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Sun W, Huang A, Wen S, Yang R, Liu X. Temporal Assessment of Protein Stability in Dried Blood Spots. J Proteome Res 2024. [PMID: 38950347 DOI: 10.1021/acs.jproteome.4c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The use of protein biomarkers in blood for clinical settings is limited by the cost and accessibility of traditional venipuncture sampling. The dried blood spot (DBS) technique offers a less invasive and more accessible alternative. However, protein stability in DBS has not been well evaluated. Herein, we deployed a quantitative LC-MS/MS system to construct proteomic atlases of whole blood, DBSs, plasma, and blood cells. Approximately 4% of detected proteins' abundance was significantly altered during blood drying into blood spots, with overwhelming disturbances in cytoplasmic fraction. We also reported a novel finding suggesting a decrease in the level of membrane/cytoskeletal proteins (SLC4A1, RHAG, DSC1, DSP, and JUP) and an increase in the level of proteins (ATG3, SEC14L4, and NRBP1) related to intracellular trafficking. Furthermore, we identified 19 temporally dynamic proteins in DBS samples stored at room temperature for up to 6 months. There were three declined cytoskeleton-related proteins (RDX, SH3BGRL3, and MYH9) and four elevated proteins (XPO7, RAN, SLC2A1, and SLC29A1) involved in cytoplasmic transport as representatives. The instability was governed predominantly by hydrophilic proteins and enhanced significantly with an increasing storage time. Our analyses provide comprehensive knowledge of both short- and long-term storage stability of DBS proteins, forming the foundation for the widespread use of DBS in clinical proteomics and other analytical applications.
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Affiliation(s)
- Weifen Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, Jiangsu Province, China
| | - Shubo Wen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, Jiangsu Province, China
| | - Ruicong Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, Yunnan Province, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
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2
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Zhekova HR, Ramirez Echemendía DP, Sejdiu BI, Pushkin A, Tieleman DP, Kurtz I. Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins. Biophys J 2024; 123:1705-1721. [PMID: 38760929 PMCID: PMC11214021 DOI: 10.1016/j.bpj.2024.05.013] [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: 07/31/2023] [Revised: 04/09/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024] Open
Abstract
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO3-, CO32-, Cl-, Na+, K+, NH3, and H+, which are necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl-/HCO3- exchanger) and NBCe1 (Na+-CO32-cotransporter). Previous computational studies of the outward-facing state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed coarse-grained and atomistic molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1, and NDCBE (an Na+-CO32-/Cl- exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin. The recently resolved inward-facing state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, phosphatidylcholine, and sphingomyelin in the three studied proteins, and their potential roles in the SLC4 transport function, conformational transition, and protein dimerization are discussed.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Daniel P Ramirez Echemendía
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Alexander Pushkin
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - D Peter Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Ira Kurtz
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Brain Research Institute, University of California, Los Angeles, Los Angeles, California.
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Lv H, Cao Y, Zhu J, Liang Q. Molecular Insights into the Effect of Cholesterol on the Binding of Bicarbonate Ions in Band 3 Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10908-10915. [PMID: 38739034 DOI: 10.1021/acs.langmuir.4c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Band 3, or anion exchanger 1 (AE1), is one of the indispensable transmembrane proteins involved in the effective respiratory process of the human body and is primarily responsible for the exchange of bicarbonate and chloride anions across the plasma membrane of erythrocyte. However, the molecular mechanism of ion transport of Band 3 is not completely understood, yet. In this work, we systematically investigate the key binding sites of bicarbonate ions in Band 3 and the impact of cholesterol (CHOL) in lipid bilayers on bicarbonate ion binding using all-atom molecular dynamics (MD) simulations. We examine the dynamics of interactions of bicarbonate ions with Band 3 in the microsecond time scale and calculate the binding free energy of the anion in Band 3. The results indicate that the residue R730 of Band 3 is the most probable binding site for bicarbonate ions. CHOL enhances the bicarbonate ion binding by influencing the conformational stability of Band 3 and compressing the volume of the Band 3 cavity. These findings provide some insights into the bicarbonate ion binding in Band 3 and are helpful for understanding the anion exchange of Band 3.
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Affiliation(s)
- Haiying Lv
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua 321004, China
| | - Yu Cao
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua 321004, China
| | - Jin Zhu
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua 321004, China
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua 321004, China
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4
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Trudel G, Stratis D, Rocheleau L, Pelchat M, Laneuville O. Transcriptomic evidence of erythropoietic adaptation from the International Space Station and from an Earth-based space analog. NPJ Microgravity 2024; 10:55. [PMID: 38740795 DOI: 10.1038/s41526-024-00400-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Space anemia affects astronauts and the underlying molecular alterations remain unknown. We evaluated the response of erythropoiesis-modulating genes to spaceflight through the analysis of leukocyte transcriptomes from astronauts during long-duration spaceflight and from an Earth model of microgravity. Differential expression analysis identified 50 genes encoding ribosomal proteins with reduced expression at the transition to bed rest and increased during the bed rest phase; a similar trend was observed in astronauts. Additional genes associated with anemia (15 genes), erythrocyte maturation (3 genes), and hemoglobin (6 genes) were down-regulated during bed rest and increased during reambulation. Transcript levels of the erythropoiesis transcription factor GATA1 and nine of most enriched erythrocyte proteins increased at reambulation after bed rest and at return to Earth from space. Dynamic changes of the leukocyte transcriptome composition while in microgravity and during reambulation supported an erythropoietic modulation accompanying the hemolysis of space anemia and of immobility-induced anemia.
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Affiliation(s)
- Guy Trudel
- Bone and Joint Research Laboratory, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.
- Department of Medicine, Division of Physiatry, Faculty of Medicine, University of Ottawa, 505 Smyth Road, Ottawa, ON, K1H 8M2, Canada.
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
| | - Daniel Stratis
- Department of Biology, Faculty of Science, University of Ottawa, 30 Marie Curie Private Drive, Ottawa, ON, K1N 6N5, Canada.
| | - Lynda Rocheleau
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
| | - Odette Laneuville
- Bone and Joint Research Laboratory, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.
- Department of Biology, Faculty of Science, University of Ottawa, 30 Marie Curie Private Drive, Ottawa, ON, K1N 6N5, Canada.
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5
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Reddy KD, Rasool B, Akher FB, Kutlešić N, Pant S, Boudker O. Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569786. [PMID: 38106174 PMCID: PMC10723334 DOI: 10.1101/2023.12.03.569786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Secondary active membrane transporters harness the energy of ion gradients to concentrate their substrates. Homologous transporters evolved to couple transport to different ions in response to changing environments and needs. The bases of such diversification, and thus principles of ion coupling, are unexplored. Employing phylogenetics and ancestral protein reconstruction, we investigated sodium-coupled transport in prokaryotic glutamate transporters, a mechanism ubiquitous across life domains and critical to neurotransmitter recycling in humans. We found that the evolutionary transition from sodium-dependent to independent substrate binding to the transporter preceded changes in the coupling mechanism. Structural and functional experiments suggest that the transition entailed allosteric mutations, making sodium binding dispensable without affecting ion-binding sites. Allosteric tuning of transporters' energy landscapes might be a widespread route of their functional diversification.
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Affiliation(s)
- Krishna D. Reddy
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Burha Rasool
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Farideh Badichi Akher
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Nemanja Kutlešić
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Swati Pant
- Dept. of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Olga Boudker
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
- Howard Hughes Medical Institute, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
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6
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Jin X, Zhang Y, Wang D, Zhang X, Li Y, Wang D, Liang Y, Wang J, Zheng L, Song H, Zhu X, Liang J, Ma J, Gao J, Tong J, Shi L. Metabolite and protein shifts in mature erythrocyte under hypoxia. iScience 2024; 27:109315. [PMID: 38487547 PMCID: PMC10937114 DOI: 10.1016/j.isci.2024.109315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
As the only cell type responsible for oxygen delivery, erythrocytes play a crucial role in supplying oxygen to hypoxic tissues, ensuring their normal functions. Hypoxia commonly occurs under physiological or pathological conditions, and understanding how erythrocytes adapt to hypoxia is fundamental for exploring the mechanisms of hypoxic diseases. Additionally, investigating acute and chronic mountain sickness caused by plateaus, which are naturally hypoxic environments, will aid in the study of hypoxic diseases. In recent years, increasingly developed proteomics and metabolomics technologies have become powerful tools for studying mature enucleated erythrocytes, which has significantly contributed to clarifying how hypoxia affects erythrocytes. The aim of this article is to summarize the composition of the cytoskeleton and cytoplasmic proteins of hypoxia-altered erythrocytes and explore the impact of hypoxia on their essential functions. Furthermore, we discuss the role of microRNAs in the adaptation of erythrocytes to hypoxia, providing new perspectives on hypoxia-related diseases.
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Affiliation(s)
- Xu Jin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yingnan Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Ding Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xiaoru Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yue Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Di Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yipeng Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jingwei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lingyue Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Haoze Song
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xu Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jing Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jinfa Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
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7
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Zheng K, Li Q, Jiang N, Zhang Y, Zheng Y, Zhang Y, Feng Y, Chen R, Sang X, Chen Q. Plasmodium falciparum selectively degrades α-spectrin of infected erythrocytes after invasion. mBio 2024; 15:e0351023. [PMID: 38470053 PMCID: PMC11005373 DOI: 10.1128/mbio.03510-23] [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: 01/08/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Remodeling the erythrocyte membrane and skeleton by the malarial parasite Plasmodium falciparum is closely associated with intraerythrocytic development. However, the mechanisms underlying this association remain unclear. In this study, we present evidence that erythrocytic α-spectrin, but not β-spectrin, was dynamically ubiquitinated and progressively degraded during the intraerythrocytic development of P. falciparum, from the ring to the schizont stage. We further observed an upregulated expression of P. falciparum phosphatidylinositol 3-kinase (PfPI3K) in the infected red blood cells during the intraerythrocytic development of the parasite. The data indicated that PfPI3K phosphorylated and activated erythrocytic ubiquitin-protein ligase, leading to increased α-spectrin ubiquitination and degradation during P. falciparum development. We further revealed that inhibition of the activity of PfPI3K impaired P. falciparum development in vitro and Plasmodium berghei infectivity in mice. These findings collectively unveil an important mechanism of PfPI3K-ubiquitin-mediated degradation of α-spectrin during the intraerythrocytic development of Plasmodium species. Proteins in the PfPI3K regulatory pathway are novel targets for effective treatment of severe malaria. IMPORTANCE Plasmodium falciparum is the causative agent of severe malaria that causes millions of deaths globally. The parasite invades human red blood cells and induces a cascade of alterations in erythrocytes for development and proliferation. Remodeling the host erythrocytic cytoskeleton is a necessary process during parasitization, but its regulatory mechanisms remain to be elucidated. In this study, we observed that erythrocytic α-spectrin is selectively degraded after P. falciparum invasion, while β-spectrin remained intact. We found that the α-spectrin chain was profoundly ubiquitinated by E3 ubiquitin ligase and degraded by the 26S proteasome. E3 ubiquitin ligase activity was regulated by P. falciparum phosphatidylinositol 3-kinase (PfPI3K) signaling. Additionally, blocking the PfPI3K-ubiquitin-proteasome pathway in P. falciparum-infected red blood cells reduced parasite proliferation and infectivity. This study deepens our understanding of the regulatory mechanisms of host and malarial parasite interactions and paves the way for the exploration of novel antimalarial drugs.
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Affiliation(s)
- Kexin Zheng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
- Engineering Research Center of Food Fermentation Technology, College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Qilong Li
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ning Jiang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Yanxin Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Yuxin Zheng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Yiwei Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ying Feng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ran Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Xiaoyu Sang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
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8
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Nogales E, Mahamid J. Bridging structural and cell biology with cryo-electron microscopy. Nature 2024; 628:47-56. [PMID: 38570716 PMCID: PMC11211576 DOI: 10.1038/s41586-024-07198-2] [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: 07/18/2023] [Accepted: 02/13/2024] [Indexed: 04/05/2024]
Abstract
Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, Institute for Quantitative Biomedicine, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Berkeley, CA, USA.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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9
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Newstead S. Future opportunities in solute carrier structural biology. Nat Struct Mol Biol 2024; 31:587-590. [PMID: 38637662 DOI: 10.1038/s41594-024-01271-0] [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: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 04/20/2024]
Abstract
Solute carriers (SLCs) control the flow of small molecules and ions across biological membranes. Over the last 20 years, the pace of research in SLC biology has accelerated markedly, opening new opportunities to treat metabolic diseases, cancer and neurological disorders. Recently, new families of atypical SLCs, with roles in organelle biology, metabolite signaling and trafficking, have expanded their roles in the cell. This Perspective discusses work leading to current advances and the emerging opportunities to target and modulate SLCs to uncover new biology and treat human disease.
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Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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10
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Floch A, Galochkina T, Pirenne F, Tournamille C, de Brevern AG. Molecular dynamics of the human RhD and RhAG blood group proteins. Front Chem 2024; 12:1360392. [PMID: 38566898 PMCID: PMC10985258 DOI: 10.3389/fchem.2024.1360392] [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: 12/22/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Blood group antigens of the RH system (formerly known as "Rhesus") play an important role in transfusion medicine because of the severe haemolytic consequences of antibodies to these antigens. No crystal structure is available for RhD proteins with its partner RhAG, and the precise stoichiometry of the trimer complex remains unknown. Methods: To analyse their structural properties, the trimers formed by RhD and/or RhAG subunits were generated by protein modelling and molecular dynamics simulations were performed. Results: No major differences in structural behaviour were found between trimers of different compositions. The conformation of the subunits is relatively constant during molecular dynamics simulations, except for three large disordered loops. Discussion: This work makes it possible to propose a reasonable stoichiometry and demonstrates the potential of studying the structural behaviour of these proteins to investigate the hundreds of genetic variants relevant to transfusion medicine.
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Affiliation(s)
- Aline Floch
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
| | - France Pirenne
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Christophe Tournamille
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
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11
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Burke SM, Avstrikova M, Noviello CM, Mukhtasimova N, Changeux JP, Thakur GA, Sine SM, Cecchini M, Hibbs RE. Structural mechanisms of α7 nicotinic receptor allosteric modulation and activation. Cell 2024; 187:1160-1176.e21. [PMID: 38382524 PMCID: PMC10950261 DOI: 10.1016/j.cell.2024.01.032] [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: 08/31/2023] [Revised: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion channel that plays an important role in cholinergic signaling throughout the nervous system. Its unique physiological characteristics and implications in neurological disorders and inflammation make it a promising but challenging therapeutic target. Positive allosteric modulators overcome limitations of traditional α7 agonists, but their potentiation mechanisms remain unclear. Here, we present high-resolution structures of α7-modulator complexes, revealing partially overlapping binding sites but varying conformational states. Structure-guided functional and computational tests suggest that differences in modulator activity arise from the stable rotation of a channel gating residue out of the pore. We extend the study using a time-resolved cryoelectron microscopy (cryo-EM) approach to reveal asymmetric state transitions for this homomeric channel and also find that a modulator with allosteric agonist activity exploits a distinct channel-gating mechanism. These results define mechanisms of α7 allosteric modulation and activation with implications across the pentameric receptor superfamily.
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Affiliation(s)
- Sean M Burke
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariia Avstrikova
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, 67081 Strasbourg Cedex, France
| | - Colleen M Noviello
- Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nuriya Mukhtasimova
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Jean-Pierre Changeux
- Neuroscience Department, Institut Pasteur, Collège de France, 75015 Paris, France
| | - Ganesh A Thakur
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Steven M Sine
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, 67081 Strasbourg Cedex, France.
| | - Ryan E Hibbs
- Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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12
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Zhang W, Ding D, Lu Y, Chen H, Jiang P, Zuo P, Wang G, Luo J, Yin Y, Luo J, Yin Y. Structural and functional insights into the lipid regulation of human anion exchanger 2. Nat Commun 2024; 15:759. [PMID: 38272905 PMCID: PMC10810954 DOI: 10.1038/s41467-024-44966-0] [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] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Anion exchanger 2 (AE2) is an electroneutral Na+-independent Cl-/HCO3- exchanger belongs to the SLC4 transporter family. The widely expressed AE2 participates in a variety of physiological processes, including transepithelial acid-base secretion and osteoclastogenesis. Both the transmembrane domains (TMDs) and the N-terminal cytoplasmic domain (NTD) are involved in regulation of AE2 activity. However, the regulatory mechanism remains unclear. Here, we report a 3.2 Å cryo-EM structure of the AE2 TMDs in complex with PIP2 and a 3.3 Å full-length mutant AE2 structure in the resting state without PIP2. We demonstrate that PIP2 at the TMD dimer interface is involved in the substrate exchange process. Mutation in the PIP2 binding site leads to the displacement of TM7 and further stabilizes the interaction between the TMD and the NTD. Reduced substrate transport activity and conformation similar to AE2 in acidic pH indicating the central contribution of PIP2 to the function of AE2.
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Affiliation(s)
- Weiqi Zhang
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Dian Ding
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yishuo Lu
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Hongyi Chen
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Peijun Jiang
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Guangxi Wang
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Juan Luo
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Yue Yin
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jianyuan Luo
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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13
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Wang L, Hoang A, Gil-Iturbe E, Laganowsky A, Quick M, Zhou M. Mechanism of anion exchange and small-molecule inhibition of pendrin. Nat Commun 2024; 15:346. [PMID: 38184688 PMCID: PMC10771415 DOI: 10.1038/s41467-023-44612-1] [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: 06/24/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024] Open
Abstract
Pendrin (SLC26A4) is an anion exchanger that mediates bicarbonate (HCO3-) exchange for chloride (Cl-) and is crucial for maintaining pH and salt homeostasis in the kidney, lung, and cochlea. Pendrin also exports iodide (I-) in the thyroid gland. Pendrin mutations in humans lead to Pendred syndrome, causing hearing loss and goiter. Inhibition of pendrin is a validated approach for attenuating airway hyperresponsiveness in asthma and for treating hypertension. However, the mechanism of anion exchange and its inhibition by drugs remains poorly understood. We applied cryo-electron microscopy to determine structures of pendrin from Sus scrofa in the presence of either Cl-, I-, HCO3- or in the apo-state. The structures reveal two anion-binding sites in each protomer, and functional analyses show both sites are involved in anion exchange. The structures also show interactions between the Sulfate Transporter and Anti-Sigma factor antagonist (STAS) and transmembrane domains, and mutational studies suggest a regulatory role. We also determine the structure of pendrin in a complex with niflumic acid (NFA), which uncovers a mechanism of inhibition by competing with anion binding and impeding the structural changes necessary for anion exchange. These results reveal directions for understanding the mechanisms of anion selectivity and exchange and their regulations by the STAS domain. This work also establishes a foundation for analyzing the pathophysiology of mutations associated with Pendred syndrome.
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Affiliation(s)
- Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony Hoang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Area Neuroscience - Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
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14
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Remigante A, Spinelli S, Patanè GT, Barreca D, Straface E, Gambardella L, Bozzuto G, Caruso D, Falliti G, Dossena S, Marino A, Morabito R. AAPH-induced oxidative damage reduced anion exchanger 1 (SLC4A1/AE1) activity in human red blood cells: protective effect of an anthocyanin-rich extract. Front Physiol 2023; 14:1303815. [PMID: 38111898 PMCID: PMC10725977 DOI: 10.3389/fphys.2023.1303815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/22/2023] [Indexed: 12/20/2023] Open
Abstract
Introduction: During their lifespan in the bloodstream, red blood cells (RBCs) are exposed to multiple stressors, including increased oxidative stress, which can affect their morphology and function, thereby contributing to disease. Aim: This investigation aimed to explore the cellular and molecular mechanisms related to oxidative stress underlying anion exchanger 1 activity (band 3, SLC4A1/AE1) in human RBCs. To achieve this aim, the relationship between RBC morphology and functional and metabolic activity has been explored. Moreover, the potential protective effect of an anthocyanin-enriched fraction extracted from Callistemon citrinus flowers was studied. Methods: Cellular morphology, parameters of oxidative stress, as well as the anion exchange capability of band 3 have been analyzed in RBCs treated for 1 h with 50 mM of the pro-oxidant 2,2'-azobis (2-methylpropionamide)-dihydrochloride (AAPH). Before or after the oxidative insult, subsets of cells were exposed to 0.01 μg/mL of an anthocyanin-enriched fraction for 1 h. Results: Exposure to AAPH caused oxidative stress, exhaustion of reduced glutathione, and over-activation of the endogenous antioxidant machinery, resulting in morphological alterations of RBCs, specifically the formation of acanthocytes, increased lipid peroxidation and oxidation of proteins, as well as abnormal distribution and hyper-phosphorylation of band 3. Expected, oxidative stress was also associated with a decreased band 3 ion transport activity and an increase of oxidized haemoglobin, which led to abnormal clustering of band 3. Exposure of cells to the anthocyanin-enriched fraction prior to, but not after, oxidative stress efficiently counteracted oxidative stress-related alterations. Importantly, protection of band3 function from oxidative stress could only be achieved in intact cells and not in RBC ghosts. Conclusion: These findings contribute a) to clarify oxidative stress-related physiological and biochemical alterations in human RBCs, b) propose anthocyanins as natural antioxidants to neutralize oxidative stress-related modifications, and 3) suggest that cell integrity, and therefore a cytosolic component, is required to reverse oxidative stress-related pathophysiological derangements in human mature RBCs.
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Affiliation(s)
- Alessia Remigante
- Department of Chemical Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Sara Spinelli
- Department of Chemical Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Giuseppe Tancredi Patanè
- Department of Chemical Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Davide Barreca
- Department of Chemical Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Elisabetta Straface
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucrezia Gambardella
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppina Bozzuto
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Daniele Caruso
- Complex Operational Unit of Clinical Pathology of Papardo Hospital, Messina, Italy
| | - Giuseppe Falliti
- Complex Operational Unit of Clinical Pathology of Papardo Hospital, Messina, Italy
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Angela Marino
- Department of Chemical Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Rossana Morabito
- Department of Chemical Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
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15
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Christensen RD, Bahr TM, Ilstrup SJ, Dizon-Townson DS. Alloimmune hemolytic disease of the fetus and newborn: genetics, structure, and function of the commonly involved erythrocyte antigens. J Perinatol 2023; 43:1459-1467. [PMID: 37848604 DOI: 10.1038/s41372-023-01785-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Hemolytic disease of the fetus and newborn (HDFN) can occur when a pregnant woman has antibody directed against an erythrocyte surface antigen expressed by her fetus. This alloimmune disorder is restricted to situations where transplacental transfer of maternal antibody to the fetus occurs, and binds to fetal erythrocytes, and significantly shortens the red cell lifespan. The pathogenesis of HDFN involves maternal sensitization to erythrocyte "non-self" antigens (those she does not express). Exposure of a woman to a non-self-erythrocyte antigen principally occurs through either a blood transfusion or a pregnancy where paternally derived erythrocyte antigens, expressed by her fetus, enter her circulation, and are immunologically recognized as foreign. This review focuses on the genetics, structure, and function of the erythrocyte antigens that are most frequently involved in the pathogenesis of alloimmune HDFN. By providing this information we aim to convey useful insights to clinicians caring for patients with this condition.
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Affiliation(s)
- Robert D Christensen
- Division of Neonatology, Department of Pediatrics, University of Utah Health, Salt Lake City, UT, USA.
- Obstetric and Neonatal Operations, Intermountain Health, Salt Lake City, UT, USA.
| | - Timothy M Bahr
- Division of Neonatology, Department of Pediatrics, University of Utah Health, Salt Lake City, UT, USA
- Obstetric and Neonatal Operations, Intermountain Health, Salt Lake City, UT, USA
| | - Sarah J Ilstrup
- Intermountain Health Transfusion Services and Department of Pathology, Intermountain Medical Center, Murray, UT, USA
| | - Donna S Dizon-Townson
- Division of Neonatology, Department of Pediatrics, University of Utah Health, Salt Lake City, UT, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Utah Health, and Intermountain Health, Salt Lake City, UT, USA
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16
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Häuser F, Rossmann H, Adenaeuer A, Shrestha A, Marandiuc D, Paret C, Faber J, Lackner KJ, Lämmle B, Beck O. Hereditary Spherocytosis: Can Next-Generation Sequencing of the Five Most Frequently Affected Genes Replace Time-Consuming Functional Investigations? Int J Mol Sci 2023; 24:17021. [PMID: 38069343 PMCID: PMC10707146 DOI: 10.3390/ijms242317021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Congenital defects of the erythrocyte membrane are common in northern Europe and all over the world. The resulting diseases, for example, hereditary spherocytosis (HS), are often underdiagnosed, partly due to their sometimes mild and asymptomatic courses. In addition to a broad clinical spectrum, this is also due to the occasionally complex diagnostics that are not available to every patient. To test whether next-generation sequencing (NGS) could replace time-consuming spherocytosis-specific functional tests, 22 consecutive patients with suspected red cell membranopathy underwent functional blood tests. We were able to identify the causative genetic defect in all patients with suspected HS who underwent genetic testing (n = 17). The sensitivity of the NGS approach, which tests five genes (ANK1 (gene product: ankyrin1), EPB42 (erythrocyte membrane protein band4.2), SLC4A1 (band3), SPTA1 (α-spectrin), and SPTB (β-spectrin)), was 100% (95% confidence interval: 81.5-100.0%). The major advantage of genetic testing in the paediatric setting is the small amount of blood required (<200 µL), and compared to functional assays, sample stability is not an issue. The combination of medical history, basic laboratory parameters, and an NGS panel with five genes is sufficient for diagnosis in most cases. Only in rare cases, a more comprehensive functional screening is required.
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Affiliation(s)
- Friederike Häuser
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Heidi Rossmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Anke Adenaeuer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Annette Shrestha
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Dana Marandiuc
- Transfusion Center, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Claudia Paret
- Department of Pediatric Hematology, Oncology & Hemostaseology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Jörg Faber
- Department of Pediatric Hematology, Oncology & Hemostaseology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Karl J. Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Bernhard Lämmle
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
- Haemostasis Research Unit, University College London, London WC1E6BT, UK
| | - Olaf Beck
- Department of Pediatric Hematology, Oncology & Hemostaseology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
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17
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Ansell TB, Song W, Coupland CE, Carrique L, Corey RA, Duncan AL, Cassidy CK, Geurts MMG, Rasmussen T, Ward AB, Siebold C, Stansfeld PJ, Sansom MSP. LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins. Nat Commun 2023; 14:7774. [PMID: 38012131 PMCID: PMC10682427 DOI: 10.1038/s41467-023-43392-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: 07/08/2022] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures. The pipeline integrates the implementation and analysis of multi-scale MD simulations for identification, ranking and refinement of lipid binding poses which superpose onto cryo-EM map densities. Thus, LipIDens enables direct integration of experimental and computational structural approaches to facilitate the interpretation of lipid-like cryo-EM densities and to reveal the molecular identities of protein-lipid interactions within a bilayer environment. We demonstrate this by application of our open-source LipIDens code to ten diverse membrane protein structures which exhibit lipid-like densities.
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Affiliation(s)
- T Bertie Ansell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- MSD R&D Innovation Centre, 120 Moorgate, London, EC2M 6UR, UK
| | - Claire E Coupland
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Loic Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Chemistry, Aarhus University, Lagelsandsgade 140, 8000, Aarhus C, Denmark
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Maxwell M G Geurts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tim Rasmussen
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, Haus D15, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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18
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Stewart GW, Gibson JS, Rees DC. The cation-leaky hereditary stomatocytosis syndromes: A tale of six proteins. Br J Haematol 2023; 203:509-522. [PMID: 37679660 DOI: 10.1111/bjh.19093] [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: 06/07/2023] [Revised: 08/13/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
This review concerns a series of dominantly inherited haemolytic anaemias in which the membrane of the erythrocyte 'leaks' the univalent cations, compromising the osmotic stability of the cell. The majority of the conditions are explained by mutations in one of six genes, coding for multispanning membrane proteins of different structure and function. These are: RhAG, coding for an ammonium carrier; SLC4A1, coding for the band 3 anion exchanger; PIEZO1, coding for a mechanosensitive cation channel; GLUT1, coding for a glucose transporter; KCNN4, coding for an internal-calcium-activated potassium channel; and ABCB6, coding for a porphyrin transporter. This review describes the five clinical syndromes associated with genetic defects in these genes and their variable genotype/phenotype relationships.
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Affiliation(s)
- Gordon W Stewart
- Division of Medicine, Faculty of Medical Sciences, University College London, London, UK
| | - John S Gibson
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - David C Rees
- Haematological Medicine, Kings College London, London, UK
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19
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Lu Y, Zuo P, Chen H, Shan H, Wang W, Dai Z, Xu H, Chen Y, Liang L, Ding D, Jin Y, Yin Y. Structural insights into the conformational changes of BTR1/SLC4A11 in complex with PIP 2. Nat Commun 2023; 14:6157. [PMID: 37788993 PMCID: PMC10547724 DOI: 10.1038/s41467-023-41924-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023] Open
Abstract
BTR1 (SLC4A11) is a NH3 stimulated H+ (OH-) transporter belonging to the SLC4 family. Dysfunction of BTR1 leads to diseases such as congenital hereditary endothelial dystrophy (CHED) and Fuchs endothelial corneal dystrophy (FECD). However, the mechanistic basis of BTR1 activation by alkaline pH, transport activity regulation and pathogenic mutations remains elusive. Here, we present cryo-EM structures of human BTR1 in the outward-facing state in complex with its activating ligands PIP2 and the inward-facing state with the pathogenic R125H mutation. We reveal that PIP2 binds at the interface between the transmembrane domain and the N-terminal cytosolic domain of BTR1. Disruption of either the PIP2 binding site or protonation of PIP2 phosphate groups by acidic pH can transform BTR1 into an inward-facing conformation. Our results provide insights into the mechanisms of how the transport activity and conformation changes of BTR1 are regulated by PIP2 binding and interaction of TMD and NTD.
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Affiliation(s)
- Yishuo Lu
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Hongyi Chen
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Hui Shan
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Weize Wang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zonglin Dai
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | | | | | - Ling Liang
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Dian Ding
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Jin
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yuxin Yin
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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20
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Capper MJ, Yang S, Stone AC, Vatansever S, Zilberg G, Mathiharan YK, Habib R, Hutchinson K, Zhao Y, Schlessinger A, Mezei M, Osman R, Zhang B, Wacker D. Substrate binding and inhibition of the anion exchanger 1 transporter. Nat Struct Mol Biol 2023; 30:1495-1504. [PMID: 37679563 PMCID: PMC11008770 DOI: 10.1038/s41594-023-01085-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/28/2023] [Indexed: 09/09/2023]
Abstract
Anion exchanger 1 (AE1), a member of the solute carrier (SLC) family, is the primary bicarbonate transporter in erythrocytes, regulating pH levels and CO2 transport between lungs and tissues. Previous studies characterized its role in erythrocyte structure and provided insight into transport regulation. However, key questions remain regarding substrate binding and transport, mechanisms of drug inhibition and modulation by membrane components. Here we present seven cryo-EM structures in apo, bicarbonate-bound and inhibitor-bound states. These, combined with uptake and computational studies, reveal important molecular features of substrate recognition and transport, and illuminate sterol binding sites, to elucidate distinct inhibitory mechanisms of research chemicals and prescription drugs. We further probe the substrate binding site via structure-based ligand screening, identifying an AE1 inhibitor. Together, our findings provide insight into mechanisms of solute carrier transport and inhibition.
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Affiliation(s)
- Michael J Capper
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shifan Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander C Stone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sezen Vatansever
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory Zilberg
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yamuna Kalyani Mathiharan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raul Habib
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yihan Zhao
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mihaly Mezei
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Wacker
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Trueba-Gómez R, Rosenfeld-Mann F, Baptista-González HA, Domínguez-López ML, Estrada-Juárez H. Use of computational biology to compare the theoretical tertiary structures of the most common forms of RhCE and RhD. Vox Sang 2023; 118:881-890. [PMID: 37559188 DOI: 10.1111/vox.13509] [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: 01/18/2023] [Revised: 07/11/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND AND OBJECTIVES Computational biology analyses the theoretical tertiary structure of proteins and identifies the 'topological' differences between RhD and RhCE. Our aim was to identify the theoretical structural differences between the four isoforms of RhCE and RhD using computational biological tools. MATERIALS AND METHODS Physicochemical profile was determined by hydrophobicity and electrostatic potential analysis. Secondary and tertiary structures were generated using computational biology tools. The structures were evaluated and validated using Ramachandran algorithm, which calculates the single score, p-value and root mean square deviation (RMSD). Structures were overlaid on local refinement of 'RhAG-RhCE-ANK' (PBDID 7uzq) and RhAG to compare their spatial distribution within the membrane. RESULTS All proteins differed in surface area and electrostatic distance due to variations in hydrophobicity and electrostatic potential. The RMSD between RhD and RhCE was 0.46 ± 0.04 Å, and the comparison within RhCE was 0.57 ± 0.08 Å. The percentage of amino acids in the hydrophobic thickness was 50.24% for RhD while for RhCE it ranged between 73.08% and 76.68%. The RHAG hydrophobic thickness was 34.2 Å, and RhCE's hydrophobic thickness was 33.83 Å. We suggest that the C/c antigens differ exofacially at loops L1 and L2. For the E/e antigens, the difference lies in L6. By contrast, L4 is the same for all proteins except Rhce. CONCLUSION The physicochemical properties of Rh proteins made them different, although their genes are homologous. Using computational biology, we model structures with sufficient precision, similar to those obtained experimentally. An amino acid variation alters the folding of the tertiary structure and the interactions with other proteins, modifying the electrostatic environment, the spatial conformations and therefore the antigenic recognition.
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Affiliation(s)
- Rocio Trueba-Gómez
- Instituto Nacional de Perinatología "Isidro Espinosa de los Reyes", Coordinación de Hematología Perinatal, Mexico City, Mexico
- Posgrado en Ciencias Químico Biológicas, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Fany Rosenfeld-Mann
- Instituto Nacional de Perinatología "Isidro Espinosa de los Reyes", Coordinación de Hematología Perinatal, Mexico City, Mexico
| | - Hector A Baptista-González
- Instituto Nacional de Perinatología "Isidro Espinosa de los Reyes", Coordinación de Hematología Perinatal, Mexico City, Mexico
| | - María L Domínguez-López
- Posgrado en Ciencias Químico Biológicas, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Higinio Estrada-Juárez
- Instituto Nacional de Perinatología "Isidro Espinosa de los Reyes", Coordinación de Hematología Perinatal, Mexico City, Mexico
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22
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Kamegawa A, Suzuki S, Suzuki H, Nishikawa K, Numoto N, Fujiyoshi Y. Structural analysis of the water channel AQP2 by single-particle cryo-EM. J Struct Biol 2023; 215:107984. [PMID: 37315821 DOI: 10.1016/j.jsb.2023.107984] [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: 04/06/2023] [Revised: 05/19/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Water channels, which are small membrane proteins almost entirely buried in lipid membranes, are challenging research targets for single-particle cryo-electron microscopy (cryo-EM), a powerful technique routinely used to determine the structures of membrane proteins. Because the single-particle method enables structural analysis of a whole protein with flexible parts that interfere with crystallization, we have focused our efforts on analyzing water channel structures. Here, utilizing this system, we analyzed the structure of full-length aquaporin-2 (AQP2), a primary regulator of vasopressin-dependent reabsorption of water at the renal collecting ducts. The 2.9 Å resolution map revealed a cytoplasmic extension of the cryo-EM density that was presumed to be the highly flexible C-terminus at which the localization of AQP2 is regulated in the renal collecting duct cells. We also observed a continuous density along the common water pathway inside the channel pore and lipid-like molecules at the membrane interface. Observations of these constructions in the AQP2 structure analyzed without any fiducial markers (e.g., a rigidly bound antibody) indicate that single-particle cryo-EM will be useful for investigating water channels in native states as well as in complexes with chemical compounds.
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Affiliation(s)
- Akiko Kamegawa
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shota Suzuki
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hiroshi Suzuki
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kouki Nishikawa
- Joint Research Course for Advanced Biomolecular Characterization, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8501, Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
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23
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Choi W, Wu H, Yserentant K, Huang B, Cheng Y. Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM. Proc Natl Acad Sci U S A 2023; 120:e2302471120. [PMID: 37487103 PMCID: PMC10401002 DOI: 10.1073/pnas.2302471120] [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: 02/12/2023] [Accepted: 06/21/2023] [Indexed: 07/26/2023] Open
Abstract
CRISPR/Cas9-based genome engineering has revolutionized our ability to manipulate biological systems, particularly in higher organisms. Here, we designed a set of homology-directed repair donor templates that enable efficient tagging of endogenous proteins with affinity tags by transient transfection and selection of genome-edited cells in various human cell lines. Combined with technological advancements in single-particle cryogenic electron microscopy, this strategy allows efficient structural studies of endogenous proteins captured in their native cellular environment and during different cellular processes. We demonstrated this strategy by tagging six different human proteins in both HEK293T and Jurkat cells. Moreover, analysis of endogenous glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in HEK293T cells allowed us to follow its behavior spatially and temporally in response to prolonged oxidative stress, correlating the increased number of oxidation-induced inactive catalytic sites in GAPDH with its translocation from cytosol to nucleus.
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Affiliation(s)
- Wooyoung Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Hao Wu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Klaus Yserentant
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA94158
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
- HHMI, University of California, San Francisco, CA94143
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24
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Azinas S, Carroni M. Cryo-EM uniqueness in structure determination of macromolecular complexes: A selected structural anthology. Curr Opin Struct Biol 2023; 81:102621. [PMID: 37315343 DOI: 10.1016/j.sbi.2023.102621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) has become in the past 10 years one of the major tools for the structure determination of proteins. Nowadays, the structure prediction field is experiencing the same revolution and, using AlphaFold2, it is possible to have high-confidence atomic models for virtually any polypeptide chain, smaller than 4000 amino acids, in a simple click. Even in a scenario where all polypeptide chain folding were to be known, cryo-EM retains specific characteristics that make it a unique tool for the structure determination of macromolecular complexes. Using cryo-EM, it is possible to obtain near-atomic structures of large and flexible mega-complexes, describe conformational panoramas, and potentially develop a structural proteomic approach from fully ex vivo specimens.
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Affiliation(s)
- Stavros Azinas
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23A, Solna, 17165, Sweden. https://twitter.com/@stav____
| | - Marta Carroni
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23A, Solna, 17165, Sweden.
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25
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Remigante A, Spinelli S, Straface E, Gambardella L, Russo M, Cafeo G, Caruso D, Falliti G, Dugo P, Dossena S, Marino A, Morabito R. Mechanisms underlying the anti-aging activity of bergamot ( Citrus bergamia) extract in human red blood cells. Front Physiol 2023; 14:1225552. [PMID: 37457030 PMCID: PMC10348362 DOI: 10.3389/fphys.2023.1225552] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction: Aging is a process characterised by a decline in physiological functions. Reactive species play a crucial role in the aging rate. Due to the close relationship between aging and oxidative stress, functional foods rich in phytochemicals are excellent candidates to neutralise age-related changes. Aim: This investigation aims to verify the potential protective role of bergamot (Citrus bergamia, Femminello cultivar) peel and juice extract in a model of aging represented by human red blood cells (RBCs) exposed to D-Galactose (DGal). Methods: Bergamot peel and juice extracts were subjected to RP-HPLC/PDA/MS for determination of their composition in bioactive compounds. Markers of oxidative stress, including ROS production, thiobarbituric acid reactive substances (TBARS) levels -a marker of lipid peroxidation, oxidation of total protein sulfhydryl groups, as well as the expression and anion exchange capability of band 3 and glycated haemoglobin (A1c) production have been investigated in RBCs treated with D-Gal for 24 h, with or without pre-incubation for 15 min with 5 μg/mL peel or juice extract. In addition, the activity of the endogenous antioxidant system, including catalase (CAT) and superoxide dismutase (SOD), as well as the diversion of the RBC metabolism from glycolysis towards the pentose phosphate pathway shunt, as denoted by activation of glucose-6-phosphate dehydrogenase (G6PDH), have been explored. Results: Data shown here suggest that bergamot peel and juice extract i) prevented the D-Gal-induced ROS production, and consequently, oxidative stress injury to biological macromolecules including membrane lipids and proteins; ii) significantly restored D-Gal-induced alterations in the distribution and ion transport kinetics of band 3; iii) blunted A1c production; iv) effectively impeded the over-activation of the endogenous antioxidant enzymes CAT and SOD; and v) significantly prevented the activation of G6PDH. Discussion: These results further contribute to shed light on aging mechanisms in human RBCs and identify bergamot as a functional food rich in natural antioxidants useful for prevention and treatment of oxidative stress-related changes, which may lead to pathological states during aging.
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Affiliation(s)
- Alessia Remigante
- Department of Chemical and Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Sara Spinelli
- Department of Chemical and Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Elisabetta Straface
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucrezia Gambardella
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Marina Russo
- Department of Chemical and Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Giovanna Cafeo
- Department of Chemical and Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Daniele Caruso
- Complex Operational Unit of Clinical Pathology of Papardo Hospital, Messina, Italy
| | - Giuseppe Falliti
- Complex Operational Unit of Clinical Pathology of Papardo Hospital, Messina, Italy
| | - Paola Dugo
- Department of Chemical and Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Angela Marino
- Department of Chemical and Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Rossana Morabito
- Department of Chemical and Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
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26
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Zhekova HR, Ramirez-Echemendía DP, Sejdiu BI, Pushkin A, Tieleman DP, Kurtz I. Coarse-grained molecular dynamics simulations of lipid-protein interactions in SLC4 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546592. [PMID: 37425774 PMCID: PMC10327080 DOI: 10.1101/2023.06.26.546592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO 3 -, CO 3 2- , Cl - , Na + , K + , NH 3 and H + necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl - /HCO 3 - exchanger) and NBCe1 (Na + -CO 3 2- cotransporter). Previous computational studies of the outward facing (OF) state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed multiple 50 µs coarse-grained molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1 and NDCBE (a Na + -CO 3 2- /Cl - exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), and sphingomyelin (POSM). The recently resolved inward-facing (IF) state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, POPC, and POSM in the three studied proteins and their potential roles in the SLC4 transport function, conformational transition and protein dimerization were discussed. Statement of significance The SLC4 protein family is involved in critical physiological processes like pH and blood pressure regulation and maintenance of ion homeostasis. Its members can be found in various tissues. A number of studies suggest possible lipid regulation of the SLC4 function. However, the protein-lipid interactions in the SLC4 family are still poorly understood. Here we make use of long coarse-grained molecular dynamics simulations to assess the protein-lipid interactions in three SLC4 proteins with different transport modes, AE1, NBCe1, and NDCBE. We identify putative lipid binding sites for several lipid types of potential mechanistic importance, discuss them in the framework of the known experimental data and provide a necessary basis for further studies on lipid regulation of SLC4 function.
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27
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Li N, Chen S, Xu K, He MT, Dong MQ, Zhang QC, Gao N. Structural basis of membrane skeleton organization in red blood cells. Cell 2023; 186:1912-1929.e18. [PMID: 37044097 DOI: 10.1016/j.cell.2023.03.017] [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: 09/12/2022] [Revised: 02/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023]
Abstract
The spectrin-based membrane skeleton is a ubiquitous membrane-associated two-dimensional cytoskeleton underneath the lipid membrane of metazoan cells. Mutations of skeleton proteins impair the mechanical strength and functions of the membrane, leading to several different types of human diseases. Here, we report the cryo-EM structures of the native spectrin-actin junctional complex (from porcine erythrocytes), which is a specialized short F-actin acting as the central organizational unit of the membrane skeleton. While an α-/β-adducin hetero-tetramer binds to the barbed end of F-actin as a flexible cap, tropomodulin and SH3BGRL2 together create an absolute cap at the pointed end. The junctional complex is strengthened by ring-like structures of dematin in the middle actin layers and by patterned periodic interactions with tropomyosin over its entire length. This work serves as a structural framework for understanding the assembly and dynamics of membrane skeleton and offers insights into mechanisms of various ubiquitous F-actin-binding factors in other F-actin systems.
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Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
| | - Siyi Chen
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China; Changping Laboratory Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Kui Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meng-Ting He
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China; National Biomedical Imaging Center, Peking University, Beijing 100871, China.
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28
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Zhang Q, Jian L, Yao D, Rao B, Xia Y, Hu K, Li S, Shen Y, Cao M, Qin A, Zhao J, Cao Y. The structural basis of the pH-homeostasis mediated by the Cl -/HCO 3- exchanger, AE2. Nat Commun 2023; 14:1812. [PMID: 37002221 PMCID: PMC10066210 DOI: 10.1038/s41467-023-37557-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
The cell maintains its intracellular pH in a narrow physiological range and disrupting the pH-homeostasis could cause dysfunctional metabolic states. Anion exchanger 2 (AE2) works at high cellular pH to catalyze the exchange between the intracellular HCO3- and extracellular Cl-, thereby maintaining the pH-homeostasis. Here, we determine the cryo-EM structures of human AE2 in five major operating states and one transitional hybrid state. Among those states, the AE2 shows the inward-facing, outward-facing, and intermediate conformations, as well as the substrate-binding pockets at two sides of the cell membrane. Furthermore, critical structural features were identified showing an interlock mechanism for interactions among the cytoplasmic N-terminal domain and the transmembrane domain and the self-inhibitory effect of the C-terminal loop. The structural and cell-based functional assay collectively demonstrate the dynamic process of the anion exchange across membranes and provide the structural basis for the pH-sensitive pH-rebalancing activity of AE2.
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Affiliation(s)
- Qing Zhang
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Liyan Jian
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Deqiang Yao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, 200127, Shanghai, China
| | - Bing Rao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Ying Xia
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Kexin Hu
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Shaobai Li
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Yafeng Shen
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Mi Cao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - An Qin
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Jie Zhao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Yu Cao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China.
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Bogusławska DM, Kraszewski S, Skulski M, Potoczek S, Kuliczkowski K, Sikorski AF. Novel Variant of the SLC4A1 Gene Associated with Hereditary Spherocytosis. Biomedicines 2023; 11:biomedicines11030784. [PMID: 36979763 PMCID: PMC10045460 DOI: 10.3390/biomedicines11030784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Hereditary spherocytosis (HS) refers to the group of the most frequently occurring non-immune hereditary hemolytic anemia in people of Caucasian central or northern European ancestry. HS is mainly associated with pathogenic variants of genes encoding defects in five membrane proteins, including anion exchanger 1 encoded by the SLC4A1 gene. In this study, in a family affected with HS, we identified a hitherto unreported AE1 defect, variant p.G720W. The result of it is most likely the HS phenotype. Molecular dynamics simulation study of the AE1 transmembrane domain may indicate reasonable changes in AE1 domain structure, i.e., significant displacement of the tryptophan residue towards the membrane surface connected with possible changes in AE1 function. The WES analysis verified by classical sequencing in conjunction with biochemical analysis and molecular simulation studies shed light on the molecular mechanism underlying this case of hereditary spherocytosis, for which the newly discovered AE1 variant p.G720W seems crucial.
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Affiliation(s)
- Dżamila M. Bogusławska
- Department of Biotechnology, Institute of Biological Sciences, University of Zielona Góra, Prof. Szafrana St. 1, 65-516 Zielona Góra, Poland
| | - Sebastian Kraszewski
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Plac Grunwaldzki 13 (D-1), 50-377 Wroclaw, Poland
| | - Michał Skulski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a St., 50-383 Wroclaw, Poland
| | - Stanisław Potoczek
- Department and Clinic of Haematology, Blood Neoplasms and Bone Marrow Transplantation, Wroclaw Medical University, Wybrzeże L. Pasteura 4, 50-367 Wroclaw, Poland
| | - Kazimierz Kuliczkowski
- Silesian Park of Medical Technology Kardio-Med Silesia, ul. M. Curie-Skłodowskiej 10c, 41-800 Zabrze, Poland
| | - Aleksander F. Sikorski
- Research and Development Centre, Regional Specialist Hospital, Kamieńskiego 73a, 51-154 Wroclaw, Poland
- Correspondence: ; Tel.: +48-71-327-05-16; Fax: +48-71-375-62-08
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30
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Beltran JL, McGrath LG, Caruso S, Bain RK, Hendrix CE, Kamran H, Johnston HG, Collings RM, Henry MCN, Abera TAL, Donoso VA, Carriker EC, Thurtle-Schmidt BH. Borate Transporters and SLC4 Bicarbonate Transporters Share Key Functional Properties. MEMBRANES 2023; 13:membranes13020235. [PMID: 36837738 PMCID: PMC9959716 DOI: 10.3390/membranes13020235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/03/2023]
Abstract
Borate transporters are membrane transport proteins that regulate intracellular borate levels. In plants, borate is a micronutrient essential for growth but is toxic in excess, while in yeast, borate is unnecessary for growth and borate export confers tolerance. Borate transporters share structural homology with human bicarbonate transporters in the SLC4 family despite low sequence identity and differences in transported solutes. Here, we characterize the S. cerevisiae borate transporter Bor1p and examine whether key biochemical features of SLC4 transporters extend to borate transporters. We show that borate transporters and SLC4 transporters share multiple properties, including lipid-promoted dimerization, sensitivity to stilbene disulfonate-derived inhibitors, and a requirement for an acidic residue at the solute binding site. We also identify several amino acids critical for Bor1p function and show that disease-causing mutations in human SLC4A1 will eliminate in vivo function when their homologous mutations are introduced in Bor1p. Our data help elucidate mechanistic features of Bor1p and reveal significant functional properties shared between borate transporters and SLC4 transporters.
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31
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Spherocytosis-Related L1340P Mutation in Ankyrin Affects Its Interactions with Spectrin. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010151. [PMID: 36676098 PMCID: PMC9864249 DOI: 10.3390/life13010151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023]
Abstract
Previously, we reported a new missense mutation in the ANK1 gene that correlated with the hereditary spherocytosis phenotype. This mutation, resulting in L1340P substitution (HGMD CM149731), likely leads to the changes in the conformation of the ankyrin ZZUD domain important for ankyrin binding to spectrin. Here, we report the molecular and physiological effects of this mutation. First, we assessed the binding activity of human β-spectrin to the mutated ZZUDL1340P domain of ankyrin using two different experimental approaches-the study of association and dissociation responses of the spectrin-ankyrin binding domain and a sedimentation assay. In addition, we documented the changes in morphology caused by the overexpressed ankyrin ZZUD domain in human cell models. Our results prove the key role of the L1340 aa residue for the correct alignment of the ZZUD domain of ankyrin, which results in binding the latter with spectrin within the erythrocyte membrane. Replacing L1340 with a proline residue disrupts the spectrin-binding activity of ankyrin.
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32
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Vaisey G, Banerjee P, North AJ, Haselwandter CA, MacKinnon R. Piezo1 as a force-through-membrane sensor in red blood cells. eLife 2022; 11:e82621. [PMID: 36515266 PMCID: PMC9750178 DOI: 10.7554/elife.82621] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Piezo1 is the stretch activated Ca2+ channel in red blood cells that mediates homeostatic volume control. Here, we study the organization of Piezo1 in red blood cells using a combination of super-resolution microscopy techniques and electron microscopy. Piezo1 adopts a non-uniform distribution on the red blood cell surface, with a bias toward the biconcave 'dimple'. Trajectories of diffusing Piezo1 molecules, which exhibit confined Brownian diffusion on short timescales and hopping on long timescales, also reflect a bias toward the dimple. This bias can be explained by 'curvature coupling' between the intrinsic curvature of the Piezo dome and the curvature of the red blood cell membrane. Piezo1 does not form clusters with itself, nor does it colocalize with F-actin, Spectrin, or the Gardos channel. Thus, Piezo1 exhibits the properties of a force-through-membrane sensor of curvature and lateral tension in the red blood cell.
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Affiliation(s)
- George Vaisey
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Priyam Banerjee
- Bio-Imaging Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Alison J North
- Bio-Imaging Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Christoph A Haselwandter
- Department of Physics and Astronomy and Department of Quantitative and Computational Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
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CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations. Commun Biol 2022; 5:1372. [PMID: 36517642 PMCID: PMC9751308 DOI: 10.1038/s42003-022-04306-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of carbon dioxide during respiration. Though structures of the transmembrane domain (TMD) of three SLC4 transporters, including AE1, have been resolved previously in their outward-facing (OF) state, no mammalian SLC4 structure has been reported in the inward-facing (IF) conformation. Here we present the cryoEM structures of full-length bovine AE1 with its TMD captured in both IF and OF conformations. Remarkably, both IF-IF homodimers and IF-OF heterodimers were detected. The IF structures feature downward movement in the core domain with significant unexpected elongation of TM11. Molecular modeling and structure guided mutagenesis confirmed the functional significance of residues involved in TM11 elongation. Our data provide direct evidence for an elevator-like mechanism of ion transport by an SLC4 family member.
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Hsu K, Lee TY, Lin JY, Chen PL. A Balance between Transmembrane-Mediated ER/Golgi Retention and Forward Trafficking Signals in Glycophorin-Anion Exchanger-1 Interaction. Cells 2022; 11:3512. [PMID: 36359907 PMCID: PMC9653601 DOI: 10.3390/cells11213512] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 12/04/2023] Open
Abstract
Anion exchanger-1 (AE1) is the main erythroid Cl-/HCO3- transporter that supports CO2 transport. Glycophorin A (GPA), a component of the AE1 complexes, facilitates AE1 expression and anion transport, but Glycophorin B (GPB) does not. Here, we dissected the structural components of GPA/GPB involved in glycophorin-AE1 trafficking by comparing them with three GPB variants-GPBhead (lacking the transmembrane domain [TMD]), GPBtail (mainly the TMD), and GP.Mur (glycophorin B-A-B hybrid). GPB-derived GP.Mur bears an O-glycopeptide that encompasses the R18 epitope, which is present in GPA but not GPB. By flow cytometry, AE1 expression in the control erythrocytes increased with the GPA-R18 expression; GYP.Mur+/+ erythrocytes bearing both GP.Mur and GPA expressed more R18 epitopes and more AE1 proteins. In contrast, heterologously expressed GPBtail and GPB were predominantly localized in the Golgi apparatus of HEK-293 cells, whereas GBhead was diffuse throughout the cytosol, suggesting that glycophorin transmembrane encoded an ER/Golgi retention signal. AE1 coexpression could reduce the ER/Golgi retention of GPB, but not of GPBtail or GPBhead. Thus, there are forward-trafficking and transmembrane-driven ER/Golgi retention signals encoded in the glycophorin sequences. How the balance between these opposite trafficking signals could affect glycophorin sorting into AE1 complexes and influence erythroid anion transport remains to be explored.
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Affiliation(s)
- Kate Hsu
- The Laboratory of Immunogenetics, Department of Medical Research, MacKay Memorial Hospital, Tamsui, New Taipei City 251020, Taiwan
- MacKay Junior College of Medicine, Nursing, and Management, New Taipei City 25245, Taiwan
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City 25245, Taiwan
- Department of Exercise & Health Sciences, University of Taipei, Taipei 100234, Taiwan
| | - Ting-Ying Lee
- The Laboratory of Immunogenetics, Department of Medical Research, MacKay Memorial Hospital, Tamsui, New Taipei City 251020, Taiwan
| | - Jian-Yi Lin
- The Laboratory of Immunogenetics, Department of Medical Research, MacKay Memorial Hospital, Tamsui, New Taipei City 251020, Taiwan
| | - Pin-Lung Chen
- The Laboratory of Immunogenetics, Department of Medical Research, MacKay Memorial Hospital, Tamsui, New Taipei City 251020, Taiwan
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Remigante A, Spinelli S, Straface E, Gambardella L, Caruso D, Falliti G, Dossena S, Marino A, Morabito R. Antioxidant Activity of Quercetin in a H2O2-Induced Oxidative Stress Model in Red Blood Cells: Functional Role of Band 3 Protein. Int J Mol Sci 2022; 23:ijms231910991. [PMID: 36232293 PMCID: PMC9569818 DOI: 10.3390/ijms231910991] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 12/12/2022] Open
Abstract
During their lifespan, red blood cells (RBCs) are exposed to a large number of stressors and are therefore considered as a suitable model to investigate cell response to oxidative stress (OS). This study was conducted to evaluate the potential beneficial effects of the natural antioxidant quercetin (Q) on an OS model represented by human RBCs treated with H2O2. Markers of OS, including % hemolysis, reactive oxygen species (ROS) production, thiobarbituric acid reactive substances (TBARS) levels, oxidation of protein sulfhydryl groups, CD47 and B3p expression, methemoglobin formation (% MetHb), as well as the anion exchange capability through Band 3 protein (B3p) have been analyzed in RBCs treated for 1 h with 20 mM H2O2 with or without pre-treatment for 1 h with 10 μM Q, or in RBCs pre-treated with 20 mM H2O2 and then exposed to 10 µM Q. The results show that pre-treatment with Q is more effective than post-treatment to counteract OS in RBCs. In particular, pre-exposure to Q avoided morphological alterations (formation of acanthocytes), prevented H2O2-induced OS damage, and restored the abnormal distribution of B3p and CD47 expression. Moreover, H2O2 exposure was associated with a decreased rate constant of SO42− uptake via B3p, as well as an increased MetHb formation. Both alterations have been attenuated by pre-treatment with 10 μM Q. These results contribute (1) to elucidate OS-related events in human RBCs, (2) propose Q as natural antioxidant to counteract OS-related alterations, and (3) identify B3p as a possible target for the treatment and prevention of OS-related disease conditions or aging-related complications impacting on RBCs physiology.
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Affiliation(s)
- Alessia Remigante
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98122 Messina, Italy
| | - Sara Spinelli
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98122 Messina, Italy
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Elisabetta Straface
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Lucrezia Gambardella
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Daniele Caruso
- Complex Operational Unit of Clinical Pathology, Papardo Hospital, 98122 Messina, Italy
| | - Giuseppe Falliti
- Complex Operational Unit of Clinical Pathology, Papardo Hospital, 98122 Messina, Italy
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Angela Marino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98122 Messina, Italy
| | - Rossana Morabito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98122 Messina, Italy
- Correspondence:
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The band 3-ankyrin multiprotein complex comes in from the cold. Nat Struct Mol Biol 2022; 29:621-623. [PMID: 35835868 DOI: 10.1038/s41594-022-00789-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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