1
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Wills MF, Alejo CB, Hundt N, Hudson AJ, Eperon IC. FluoroTensor: Identification and tracking of colocalised molecules and their stoichiometries in multi-colour single molecule imaging via deep learning. Comput Struct Biotechnol J 2024; 23:918-928. [PMID: 38375530 PMCID: PMC10875188 DOI: 10.1016/j.csbj.2024.02.004] [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: 11/17/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
The identification of photobleaching steps in single molecule fluorescence imaging is a well-established procedure for analysing the stoichiometries of molecular complexes. Nonetheless, the method is challenging with protein fluorophores because of the high levels of noise, rapid bleaching and highly variable signal intensities, all of which complicate methods based on statistical analyses of intensities to identify bleaching steps. It has recently been shown that deep learning by convolutional neural networks can yield an accurate analysis with a relatively short computational time. We describe here an improved use of such an approach that detects bleaching events even in the first time point of observation, and we have included this within an integrated software package incorporating fluorescence spot detection, colocalisation, tracking, FRET and photobleaching step analyses of single molecules or complexes. This package, known as FluoroTensor, is written in Python with a self-explanatory user interface.
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Affiliation(s)
- Max F.K. Wills
- Institute for Structural and Chemical Biology, University of Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Carlos Bueno Alejo
- Institute for Structural and Chemical Biology, University of Leicester, UK
- Department of Chemistry, University of Leicester, UK
| | - Nikolas Hundt
- Department of Cellular Physiology, Ludwig-Maximilians-Universität München, Germany
| | - Andrew J. Hudson
- Institute for Structural and Chemical Biology, University of Leicester, UK
- Department of Chemistry, University of Leicester, UK
| | - Ian C. Eperon
- Institute for Structural and Chemical Biology, University of Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, UK
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2
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Yin Q, Aryal SP, Song Y, Fu X, Richards CI. Quantitative Single-Molecule Analysis of Ryanodine Receptor 2 Subunit Assembly in Cardiac and Neuronal Tissues. Anal Chem 2024. [PMID: 39359032 DOI: 10.1021/acs.analchem.4c03314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
We developed a method for ex vivo receptor encapsulation and single-molecule imaging techniques from neuronal and cardiac tissues, illustrating the method's broad applicability for measuring membrane receptor assembly. Ryanodine receptor 2 (RyR2) is a tetrameric Ca2+ channel governing intracellular Ca2+ dynamics, which is critical for muscle contraction. Employing GFP-RyR2 knock-in mice, we isolated individual receptor proteins in tissue-specific nanovesicles and performed subunit counting analyses to yield quantitative assessment of stoichiometric distributions across different organs. With this method, we explored the potential heterogeneity of brain-derived RyR2, which has been reported to form heteromeric assemblies with other ryanodine receptor isoforms.
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Affiliation(s)
- Qianye Yin
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Surya P Aryal
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yongwook Song
- Computational Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Xu Fu
- Light Microscopy Center, University of Kentucky, Lexington, Kentucky 40508, United States
| | - Christopher I Richards
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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3
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Margheritis E, Kappelhoff S, Danial J, Gehle N, Kohl W, Kurre R, González Montoro A, Cosentino K. Gasdermin D cysteine residues synergistically control its palmitoylation-mediated membrane targeting and assembly. EMBO J 2024; 43:4274-4297. [PMID: 39143238 PMCID: PMC11445239 DOI: 10.1038/s44318-024-00190-6] [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: 02/12/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 08/16/2024] Open
Abstract
Gasdermin D (GSDMD) executes the cell death program of pyroptosis by assembling into oligomers that permeabilize the plasma membrane. Here, by single-molecule imaging, we elucidate the yet unclear mechanism of Gasdermin D pore assembly and the role of cysteine residues in GSDMD oligomerization. We show that GSDMD preassembles at the membrane into dimeric and trimeric building blocks that can either be inserted into the membrane, or further assemble into higher-order oligomers prior to insertion into the membrane. The GSDMD residues Cys39, Cys57, and Cys192 are the only relevant cysteines involved in GSDMD oligomerization. S-palmitoylation of Cys192, combined with the presence of negatively-charged lipids, controls GSDMD membrane targeting. Simultaneous Cys39/57/192-to-alanine (Ala) mutations, but not Ala mutations of Cys192 or the Cys39/57 pair individually, completely abolish GSDMD insertion into artificial membranes as well as into the plasma membrane. Finally, either Cys192 or the Cys39/Cys57 pair are sufficient to enable formation of GSDMD dimers/trimers, but they are all required for functional higher-order oligomer formation. Overall, our study unveils a cooperative role of Cys192 palmitoylation-mediated membrane binding and Cys39/57/192-mediated oligomerization in GSDMD pore assembly. This study supports a model in which Gasdermin D oligomerization relies on a two-step mechanism mediated by specific cysteine residues.
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Affiliation(s)
- Eleonora Margheritis
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Shirin Kappelhoff
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - John Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, UK
| | - Nadine Gehle
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Wladislaw Kohl
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Ayelén González Montoro
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Katia Cosentino
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany.
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4
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Islas P, Platnich CM, Gidi Y, Karimi R, Ginot L, Saliba D, Luo X, Cosa G, Sleiman HF. Automated Synthesis of DNA Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2403477. [PMID: 39049795 DOI: 10.1002/adma.202403477] [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: 03/07/2024] [Revised: 07/10/2024] [Indexed: 07/27/2024]
Abstract
DNA nanotechnology has revolutionized the ability to position matter at the nanoscale, but the preparation of DNA-based architectures remains laborious. To facilitate the formation of custom structures, a fully automated method is reported to produce sequence- and size-defined DNA nanotubes. By programming the sequential addition of desired building blocks, rigid DX-tile-based DNA nanotubes and flexible wireframe DNA structures are attained, where the total number of possible constructs increases as a power function of the number of different units available. Using single-molecule fluorescence imaging, the kinetics and yield of each synthetic step can be quantitatively determined, revealing differences in self-assembly dynamics as the nanotube is built up from the solid support and providing new insights into DNA self-assembly. The exploitation of automation for both assembly and analysis (through an ad-hoc developed K-means clustering algorithm) facilitates a workflow wherein the synthesis parameters may be iteratively improved upon, demonstrating how a single-molecule "assembly-analysis-optimization" sequence can be used to generate complex, noncovalent materials in good yield. The presented synthetic strategy is generalizable, making use of equipment already available in most standard laboratories and represents the first fully automated supramolecular assembly on a solid support.
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Affiliation(s)
- Patricia Islas
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Yasser Gidi
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Ryan Karimi
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Lorianne Ginot
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
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5
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Bartels N, van der Voort NTM, Opanasyuk O, Felekyan S, Greife A, Shang X, Bister A, Wiek C, Seidel CAM, Monzel C. Advanced multiparametric image spectroscopy and super-resolution microscopy reveal a minimal model of CD95 signal initiation. SCIENCE ADVANCES 2024; 10:eadn3238. [PMID: 39213362 DOI: 10.1126/sciadv.adn3238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Unraveling the concentration-dependent spatiotemporal organization of receptors in the plasma membrane is crucial to understand cell signal initiation. A paradigm of this process is the oligomerization of CD95 during apoptosis signaling, with different oligomerization models being discussed. Here, we establish the molecular-sensitive approach cell lifetime Förster resonance energy transfer image spectroscopy to determine CD95 configurations in live cells. These data are corroborated by stimulated emission depletion microscopy, confocal photobleaching step analysis, and fluorescence correlation spectroscopy. We probed CD95 interactions for concentrations of ~10 to 1000 molecules per square micrometer, over nanoseconds to hours, and molecular to cellular scales. Quantitative benchmarking was achieved establishing high-fidelity monomer and dimer controls. While CD95 alone is primarily monomeric (~96%) and dimeric (4%), the addition of ligand induces oligomerization to dimers/trimers (~15%) leading to cell death. This study highlights molecular concentration effects and oligomerization dynamics. It reveals a minimal model, where small CD95 oligomers suffice to efficiently initiate signaling.
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Affiliation(s)
- Nina Bartels
- Experimental Medical Physics, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Oleg Opanasyuk
- Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Suren Felekyan
- Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Annemarie Greife
- Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Xiaoyue Shang
- Experimental Medical Physics, Heinrich-Heine University, Düsseldorf, Germany
| | - Arthur Bister
- Department of Otorhinolaryngology, Head & Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany
| | - Constanze Wiek
- Department of Otorhinolaryngology, Head & Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Heinrich-Heine University, Düsseldorf, Germany
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6
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Li J, Zhang L, Johnson-Buck A, Walter NG. Foundation model for efficient biological discovery in single-molecule data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609721. [PMID: 39253410 PMCID: PMC11383305 DOI: 10.1101/2024.08.26.609721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Modern data-intensive techniques offer ever deeper insights into biology, but render the process of discovery increasingly complex. For example, exploiting the unique ability of single-molecule fluorescence microscopy (SMFM)1-5. to uncover rare but critical intermediates often demands manual inspection of time traces and iterative ad hoc approaches that are difficult to systematize. To facilitate systematic and efficient discovery from SMFM data, we introduce META-SiM, a transformer-based foundation model pre-trained on diverse SMFM analysis tasks. META-SiM achieves high performance-rivaling best-in-class algorithms-on a broad range of analysis tasks including trace selection, classification, segmentation, idealization, and stepwise photobleaching analysis. Additionally, the model produces high-dimensional embedding vectors that encapsulate detailed information about each trace, which the web-based META-SiM Projector (https://www.simol-projector.org) casts into lower-dimensional space for efficient whole-dataset visualization, labeling, comparison, and sharing. Combining this Projector with the objective metric of Local Shannon Entropy enables rapid identification of condition-specific behaviors, even if rare or subtle. As a result, by applying META-SiM to an existing single-molecule Förster resonance energy transfer (smFRET) dataset6, we discover a previously unobserved intermediate state in pre-mRNA splicing. META-SiM thus removes bottlenecks, improves objectivity, and both systematizes and accelerates biological discovery in complex single-molecule data.
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Affiliation(s)
- Jieming Li
- Bristol Myers Squibb, New Brunswick, NJ, USA
| | | | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
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7
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Haskel MVL, da Silva Correa V, Queiroz R, Bonini JS, da Silva WC. On the participation of glycine receptors in the reconsolidation of spatial long-term memory in male rats. Behav Brain Res 2024; 471:115086. [PMID: 38825024 DOI: 10.1016/j.bbr.2024.115086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/14/2024] [Accepted: 05/31/2024] [Indexed: 06/04/2024]
Abstract
The effects of intra-hippocampal manipulation of glycine receptors on the reconsolidation of recent and late long-term spatial memory were evaluated and assessed in the Morris water maze. The results obtained from the intra-hippocampal infusion of glycine and taurine demonstrated that taurine at a 100 nmol/side dose impaired the reconsolidation of recent and late long-term spatial memory. In comparison, at a dose of 10 nmol/side, it only affected the reconsolidation of late long-term spatial memory, reinforcing that there are differences between molecular mechanisms underlying recent and late long-term memory reconsolidation. On the other hand, glycine impaired the reconsolidation of early and late spatial memory when infused at a dose of 10 nmol/side, but not at a dose of 100 nmol/side, unless it is co-infused with an allosteric site antagonist of the NMDA receptor. Altogether these results show that glycine acting in situ in the hippocampal CA1 region exerts a pharmacological effect on U-curve, which can be explained by its concomitant action on its ionotropic receptor GlyR and on its NMDA receptor co-agonist site.
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MESH Headings
- Animals
- Receptors, Glycine/metabolism
- Receptors, Glycine/drug effects
- Male
- Glycine/pharmacology
- Rats
- Spatial Memory/drug effects
- Spatial Memory/physiology
- Memory, Long-Term/drug effects
- Memory, Long-Term/physiology
- Rats, Wistar
- Taurine/pharmacology
- Taurine/administration & dosage
- Hippocampus/drug effects
- Hippocampus/metabolism
- Memory Consolidation/drug effects
- Memory Consolidation/physiology
- Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors
- Receptors, N-Methyl-D-Aspartate/metabolism
- Receptors, N-Methyl-D-Aspartate/drug effects
- CA1 Region, Hippocampal/drug effects
- CA1 Region, Hippocampal/metabolism
- CA1 Region, Hippocampal/physiology
- Maze Learning/drug effects
- Maze Learning/physiology
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Affiliation(s)
- Maria Vaitsa Loch Haskel
- Program in Physiology, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Brazil; Laboratory of Neuropsychopharmacology, Department of Pharmacy, State University of Centre-West of Paraná, Guarapuava 85040-167, Brazil
| | - Vinicius da Silva Correa
- Laboratory of Neuropsychopharmacology, Department of Pharmacy, State University of Centre-West of Paraná, Guarapuava 85040-167, Brazil
| | - Ruliam Queiroz
- Program in Physiology, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Brazil; Laboratory of Neuropsychopharmacology, Department of Pharmacy, State University of Centre-West of Paraná, Guarapuava 85040-167, Brazil
| | - Juliana Sartori Bonini
- Laboratory of Neuropsychopharmacology, Department of Pharmacy, State University of Centre-West of Paraná, Guarapuava 85040-167, Brazil
| | - Weber Claudio da Silva
- Program in Physiology, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Brazil; Laboratory of Neuropsychopharmacology, Department of Pharmacy, State University of Centre-West of Paraná, Guarapuava 85040-167, Brazil.
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8
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Cichos F, Xia T, Yang H, Zijlstra P. The ever-expanding optics of single-molecules and nanoparticles. J Chem Phys 2024; 161:010401. [PMID: 38949895 DOI: 10.1063/5.0221680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024] Open
Affiliation(s)
- F Cichos
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - T Xia
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
| | - H Yang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - P Zijlstra
- Department of Applied Physics and Science Education, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands
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9
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Wang Y, Qiu L, Wang B, Guan Z, Dong Z, Zhang J, Cao S, Yang L, Wang B, Gong Z, Zhang L, Ma W, Liu Z, Zhang D, Wang G, Yin P. Structural basis for odorant recognition of the insect odorant receptor OR-Orco heterocomplex. Science 2024; 384:1453-1460. [PMID: 38870272 DOI: 10.1126/science.adn6881] [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: 12/21/2023] [Accepted: 05/29/2024] [Indexed: 06/15/2024]
Abstract
Insects detect and discriminate a diverse array of chemicals using odorant receptors (ORs), which are ligand-gated ion channels comprising a divergent odorant-sensing OR and a conserved odorant receptor co-receptor (Orco). In this work, we report structures of the ApOR5-Orco heterocomplex from the pea aphid Acyrthosiphon pisum alone and bound to its known activating ligand, geranyl acetate. In these structures, three ApOrco subunits serve as scaffold components that cannot bind the ligand and remain relatively unchanged. Upon ligand binding, the pore-forming helix S7b of ApOR5 shifts outward from the central pore axis, causing an asymmetrical pore opening for ion influx. Our study provides insights into odorant recognition and channel gating of the OR-Orco heterocomplex and offers structural resources to support development of innovative insecticides and repellents for pest control.
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Affiliation(s)
- Yidong Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Synthetic Biology Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Qiu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Bing Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhi Dong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Song Cao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Synthetic Biology Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lulu Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bo Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhou Gong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Liwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Synthetic Biology Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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10
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Chien CT, Puhl H, Vogel SS, Molloy JE, Chiu W, Khan S. Hub stability in the calcium calmodulin-dependent protein kinase II. Commun Biol 2024; 7:766. [PMID: 38918547 PMCID: PMC11199487 DOI: 10.1038/s42003-024-06423-y] [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: 06/20/2023] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.
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Affiliation(s)
- Chih-Ta Chien
- Department of Bioengineering, and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Henry Puhl
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, MD, 208952, USA
| | - Steven S Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, MD, 208952, USA
| | - Justin E Molloy
- The Francis Crick Institute, London, UK
- CMCB, Warwick Medical School, Coventry, CV4 7AL, UK
| | - Wah Chiu
- Department of Bioengineering, and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA.
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Light source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
| | - Shahid Khan
- Molecular Biology Consortium @ Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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11
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Schuck RJ, Ward AE, Sahoo AR, Rybak JA, Pyron RJ, Trybala TN, Simmons TB, Baccile JA, Sgouralis I, Buck M, Lamichhane R, Barrera FN. Cholesterol inhibits assembly and activation of the EphA2 receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598255. [PMID: 38915729 PMCID: PMC11195142 DOI: 10.1101/2024.06.10.598255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The receptor tyrosine kinase EphA2 drives cancer malignancy by facilitating metastasis. EphA2 can be found in different self-assembly states: as a monomer, dimer, and oligomer. However, our understanding remains limited regarding which EphA2 state is responsible for driving pro-metastatic signaling. To address this limitation, we have developed SiMPull-POP, a single-molecule method for accurate quantification of membrane protein self-assembly. Our experiments revealed that a reduction of plasma membrane cholesterol strongly promoted EphA2 self-assembly. Indeed, low cholesterol caused a similar effect to the EphA2 ligand ephrinA1-Fc. These results indicate that cholesterol inhibits EphA2 assembly. Phosphorylation studies in different cell lines revealed that low cholesterol increased phospho-serine levels, the signature of oncogenic signaling. Investigation of the mechanism that cholesterol uses to inhibit the assembly and activity of EphA2 indicate an in-trans effect, where EphA2 is phosphorylated by protein kinase A downstream of beta-adrenergic receptor activity, which cholesterol also inhibits. Our study not only provides new mechanistic insights on EphA2 oncogenic function, but also suggests that cholesterol acts as a molecular safeguard mechanism that prevents uncontrolled self-assembly and activation of EphA2.
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Affiliation(s)
- Ryan J Schuck
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Alyssa E Ward
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, USA
| | - Jennifer A Rybak
- Genome Science and Technology, University of Tennessee, Knoxville, USA
| | - Robert J Pyron
- Genome Science and Technology, University of Tennessee, Knoxville, USA
| | - Thomas N Trybala
- Department of Chemistry, University of Tennessee, Knoxville, USA
| | - Timothy B Simmons
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, USA
| | | | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, USA
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
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12
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Li C, Krishnan S, Zhang M, Hu D, Meng D, Riedelsberger J, Dougherty L, Xu K, Piñeros MA, Cheng L. Alternative Splicing Underpins the ALMT9 Transporter Function for Vacuolar Malic Acid Accumulation in Apple. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310159. [PMID: 38514904 PMCID: PMC11165477 DOI: 10.1002/advs.202310159] [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: 12/23/2023] [Revised: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Vacuolar malic acid accumulation largely determines fruit acidity, a key trait for the taste and flavor of apple and other fleshy fruits. Aluminum-activated malate transporter 9 (ALMT9/Ma1) underlies a major genetic locus, Ma, for fruit acidity in apple, but how the protein transports malate across the tonoplast is unclear. Here, it is shown that overexpression of the coding sequence of Ma1 (Ma1α) drastically decreases fruit acidity in "Royal Gala" apple, leading to uncovering alternative splicing underpins Ma1's function. Alternative splicing generates two isoforms: Ma1β is 68 amino acids shorter with much lower expression than the full-length protein Ma1α. Ma1β does not transport malate itself but interacts with the functional Ma1α to form heterodimers, creating synergy with Ma1α for malate transport in a threshold manner (When Ma1β/Ma1α ≥ 1/8). Overexpression of Ma1α triggers feedback inhibition on the native Ma1 expression via transcription factor MYB73, decreasing the Ma1β level well below the threshold that leads to significant reductions in Ma1 function and malic acid accumulation in fruit. Overexpression of Ma1α and Ma1β or genomic Ma1 increases both isoforms proportionally and enhances fruit malic acid accumulation. These findings reveal an essential role of alternative splicing in ALMT9-mediated malate transport underlying apple fruit acidity.
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Affiliation(s)
- Chunlong Li
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan430070China
| | | | - Mengxia Zhang
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dagang Hu
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dong Meng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Janin Riedelsberger
- Center for Bioinformatics, Simulation and Modeling, Department of Bioinformatics, Faculty of EngineeringUniversity of TalcaTalca3460000Chile
| | - Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Miguel A. Piñeros
- Plant Biology Section, School of Integrative Plant Science and Robert W. Holley Center for Agriculture and HealthUSDA‐ARS Cornell UniversityIthacaNY14853USA
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
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13
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Feld LG, Boehme SC, Morad V, Sahin Y, Kaul CJ, Dirin DN, Rainò G, Kovalenko MV. Quantifying Förster Resonance Energy Transfer from Single Perovskite Quantum Dots to Organic Dyes. ACS NANO 2024; 18:9997-10007. [PMID: 38547379 PMCID: PMC11008358 DOI: 10.1021/acsnano.3c11359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
Colloidal quantum dots (QDs) are promising regenerable photoredox catalysts offering broadly tunable redox potentials along with high absorption coefficients. QDs have thus far been examined for various organic transformations, water splitting, and CO2 reduction. Vast opportunities emerge from coupling QDs with other homogeneous catalysts, such as transition metal complexes or organic dyes, into hybrid nanoassemblies exploiting energy transfer (ET), leveraging a large absorption cross-section of QDs and long-lived triplet states of cocatalysts. However, a thorough understanding and further engineering of the complex operational mechanisms of hybrid nanoassemblies require simultaneously controlling the surface chemistry of the QDs and probing dynamics at sufficient spatiotemporal resolution. Here, we probe the ET from single lead halide perovskite QDs, capped by alkylphospholipid ligands, to organic dye molecules employing single-particle photoluminescence spectroscopy with single-photon resolution. We identify a Förster-type ET by spatial, temporal, and photon-photon correlations in the QD and dye emission. Discrete quenching steps in the acceptor emission reveal stochastic photobleaching events of individual organic dyes, allowing a precise quantification of the transfer efficiency, which is >70% for QD-dye complexes with strong donor-acceptor spectral overlap. Our work explores the processes occurring at the QD/molecule interface and demonstrates the feasibility of sensitizing organic photocatalysts with QDs.
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Affiliation(s)
- Leon G. Feld
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Simon C. Boehme
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Viktoriia Morad
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Yesim Sahin
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Christoph J. Kaul
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Dmitry N. Dirin
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Gabriele Rainò
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Maksym V. Kovalenko
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
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14
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Stuebler M, Manzer ZA, Liu HY, Miller J, Richter A, Krishnan S, Selivanovitch E, Banuna B, Jander G, Reimhult E, Zipfel WR, Roeder AHK, Piñeros MA, Daniel S. Plant Membrane-On-A-Chip: A Platform for Studying Plant Membrane Proteins and Lipids. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38593404 DOI: 10.1021/acsami.3c18562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The cell plasma membrane is a two-dimensional, fluid mosaic material composed of lipids and proteins that create a semipermeable barrier defining the cell from its environment. Compared with soluble proteins, the methodologies for the structural and functional characterization of membrane proteins are challenging. An emerging tool for studies of membrane proteins in mammalian systems is a "plasma membrane on a chip," also known as a supported lipid bilayer. Here, we create the "plant-membrane-on-a-chip,″ a supported bilayer made from the plant plasma membranes of Arabidopsis thaliana, Nicotiana benthamiana, or Zea mays. Membrane vesicles from protoplasts containing transgenic membrane proteins and their native lipids were incorporated into supported membranes in a defined orientation. Membrane vesicles fuse and orient systematically, where the cytoplasmic side of the membrane proteins faces the chip surface and constituents maintain mobility within the membrane plane. We use plant-membrane-on-a-chip to perform fluorescent imaging to examine protein-protein interactions and determine the protein subunit stoichiometry of FLOTILLINs. We report here that like the mammalian FLOTILLINs, FLOTILLINs expressed in Arabidopsis form a tetrameric complex in the plasma membrane. This plant-membrane-on-a-chip approach opens avenues to studies of membrane properties of plants, transport phenomena, biophysical processes, and protein-protein and protein-lipid interactions in a convenient, cell-free platform.
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Affiliation(s)
- Martin Stuebler
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- University of Natural Resources and Life Sciences, Vienna 1180, Austria
| | - Zachary A Manzer
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Han-Yuan Liu
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Julia Miller
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, United States
| | - Annett Richter
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | | | - Ekaterina Selivanovitch
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Barituziga Banuna
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Georg Jander
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Erik Reimhult
- University of Natural Resources and Life Sciences, Vienna 1180, Austria
| | - Warren R Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Adrienne H K Roeder
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Miguel A Piñeros
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, United States
- Robert W. Holley Center for Agriculture & Health, ARS-USDA, Ithaca, New York 14853, United States
| | - Susan Daniel
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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15
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Khan S, Molloy JE, Puhl H, Schulman H, Vogel SS. Real-time single-molecule imaging of CaMKII-calmodulin interactions. Biophys J 2024; 123:824-838. [PMID: 38414237 DOI: 10.1016/j.bpj.2024.02.021] [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: 08/03/2023] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
The binding of calcium/calmodulin (CAM) to calcium/calmodulin-dependent protein kinase II (CaMKII) initiates an ATP-driven cascade that triggers CaMKII autophosphorylation. The autophosphorylation in turn increases the CaMKII affinity for CAM. Here, we studied the ATP dependence of CAM association with the actin-binding CaMKIIβ isoform using single-molecule total internal reflection fluorescence microscopy. Rhodamine-CAM associations/dissociations to surface-immobilized Venus-CaMKIIβ were resolved with 0.5 s resolution from video records, batch-processed with a custom algorithm. CAM occupancy was determined simultaneously with spot-photobleaching measurement of CaMKII holoenzyme stoichiometry. We show the ATP-dependent increase of the CAM association requires dimer formation for both the α and β isoforms. The study of mutant β holoenzymes revealed that the ATP-dependent increase in CAM affinity results in two distinct states. The phosphorylation-defective (T287.306-307A) holoenzyme resides only in the low-affinity state. CAM association is further reduced in the T287A holoenzyme relative to T287.306-307A. In the absence of ATP, the affinity of CAM for the T287.306-307A mutant and the wild-type monomer are comparable. The affinity of the ATP-binding impaired (K43R) mutant is even weaker. In ATP, the K43R holoenzyme resides in the low-affinity state. The phosphomimetic mutant (T287D) resides only in a 1000-fold higher-affinity state, with mean CAM occupancy of more than half of the 14-mer holoenzyme stoichiometry in picomolar CAM. ATP promotes T287D holoenzyme disassembly but does not elevate CAM occupancy. Single Poisson distributions characterized the ATP-dependent CAM occupancy of mutant holoenzymes. In contrast, the CAM occupancy of the wild-type population had a two-state distribution with both low- and high-affinity states represented. The low-affinity state was the dominant state, a result different from published in vitro assays. Differences in assay conditions can alter the balance between activating and inhibitory autophosphorylation. Bound ATP could be sufficient for CaMKII structural function, while antagonistic autophosphorylations may tune CaMKII kinase-regulated action-potential frequency decoding in vivo.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium at Lawrence Berkeley National Laboratory, Berkeley, California.
| | | | - Henry Puhl
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Howard Schulman
- Panorama Research Institute, Sunnyvale, California; Stanford University School of Medicine, Stanford, California
| | - Steven S Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
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16
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Kashyap P, Bertelli S, Cao F, Kostritskaia Y, Blank F, Srikanth NA, Schlack-Leigers C, Saleppico R, Bierhuizen D, Lu X, Nickel W, Campbell RE, Plested AJR, Stauber T, Taylor MJ, Ewers H. An optogenetic method for the controlled release of single molecules. Nat Methods 2024; 21:666-672. [PMID: 38459384 PMCID: PMC11009104 DOI: 10.1038/s41592-024-02204-x] [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: 01/23/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
We developed a system for optogenetic release of single molecules in cells. We confined soluble and transmembrane proteins to the Golgi apparatus via a photocleavable protein and released them by short pulses of light. Our method allows for a light dose-dependent delivery of functional proteins to the cytosol and plasma membrane in amounts compatible with single-molecule imaging, greatly simplifying access to single-molecule microscopy of any protein in live cells. We were able to reconstitute ion conductance by delivering BK and LRRC8/volume-regulated anion channels to the plasma membrane. Finally we were able to induce NF-kB signaling in T lymphoblasts stimulated by interleukin-1 by controlled release of a signaling protein that had been knocked out. We observed light-induced formation of functional inflammatory signaling complexes that triggered phosphorylation of the inhibitor of nuclear factor kappa-B kinase only in activated cells. We thus developed an optogenetic method for the reconstitution and investigation of cellular function at the single-molecule level.
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Affiliation(s)
- Purba Kashyap
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Sara Bertelli
- Humboldt-Universität zu Berlin and Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Fakun Cao
- Max-Planck-Institute for Infection Biology, Berlin, Germany
| | - Yulia Kostritskaia
- Institute for Molecular Medicine, MSH Medical School Hamburg, Hamburg, Germany
| | - Fenja Blank
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Niranjan A Srikanth
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
- Max-Planck-Institute for Infection Biology, Berlin, Germany
| | | | | | - Dolf Bierhuizen
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Xiaocen Lu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Andrew J R Plested
- Humboldt-Universität zu Berlin and Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Tobias Stauber
- Institute for Molecular Medicine, MSH Medical School Hamburg, Hamburg, Germany
| | | | - Helge Ewers
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany.
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17
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Li L, Liu X, Yang S, Li M, Wu Y, Hu S, Wang W, Jiang A, Zhang Q, Zhang J, Ma X, Hu J, Zhao Q, Liu Y, Li D, Hu J, Yang C, Feng W, Wang X. The HEAT repeat protein HPO-27 is a lysosome fission factor. Nature 2024; 628:630-638. [PMID: 38538795 DOI: 10.1038/s41586-024-07249-8] [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: 01/03/2023] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
Lysosomes are degradation and signalling centres crucial for homeostasis, development and ageing1. To meet diverse cellular demands, lysosomes remodel their morphology and function through constant fusion and fission2,3. Little is known about the molecular basis of fission. Here we identify HPO-27, a conserved HEAT repeat protein, as a lysosome scission factor in Caenorhabditis elegans. Loss of HPO-27 impairs lysosome fission and leads to an excessive tubular network that ultimately collapses. HPO-27 and its human homologue MROH1 are recruited to lysosomes by RAB-7 and enriched at scission sites. Super-resolution imaging, negative-staining electron microscopy and in vitro reconstitution assays reveal that HPO-27 and MROH1 self-assemble to mediate the constriction and scission of lysosomal tubules in worms and mammalian cells, respectively, and assemble to sever supported membrane tubes in vitro. Loss of HPO-27 affects lysosomal morphology, integrity and degradation activity, which impairs animal development and longevity. Thus, HPO-27 and MROH1 act as self-assembling scission factors to maintain lysosomal homeostasis and function.
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Affiliation(s)
- Letao Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Xilu Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Meijiao Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
- Southwest United Graduate School, Kunming, China
| | - Yanwei Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Siqi Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjuan Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Amin Jiang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qianqian Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Junbing Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Junyan Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qiaohong Zhao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Yubing Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junjie Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chonglin Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
- Southwest United Graduate School, Kunming, China
| | - Wei Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Xiaochen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Southwest United Graduate School, Kunming, China.
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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18
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Bestsennaia E, Maslov I, Balandin T, Alekseev A, Yudenko A, Abu Shamseye A, Zabelskii D, Baumann A, Catapano C, Karathanasis C, Gordeliy V, Heilemann M, Gensch T, Borshchevskiy V. Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy. Angew Chem Int Ed Engl 2024; 63:e202307555. [PMID: 38226794 DOI: 10.1002/anie.202307555] [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: 06/06/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Microbial rhodopsins are retinal membrane proteins that found a broad application in optogenetics. The oligomeric state of rhodopsins is important for their functionality and stability. Of particular interest is the oligomeric state in the cellular native membrane environment. Fluorescence microscopy provides powerful tools to determine the oligomeric state of membrane proteins directly in cells. Among these methods is quantitative photoactivated localization microscopy (qPALM) allowing the investigation of molecular organization at the level of single protein clusters. Here, we apply qPALM to investigate the oligomeric state of the first and most used optogenetic tool Channelrhodopsin-2 (ChR2) in the plasma membrane of eukaryotic cells. ChR2 appeared predominantly as a dimer in the cell membrane and did not form higher oligomers. The disulfide bonds between Cys34 and Cys36 of adjacent ChR2 monomers were not required for dimer formation and mutations disrupting these bonds resulted in only partial monomerization of ChR2. The monomeric fraction increased when the total concentration of mutant ChR2 in the membrane was low. The dissociation constant was estimated for this partially monomerized mutant ChR2 as 2.2±0.9 proteins/μm2 . Our findings are important for understanding the mechanistic basis of ChR2 activity as well as for improving existing and developing future optogenetic tools.
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Affiliation(s)
- Ekaterina Bestsennaia
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Maslov
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and the Biomedical Research Institute, Hasselt University, B3590, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium
| | - Taras Balandin
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexey Alekseev
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Anna Yudenko
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Assalla Abu Shamseye
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Dmitrii Zabelskii
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
- European XFEL, 22869, Schenefeld, Germany
| | - Arnd Baumann
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Claudia Catapano
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
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19
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Moochickal Assainar B, Ragunathan K, Baldridge RD. Direct observation of autoubiquitination for an integral membrane ubiquitin ligase in ERAD. Nat Commun 2024; 15:1340. [PMID: 38351109 PMCID: PMC10864399 DOI: 10.1038/s41467-024-45541-3] [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: 08/02/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
The endoplasmic reticulum associated degradation (ERAD) pathway regulates protein quality control at the endoplasmic reticulum. ERAD of lumenal and membrane proteins requires a conserved E3 ubiquitin ligase, called Hrd1. We do not understand the molecular configurations of Hrd1 that enable autoubiquitination and the subsequent retrotranslocation of misfolded protein substrates from the ER to the cytosol. Here, we have established a generalizable, single-molecule platform that enables high-efficiency labeling, stoichiometry determination, and functional assays for any integral membrane protein. Using this approach, we directly count Hrd1 proteins reconstituted into individual proteoliposomes. We report that Hrd1 assembles in different oligomeric configurations with mostly monomers and dimers detected at limiting dilution. By correlating oligomeric states with ubiquitination in vitro, we conclude that Hrd1 monomers are inefficient in autoubiquitination while dimers efficiently assemble polyubiquitin chains. Therefore, our results reveal the minimal composition of a Hrd1 oligomer that is capable of autoubiquitination. Our methods are broadly applicable to studying other complex membrane protein functions using reconstituted bilayer systems.
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Affiliation(s)
- Basila Moochickal Assainar
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Kaushik Ragunathan
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
| | - Ryan D Baldridge
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA.
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20
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Leek AN, Quinn JA, Krapf D, Tamkun MM. GLT-1a glutamate transporter nanocluster localization is associated with astrocytic actin and neuronal Kv2 clusters at sites of neuron-astrocyte contact. Front Cell Dev Biol 2024; 12:1334861. [PMID: 38362041 PMCID: PMC10867268 DOI: 10.3389/fcell.2024.1334861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Introduction: Astrocytic GLT-1 glutamate transporters ensure the fidelity of glutamic neurotransmission by spatially and temporally limiting glutamate signals. The ability to limit neuronal hyperactivity relies on the localization and diffusion of GLT-1 on the astrocytic surface, however, little is known about the underlying mechanisms. We show that two isoforms of GLT-1, GLT-1a and GLT-1b, form nanoclusters on the surface of transfected astrocytes and HEK-293 cells. Methods: We used both fixed and live cell super-resolution imaging of fluorescent protein and epitope tagged proteins in co-cultures of rat astrocytes and neurons. Immunofluorescence techniques were also used. GLT1 diffusion was assessed via single particle tracking and fluorescence recovery after photobleach (FRAP). Results: We found GLT-1a, but not GLT-1b, nanoclusters concentrated adjacent to actin filaments which was maintained after addition of glutamate. GLT-1a nanocluster concentration near actin filaments was prevented by expression of a cytosolic GLT-1a C-terminus, suggesting the C-terminus is involved in the localization adjacent to cortical actin. Using super-resolution imaging, we show that astrocytic GLT-1a and actin co-localize in net-like structures around neuronal Kv2.1 clusters at points of neuron/astrocyte contact. Conclusion: Overall, these data describe a novel relationship between GLT-1a and cortical actin filaments, which localizes GLT-1a near neuronal structures responsive to ischemic insult.
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Affiliation(s)
- Ashley N. Leek
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
- Molecular, Cellular and Integrative Neuroscience Program, Colorado State University, Fort Collins, CO, United States
| | - Josiah A. Quinn
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO, United States
| | - Michael M. Tamkun
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
- Molecular, Cellular and Integrative Neuroscience Program, Colorado State University, Fort Collins, CO, United States
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
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21
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Chen H, Chen TY. From Monomers to Hexamers: A Theoretical Probability of the Neighbor Density Approach to Dissect Protein Oligomerization in Cells. Anal Chem 2024; 96:895-903. [PMID: 38156958 PMCID: PMC10842889 DOI: 10.1021/acs.analchem.3c04728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Deciphering the oligomeric state of proteins within cells is pivotal to understanding their role in intricate cellular processes. With the recent advances in single-molecule localization microscopy, previous efforts have harnessed protein location density approaches, coupled with simulations, to extract membrane protein oligomeric states in cells, highlighting the value of such techniques. However, a comprehensive theoretical approach that can be universally applied across different proteins (e.g., membrane and cytosolic proteins) remains elusive. Here, we introduce the theoretical probability of neighbor density (PND) as a robust tool to discern protein oligomeric states in cellular environments. Utilizing our approach, the theoretical PND was validated against simulated data for both membrane and cytosolic proteins, consistently aligning with experimental baselines for membrane proteins. This congruence was maintained even when adjusting for protein concentrations or exploring proteins of various oligomeric states. The strength of our method lies not only in its precision but also in its adaptability, accommodating diverse cellular protein scenarios without compromising the accuracy. The development and validation of the theoretical PND facilitate accurate protein oligomeric state determination and bolster our understanding of protein-mediated cellular functions.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204
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22
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Walker G, Brown C, Ge X, Kumar S, Muzumdar MD, Gupta K, Bhattacharyya M. Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution. NATURE NANOTECHNOLOGY 2024; 19:85-94. [PMID: 38012273 PMCID: PMC10981947 DOI: 10.1038/s41565-023-01547-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
The oligomeric organization of membrane proteins in native cell membranes is a critical regulator of their function. High-resolution quantitative measurements of oligomeric assemblies and how they change under different conditions are indispensable to understanding membrane protein biology. We report Native-nanoBleach, a total internal reflection fluorescence microscopy-based single-molecule photobleaching step analysis technique to determine the oligomeric distribution of membrane proteins directly from native membranes at an effective spatial resolution of ~10 nm. We achieved this by capturing target membrane proteins in native nanodiscs with their proximal native membrane environment using amphipathic copolymers. We applied Native-nanoBleach to quantify the oligomerization status of structurally and functionally diverse membrane proteins, including a receptor tyrosine kinase (TrkA) and a small GTPase (KRas) under growth-factor binding and oncogenic mutations, respectively. Our data suggest that Native-nanoBleach provides a sensitive, single-molecule platform to quantify membrane protein oligomeric distributions in native membranes under physiologically and clinically relevant conditions.
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Affiliation(s)
- Gerard Walker
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Caroline Brown
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Xiangyu Ge
- Department of Pathology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Shailesh Kumar
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Mandar D Muzumdar
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- Department of Genetics, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Yale University, New Haven, CT, USA
- Yale Cancer Center, New Haven, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
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23
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Mitra K, Krishnan Y. Lightly counting membrane proteins in native nanodiscs. NATURE NANOTECHNOLOGY 2024; 19:5-6. [PMID: 38012272 DOI: 10.1038/s41565-023-01538-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Affiliation(s)
- Koushambi Mitra
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA.
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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24
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Kim S, Kim Y, Lee JY. Real-time single-molecule visualization using DNA curtains reveals the molecular mechanisms underlying DNA repair pathways. DNA Repair (Amst) 2024; 133:103612. [PMID: 38128155 DOI: 10.1016/j.dnarep.2023.103612] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
The demand for direct observation of biomolecular interactions provides new insights into the molecular mechanisms underlying many biological processes. Single-molecule imaging techniques enable real-time visualization of individual biomolecules, providing direct observations of protein machines. Various single-molecule imaging techniques have been developed and have contributed to breakthroughs in biological research. One such technique is the DNA curtain, a novel, high-throughput, single-molecule platform that integrates lipid fluidity, nano-fabrication, microfluidics, and fluorescence imaging. Many DNA metabolic reactions, such as replication, transcription, and chromatin dynamics, have been studied using DNA curtains. In particular, the DNA curtain platform has been intensively applied in investigating the molecular details of DNA repair processes. This article reviews DNA curtain techniques and their applications for imaging DNA repair proteins.
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Affiliation(s)
- Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Youngseo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea.
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25
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Lee J, Gonzalez-Hernandez AJ, Kristt M, Abreu N, Roßmann K, Arefin A, Marx DC, Broichhagen J, Levitz J. Distinct beta-arrestin coupling and intracellular trafficking of metabotropic glutamate receptor homo- and heterodimers. SCIENCE ADVANCES 2023; 9:eadi8076. [PMID: 38055809 PMCID: PMC10699790 DOI: 10.1126/sciadv.adi8076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023]
Abstract
The metabotropic glutamate receptors (mGluRs) are family C, dimeric G protein-coupled receptors (GPCRs), which play critical roles in synaptic transmission. Despite an increasing appreciation of the molecular diversity of this family, how distinct mGluR subtypes are regulated remains poorly understood. We reveal that different group II/III mGluR subtypes show markedly different beta-arrestin (β-arr) coupling and endocytic trafficking. While mGluR2 is resistant to internalization and mGluR3 shows transient β-arr coupling, which enables endocytosis and recycling, mGluR8 and β-arr form stable complexes, which leads to efficient lysosomal targeting and degradation. Using chimeras and mutagenesis, we pinpoint carboxyl-terminal domain regions that control β-arr coupling and trafficking, including the identification of an mGluR8 splice variant with impaired internalization. We then use a battery of high-resolution fluorescence assays to find that heterodimerization further expands the diversity of mGluR regulation. Together, this work provides insight into the relationship between GPCR/β-arr complex formation and trafficking while revealing diversity and intricacy in the regulation of mGluRs.
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Affiliation(s)
- Joon Lee
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Melanie Kristt
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nohely Abreu
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Kilian Roßmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Anisul Arefin
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dagan C. Marx
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Psychiatry, Weill Cornell Medicine, New York, NY 10065, USA
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26
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Asada R, Dominguez A, Montpetit B. Single-molecule quantitation of RNA-binding protein occupancy and stoichiometry defines a role for Yra1 (Aly/REF) in nuclear mRNP organization. Cell Rep 2023; 42:113415. [PMID: 37963019 PMCID: PMC10841842 DOI: 10.1016/j.celrep.2023.113415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/09/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
RNA-binding proteins (RBPs) interact with mRNA to form supramolecular complexes called messenger ribonucleoprotein (mRNP) particles. These dynamic assemblies direct and regulate individual steps of gene expression; however, their composition and functional importance remain largely unknown. Here, we develop a total internal reflection fluorescence-based single-molecule imaging assay to investigate stoichiometry and co-occupancy of 15 RBPs within mRNPs from Saccharomyces cerevisiae. We show compositional heterogeneity of single mRNPs and plasticity across different growth conditions, with major co-occupants of mRNPs containing the nuclear cap-binding complex identified as Yra1 (1-10 copies), Nab2 (1-6 copies), and Npl3 (1-6 copies). Multicopy Yra1-bound mRNPs are specifically co-occupied by the THO complex and assembled on mRNAs biased by transcript length and RNA secondary structure. Yra1 depletion results in decreased compaction of nuclear mRNPs demonstrating a packaging function. Together, we provide a quantitative framework for gene- and condition-dependent RBP occupancy and stoichiometry in individual nuclear mRNPs.
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Affiliation(s)
- Ryuta Asada
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Andrew Dominguez
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA.
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27
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Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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28
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Kang Y, Han YG, Khim KW, Choi WG, Ju MK, Park K, Shin KJ, Chae YC, Choi JH, Kim H, Lee JY. Alteration of replication protein A binding mode on single-stranded DNA by NSMF potentiates RPA phosphorylation by ATR kinase. Nucleic Acids Res 2023; 51:7936-7950. [PMID: 37378431 PMCID: PMC10450186 DOI: 10.1093/nar/gkad543] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Replication protein A (RPA), a eukaryotic single-stranded DNA (ssDNA) binding protein, dynamically interacts with ssDNA in different binding modes and plays essential roles in DNA metabolism such as replication, repair, and recombination. RPA accumulation on ssDNA due to replication stress triggers the DNA damage response (DDR) by activating the ataxia telangiectasia and RAD3-related (ATR) kinase, which phosphorylates itself and downstream DDR factors, including RPA. We recently reported that the N-methyl-D-aspartate receptor synaptonuclear signaling and neuronal migration factor (NSMF), a neuronal protein associated with Kallmann syndrome, promotes RPA32 phosphorylation via ATR upon replication stress. However, how NSMF enhances ATR-mediated RPA32 phosphorylation remains elusive. Here, we demonstrate that NSMF colocalizes and physically interacts with RPA at DNA damage sites in vivo and in vitro. Using purified RPA and NSMF in biochemical and single-molecule assays, we find that NSMF selectively displaces RPA in the more weakly bound 8- and 20-nucleotide binding modes from ssDNA, allowing the retention of more stable RPA molecules in the 30-nt binding mode. The 30-nt binding mode of RPA enhances RPA32 phosphorylation by ATR, and phosphorylated RPA becomes stabilized on ssDNA. Our findings provide new mechanistic insight into how NSMF facilitates the role of RPA in the ATR pathway.
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Affiliation(s)
- Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ye Gi Han
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Keon Woo Khim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Woo Gyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Min Kyung Ju
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kibeom Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyeong Jin Shin
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Young Chan Chae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jang Hyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
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29
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Lan C, Kim J, Ulferts S, Aprile-Garcia F, Weyrauch S, Anandamurugan A, Grosse R, Sawarkar R, Reinhardt A, Hugel T. Quantitative real-time in-cell imaging reveals heterogeneous clusters of proteins prior to condensation. Nat Commun 2023; 14:4831. [PMID: 37582808 PMCID: PMC10427612 DOI: 10.1038/s41467-023-40540-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Our current understanding of biomolecular condensate formation is largely based on observing the final near-equilibrium condensate state. Despite expectations from classical nucleation theory, pre-critical protein clusters were recently shown to form under subsaturation conditions in vitro; if similar long-lived clusters comprising more than a few molecules are also present in cells, our understanding of the physical basis of biological phase separation may fundamentally change. Here, we combine fluorescence microscopy with photobleaching analysis to quantify the formation of clusters of NELF proteins in living, stressed cells. We categorise small and large clusters based on their dynamics and their response to p38 kinase inhibition. We find a broad distribution of pre-condensate cluster sizes and show that NELF protein cluster formation can be explained as non-classical nucleation with a surprisingly flat free-energy landscape for a wide range of sizes and an inhibition of condensation in unstressed cells.
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Affiliation(s)
- Chenyang Lan
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- BIOSS and CIBSS Signalling Research Centres, University of Freiburg, Freiburg, Germany
- PicoQuant GmbH, Rudower Chaussee 29, 12489, Berlin, Germany
| | - Juhyeong Kim
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Svenja Ulferts
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg, Germany
| | | | - Sophie Weyrauch
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Chemistry and Pharmacology, University of Freiburg, Freiburg, Germany
| | | | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg, Germany
| | - Ritwick Sawarkar
- Medical Research Council (MRC), University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom.
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany.
- BIOSS and CIBSS Signalling Research Centres, University of Freiburg, Freiburg, Germany.
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30
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Lučić I, Héluin L, Jiang PL, Castro Scalise AG, Wang C, Franz A, Heyd F, Wahl MC, Liu F, Plested AJR. CaMKII autophosphorylation can occur between holoenzymes without subunit exchange. eLife 2023; 12:e86090. [PMID: 37566455 PMCID: PMC10468207 DOI: 10.7554/elife.86090] [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: 01/10/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
The dodecameric protein kinase CaMKII is expressed throughout the body. The alpha isoform is responsible for synaptic plasticity and participates in memory through its phosphorylation of synaptic proteins. Its elaborate subunit organization and propensity for autophosphorylation allow it to preserve neuronal plasticity across space and time. The prevailing hypothesis for the spread of CaMKII activity, involving shuffling of subunits between activated and naive holoenzymes, is broadly termed subunit exchange. In contrast to the expectations of previous work, we found little evidence for subunit exchange upon activation, and no effect of restraining subunits to their parent holoenzymes. Rather, mass photometry, crosslinking mass spectrometry, single molecule TIRF microscopy and biochemical assays identify inter-holoenzyme phosphorylation (IHP) as the mechanism for spreading phosphorylation. The transient, activity-dependent formation of groups of holoenzymes is well suited to the speed of neuronal activity. Our results place fundamental limits on the activation mechanism of this kinase.
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Affiliation(s)
- Iva Lučić
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu BerlinBerlinGermany
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Léonie Héluin
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu BerlinBerlinGermany
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Pin-Lian Jiang
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Alejandro G Castro Scalise
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu BerlinBerlinGermany
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Cong Wang
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Andreas Franz
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Florian Heyd
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Markus C Wahl
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular CrystallographyBerlinGermany
| | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
- Charité-Universitätsmedizin BerlinBerlinGermany
| | - Andrew JR Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu BerlinBerlinGermany
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
- NeuroCure, Charité UniversitätsmedizinBerlinGermany
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31
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Petrich A, Aji AK, Dunsing V, Chiantia S. Benchmarking of novel green fluorescent proteins for the quantification of protein oligomerization in living cells. PLoS One 2023; 18:e0285486. [PMID: 37535571 PMCID: PMC10399874 DOI: 10.1371/journal.pone.0285486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/25/2023] [Indexed: 08/05/2023] Open
Abstract
Protein-protein-interactions play an important role in many cellular functions. Quantitative non-invasive techniques are applied in living cells to evaluate such interactions, thereby providing a broader understanding of complex biological processes. Fluorescence fluctuation spectroscopy describes a group of quantitative microscopy approaches for the characterization of molecular interactions at single cell resolution. Through the obtained molecular brightness, it is possible to determine the oligomeric state of proteins. This is usually achieved by fusing fluorescent proteins (FPs) to the protein of interest. Recently, the number of novel green FPs has increased, with consequent improvements to the quality of fluctuation-based measurements. The photophysical behavior of FPs is influenced by multiple factors (including photobleaching, protonation-induced "blinking" and long-lived dark states). Assessing these factors is critical for selecting the appropriate fluorescent tag for live cell imaging applications. In this work, we focus on novel green FPs that are extensively used in live cell imaging. A systematic performance comparison of several green FPs in living cells under different pH conditions using Number & Brightness (N&B) analysis and scanning fluorescence correlation spectroscopy was performed. Our results show that the new FP Gamillus exhibits higher brightness at the cost of lower photostability and fluorescence probability (pf), especially at lower pH. mGreenLantern, on the other hand, thanks to a very high pf, is best suited for multimerization quantification at neutral pH. At lower pH, mEGFP remains apparently the best choice for multimerization investigation. These guidelines provide the information needed to plan quantitative fluorescence microscopy involving these FPs, both for general imaging or for protein-protein-interactions quantification via fluorescence fluctuation-based methods.
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Affiliation(s)
- Annett Petrich
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
| | - Amit Koikkarah Aji
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
| | - Valentin Dunsing
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
- Aix-Marseille University, CNRS, UMR 7288, IBDM, Turing Center for Living Systems, Marseille, France
| | - Salvatore Chiantia
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
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Torres A, Cockerell S, Phillips M, Balázsi G, Ghosh K. MaxCal can infer models from coupled stochastic trajectories of gene expression and cell division. Biophys J 2023; 122:2623-2635. [PMID: 37218129 PMCID: PMC10397576 DOI: 10.1016/j.bpj.2023.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023] Open
Abstract
Gene expression is inherently noisy due to small numbers of proteins and nucleic acids inside a cell. Likewise, cell division is stochastic, particularly when tracking at the level of a single cell. The two can be coupled when gene expression affects the rate of cell division. Single-cell time-lapse experiments can measure both fluctuations by simultaneously recording protein levels inside a cell and its stochastic division. These information-rich noisy trajectory data sets can be harnessed to learn about the underlying molecular and cellular details that are often not known a priori. A critical question is: How can we infer a model given data where fluctuations at two levels-gene expression and cell division-are intricately convoluted? We show the principle of maximum caliber (MaxCal)-integrated within a Bayesian framework-can be used to infer several cellular and molecular details (division rates, protein production, and degradation rates) from these coupled stochastic trajectories (CSTs). We demonstrate this proof of concept using synthetic data generated from a known model. An additional challenge in data analysis is that trajectories are often not in protein numbers, but in noisy fluorescence that depends on protein number in a probabilistic manner. We again show that MaxCal can infer important molecular and cellular rates even when data are in fluorescence, another example of CST with three confounding factors-gene expression noise, cell division noise, and fluorescence distortion-all coupled. Our approach will provide guidance to build models in synthetic biology experiments as well as general biological systems where examples of CSTs are abundant.
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Affiliation(s)
- Andrew Torres
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Spencer Cockerell
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Gábor Balázsi
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Kingshuk Ghosh
- Molecular and Cellular Biophysics, University of Denver, Denver, Colorado; Department of Physics and Astronomy, University of Denver, Denver, Colorado.
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Yu C, Runge HFP, Mukhopadhyay A, Zolles G, Ulbrich MH. γ-2 and GSG1L bind with comparable affinities to the tetrameric GluA1 core. Cell Mol Biol Lett 2023; 28:54. [PMID: 37430208 PMCID: PMC10332039 DOI: 10.1186/s11658-023-00470-9] [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: 04/21/2023] [Accepted: 06/24/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND The AMPA-type ionotropic glutamate receptor mediates fast excitatory neurotransmission in the brain. A variety of auxiliary subunits regulate its gating properties, assembly, and trafficking, but it is unknown if the binding of these auxiliary subunits to the receptor core is dynamically regulated. Here we investigate the interplay of the two auxiliary subunits γ-2 and GSG1L when binding to the AMPA receptor composed of four GluA1 subunits. METHODS We use a three-color single-molecule imaging approach in living cells, which allows the direct observation of the receptors and both auxiliary subunits. Colocalization of different colors can be interpreted as interaction of the respective receptor subunits. RESULTS Depending on the relative expression levels of γ-2 and GSG1L, the occupancy of binding sites shifts from one auxiliary subunit to the other, supporting the idea that they compete for binding to the receptor. Based on a model where each of the four binding sites at the receptor core can be either occupied by γ-2 or GSG1L, our experiments yield apparent dissociation constants for γ-2 and GSG1L in the range of 2.0-2.5/µm2. CONCLUSIONS The result that both binding affinities are in the same range is a prerequisite for dynamic changes of receptor composition under native conditions.
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Affiliation(s)
- Chenlu Yu
- Internal Medicine IV, Department of Medicine, University Medical Center, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Hendrik F P Runge
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Antara Mukhopadhyay
- Internal Medicine IV, Department of Medicine, University Medical Center, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Gerd Zolles
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian H Ulbrich
- Internal Medicine IV, Department of Medicine, University Medical Center, and Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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Tan HL, Bungert-Plümke S, Kortzak D, Fahlke C, Stölting G. Dual-color Colocalization in Single-molecule Localization Microscopy to Determine the Oligomeric State of Proteins in the Plasma Membrane. Bio Protoc 2023; 13:e4749. [PMID: 37456335 PMCID: PMC10339340 DOI: 10.21769/bioprotoc.4749] [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: 02/16/2023] [Revised: 03/15/2023] [Accepted: 05/21/2023] [Indexed: 07/18/2023] Open
Abstract
Determining the oligomeric state of membrane proteins is critical for understanding their function. However, traditional ex situ methods like clear native gel electrophoresis can disrupt protein subunit interactions during sample preparation. In situ methods such as stepwise photobleaching have limitations due to high expression levels and limitations of optical resolution in microscopy. Super-resolution microscopy techniques such as single-molecule localization microscopy (SMLM) have the potential to overcome these limitations, but the stochastic nature of signals can lead to miscounting due to over-expression, background noise, and temporal separation of signals. Additionally, this technique has limited application due to the limited selection of fluorescent labels and the demanding control of laser power. To address these issues, we developed a dual color colocalization (DCC) strategy that offers higher tolerance to background noise and simplifies data acquisition and processing for high-throughput and reliable counting. The DCC strategy was used to determine the oligomeric states of membrane proteins of the SLC17 and SLC26 family with SMLM, providing a robust and efficient method for studying protein interactions.
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Affiliation(s)
- Hua Leonhard Tan
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Stefanie Bungert-Plümke
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Kortzak
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Christoph Fahlke
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Gabriel Stölting
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Center of Functional Genomics, Hypertension and Molecular Biology of Endocrine Tumors, Berlin, Germany
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Façanha Wendel C, Hapuque Oliveira Alencar Q, Viana Vieira R, Teixeira KN. In silico insight into Amurensinine - an N-Methyl-D-Aspartate receptor antagonist. World J Pharmacol 2023; 12:25-34. [DOI: 10.5497/wjp.v12.i3.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Some isopavines can exhibit important biological activity in the treatment of neurological disorders since it is considered an antagonist of the specific N-methyl-D-Aspartate (NMDA) receptor. Amurensinine is an isopavine which still has few studies. In view of the potential of isopavines as NMDA receptor antagonists, theoretical studies using bioinformatics were carried out in order to investigate whether Amurensinine binds to the NMDA receptor and to analyze the receptor/Ligand complex. This data can contribute to understanding of the onset of neurological diseases and contribute to the planning of drugs for the treatment of neurological diseases involving the NMDA receptor.
AIM To investigate the interaction of the antagonist Amurensinine on the GluN1A/ GluN2B isoform of the NMDA receptor using bioinformatics.
METHODS The three-dimen-sional structure of the GluN1A/GluN2B NMDA receptor was selected from the Protein Data Bank (PDB) - PDB: 4PE5, and the three-dimen-sional structure of Amurensinine (ligand) was designed and optimized using ACD/SchemsketchTM software. Prediction of the protonation state of Amur-ensinine at physiological pH was performed using MarvinSketch software (ChemAxon). Protonated and non-protonated Amurensin were prepared using AutoDock Tools 4 software and simulations were performed using Autodock Vina v.1.2.0. The receptor/Ligand complexes were analyzed using PyMol (Schrödinger, Inc) and BIOVIA Discovery Studio (Dassault Systemes) software. To evaluate the NMDA receptor/Amurensinine complex and validate the molecular docking, simulations using NMDA receptor and Ifenprodil antagonist were performed under the same conditions. Ifenprodil was also designed, optimized and protonated, under the same conditions as Amurensinine.
RESULTS Molecular docking simulations showed that both non-protonated and protonated Amurensinine bind to the amino terminal domain (ATD) domain of the GluN1A/GluN2B NMDA receptor with significant affinity energy, -7.9 Kcal/mol and -8.1 Kcal/mol, respectively. The NMDA receptor/non-protonated Amurensinine complex was stabilized by 15 bonds, while the NMDA receptor/protonated Amurensinine complex was stabilized by less than half, 6 bonds. Despite the difference in the number of bonds, the variation in bond length and the average bond length values are similar in both complexes. The complex formed by the NMDA receptor and Ifenprodil showed an affinity energy of -8.2 Kcal/mol, a value very close to that obtained for the NMDA receptor/Amurensinine complex. Molecular docking between Ifenprodil and the GluN1A /GluN2B NMDA receptor demonstrated that this antagonist interacts with the ATD of the receptor, which validates the simulations performed with Amurensinine.
CONCLUSION Amurensinine binds to the NMDA receptor on ATD, similar to Ifenprodil, and the affinity energy is closer. These data suggest that Amurensinine could behave as a receptor inhibitor, indicating that this compound may have a potential biological application, which should be evaluated by in vitro and preclinical assays.
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Affiliation(s)
- Cinthia Façanha Wendel
- Campus Toledo, Universidade Federal do Paraná, Toledo 85.919-899, Paraná, Brazil
- Programa Multicêntrico de Pós-graduação em Bioquímica e Biologia Molecular - Setor Palotina, Universidade Federal do Paraná, Palotina 85.950-000, Paraná, Brazil
| | | | - Rafaela Viana Vieira
- Campus Toledo, Universidade Federal do Paraná, Toledo 85.919-899, Paraná, Brazil
| | - Kádima Nayara Teixeira
- Campus Toledo, Universidade Federal do Paraná, Toledo 85.919-899, Paraná, Brazil
- Programa Multicêntrico de Pós-graduação em Bioquímica e Biologia Molecular - Setor Palotina, Universidade Federal do Paraná, Palotina 85.950-000, Paraná, Brazil
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Yin F, Zhao H, Lu S, Shen J, Li M, Mao X, Li F, Shi J, Li J, Dong B, Xue W, Zuo X, Yang X, Fan C. DNA-framework-based multidimensional molecular classifiers for cancer diagnosis. NATURE NANOTECHNOLOGY 2023; 18:677-686. [PMID: 36973399 DOI: 10.1038/s41565-023-01348-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
A molecular classification of diseases that accurately reflects clinical behaviour lays the foundation of precision medicine. The development of in silico classifiers coupled with molecular implementation based on DNA reactions marks a key advance in more powerful molecular classification, but it nevertheless remains a challenge to process multiple molecular datatypes. Here we introduce a DNA-encoded molecular classifier that can physically implement the computational classification of multidimensional molecular clinical data. To produce unified electrochemical sensing signals across heterogeneous molecular binding events, we exploit DNA-framework-based programmable atom-like nanoparticles with n valence to develop valence-encoded signal reporters that enable linearity in translating virtually any biomolecular binding events to signal gains. Multidimensional molecular information in computational classification is thus precisely assigned weights for bioanalysis. We demonstrate the implementation of a molecular classifier based on programmable atom-like nanoparticles to perform biomarker panel screening and analyse a panel of six biomarkers across three-dimensional datatypes for a near-deterministic molecular taxonomy of prostate cancer patients.
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Affiliation(s)
- Fangfei Yin
- Institute of Molecular Medicine, Department of Urology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haipei Zhao
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shasha Lu
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Juwen Shen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Min Li
- Institute of Molecular Medicine, Department of Urology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Urology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Urology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Baijun Dong
- Institute of Molecular Medicine, Department of Urology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Xue
- Institute of Molecular Medicine, Department of Urology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Urology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Xiurong Yang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Department of Urology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
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37
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Bossi S, Pizzamiglio L, Paoletti P. Excitatory GluN1/GluN3A glycine receptors (eGlyRs) in brain signaling. Trends Neurosci 2023:S0166-2236(23)00127-3. [PMID: 37248111 DOI: 10.1016/j.tins.2023.05.002] [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: 03/17/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
GluN3A is a glycine-binding subunit belonging to the NMDA receptor (NMDAR) family that can assemble with GluN1 subunits to form unconventional NMDARs insensitive to glutamate and activated by glycine only. The existence of such excitatory glycine receptors (eGlyRs) in the central nervous system (CNS) has long remained elusive. Recently, eGlyRs have been identified in specific brain regions, where they represent a novel neuronal signaling modality by which extracellular glycine tunes neuronal excitability, circuit function, and behavior. In this review, we summarize the emerging knowledge regarding these underappreciated receptors. The existence of eGlyRs reshapes current understanding of NMDAR diversity and of glycinergic signaling, previously thought to be primarily inhibitory. Given that GluN3A expression is concentrated in brain regions regulating emotional responses, eGlyRs are potential new targets of therapeutic interest in neuropsychiatry.
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Affiliation(s)
- Simon Bossi
- Institut de Biologie de l'École Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | - Lara Pizzamiglio
- Institut de Biologie de l'École Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | - Pierre Paoletti
- Institut de Biologie de l'École Normale Supérieure (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France.
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38
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Singh V, Macharová S, Riegerová P, Steringer JP, Müller HM, Lolicato F, Nickel W, Hof M, Šachl R. Determining the Functional Oligomeric State of Membrane-Associated Protein Oligomers Forming Membrane Pores on Giant Lipid Vesicles. Anal Chem 2023. [PMID: 37148264 DOI: 10.1021/acs.analchem.2c05692] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Several peripheral membrane proteins are known to form membrane pores through multimerization. In many cases, in biochemical reconstitution experiments, a complex distribution of oligomeric states has been observed that may, in part, be irrelevant to their physiological functions. This phenomenon makes it difficult to identify the functional oligomeric states of membrane lipid interacting proteins, for example, during the formation of transient membrane pores. Using fibroblast growth factor 2 (FGF2) as an example, we present a methodology applicable to giant lipid vesicles by which functional oligomers can be distinguished from nonspecifically aggregated proteins without functionality. Two distinct populations of fibroblast growth factor 2 were identified with (i) dimers to hexamers and (ii) a broad population of higher oligomeric states of membrane-associated FGF2 oligomers significantly distorting the original unfiltered histogram of all detectable oligomeric species of FGF2. The presented statistical approach is relevant for various techniques for characterizing membrane-dependent protein oligomerization.
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Affiliation(s)
- Vandana Singh
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu, 2027/3, 121 16 Prague, Czech Republic
| | - Sabína Macharová
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Petra Riegerová
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Julia P Steringer
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Hans-Michael Müller
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
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Ritter N, Disse P, Wünsch B, Seebohm G, Strutz-Seebohm N. Pharmacological Potential of 3-Benzazepines in NMDAR-Linked Pathophysiological Processes. Biomedicines 2023; 11:1367. [PMID: 37239037 PMCID: PMC10216354 DOI: 10.3390/biomedicines11051367] [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: 03/14/2023] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The number of N-Methyl-D-aspartate receptor (NMDAR) linked neurodegenerative diseases such as Alzheimer's disease and dementia is constantly increasing. This is partly due to demographic change and presents new challenges to societies. To date, there are no effective treatment options. Current medications are nonselective and can lead to unwanted side effects in patients. A promising therapeutic approach is the targeted inhibition of NMDARs in the brain. NMDARs containing different subunits and splice variants display different physiological properties and play a crucial role in learning and memory, as well as in inflammatory or injury processes. They become overactivated during the course of the disease, leading to nerve cell death. Until now, there has been a lack of understanding of the general functions of the receptor and the mechanism of inhibition, which need to be understood in order to develop inhibitors. Ideal compounds should be highly targeted and even splice-variant-selective. However, a potent and splice-variant-selective NMDAR-targeting drug has yet to be developed. Recently developed 3-benzazepines are promising inhibitors for further drug development. The NMDAR splice variants GluN1-1b-4b carry a 21-amino-acid-long, flexible exon 5. Exon 5 lowers the NMDAR's sensitivity to allosteric modulators by probably acting as an NMDAR modulator itself. The role of exon 5 in NMDAR modulation is still poorly understood. In this review, we summarize the structure and pharmacological relevance of tetrahydro-3-benzazepines.
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Affiliation(s)
- Nadine Ritter
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, D-48149 Münster, Germany; (P.D.); (G.S.); (N.S.-S.)
- Chembion, University of Münster, D-48149 Münster, Germany;
| | - Paul Disse
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, D-48149 Münster, Germany; (P.D.); (G.S.); (N.S.-S.)
- Chembion, University of Münster, D-48149 Münster, Germany;
| | - Bernhard Wünsch
- Chembion, University of Münster, D-48149 Münster, Germany;
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstr. 48, D-48149 Münster, Germany
| | - Guiscard Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, D-48149 Münster, Germany; (P.D.); (G.S.); (N.S.-S.)
- Chembion, University of Münster, D-48149 Münster, Germany;
| | - Nathalie Strutz-Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, D-48149 Münster, Germany; (P.D.); (G.S.); (N.S.-S.)
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Cha M, Jeong SH, Jung J, Baeg Y, Park S, Bae S, Lim CS, Park JH, Lee J, Gho YS, Oh SW, Shon MJ. Quantitative imaging of vesicle-protein interactions reveals close cooperation among proteins. J Extracell Vesicles 2023; 12:e12322. [PMID: 37186457 PMCID: PMC10130417 DOI: 10.1002/jev2.12322] [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: 10/12/2022] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Membrane-bound vesicles such as extracellular vesicles (EVs) can function as biochemical effectors on target cells. Docking of the vesicles onto recipient plasma membranes depends on their interaction with cell-surface proteins, but a generalizable technique that can quantitatively observe these vesicle-protein interactions (VPIs) is lacking. Here, we describe a fluorescence microscopy that measures VPIs between single vesicles and cell-surface proteins, either in a surface-tethered or in a membrane-embedded state. By employing cell-derived vesicles (CDVs) and intercellular adhesion molecule-1 (ICAM-1) as a model system, we found that integrin-driven VPIs exhibit distinct modes of affinity depending on vesicle origin. Controlling the surface density of proteins also revealed a strong support from a tetraspanin protein CD9, with a critical dependence on molecular proximity. An adsorption model accounting for multiple protein molecules was developed and captured the features of density-dependent cooperativity. We expect that VPI imaging will be a useful tool to dissect the molecular mechanisms of vesicle adhesion and uptake, and to guide the development of therapeutic vesicles.
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Affiliation(s)
- Minkwon Cha
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
- POSTECH Biotech CenterPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Sang Hyeok Jeong
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Jaehun Jung
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Yoonjin Baeg
- Biodrone Research InstituteMDimune Inc.SeoulRepublic of Korea
| | - Sung‐Soo Park
- Biodrone Research InstituteMDimune Inc.SeoulRepublic of Korea
| | - Seoyoon Bae
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Chan Seok Lim
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Jun Hyuk Park
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Jie‐Oh Lee
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
- Institute of Membrane ProteinsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Yong Song Gho
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Seung Wook Oh
- Biodrone Research InstituteMDimune Inc.SeoulRepublic of Korea
| | - Min Ju Shon
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
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41
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Danial JSH, Jenner A, Garcia-Saez AJ, Cosentino K. Real-Time Growth Kinetics Analysis of Macromolecular Assemblies in Cells with Single Molecule Resolution. J Phys Chem A 2023; 127:3490-3496. [PMID: 37023388 DOI: 10.1021/acs.jpca.3c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Single molecule fluorescence microscopy has the unique advantage to provide real-time information on the spatiotemporal assembly of individual protein complexes in cellular membranes. This includes the assembly of proteins into oligomer species of numerous copy numbers. However, there is a need for improved tracing analysis of the real-time growth kinetics of these assemblies in cells with single molecule resolution. Here, we present an automated analysis software to accurately measure the real-time kinetics of assembly of individual high-order oligomer complexes. Our software comes with a simple Graphical User Interface (GUI), is available as a source code and an executable, and can analyze a full data set of several hundred to thousand molecules in less than 2 minutes. Importantly, this software is suitable for the analysis of intracellular protein oligomers, whose stoichiometry is usually more difficult to quantify due to variability in signal detection in the different areas of the cell. We validated our method with simulated ground-truth data and time-lapse images of diffraction-limited oligomeric assemblies of BAX and BAK proteins on mitochondria of cells undergoing apoptosis. Our approach provides the broad community of biologists with a fast, user-friendly tool to trace the compositional evolution of macromolecular assemblies, and potentially model their growth for a deeper understanding of the structural and biophysical mechanisms underlying their functions.
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Affiliation(s)
- John S H Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Andreas Jenner
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Ana J Garcia-Saez
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Katia Cosentino
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, 49076 Osnabrück, Germany
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42
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Scalisi S, Pisignano D, Cella Zanacchi F. Single-molecule localization microscopy goes quantitative. Microsc Res Tech 2023; 86:494-504. [PMID: 36601697 DOI: 10.1002/jemt.24281] [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: 11/15/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023]
Abstract
In the last few years, single-molecule localization (SMLM) techniques have been used to address biological questions in different research fields. More recently, super-resolution has also been proposed as a quantitative tool for quantifying protein copy numbers at the nanoscale level. In this scenario, quantitative approaches, mainly based on stepwise photobleaching and quantitative SMLM assisted by calibration standards, offer an exquisite tool for investigating protein complexes. This primer focuses on the basic concepts behind quantitative super-resolution microscopy, also providing strategies to overcome the technical hurdles that could limit their application.
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Affiliation(s)
- Silvia Scalisi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Dario Pisignano
- Dipartimento di Fisica "E. Fermi", Università di Pisa, Pisa, Italy
| | - Francesca Cella Zanacchi
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Fisica "E. Fermi", Università di Pisa, Pisa, Italy
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43
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Steiert F, Schultz P, Höfinger S, Müller TD, Schwille P, Weidemann T. Insights into receptor structure and dynamics at the surface of living cells. Nat Commun 2023; 14:1596. [PMID: 36949079 PMCID: PMC10033668 DOI: 10.1038/s41467-023-37284-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/10/2023] [Indexed: 03/24/2023] Open
Abstract
Evaluating protein structures in living cells remains a challenge. Here, we investigate Interleukin-4 receptor alpha (IL-4Rα) into which the non-canonical amino acid bicyclo[6.1.0]nonyne-lysine (BCNK) is incorporated by genetic code expansion. Bioorthogonal click labeling is performed with tetrazine-conjugated dyes. To quantify the reaction yield in situ, we develop brightness-calibrated ratiometric imaging, a protocol where fluorescent signals in confocal multi-color images are ascribed to local concentrations. Screening receptor mutants bearing BCNK in the extracellular domain uncovered site-specific variations of both click efficiency and Interleukin-4 binding affinity, indicating subtle well-defined structural perturbations. Molecular dynamics and continuum electrostatics calculations suggest solvent polarization to determine site-specific variations of BCNK reactivity. Strikingly, signatures of differential click efficiency, measured for IL-4Rα in ligand-bound and free form, mirror sub-angstrom deformations of the protein backbone at corresponding locations. Thus, click efficiency by itself represents a remarkably informative readout linked to protein structure and dynamics in the native plasma membrane.
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Affiliation(s)
- Frederik Steiert
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Physics, Technical University Munich, 85748, Garching, Germany
| | - Peter Schultz
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Siegfried Höfinger
- VSC Research Center, TU Wien, Operngasse 11 / E057-09, 1040, Wien, Austria
- Department of Physics, Michigan Technological University, 1400 Townsend Drive, 49931, Houghton, MI, USA
| | - Thomas D Müller
- Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik - Botanik I, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Thomas Weidemann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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44
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Margheritis E, Kappelhoff S, Cosentino K. Pore-Forming Proteins: From Pore Assembly to Structure by Quantitative Single-Molecule Imaging. Int J Mol Sci 2023; 24:ijms24054528. [PMID: 36901959 PMCID: PMC10003378 DOI: 10.3390/ijms24054528] [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: 01/05/2023] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Pore-forming proteins (PFPs) play a central role in many biological processes related to infection, immunity, cancer, and neurodegeneration. A common feature of PFPs is their ability to form pores that disrupt the membrane permeability barrier and ion homeostasis and generally induce cell death. Some PFPs are part of the genetically encoded machinery of eukaryotic cells that are activated against infection by pathogens or in physiological programs to carry out regulated cell death. PFPs organize into supramolecular transmembrane complexes that perforate membranes through a multistep process involving membrane insertion, protein oligomerization, and finally pore formation. However, the exact mechanism of pore formation varies from PFP to PFP, resulting in different pore structures with different functionalities. Here, we review recent insights into the molecular mechanisms by which PFPs permeabilize membranes and recent methodological advances in their characterization in artificial and cellular membranes. In particular, we focus on single-molecule imaging techniques as powerful tools to unravel the molecular mechanistic details of pore assembly that are often obscured by ensemble measurements, and to determine pore structure and functionality. Uncovering the mechanistic elements of pore formation is critical for understanding the physiological role of PFPs and developing therapeutic approaches.
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45
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Walker G, Brown C, Ge X, Kumar S, Muzumdar MD, Gupta K, Bhattacharyya M. Determination of oligomeric organization of membrane proteins from native membranes at nanoscale-spatial and single-molecule resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.529138. [PMID: 36865290 PMCID: PMC9980011 DOI: 10.1101/2023.02.19.529138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The oligomeric organization of membrane proteins in native cell membranes is a critical regulator of their function. High-resolution quantitative measurements of oligomeric assemblies and how they change under different conditions are indispensable to the understanding of membrane protein biology. We report a single-molecule imaging technique (Native-nanoBleach) to determine the oligomeric distribution of membrane proteins directly from native membranes at an effective spatial resolution of ∼10 nm. We achieved this by capturing target membrane proteins in "native nanodiscs" with their proximal native membrane environment using amphipathic copolymers. We established this method using structurally and functionally diverse membrane proteins with well-established stoichiometries. We then applied Native-nanoBleach to quantify the oligomerization status of a receptor tyrosine kinase (TrkA) and a small GTPase (KRas) under conditions of growth-factor binding or oncogenic mutations, respectively. Native-nanoBleach provides a sensitive, single-molecule platform to quantify membrane protein oligomeric distributions in native membranes at an unprecedented spatial resolution.
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46
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Bohr F, Bohr SSR, Mishra NK, González-Foutel NS, Pinholt HD, Wu S, Nielsen EM, Zhang M, Kjaergaard M, Jensen KJ, Hatzakis NS. Enhanced hexamerization of insulin via assembly pathway rerouting revealed by single particle studies. Commun Biol 2023; 6:178. [PMID: 36792809 PMCID: PMC9932072 DOI: 10.1038/s42003-022-04386-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/20/2022] [Indexed: 02/17/2023] Open
Abstract
Insulin formulations with diverse oligomerization states are the hallmark of interventions for the treatment of diabetes. Here using single-molecule recordings we firstly reveal that insulin oligomerization can operate via monomeric additions and secondly quantify the existence, abundance and kinetic characterization of diverse insulin assembly and disassembly pathways involving addition of monomeric, dimeric or tetrameric insulin species. We propose and experimentally validate a model where the insulin self-assembly pathway is rerouted, favoring monomeric or oligomeric assembly, by solution concentration, additives and formulations. Combining our practically complete kinetic characterization with rate simulations, we calculate the abundance of each oligomeric species from nM to mM offering mechanistic insights and the relative abundance of all oligomeric forms at concentrations relevant both for secreted and administrated insulin. These reveal a high abundance of all oligomers and a significant fraction of hexamer resulting in practically halved bioavailable monomer concentration. In addition to providing fundamental new insights, the results and toolbox presented here can be universally applied, contributing to the development of optimal insulin formulations and the deciphering of oligomerization mechanisms for additional proteins.
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Affiliation(s)
- Freja Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Narendra Kumar Mishra
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
| | - Nicolás Sebastian González-Foutel
- Department of Molecular Biology and Genetics, The Danish Research Institute for Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, and Center for Proteins in Memory PROMEMO, Danish National Research Foundation, Aarhus University, Aarhus, Denmark
| | - Henrik Dahl Pinholt
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Physics Department, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shunliang Wu
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
| | - Emilie Milan Nielsen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, The Danish Research Institute for Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, and Center for Proteins in Memory PROMEMO, Danish National Research Foundation, Aarhus University, Aarhus, Denmark
| | - Knud J Jensen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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47
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Ernst M, Ozturk TN, Robertson JL. A single-molecule method for measuring fluorophore labeling yields for the study of membrane protein oligomerization in membranes. PLoS One 2023; 18:e0280693. [PMID: 36662827 PMCID: PMC9858377 DOI: 10.1371/journal.pone.0280693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Membrane proteins are often observed as higher-order oligomers, and in some cases in multiple stoichiometric forms, raising the question of whether dynamic oligomerization can be linked to modulation of function. To better understand this potential regulatory mechanism, there is an ongoing effort to quantify equilibrium reactions of membrane protein oligomerization directly in membranes. Single-molecule photobleaching analysis is particularly useful for this as it provides a binary readout of fluorophores attached to protein subunits at dilute conditions. However, any quantification of stoichiometry also critically requires knowing the probability that a subunit is fluorescently labeled. Since labeling uncertainty is often unavoidable, we developed an approach to estimate labeling yields using the photobleaching probability distribution of an intrinsic dimeric control. By iterative fitting of an experimental dimeric photobleaching probability distribution to an expected dimer model, we estimate the fluorophore labeling yields and find agreement with direct measurements of labeling of the purified protein by UV-VIS absorbance before reconstitution. Using this labeling prediction, similar estimation methods are applied to determine the dissociation constant of reactive CLC-ec1 dimerization constructs without prior knowledge of the fluorophore labeling yield. Finally, we estimate the operational range of subunit labeling yields that allows for discrimination of monomer and dimer populations across the reactive range of mole fraction densities. Thus, our study maps out a practical method for quantifying fluorophore labeling directly from single-molecule photobleaching data, improving the ability to quantify reactive membrane protein stoichiometry in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tugba N. Ozturk
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Janice L. Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
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48
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Senior MJT, Monico C, Weatherill EE, Gilbert RJ, Heuck AP, Wallace MI. Single-molecule tracking of perfringolysin O assembly and membrane insertion uncoupling. FEBS J 2023; 290:428-441. [PMID: 35989549 PMCID: PMC10086847 DOI: 10.1111/febs.16596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/22/2022] [Accepted: 08/15/2022] [Indexed: 02/05/2023]
Abstract
We exploit single-molecule tracking and optical single channel recording in droplet interface bilayers to resolve the assembly pathway and pore formation of the archetypical cholesterol-dependent cytolysin nanopore, Perfringolysin O. We follow the stoichiometry and diffusion of Perfringolysin O complexes during assembly with 60 ms temporal resolution and 20 nm spatial precision. Our results suggest individual nascent complexes can insert into the lipid membrane where they continue active assembly. Overall, these data support a model of stepwise irreversible assembly dominated by monomer addition, but with infrequent assembly from larger partial complexes.
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Affiliation(s)
| | - Carina Monico
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordUK
- Department of ChemistryKing's College LondonUK
| | - Eve E. Weatherill
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordUK
- Department of ChemistryKing's College LondonUK
| | - Robert J. Gilbert
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordUK
| | - Alejandro P. Heuck
- Departments of Biochemistry and Molecular BiologyUniversity of MassachusettsAmherstMAUSA
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49
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Shin S, Hyun K, Lee J, Joo D, Kulikowicz T, Bohr V, Kim J, Hohng S. Werner syndrome protein works as a dimer for unwinding and replication fork regression. Nucleic Acids Res 2022; 51:337-348. [PMID: 36583333 PMCID: PMC9841404 DOI: 10.1093/nar/gkac1200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/31/2022] Open
Abstract
The determination of the oligomeric state of functional enzymes is essential for the mechanistic understanding of their catalytic activities. RecQ helicases have diverse biochemical activities, but it is still unclear how their activities are related to their oligomeric states. We use single-molecule multi-color fluorescence imaging to determine the oligomeric states of Werner syndrome protein (WRN) during its unwinding and replication fork regression activities. We reveal that WRN binds to a forked DNA as a dimer, and unwinds it without any change of its oligomeric state. In contrast, WRN binds to a replication fork as a tetramer, and is dimerized during activation of replication fork regression. By selectively inhibiting the helicase activity of WRN on specific strands, we reveal how the active dimers of WRN distinctly use the energy of ATP hydrolysis for repetitive unwinding and replication fork regression.
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Affiliation(s)
| | | | - Jinwoo Lee
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
| | - Dongwon Joo
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
| | - Tomasz Kulikowicz
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vilhelm A Bohr
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sungchul Hohng
- To whom correspondence should be addressed. Tel: +82 2 880 6593;
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50
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Liu Y, Bafaro EM, Cowan AE, Dempski RE. The transmembrane domains mediate oligomerization of the human ZIP4 transporter in vivo. Sci Rep 2022; 12:21083. [PMID: 36473915 PMCID: PMC9727157 DOI: 10.1038/s41598-022-24782-6] [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: 07/19/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The human (h) ZIP4 is a plasma membrane transporter that functions to increase cytosolic zinc levels. hZIP4 encodes eight transmembrane domains and a large extracellular domain (ECD). This ECD is cleaved from the holo-transporter when cells are zinc-deficient. At the same time, mutations in the ECD can result in the zinc-deficiency disease Acrodermatitis enteropathica. Previously, it was shown that hZIP4's ECD is comprised of two structurally independent subdomains where contacts between the ECD monomeric units are centered at the PAL motif. These results lead to the hypothesis that ZIP4-ECD is essential to the dimerization of the holo-transporter. To test this hypothesis, we used Fluorescence Correlation Spectroscopy (FCS) to quantify the oligomeric state of full-length hZIP4 and hZIP4 lacking the ECD domain, each tagged with eGFP. Inspection of our experimental results demonstrate that both the full-length and truncated hZIP4 is a dimer when expressed in HEK293 cells. Parallel functional experiments demonstrate that the Km and Vmax for truncated and full-length hZIP4/eGFP are similar. Determining that truncated hZIP4/eGFP forms a dimer is a crucial step for understanding the function of the hZIP4-ECD, which provides more insight into how the diseases related to hZIP4 protein.
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Affiliation(s)
- Yuting Liu
- grid.268323.e0000 0001 1957 0327Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609 USA
| | - Elizabeth M. Bafaro
- grid.268323.e0000 0001 1957 0327Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609 USA
| | - Ann E. Cowan
- grid.63054.340000 0001 0860 4915Department of Molecular Biology and Biophysics and Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT 06030 USA
| | - Robert E. Dempski
- grid.268323.e0000 0001 1957 0327Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609 USA
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