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Denisov IG, Sligar SG. Nanodiscs for the study of membrane proteins. Curr Opin Struct Biol 2024; 87:102844. [PMID: 38795563 PMCID: PMC11283964 DOI: 10.1016/j.sbi.2024.102844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/28/2024]
Abstract
Nanodiscs represent a versatile tool for studies of membrane proteins and protein-membrane interactions under native-like conditions. Multiple variations of the Nanodisc platform, as well as new experimental methods, have been recently developed to understand various aspects of structure, dynamics and functional properties of systems involved in signaling, transport, blood coagulation and many other critically important processes. In this mini-review, we focus on some of these exciting recent developments that utilize the Nanodisc platform.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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Zhang J, Liu B, Chen H, Zhang L, Jiang X. Application and Method of Surface Plasmon Resonance Technology in the Preparation and Characterization of Biomedical Nanoparticle Materials. Int J Nanomedicine 2024; 19:7049-7069. [PMID: 39011388 PMCID: PMC11249113 DOI: 10.2147/ijn.s468695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
Surface Plasmon Resonance (SPR) technology, as a powerful analytical tool, plays a crucial role in the preparation, performance evaluation, and biomedical applications of nanoparticles due to its real-time, label-free, and highly sensitive detection capabilities. In the nanoparticle preparation process, SPR technology can monitor synthesis reactions and surface modifications in real-time, optimizing preparation techniques and conditions. SPR enables precise measurement of interactions between nanoparticles and biomolecules, including binding affinities and kinetic parameters, thereby assessing nanoparticle performance. In biomedical applications, SPR technology is extensively used in the study of drug delivery systems, biomarker detection for disease diagnosis, and nanoparticle-biomolecule interactions. This paper reviews the latest advancements in SPR technology for nanoparticle preparation, performance evaluation, and biomedical applications, discussing its advantages and challenges in biomedical applications, and forecasting future development directions.
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Affiliation(s)
- Jingyao Zhang
- Core Facilities of West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Beibei Liu
- Core Facilities of West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Hongying Chen
- Core Facilities of West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Lingshu Zhang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xia Jiang
- Division of Biliary Tract Surgery, Department of General Surgery and Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
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Baskakova KO, Kuzmichev PK, Karbyshev MS. Advanced applications of Nanodiscs-based platforms for antibodies discovery. Biophys Chem 2024; 313:107290. [PMID: 39002246 DOI: 10.1016/j.bpc.2024.107290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
Due to their fundamental biological importance, membrane proteins (MPs) are attractive targets for drug discovery, with cell surface receptors, transporters, ion channels, and membrane-bound enzymes being of particular interest. However, due to numerous challenges, these proteins present underutilized opportunities for discovering biotherapeutics. Antibodies hold the promise of exquisite specificity and adaptability, making them the ideal candidates for targeting complex membrane proteins. They can target specific conformations of a particular membrane protein and can be engineered into various formats. Generating specific and effective antibodies targeting these proteins is no easy task due to several factors. The antigen's design, antibody-generation strategies, lead optimization technologies, and antibody modalities can be modified to tackle these challenges. The rational employment of cutting-edge lipid nanoparticle systems for retrieving the membrane antigen has been successfully implemented to simplify the mechanism-based therapeutic antibody discovery approach. Despite the highlighted MP production challenges, this review unequivocally underscores the advantages of targeting complex membrane proteins with antibodies and designing membrane protein antigens. Selected examples of lipid nanoparticle success have been illustrated, emphasizing the potential of therapeutic antibody discovery in this regard. With further research and development, we can overcome these challenges and unlock the full potential of therapeutic antibodies directed to target complex MPs.
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Affiliation(s)
- Kristina O Baskakova
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation
| | - Pavel K Kuzmichev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudniy, Russian Federation
| | - Mikhail S Karbyshev
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation; Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, Moscow, Russian Federation.
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Henze E, Ehrlich JJ, Robertson JL, Kawate T. The C-terminal activating domain promotes Panx1 channel opening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598903. [PMID: 38915727 PMCID: PMC11195165 DOI: 10.1101/2024.06.13.598903] [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
Pannexin 1 (Panx1) constitutes a large pore channel responsible for the release of ATP from apoptotic cells. Strong evidence indicates that caspase-mediated cleavage of the C-terminus promotes the opening of the Panx1 channel by unplugging the pore. However, this simple pore-plugging mechanism alone cannot account for the observation that a Panx1 construct ending before the caspase cleavage site remains closed. Here, we show that a helical region located immediately before the caspase cleavage site, referred to as the "C-terminal activating domain (CAD)," plays a pivotal role in facilitating Panx1 activation. Electrophysiology and mutagenesis studies uncovered that two conserved leucine residues within the CAD plays a pivotal role. Cryo-EM analysis of the construct ending before reaching the CAD demonstrated that the N-terminus extends into an intracellular pocket. In contrast, the construct including the CAD revealed that this domain occupies the intracellular pocket, causing the N-terminus to flip upward within the pore. Analysis of electrostatic free energy landscape in the closed conformation indicated that the intracellular side of the ion permeation pore may be occupied by anions like ATP, creating an electrostatic barrier for anions attempting to permeate the pore. When the N-terminus flips up, it diminishes the positively charged surface, thereby reducing the drive to accumulate anions inside the pore. This dynamic change in the electrostatic landscape likely contributes to the selection of permeant ions. Collectively, these experiments put forth a novel mechanism in which C-terminal cleavage liberates the CAD, causing the repositioning of the N-terminus to promote Panx1 channel opening.
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Affiliation(s)
- Erik Henze
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Janice L. Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Toshimitsu Kawate
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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Young JW, Pfitzner E, van Wee R, Kirschbaum C, Kukura P, Robinson CV. Characterization of membrane protein interactions by peptidisc-mediated mass photometry. iScience 2024; 27:108785. [PMID: 38303728 PMCID: PMC10831248 DOI: 10.1016/j.isci.2024.108785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Membrane proteins perform numerous critical functions in the cell, making many of them primary drug targets. However, their preference for a lipid environment makes them challenging to study using established solution-based methods. Here, we show that peptidiscs, a recently developed membrane mimetic, provide an ideal platform to study membrane proteins and their interactions with mass photometry (MP) in detergent-free conditions. The mass resolution for membrane protein complexes is similar to that achievable with soluble proteins owing to the low carrier heterogeneity. Using the ABC transporter BtuCD, we show that MP can quantify interactions between peptidisc-reconstituted membrane protein receptors and their soluble protein binding partners. Using the BAM complex, we further show that MP reveals interactions between a membrane protein receptor and a bactericidal antibody. Our results highlight the utility of peptidiscs for membrane protein characterization in detergent-free solution and provide a rapid and powerful platform for quantifying membrane protein interactions.
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Affiliation(s)
- John William Young
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Emanuel Pfitzner
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Raman van Wee
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Carla Kirschbaum
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Philipp Kukura
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Wu YL, Yang AH, Chiu YH. Recent advances in the structure and activation mechanisms of metabolite-releasing Pannexin 1 channels. Biochem Soc Trans 2023; 51:1687-1699. [PMID: 37622532 DOI: 10.1042/bst20230038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
Pannexin 1 (PANX1) is a widely expressed large-pore ion channel located in the plasma membrane of almost all vertebrate cells. It possesses a unique ability to act as a conduit for both inorganic ions (e.g. potassium or chloride) and bioactive metabolites (e.g. ATP or glutamate), thereby activating varying signaling pathways in an autocrine or paracrine manner. Given its crucial role in cell-cell interactions, the activity of PANX1 has been implicated in maintaining homeostasis of cardiovascular, immune, and nervous systems. Dysregulation of PANX1 has also been linked to numerous diseases, such as ischemic stroke, seizure, and inflammatory disorders. Therefore, the mechanisms underlying different modes of PANX1 activation and its context-specific channel properties have gathered significant attention. In this review, we summarize the roles of PANX1 in various physiological processes and diseases, and analyze the accumulated lines of evidence supporting diverse molecular mechanisms associated with different PANX1 activation modalities. We focus on examining recent discoveries regarding PANX1 regulations by reversible post-translational modifications, elevated intracellular calcium concentration, and protein-protein interactions, as well as by irreversible cleavage of its C-terminal tail. Additionally, we delve into the caveats in the proposed PANX1 gating mechanisms and channel open-closed configurations by critically analyzing the structural insights derived from cryo-EM studies and the unitary properties of PANX1 channels. By doing so, we aim to identify potential research directions for a better understanding of the functions and regulations of PANX1 channels.
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Affiliation(s)
- Yi-Ling Wu
- Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 300044, Taiwan
| | - Ai-Hsing Yang
- Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 300044, Taiwan
| | - Yu-Hsin Chiu
- Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 300044, Taiwan
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 300044, Taiwan
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Harrison PJ, Vecerkova T, Clare DK, Quigley A. A review of the approaches used to solve sub-100 kDa membrane proteins by cryo-electron microscopy. J Struct Biol 2023; 215:107959. [PMID: 37004781 DOI: 10.1016/j.jsb.2023.107959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/07/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Membrane proteins (MPs) are essential components of all biological membranes, contributing to key cellular functions that include signalling, molecular transport and energy metabolism. Consequently, MPs are important biomedical targets for therapeutics discovery. Despite hardware and software developments in cryo-electron microscopy, as well as MP sample preparation, MPs smaller than 100 kDa remain difficult to study structurally. Significant investment is required to overcome low levels of naturally abundant protein, MP hydrophobicity as well as conformational and compositional instability. Here we have reviewed the sample preparation approaches that have been taken to successfully express, purify and prepare small MPs for analysis by cryo-EM (those with a total solved molecular weight of under 100 kDa), as well as examining the differing approaches towards data processing and ultimately obtaining a structural solution. We highlight common challenges at each stage in the process as well as strategies that have been developed to overcome these issues. Finally, we discuss future directions and opportunities for the study of sub-100 kDa membrane proteins by cryo-EM.
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