unique advantages and limitations of the use of synthetic polymers are also discussed.
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Affiliation(s)
- Bankala Krishnarjuna
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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43
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Zhang Y, Ma L, Bao H. Energetics, kinetics, and pathways of SNARE assembly in membrane fusion. Crit Rev Biochem Mol Biol 2022; 57:443-460. [PMID: 36151854 PMCID: PMC9588726 DOI: 10.1080/10409238.2022.2121804] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fusion of transmitter-containing vesicles with plasma membranes at the synaptic and neuromuscular junctions mediates neurotransmission and muscle contractions, respectively, thereby underlying all thoughts and actions. The fusion process is driven by the coupled folding and assembly of three synaptic SNARE proteins--syntaxin-1 and SNAP-25 on the target plasma membrane (t-SNAREs) and VAMP2 on the vesicular membrane (v-SNARE) into a four-helix bundle. Their assembly is chaperoned by Munc18-1 and many other proteins to achieve the speed and accuracy required for neurotransmission. However, the physiological pathway of SNARE assembly and its coupling to membrane fusion remains unclear. Here, we review recent progress in understanding SNARE assembly and membrane fusion, with a focus on results obtained by single-molecule manipulation approaches and electric recordings of single fusion pores. We describe two pathways of synaptic SNARE assembly, their associated intermediates, energetics, and kinetics. Assembly of the three SNAREs in vitro begins with the formation of a t-SNARE binary complex, on which VAMP2 folds in a stepwise zipper-like fashion. Munc18-1 significantly alters the SNARE assembly pathway: syntaxin-1 and VAMP2 first bind on the surface of Munc18-1 to form a template complex, with which SNAP-25 associates to conclude SNARE assembly and displace Munc18-1. During membrane fusion, multiple trans-SNARE complexes cooperate to open a dynamic fusion pore in a manner dependent upon their copy number and zippering states. Together, these results demonstrate that stepwise and cooperative SNARE assembly drive stagewise membrane fusion.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA;,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA;,Conatct: and
| | - Lu Ma
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA;,Present address: Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Huan Bao
- Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida, 33458,Conatct: and
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44
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Hermansen S, Ryoo D, Orwick-Rydmark M, Saragliadis A, Gumbart JC, Linke D. The Role of Extracellular Loops in the Folding of Outer Membrane Protein X (OmpX) of Escherichia coli. Front Mol Biosci 2022; 9:918480. [PMID: 35911955 PMCID: PMC9329534 DOI: 10.3389/fmolb.2022.918480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022] Open
Abstract
The outer membrane of Gram-negative bacteria acts as an additional diffusion barrier for solutes and nutrients. It is perforated by outer membrane proteins (OMPs) that function most often as diffusion pores, but sometimes also as parts of larger cellular transport complexes, structural components of the cell wall, or even as enzymes. These OMPs often have large loops that protrude into the extracellular environment, which have promise for biotechnological applications and as therapeutic targets. Thus, understanding how modifications to these loops affect OMP stability and folding is critical for their efficient application. In this work, the small outer membrane protein OmpX was used as a model system to quantify the effects of loop insertions on OMP folding and stability. The insertions were varied according to both hydrophobicity and size, and their effects were determined by assaying folding into detergent micelles in vitro by SDS-PAGE and in vivo by isolating the outer membrane of cells expressing the constructs. The different insertions were also examined in molecular dynamics simulations to resolve how they affect OmpX dynamics in its native outer membrane. The results indicate that folding of OMPs is affected by both the insert length and by its hydrophobic character. Small insertions sometimes even improved the folding efficiency of OmpX, while large hydrophilic inserts reduced it. All the constructs that were found to fold in vitro could also do so in their native environment. One construct that could not fold in vitro was transported to the OM in vivo, but remained unfolded. Our results will help to improve the design and efficiency of recombinant OMPs used for surface display.
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Affiliation(s)
- Simen Hermansen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Ryoo
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, United States
| | - Marcella Orwick-Rydmark
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Athanasios Saragliadis
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- *Correspondence: Dirk Linke,
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45
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Li J, Byrd RA. A simple protocol for the production of highly deuterated proteins for biophysical studies. J Biol Chem 2022; 298:102253. [PMID: 35835218 PMCID: PMC9386462 DOI: 10.1016/j.jbc.2022.102253] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/06/2022] Open
Abstract
Highly deuterated protein samples expand the biophysics and biological tool kit by providing, among other qualities, contrast matching in neutron diffraction experiments and reduction of dipolar spin interactions from normally protonated proteins in magnetic resonance studies, impacting both electron paramagnetic resonance and NMR spectroscopy. In NMR applications, deuteration is often combined with other isotopic labeling patterns to expand the range of conventional NMR spectroscopy research in both solution and solid-state conditions. However, preparation of deuterated proteins is challenging. We present here a simple, effective, and user-friendly protocol to produce highly deuterated proteins in Escherichia coli cells. The protocol utilizes the common shaker flask growth method and the well-known pET system (which provides expression control via the T7 promotor) for large-scale recombinant protein expression. One liter expression typically yields 5 to 50 mg of highly deuterated protein. Our data demonstrate that the optimized procedure produces a comparable quantity of protein in deuterium (2H2O) oxide M9 medium compared with that in 1H2O M9 medium. The protocol will enable a broader utilization of deuterated proteins in a number of biophysical techniques.
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Affiliation(s)
- Jess Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201.
| | - R Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201.
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46
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Anada C, Ikeda K, Nakao H, Nakano M. Improvement of Thermal Stability of Amphipathic Peptide-Phospholipid Nanodiscs via Lateral Association of α-Helices by Disulfide Cross-Linking. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6977-6983. [PMID: 35613431 DOI: 10.1021/acs.langmuir.2c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Amphipathic α-helical peptides have been reported to form discoidal particles or nanodiscs with phospholipids, in which a lipid bilayer patch is encircled by peptides. Peptide-based nanodiscs have broad applicability because of their ease of preparation, size flexibility, and structural plasticity. We previously revealed that the nanodiscs formed by apolipoprotein-A-I-derived peptide 18A showed temperature-dependent structural destabilization above the gel-to-liquid-crystalline phase transition temperature of the lipid bilayer. It has been suggested that this destabilization is due to the migration of peptides bound to the edge of the discs to the bilayer surface. In this study, we designed a peptide that could stabilize nanodisc structures against the phase transition of lipid bilayers by disulfide cross-linking of peptides. An 18A-dimer cross-linked by a proline residue, 37pA (Ac-18A-P-18A-CONH2), also showed thermal destabilization of nanodiscs like 18A. However, cross-linking the sides of the two α-helices of the cysteine-substituted analogue 37pA-C2 with disulfide bonds led to the formation of nanodiscs that were more stable to temperature changes. This stabilizing effect was mainly due to the formation of a cyclic 37pA-C2 monomer by intramolecular disulfide cross-linking. These results suggest that the lateral association of two α-helices, which is the basis of the double-belt structure, is an important factor for the implementation of stable nanodiscs. The results of this study will help in development of more stable nanoparticles with membrane proteins in the future.
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Affiliation(s)
- Chiharu Anada
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
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47
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Tidemand FG, Blemmer S, Johansen NT, Arleth L, Pedersen MC. Non-ionic detergent assists formation of supercharged nanodiscs and insertion of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183884. [PMID: 35182589 DOI: 10.1016/j.bbamem.2022.183884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 12/12/2022]
Abstract
Nanodiscs are used to stabilize membrane proteins in a lipid environment and enable investigations of the function and structure of these. Membrane proteins are often only available in small amounts, and thus the stability and ease of use of the nanodiscs are essential. We have recently explored circularizing and supercharging membrane scaffolding proteins (MSPs) for nanodisc formation and found increased temporal stability at elevated temperatures. In the present study, we investigate six different supercharged MSPs and their ability to form nanodiscs: three covalently circularized and the three non-circularized, linear versions. Using standard reconstitution protocols using cholate as the reconstitution detergent, we found that two of the linear constructs formed multiple lipid-protein species, whereas adding n-Dodecyl-B-D-maltoside (DDM) with the cholate in the reconstitution gave rise to single-species nanodisc formation for these MSPs. For all MSPs, the formed nanodiscs were analyzed by small-angle X-ray scattering (SAXS), which showed similar structures for each MSP, respectively, suggesting that the structures of the formed nanodiscs are independent of the initial DDM content, as long as cholate is present. Lastly, we incorporated the membrane protein proteorhodopsin into the supercharged nanodiscs and observed a considerable increase in incorporation yield with the addition of DDM. For the three circularized MSPs, a single major species appeared in the size exclusion chromatography (SEC) chromatogram, suggesting monodisperse nanodiscs with proteorhodopsin incorporated, which is in strong contrast to the samples without DDM showing almost no incorporation and high polydispersity.
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Affiliation(s)
- Frederik G Tidemand
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Sara Blemmer
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nicolai T Johansen
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark; Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Martin Cramer Pedersen
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
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48
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Formation of styrene maleic acid lipid nanoparticles (SMALPs) using SMA thin film on a substrate. Anal Biochem 2022; 647:114692. [DOI: 10.1016/j.ab.2022.114692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022]
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49
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Pozza A, Giraud F, Cece Q, Casiraghi M, Point E, Damian M, Le Bon C, Moncoq K, Banères JL, Lescop E, Catoire LJ. Exploration of the dynamic interplay between lipids and membrane proteins by hydrostatic pressure. Nat Commun 2022; 13:1780. [PMID: 35365643 PMCID: PMC8975810 DOI: 10.1038/s41467-022-29410-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Cell membranes represent a complex and variable medium in time and space of lipids and proteins. Their physico-chemical properties are determined by lipid components which can in turn influence the biological function of membranes. Here, we used hydrostatic pressure to study the close dynamic relationships between lipids and membrane proteins. Experiments on the β–barrel OmpX and the α–helical BLT2 G Protein-Coupled Receptor in nanodiscs of different lipid compositions reveal conformational landscapes intimately linked to pressure and lipids. Pressure can modify the conformational landscape of the membrane protein per se, but also increases the gelation of lipids, both being monitored simultaneously at high atomic resolution by NMR. Our study also clearly shows that a membrane protein can modulate, at least locally, the fluidity of the bilayer. The strategy proposed herein opens new perspectives to scrutinize the dynamic interplay between membrane proteins and their surrounding lipids. Direct information on the dynamic interplay between membrane proteins and lipids is scarce. Here the authors report a detailed description of these close relationships by combining lipid nanodiscs and high-pressure NMR. They report the link between pressure and lipid compositions to the conformational landscape of the β-barrel OmpX and the α-helical BLT2 G Protein-Coupled Receptor in nanodiscs.
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Affiliation(s)
- Alexandre Pozza
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France
| | - François Giraud
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Quentin Cece
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France.,Laboratoire Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), UMR 8038, CNRS/Université de Paris, Faculté de Pharmacie, 75270, Paris, Cedex 06, France
| | - Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 94305, Stanford, CA, USA
| | - Elodie Point
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Pôle Chimie Balard Recherche, 34293, Montpellier, cedex 5, France
| | - Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Pôle Chimie Balard Recherche, 34293, Montpellier, cedex 5, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France.
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50
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Barclay A, Tidemand Johansen N, Tidemand FG, Arleth L, Pedersen MC. Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:483-493. [PMID: 35362471 PMCID: PMC8972807 DOI: 10.1107/s2059798322001838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022]
Abstract
The combination of online size-exclusion chromatography and small-angle X-ray scattering (SEC–SAXS) is rapidly becoming a key technique for structural investigations of elaborate biophysical samples in solution. Here, a novel model-refinement strategy centred around the technique is outlined and its utility is demonstrated by analysing data series from several SEC–SAXS experiments on phospholipid bilayer nanodiscs. Using this method, a single model was globally refined against many frames from the same data series, thereby capturing the frame-to-frame tendencies of the irradiated sample. These are compared with models refined in the traditional manner, in which refinement is based on the average profile of a set of consecutive frames from the same data series without an in-depth comparison of individual frames. This is considered to be an attractive model-refinement scheme as it considerably lowers the total number of parameters refined from the data series, produces tendencies that are automatically consistent between frames, and utilizes a considerably larger portion of the recorded data than is often performed in such experiments. Additionally, a method is outlined for correcting a measured UV absorption signal by accounting for potential peak broadening by the experimental setup.
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