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Swapna GVT, Dube N, Roth MJ, Montelione GT. Modeling Alternative Conformational States of Pseudo-Symmetric Solute Carrier Transporters using Methods from Machine Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603529. [PMID: 39071413 PMCID: PMC11275918 DOI: 10.1101/2024.07.15.603529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The Solute Carrier (SLC) superfamily of integral membrane proteins function to transport a wide array of solutes across the plasma and organelle membranes. SLC proteins also function as important drug transporters and as viral receptors. Despite being classified as a single superfamily, SLC proteins do not share a single common fold classification; however, most belong to multi-pass transmembrane helical protein fold families. SLC proteins populate different conformational states during the solute transport process, including outward open, intermediate (occluded), and inward open conformational states. For some SLC fold families this structural "flipping" corresponds to swapping between conformations of their N-terminal and C-terminal symmetry-related sub-structures. Conventional AlphaFold2 or Evolutionary Scale Modeling methods typically generate models for only one of these multiple conformational states of SLC proteins. Here we describe a fast and simple approach for modeling multiple conformational states of SLC proteins using a combined ESM - AF2 process. The resulting multi-state models are validated by comparison with sequence-based evolutionary co-variance data (ECs) that encode information about contacts present in the various conformational states adopted by the protein. We also explored the impact of mutations on conformational distributions of SLC proteins modeled by AlphaFold2 using both conventional and enhanced sampling methods. This approach for modeling conformational landscapes of pseudo-symmetric SLC proteins is demonstrated for several integral membrane protein transporters, including SLC35F2 the receptor of a feline leukemia virus envelope protein required for viral entry into eukaryotic cells.
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Affiliation(s)
- G V T Swapna
- Dept. of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway NJ 08854 USA
| | - Namita Dube
- Dept. of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
| | - Monica J Roth
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway NJ 08854 USA
| | - Gaetano T Montelione
- Dept. of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
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2
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Nguyen K, Strauss T, Refaeli B, Hiller R, Vinogradova O, Khananshvili D. 19F-NMR Probing of Ion-Induced Conformational Changes in Detergent-Solubilized and Nanodisc-Reconstituted NCX_Mj. Int J Mol Sci 2024; 25:6909. [PMID: 39000018 PMCID: PMC11241019 DOI: 10.3390/ijms25136909] [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: 06/06/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Consecutive interactions of 3Na+ or 1Ca2+ with the Na+/Ca2+ exchanger (NCX) result in an alternative exposure (access) of the cytosolic and extracellular vestibules to opposite sides of the membrane, where ion-induced transitions between the outward-facing (OF) and inward-facing (IF) conformational states drive a transport cycle. Here, we investigate sub-state populations of apo and ion-bound species in the OF and IF states by analyzing detergent-solubilized and nanodisc-reconstituted preparations of NCX_Mj with 19F-NMR. The 19F probe was covalently attached to the cysteine residues at entry locations of the cytosolic and extracellular vestibules. Multiple sub-states of apo and ion-bound species were observed in nanodisc-reconstituted (but not in detergent-solubilized) NCX_Mj, meaning that the lipid-membrane environment preconditions multiple sub-state populations toward the OF/IF swapping. Most importantly, ion-induced sub-state redistributions occur within each major (OF or IF) state, where sub-state interconversions may precondition the OF/IF swapping. In contrast with large changes in population redistributions, the sum of sub-state populations within each inherent state (OF or IF) remains nearly unchanged upon ion addition. The present findings allow the further elucidation of structure-dynamic modules underlying ion-induced conformational changes that determine a functional asymmetry of ion access/translocation at opposite sides of the membrane and ion transport rates concurring physiological demands.
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Affiliation(s)
- Khiem Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Tali Strauss
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Bosmat Refaeli
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
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3
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Gök C, Fuller W. Rise of palmitoylation: A new trick to tune NCX1 activity. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119719. [PMID: 38574822 DOI: 10.1016/j.bbamcr.2024.119719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
The cardiac Na+/Ca2+ Exchanger (NCX1) controls transmembrane calcium flux in numerous tissues. The only reversible post-translational modification established to regulate NCX1 is palmitoylation, which alters the ability of the exchanger to inactivate. Palmitoylation creates a binding site for the endogenous XIP domain, a region of the NCX1 intracellular loop established to inactivate NCX1. The binding site created by NCX1 palmitoylation sensitizes the transporter to XIP. Herein we summarize our recent knowledge on NCX1 palmitoylation and its association with cardiac pathologies, and discuss these findings in the light of the recent cryo-EM structures of human NCX1.
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Affiliation(s)
- Caglar Gök
- School of Cardiovascular and Metabolic Health (SCMH), Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | - William Fuller
- School of Cardiovascular and Metabolic Health (SCMH), Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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4
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Khananshvili D. Newly uncovered Cryo-EM structures of mammalian NCXs set a new stage for resolving the underlying molecular mechanisms and drug discovery. Cell Calcium 2024; 119:102867. [PMID: 38422779 DOI: 10.1016/j.ceca.2024.102867] [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: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 03/02/2024]
Abstract
The membrane-abundant NCX proteins mediate an electrogenic ion exchange (3Na+:1Ca2+) in the Ca2+-exit or Ca2+-entry mode. The structurally related isoform/splice variants of NCX are expressed in a tissue-specific manner to shape Ca2+ signalling/homeostasis in diverse cell types. The lack of mammalian NCX structure hampered the functional and regulatory resolution of tissue-specific NCX variants and their pharmacological targeting. Recently unveiled Cryo-EM structures of human cardiac NCX1.1[1] and kidney NCX1.3[2] provide new opportunities for resolving structure/functional divergences among NCX variants and their pharmacological targeting.
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Affiliation(s)
- Daniel Khananshvili
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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5
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Giladi M, Fojtík L, Strauss T, Da'adoosh B, Hiller R, Man P, Khananshvili D. Structural dynamics of Na + and Ca 2+ interactions with full-size mammalian NCX. Commun Biol 2024; 7:463. [PMID: 38627576 PMCID: PMC11021524 DOI: 10.1038/s42003-024-06159-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Cytosolic Ca2+ and Na+ allosterically regulate Na+/Ca2+ exchanger (NCX) proteins to vary the NCX-mediated Ca2+ entry/exit rates in diverse cell types. To resolve the structure-based dynamic mechanisms underlying the ion-dependent allosteric regulation in mammalian NCXs, we analyze the apo, Ca2+, and Na+-bound species of the brain NCX1.4 variant using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations. Ca2+ binding to the cytosolic regulatory domains (CBD1 and CBD2) rigidifies the intracellular regulatory loop (5L6) and promotes its interaction with the membrane domains. Either Na+ or Ca2+ stabilizes the intracellular portions of transmembrane helices TM3, TM4, TM9, TM10, and their connecting loops (3L4 and 9L10), thereby exposing previously unappreciated regulatory sites. Ca2+ or Na+ also rigidifies the palmitoylation domain (TMH2), and neighboring TM1/TM6 bundle, thereby uncovering a structural entity for modulating the ion transport rates. The present analysis provides new structure-dynamic clues underlying the regulatory diversity among tissue-specific NCX variants.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel.
- Tel-Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel.
| | - Lukáš Fojtík
- Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Prumyslova, 595, 252 50 Vestec, Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, 128 00, Prague, Czech Republic
| | - Tali Strauss
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel
| | - Benny Da'adoosh
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel
| | - Petr Man
- Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Prumyslova, 595, 252 50 Vestec, Prague, Czech Republic.
- Department of Biochemistry, Faculty of Science, Charles University, 128 00, Prague, Czech Republic.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel.
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6
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Marinelli F, Faraldo-Gómez JD. Conformational free-energy landscapes of a Na +/Ca 2+ exchanger explain its alternating-access mechanism and functional specificity. Proc Natl Acad Sci U S A 2024; 121:e2318009121. [PMID: 38588414 PMCID: PMC11032461 DOI: 10.1073/pnas.2318009121] [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: 10/25/2023] [Accepted: 02/20/2024] [Indexed: 04/10/2024] Open
Abstract
Secondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na+/Ca2+ exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na+ and Ca2+, and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H+ for either Ca2+ or Na+, despite being able to bind H+ and its high similarity with H+/Ca2+ exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.
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Affiliation(s)
- Fabrizio Marinelli
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20814
| | - José D. Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20814
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7
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Tan X, Qu S, Wang G, Zhang G, Liu T, Ling F, Wang G. Structure-based discovery of potent myosin inhibitors to guide antiparasite drug development. Eur J Med Chem 2024; 269:116338. [PMID: 38522112 DOI: 10.1016/j.ejmech.2024.116338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
Monogenea, a prevalent parasite in aquaculture, poses significant threats to the industry, leading to substantial losses. Current preventive measures have proven insufficient, necessitating the development of novel and effective anti-parasitic drugs. In this investigation, we obtained the full-length myosin cDNA sequence by analyzing three-generation transcriptome data, revealing a 5817-base sequence encoding 1938 amino acids. Subsequently, we modeled and analyzed the characteristics of the secondary and tertiary of myosin, pinpointing the crucial functional region within the motor domain (amino acids 1-768). The prokaryotic expression of this domain yielded a protein of 87.44 kDa, confirmed as myosin by Western Blotting. Molecular docking identified ASN439 as the key amino acid residue involved in arctigenin and myosin binding, a result corroborated by site-directed mutagenesis, affirming the active cavity of this interaction. Chalcone and shikonin were chosen from a virtual sieve of molecular library of natural drugs based on the active cavity. Chalcone and shikonin exhibited EC50 values of 1.085 mg/L and 0.371 mg/L, respectively, with corresponding IC50 values for myosin of 0.44 mM and 0.14 mM. Given its superior activity and structure, shikonin was selected for further optimization of drug molecule design, culminating in the discovery of 1,4-naphthoquinone as a potent antiparasitic agent. This compound demonstrated an EC50 of 0.047 mg/L, LC50 of 0.23 mg/L, and a TI index of 4.893. These findings collectively highlight the potential of shikonin and 1,4-naphthoquinone as alternative compounds to control Gyrodactylus infections. Further optimization of medicinal chemistry holds promise for the development of more potent 1,4-naphthoquinone analogues, offering prospects for future anthelmintic control through combinatorial or replacement strategies.
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Affiliation(s)
- Xiaoping Tan
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Shenye Qu
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Guangshuo Wang
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Gengrong Zhang
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Tianqiang Liu
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Fei Ling
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China.
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China.
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8
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Ding Y, Xue X. Medicinal Chemistry Strategies for the Modification of Bioactive Natural Products. Molecules 2024; 29:689. [PMID: 38338433 PMCID: PMC10856770 DOI: 10.3390/molecules29030689] [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: 12/14/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Natural bioactive compounds are valuable resources for drug discovery due to their diverse and unique structures. However, these compounds often lack optimal drug-like properties. Therefore, structural optimization is a crucial step in the drug development process. By employing medicinal chemistry principles, targeted molecular operations can be applied to natural products while considering their size and complexity. Various strategies, including structural fragmentation, elimination of redundant atoms or groups, and exploration of structure-activity relationships, are utilized. Furthermore, improvements in physicochemical properties, chemical and metabolic stability, biophysical properties, and pharmacokinetic properties are sought after. This article provides a concise analysis of the process of modifying a few marketed drugs as illustrative examples.
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Affiliation(s)
- Yuyang Ding
- Shenzhen Borui Pharmaceutical Technology Co., Ltd., Shenzhen 518055, China;
| | - Xiaoqian Xue
- Medi-X Pingshan, Southern University of Science and Technology, Shenzhen 518055, China
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9
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Liu X, Zuo Z, Xie X, Gao S, Wu S, Gu W, Wang G. SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway. THE ISME JOURNAL 2024; 18:wrae039. [PMID: 38457651 PMCID: PMC10982851 DOI: 10.1093/ismejo/wrae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Diatom bloom is characterized by a rapid increase of population density. Perception of population density and physiological responses can significantly influence their survival strategies, subsequently impacting bloom fate. The population density itself can serve as a signal, which is perceived through chemical signals or chlorophyll fluorescence signals triggered by high cell density, and their intracellular signaling mechanisms remain to be elucidated. In this study, we focused on the model diatom, Phaeodactylum tricornutum, and designed an orthogonal experiment involving varying cell densities and light conditions, to stimulate the release of chemical signals and light-induced chlorophyll fluorescence signals. Utilizing RNA-Seq and Weighted Gene Co-expression Network Analysis, we identified four gene clusters displaying density-dependent expression patterns. Within these, a potential hub gene, PtSLC24A, encoding a Na+/Ca2+ exchanger, was identified. Based on molecular genetics, cellular physiology, computational structural biology, and in situ oceanic data, we propose a potential intracellular signaling mechanism related to cell density in marine diatoms using Ca2+: upon sensing population density signals mediated by chemical cues, the membrane-bound PtSLC24A facilitates the efflux of Ca2+ to maintain specific intracellular calcium levels, allowing the transduction of intracellular density signals, subsequently regulating physiological responses, including cell apoptosis, ultimately affecting algal blooms fate. These findings shed light on the calcium-mediated intracellular signaling mechanism of marine diatoms to changing population densities, and enhances our understanding of diatom bloom dynamics and their ecological implications.
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Affiliation(s)
- Xuehua Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, Shandong Province, China
| | - Zhicheng Zuo
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Xiujun Xie
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, Shandong Province, China
| | - Shan Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, Shandong Province, China
| | - Songcui Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, Shandong Province, China
| | - Wenhui Gu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, Shandong Province, China
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266404, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, Shandong Province, China
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10
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Dong Y, Yu Z, Li Y, Huang B, Bai Q, Gao Y, Chen Q, Li N, He L, Zhao Y. Structural insight into the allosteric inhibition of human sodium-calcium exchanger NCX1 by XIP and SEA0400. EMBO J 2024; 43:14-31. [PMID: 38177313 PMCID: PMC10897212 DOI: 10.1038/s44318-023-00013-0] [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: 02/16/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
Sodium-calcium exchanger proteins influence calcium homeostasis in many cell types and participate in a wide range of physiological and pathological processes. Here, we elucidate the cryo-EM structure of the human Na+/Ca2+ exchanger NCX1.3 in the presence of a specific inhibitor, SEA0400. Conserved ion-coordinating residues are exposed on the cytoplasmic face of NCX1.3, indicating that the observed structure is stabilized in an inward-facing conformation. We show how regulatory calcium-binding domains (CBDs) assemble with the ion-translocation transmembrane domain (TMD). The exchanger-inhibitory peptide (XIP) is trapped within a groove between the TMD and CBD2 and predicted to clash with gating helices TMs1/6 at the outward-facing state, thus hindering conformational transition and promoting inactivation of the transporter. A bound SEA0400 molecule stiffens helix TM2ab and affects conformational rearrangements of TM2ab that are associated with the ion-exchange reaction, thus allosterically attenuating Ca2+-uptake activity of NCX1.3.
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Affiliation(s)
- Yanli Dong
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhuoya Yu
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Huang
- Beijing StoneWise Technology Co Ltd., 15 Haidian street, Haidian district, Beijing, China
| | - Qinru Bai
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiwei Gao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qihao Chen
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Li
- Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
| | - Lingli He
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Zhao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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11
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Zayats V, Sikora M, Perlinska AP, Stasiulewicz A, Gren BA, Sulkowska JI. Conservation of knotted and slipknotted topology in transmembrane transporters. Biophys J 2023; 122:4528-4541. [PMID: 37919904 PMCID: PMC10719070 DOI: 10.1016/j.bpj.2023.10.031] [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: 02/21/2023] [Revised: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023] Open
Abstract
The existence of nontrivial topology is well accepted in globular proteins but not in membrane proteins. Our comprehensive topological analysis of the Protein Data Bank structures reveals 18 families of transmembrane proteins with nontrivial topology, showing that they constitute a significant number of membrane proteins. Moreover, we found that they comprise one of the largest groups of secondary active transporters. We classified them based on their knotted fingerprint into four groups: three slipknotted and one knotted. Unexpectedly, we found that the same protein can possess two distinct slipknot motifs that correspond to its outward- and inward-open conformational state. Based on the analysis of structures and knotted fingerprints, we show that slipknot topology is directly involved in the conformational transition and substrate transfer. Therefore, entanglement can be used to classify proteins and to find their structure-function relationship. Furthermore, based on the topological analysis of the transmembrane protein structures predicted by AlphaFold, we identified new potentially slipknotted protein families.
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Affiliation(s)
- Vasilina Zayats
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maciej Sikora
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | | | - Adam Stasiulewicz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Department of Drug Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
| | - Bartosz A Gren
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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12
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Khananshvili D. Neuronal and astrocyte NCX isoform/splice variants: How do they participate in Na + and Ca 2+ signalling? Cell Calcium 2023; 116:102818. [PMID: 37918135 DOI: 10.1016/j.ceca.2023.102818] [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: 10/16/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
NCX1, NCX2, and NCX3 gene isoforms and their splice variants are characteristically expressed in different regions of the brain. The tissue-specific splice variants of NCX1-3 isoforms show specific expression profiles in neurons and astrocytes, whereas the relevant NCX isoform/splice variants exhibit diverse allosteric modes of Na+- and Ca2+-dependent regulation. In general, overexpression of NCX1-3 genes leads to neuroprotective effects, whereas their ablation gains the opposite results. At this end, the partial contributions of NCX isoform/splice variants to neuroprotective effects remain unresolved. The glutamate-dependent Na+ entry generates Na+ transients (in response to neuronal cell activities), whereas the Na+-driven Ca2+ entry (through the reverse NCX mode) raises Ca2+ transients. This special mode of signal coupling translates Na+ transients into the Ca2+ signals while being a part of synaptic neurotransmission. This mechanism is of general interest since disease-related conditions (ischemia, metabolic stress, and stroke among many others) trigger Na+ and Ca2+ overload with deadly outcomes of downstream apoptosis and excitotoxicity. The recently discovered mechanisms of NCX allosteric regulation indicate that some NCX variants might play a critical role in the dynamic coupling of Na+-driven Ca2+ entry. In contrast, the others are less important or even could be dangerous under altered conditions (e.g., metabolic stress). This working hypothesis can be tested by applying advanced experimental approaches and highly focused computational simulations. This may allow the development of structure-based blockers/activators that can selectively modulate predefined NCX variants to lessen the life-threatening outcomes of excitotoxicity, ischemia, apoptosis, metabolic deprivation, brain injury, and stroke.
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Affiliation(s)
- Daniel Khananshvili
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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13
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Xue J, Zeng W, Han Y, John S, Ottolia M, Jiang Y. Structural mechanisms of the human cardiac sodium-calcium exchanger NCX1. Nat Commun 2023; 14:6181. [PMID: 37794011 PMCID: PMC10550945 DOI: 10.1038/s41467-023-41885-4] [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: 06/08/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
Abstract
Na+/Ca2+ exchangers (NCX) transport Ca2+ in or out of cells in exchange for Na+. They are ubiquitously expressed and play an essential role in maintaining cytosolic Ca2+ homeostasis. Although extensively studied, little is known about the global structural arrangement of eukaryotic NCXs and the structural mechanisms underlying their regulation by various cellular cues including cytosolic Na+ and Ca2+. Here we present the cryo-EM structures of human cardiac NCX1 in both inactivated and activated states, elucidating key structural elements important for NCX ion exchange function and its modulation by cytosolic Ca2+ and Na+. We demonstrate that the interactions between the ion-transporting transmembrane (TM) domain and the cytosolic regulatory domain define the activity of NCX. In the inward-facing state with low cytosolic [Ca2+], a TM-associated four-stranded β-hub mediates a tight packing between the TM and cytosolic domains, resulting in the formation of a stable inactivation assembly that blocks the TM movement required for ion exchange function. Ca2+ binding to the cytosolic second Ca2+-binding domain (CBD2) disrupts this inactivation assembly which releases its constraint on the TM domain, yielding an active exchanger. Thus, the current NCX1 structures provide an essential framework for the mechanistic understanding of the ion transport and cellular regulation of NCX family proteins.
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Affiliation(s)
- Jing Xue
- Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Weizhong Zeng
- Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Han
- Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Scott John
- Department of Medicine (Cardiology), David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Michela Ottolia
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Youxing Jiang
- Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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14
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Berger F, Gomez GM, Sanchez CP, Posch B, Planelles G, Sohraby F, Nunes-Alves A, Lanzer M. pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle. Nat Commun 2023; 14:4234. [PMID: 37454114 PMCID: PMC10349806 DOI: 10.1038/s41467-023-39969-2] [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: 11/16/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The chloroquine resistance transporter, PfCRT, of the human malaria parasite Plasmodium falciparum is sensitive to acidic pH. Consequently, PfCRT operates at 60% of its maximal drug transport activity at the pH of 5.2 of the digestive vacuole, a proteolytic organelle from which PfCRT expels drugs interfering with heme detoxification. Here we show by alanine-scanning mutagenesis that E207 is critical for pH sensing. The E207A mutation abrogates pH-sensitivity, while preserving drug substrate specificity. Substituting E207 with Asp or His, but not other amino acids, restores pH-sensitivity. Molecular dynamics simulations and kinetics analyses suggest an allosteric binding model in which PfCRT can accept both protons and chloroquine in a partial noncompetitive manner, with increased proton concentrations decreasing drug transport. Further simulations reveal that E207 relocates from a peripheral to an engaged location during the transport cycle, forming a salt bridge with residue K80. We propose that the ionized carboxyl group of E207 acts as a hydrogen acceptor, facilitating transport cycle progression, with pH sensing as a by-product.
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Affiliation(s)
- Fiona Berger
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Guillermo M Gomez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Cecilia P Sanchez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Britta Posch
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Gabrielle Planelles
- INSERM, Centre de Recherche des Cordeliers, Unité 1138, CNRS ERL8228, Université Pierre et Marie Curie and Université Paris-Descartes, Paris, 75006, France
| | - Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
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15
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ONO N, HORIKOSHI J, IZAWA T, NISHIYAMA K, TANAKA M, KUWAMURA M, AZUMA YT. L-arginine-induced pancreatitis aggravated by inhibiting Na +/Ca 2+ exchanger 1. J Vet Med Sci 2023; 85:657-666. [PMID: 37100607 PMCID: PMC10315542 DOI: 10.1292/jvms.22-0569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Na+/Ca2+ exchangers (NCX) are an exchange transporter of Na+ and Ca2+ ions on the plasma membrane. There are three types of NCX: NCX1, NCX2, and NCX3. We have been working for many years to understand the role of NCX1 and NCX2 in gastrointestinal motility. In this study, we focused on the pancreas, an organ closely related to the gastrointestinal tract, and used a mouse model of acute pancreatitis to investigate a possible role for NCX1 in the pathogenesis of pancreatitis. We characterized a model of acute pancreatitis induced by excessive doses of L-arginine. We administered the NCX1 inhibitor SEA0400 (1 mg/kg) 1 hr prior to L-arginine-induced pancreatitis and evaluated pathological changes. Mice treated with NCX1 inhibitors show exacerbation of the disease with decreased survival and increased amylase activity in response to L-arginine-induced experimental acute pancreatitis, and this exacerbation correlates with increased autophagy mediated by LC3B and p62. These results suggest that NCX1 has a role in regulating pancreatic inflammation and acinar cell homeostasis.
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Affiliation(s)
- Naoshige ONO
- Laboratory of Prophylactic Pharmacology, Osaka Metropolitan
University Graduate School of Veterinary Science, Osaka, Japan
| | - Joji HORIKOSHI
- Laboratory of Prophylactic Pharmacology, Osaka Metropolitan
University Graduate School of Veterinary Science, Osaka, Japan
| | - Takeshi IZAWA
- Laboratory of Veterinary Pathology, Osaka Metropolitan
University Graduate School of Veterinary Science, Osaka, Japan
| | - Kazuhiro NISHIYAMA
- Laboratory of Prophylactic Pharmacology, Osaka Metropolitan
University Graduate School of Veterinary Science, Osaka, Japan
| | - Miyuu TANAKA
- Laboratory of Veterinary Pathology, Osaka Metropolitan
University Graduate School of Veterinary Science, Osaka, Japan
| | - Mitsuru KUWAMURA
- Laboratory of Veterinary Pathology, Osaka Metropolitan
University Graduate School of Veterinary Science, Osaka, Japan
| | - Yasu-Taka AZUMA
- Laboratory of Prophylactic Pharmacology, Osaka Metropolitan
University Graduate School of Veterinary Science, Osaka, Japan
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16
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Niu W, Zhou W, Lu S, Vu T, Jayaraman V, Faraldo-Gómez JD, Zheng L. Ca 2+ efflux facilitated by co-transport of inorganic phosphate anion in the H +/Ca 2+ antiporter YfkE. Commun Biol 2023; 6:573. [PMID: 37248347 PMCID: PMC10227063 DOI: 10.1038/s42003-023-04944-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
Ca2+ is an important signaling messenger. In microorganisms, fungi, and plants, H+/Ca2+ antiporters (CAX) are known to play key roles in the homeostasis of intracellular Ca2+ by catalyzing its efflux across the cell membrane. Here, we reveal that the bacterial CAX homolog YfkE transports Ca2+ in two distinct modes: a low-flux H+/Ca2+ exchange mode and a high-flux mode in which Ca2+ and phosphate ions are co-transported (1:1) in exchange for H+. Coupling with phosphate greatly accelerates the Ca2+ efflux activity of YfkE. Our studies reveal that Ca2+ and phosphate bind to adjacent sites in a central translocation pathway and lead to mechanistic insights that explain how this CAX alters its conserved alpha-repeat motifs to adopt phosphate as a specific "transport chaperon" for Ca2+ translocation. This finding uncovers a co-transport mechanism within the CAX family that indicates this class of proteins contributes to the cellular homeostasis of both Ca2+ and phosphate.
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Affiliation(s)
- Wei Niu
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shuo Lu
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Trung Vu
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Vasanthi Jayaraman
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lei Zheng
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.
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17
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Loeck T, Schwab A. The role of the Na +/Ca 2+-exchanger (NCX) in cancer-associated fibroblasts. Biol Chem 2023; 404:325-337. [PMID: 36594183 DOI: 10.1515/hsz-2022-0253] [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: 08/17/2022] [Accepted: 12/09/2022] [Indexed: 01/04/2023]
Abstract
Cancer is characterized by uncontrolled growth, invasion, and metastasis. In addition to solid cancer cells, cancer-associated fibroblasts (CAFs) play important roles in cancer pathophysiology. They arise from "healthy" cells but get manipulated by solid cancer cells to supply them and develop a tumor microenvironment (TME) that protects the cancer cells from the immune defense. A wide variety of cell types can differentiate into CAFs, including fibroblasts, endothelial cells, and epithelial cells. Precise Ca2+ regulation is essential for each cell including CAFs. The electrogenic Na+/Ca2+ exchanger (NCX) is one of the ubiquitously expressed regulatory Ca2+ transport proteins that rapidly responds to changes of the intracellular ion concentrations. Its transport function is also influenced by the membrane potential and thereby indirectly by the activity of ion channels. NCX transports Ca2+ out of the cell (forward mode) or allows its influx (reverse mode), always in exchange for 3 Na+ ions that are moved into the opposite direction. In this review, we discuss the functional roles NCX has in CAFs and how these depend on the properties of the TME. NCX activity modifies migration and leads to a reduced proliferation and apoptosis. The effect of the NCX in fibrosis is still largely unknown.
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Affiliation(s)
- Thorsten Loeck
- Institut für Physiologie II, Westfälische Wilhelms-Universität Münster, Robert-Koch-Str. 27b, D-48149 Münster, Germany
| | - Albrecht Schwab
- Institut für Physiologie II, Westfälische Wilhelms-Universität Münster, Robert-Koch-Str. 27b, D-48149 Münster, Germany
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18
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Structure-Based Function and Regulation of NCX Variants: Updates and Challenges. Int J Mol Sci 2022; 24:ijms24010061. [PMID: 36613523 PMCID: PMC9820601 DOI: 10.3390/ijms24010061] [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: 10/09/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
The plasma-membrane homeostasis Na+/Ca2+ exchangers (NCXs) mediate Ca2+ extrusion/entry to dynamically shape Ca2+ signaling/in biological systems ranging from bacteria to humans. The NCX gene orthologs, isoforms, and their splice variants are expressed in a tissue-specific manner and exhibit nearly 104-fold differences in the transport rates and regulatory specificities to match the cell-specific requirements. Selective pharmacological targeting of NCX variants could benefit many clinical applications, although this intervention remains challenging, mainly because a full-size structure of eukaryotic NCX is unavailable. The crystal structure of the archaeal NCX_Mj, in conjunction with biophysical, computational, and functional analyses, provided a breakthrough in resolving the ion transport mechanisms. However, NCX_Mj (whose size is nearly three times smaller than that of mammalian NCXs) cannot serve as a structure-dynamic model for imitating high transport rates and regulatory modules possessed by eukaryotic NCXs. The crystal structures of isolated regulatory domains (obtained from eukaryotic NCXs) and their biophysical analyses by SAXS, NMR, FRET, and HDX-MS approaches revealed structure-based variances of regulatory modules. Despite these achievements, it remains unclear how multi-domain interactions can decode and integrate diverse allosteric signals, thereby yielding distinct regulatory outcomes in a given ortholog/isoform/splice variant. This article summarizes the relevant issues from the perspective of future developments.
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19
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Conformational transition induced in the aspartate:alanine antiporter by L-Ala binding. Sci Rep 2022; 12:15871. [PMID: 36151227 PMCID: PMC9508256 DOI: 10.1038/s41598-022-19974-z] [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] [Received: 05/02/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
An aspartate:alanine antiporter (AspT) from the lactic acid bacterium Tetragenococcus halophilus catalyzes the electrogenic aspartate<sup>1-</sup>:alanine<sup>0</sup> exchange reaction. Our previous kinetic analyses of transport reactions mediated by AspT in reconstituted liposomes suggested that, although the substrate transport reactions are physiologically coupled, the putative binding sites of L-aspartate (-Asp) and L-alanine (-Ala) are independently located on AspT. By using the fluorescent probe Oregon Green maleimide (OGM), which reacts specifically with cysteine, we also found that the presence of L-Asp changes the conformation of AspT. In this study, we conducted an OGM labeling assay in the presence of L-Ala. The labeling efficiency of single cysteine mutants (G62C and P79C) in transmembrane helix 3 of the AspT showed novel patterns depending on the presence of L-Ala or analogs. A concentration-dependent shift of AspT from the conformation in the presence of one substrate to that specific to the substrate added subsequently (L-Ala or L-Asp) was observed. Moreover, size-exclusion-chromatography-based thermostability assays indicated that the thermal stability of AspT in the presence of L-Ala differed from that in the presence of L-Asp. From these results, we concluded that L-Ala binding yields a conformation different from the apo or L-Asp binding conformations.
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20
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Giladi M, Mitra S, Simhaev L, Hiller R, Refaeli B, Strauss T, Baiz CR, Khananshvili D. Exploring the Li + transporting mutant of NCX_Mj for assigning ion binding sites of mitochondrial NCLX. Cell Calcium 2022; 107:102651. [PMID: 36116246 PMCID: PMC10124574 DOI: 10.1016/j.ceca.2022.102651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/02/2022]
Abstract
The plasma membrane (NCX) and mitochondrial (NCLX) Na+/Ca2+ exchangers are structurally related proteins, although they operate under strictly different ionic conditions and membrane potentials. In contrast with NCX, NCLX can transport either Li+ or Na+ in exchange for Ca2+. Whereas the crystal structure of the archaeal NCX (NCX_Mj) describes the binding sites for alternative binding of 3Na+ or 1Ca2+, these features remain elusive for NCLX due to the lack of structural information. To elucidate the ion-binding features of mitochondrial NCLX, we analyzed here the Li+-transporting NCLX_Mj mutant, produced by replacing the ion-coordinating residues in the archaeal NCX (NCX_Mj) to match the ion-coordinating residues of human NCLX. The NCLX_Mj-mediated Na+/Ca2+ or Li+/Ca2+ exchange rates are insensitive to varying voltage, consistent with an electroneutral ion exchange. Molecular dynamics (MD) simulations revealed that NCLX_Mj contains two novel Li+ binding sites with four ion-coordinating residues, derived from the three Na+ binding sites of NCX_Mj. The ion-coordination modes, observed in the MD simulations, were further supported by two-dimensional infrared (2D IR) spectroscopy and by testing the mutational effects on the ion fluxes. Collectively, our results revealed a structural basis for Li+ binding and electroneutral transport (2Na+/Li+:1Ca2+) by NCLX_Mj, meaning that the NCLX-mediated electroneutral transport may predefine mitochondrial Ca2+ and Na+ signaling to modulate cellular functions.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel; Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Sunayana Mitra
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
| | - Luba Simhaev
- Computer-Assisted Drug Design Unit, Blavatnik Center for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Bosmat Refaeli
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Tali Strauss
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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21
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King DR, Sedovy MW, Eaton X, Dunaway LS, Good ME, Isakson BE, Johnstone SR. Cell-To-Cell Communication in the Resistance Vasculature. Compr Physiol 2022; 12:3833-3867. [PMID: 35959755 DOI: 10.1002/cphy.c210040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The arterial vasculature can be divided into large conduit arteries, intermediate contractile arteries, resistance arteries, arterioles, and capillaries. Resistance arteries and arterioles primarily function to control systemic blood pressure. The resistance arteries are composed of a layer of endothelial cells oriented parallel to the direction of blood flow, which are separated by a matrix layer termed the internal elastic lamina from several layers of smooth muscle cells oriented perpendicular to the direction of blood flow. Cells within the vessel walls communicate in a homocellular and heterocellular fashion to govern luminal diameter, arterial resistance, and blood pressure. At rest, potassium currents govern the basal state of endothelial and smooth muscle cells. Multiple stimuli can elicit rises in intracellular calcium levels in either endothelial cells or smooth muscle cells, sourced from intracellular stores such as the endoplasmic reticulum or the extracellular space. In general, activation of endothelial cells results in the production of a vasodilatory signal, usually in the form of nitric oxide or endothelial-derived hyperpolarization. Conversely, activation of smooth muscle cells results in a vasoconstriction response through smooth muscle cell contraction. © 2022 American Physiological Society. Compr Physiol 12: 1-35, 2022.
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Affiliation(s)
- D Ryan King
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Vascular and Heart Research, Virginia Tech, Roanoke, Virginia, USA
| | - Meghan W Sedovy
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Vascular and Heart Research, Virginia Tech, Roanoke, Virginia, USA.,Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, Virginia, USA
| | - Xinyan Eaton
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Vascular and Heart Research, Virginia Tech, Roanoke, Virginia, USA
| | - Luke S Dunaway
- Robert M. Berne Cardiovascular Research Centre, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Miranda E Good
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, Massachusetts, USA
| | - Brant E Isakson
- Robert M. Berne Cardiovascular Research Centre, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Scott R Johnstone
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Vascular and Heart Research, Virginia Tech, Roanoke, Virginia, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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22
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Shan X, Luo L, Yu Z, You J. Recent advances in versatile inverse lyotropic liquid crystals. J Control Release 2022; 348:1-21. [PMID: 35636617 DOI: 10.1016/j.jconrel.2022.05.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 01/01/2023]
Abstract
Owing to the rapid and significant progress in advanced materials and life sciences, nanotechnology is increasingly gaining in popularity. Among numerous bio-mimicking carriers, inverse lyotropic liquid crystals are known for their unique properties. These carriers make accommodation of molecules with varied characteristics achievable due to their complicated topologies. Besides, versatile symmetries of inverse LCNPs (lyotropic crystalline nanoparticles) and their aggregating bulk phases allow them to be applied in a wide range of fields including drug delivery, food, cosmetics, material sciences etc. In this review, in-depth summary, discussion and outlook for inverse lyotropic liquid crystals are provided.
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Affiliation(s)
- Xinyu Shan
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Lihua Luo
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Zhixin Yu
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Jian You
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China.
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23
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Staritzbichler R, Yaklich E, Sarti E, Ristic N, Hildebrand PW, Forrest LR. AlignMe: an update of the web server for alignment of membrane protein sequences. Nucleic Acids Res 2022; 50:W29-W35. [PMID: 35609986 PMCID: PMC9252776 DOI: 10.1093/nar/gkac391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
The AlignMe web server is dedicated to accurately aligning sequences of membrane proteins, a particularly challenging task due to the strong evolutionary divergence and the low compositional complexity of hydrophobic membrane-spanning proteins. AlignMe can create pairwise alignments of either two primary amino acid sequences or two hydropathy profiles. The web server for AlignMe has been continuously available for >10 years, supporting 1000s of users per year. Recent improvements include anchoring, multiple submissions, and structure visualization. Anchoring is the ability to constrain a position in an alignment, which allows expert information about related residues in proteins to be incorporated into an alignment without manual modification. The original web interface to the server limited the user to one alignment per submission, hindering larger scale studies. Now, batches of alignments can be initiated with a single submission. Finally, to provide structural context for the relationship between proteins, sequence similarity can now be mapped onto one or more structures (or structural models) of the proteins being aligned, by links to MutationExplorer, a web-based visualization tool. Together with a refreshed user interface, these features further enhance an important resource in the membrane protein community. The AlignMe web server is freely available at https://www.bioinfo.mpg.de/AlignMe/.
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Affiliation(s)
- René Staritzbichler
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Emily Yaklich
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edoardo Sarti
- Algorithms, Biology, Structure Unit Inria Sophia Antipolis - Méditerranée, 06902 Valbonne, France
| | - Nikola Ristic
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Peter W Hildebrand
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany.,Charité -Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, 10117 Berlin, Germany
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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Disturbance of calcium homeostasis and myogenesis caused by TET2 deletion in muscle stem cells. Cell Death Dis 2022; 8:236. [PMID: 35490157 PMCID: PMC9056526 DOI: 10.1038/s41420-022-01041-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 01/22/2023]
Abstract
Skeletal muscle myogenesis is a sophisticated process controlled by genetic and epigenetic regulators. In animals, one of the key enzymes for the DNA demethylation of 5-methylcytosine is TET2. Although TET2 is essential for muscle development, the mechanisms by which TET2 regulates myogenesis, particularly the implication for muscle stem cells, remains unclear. In the present study, we employed the TET2 knockout mouse model to investigate the function of TET2 in muscle development and regeneration. We observed that TET2 deficiency caused impaired muscle stem cell proliferation and differentiation, resulting in the reduction in both myofiber number and muscle tissue size. Specifically, TET2 maintains calcium homeostasis in muscle stem cells by controlling the DNA methylation levels of the calcium pathway genes. Forced expression of the sodium/calcium exchanger protein SLC8A3 could rescue the myogenic defects in TET2 knockout cells. Our data not only illustrated the vital function of TET2 during myogenesis but also identified novel targets that contribute to calcium homeostasis for enhancing muscle function.
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The Oxidative Balance Orchestrates the Main Keystones of the Functional Activity of Cardiomyocytes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7714542. [PMID: 35047109 PMCID: PMC8763515 DOI: 10.1155/2022/7714542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/03/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
Abstract
This review is aimed at providing an overview of the key hallmarks of cardiomyocytes in physiological and pathological conditions. The main feature of cardiac tissue is the force generation through contraction. This process requires a conspicuous energy demand and therefore an active metabolism. The cardiac tissue is rich of mitochondria, the powerhouses in cells. These organelles, producing ATP, are also the main sources of ROS whose altered handling can cause their accumulation and therefore triggers detrimental effects on mitochondria themselves and other cell components thus leading to apoptosis and cardiac diseases. This review highlights the metabolic aspects of cardiomyocytes and wanders through the main systems of these cells: (a) the unique structural organization (such as different protein complexes represented by contractile, regulatory, and structural proteins); (b) the homeostasis of intracellular Ca2+ that represents a crucial ion for cardiac functions and E-C coupling; and (c) the balance of Zn2+, an ion with a crucial impact on the cardiovascular system. Although each system seems to be independent and finely controlled, the contractile proteins, intracellular Ca2+ homeostasis, and intracellular Zn2+ signals are strongly linked to each other by the intracellular ROS management in a fascinating way to form a "functional tetrad" which ensures the proper functioning of the myocardium. Nevertheless, if ROS balance is not properly handled, one or more of these components could be altered resulting in deleterious effects leading to an unbalance of this "tetrad" and promoting cardiovascular diseases. In conclusion, this "functional tetrad" is proposed as a complex network that communicates continuously in the cardiomyocytes and can drive the switch from physiological to pathological conditions in the heart.
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Characteristic attributes limiting the transport rates in NCX orthologs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183792. [PMID: 34582763 DOI: 10.1016/j.bbamem.2021.183792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022]
Abstract
The Na+/Ca2+ exchangers (NCXs) modulate the Ca2+ signaling and homeostasis in health and disease. The transport cycle turnover rates (kcat) and the kcat/Km values of eukaryotic NCXs are ~104-times higher than those of prokaryotic NCXs. Three ion-coordinating residues (out of twelve) differ between eukaryotic NCXs and NCX_Mj. The replacement of three ion-coordinating residues in NCX_Mj does not increase kcat, probably due to the structural rigidity of NCX_Mj. Phospholipids and cholesterol increase (up to 10-fold) the transport rates in the cardiac NCX1.1, but not in NCX_Mj. A lipid environment can partially contribute to the huge kinetic variances among NCXs.
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27
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Ottolia M, John S, Hazan A, Goldhaber JI. The Cardiac Na + -Ca 2+ Exchanger: From Structure to Function. Compr Physiol 2021; 12:2681-2717. [PMID: 34964124 DOI: 10.1002/cphy.c200031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ca2+ homeostasis is essential for cell function and survival. As such, the cytosolic Ca2+ concentration is tightly controlled by a wide number of specialized Ca2+ handling proteins. One among them is the Na+ -Ca2+ exchanger (NCX), a ubiquitous plasma membrane transporter that exploits the electrochemical gradient of Na+ to drive Ca2+ out of the cell, against its concentration gradient. In this critical role, this secondary transporter guides vital physiological processes such as Ca2+ homeostasis, muscle contraction, bone formation, and memory to name a few. Herein, we review the progress made in recent years about the structure of the mammalian NCX and how it relates to function. Particular emphasis will be given to the mammalian cardiac isoform, NCX1.1, due to the extensive studies conducted on this protein. Given the degree of conservation among the eukaryotic exchangers, the information highlighted herein will provide a foundation for our understanding of this transporter family. We will discuss gene structure, alternative splicing, topology, regulatory mechanisms, and NCX's functional role on cardiac physiology. Throughout this article, we will attempt to highlight important milestones in the field and controversial topics where future studies are required. © 2021 American Physiological Society. Compr Physiol 12:1-37, 2021.
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Affiliation(s)
- Michela Ottolia
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Scott John
- Department of Medicine (Cardiology), UCLA, Los Angeles, California, USA
| | - Adina Hazan
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Joshua I Goldhaber
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
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28
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Magli E, Fattorusso C, Persico M, Corvino A, Esposito G, Fiorino F, Luciano P, Perissutti E, Santagada V, Severino B, Tedeschi V, Pannaccione A, Pignataro G, Caliendo G, Annunziato L, Secondo A, Frecentese F. New Insights into the Structure-Activity Relationship and Neuroprotective Profile of Benzodiazepinone Derivatives of Neurounina-1 as Modulators of the Na +/Ca 2+ Exchanger Isoforms. J Med Chem 2021; 64:17901-17919. [PMID: 34845907 PMCID: PMC8713167 DOI: 10.1021/acs.jmedchem.1c01212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Due to the neuroprotective role of the Na+/Ca2+ exchanger (NCX) isoforms NCX1 and NCX3, we synthesized novel benzodiazepinone derivatives of the unique NCX activator Neurounina-1, named compounds 1-19. The derivatives are characterized by a benzodiazepinonic nucleus linked to five- or six-membered cyclic amines via a methylene, ethylene, or acetyl spacer. The compounds have been screened on NCX1/NCX3 isoform activities by a high-throughput screening approach, and the most promising were characterized by patch-clamp electrophysiology and Fura-2AM video imaging. We identified two novel modulators of NCX: compound 4, inhibiting NCX1 reverse mode, and compound 14, enhancing NCX1 and NCX3 activity. Compound 1 displayed neuroprotection in two preclinical models of brain ischemia. The analysis of the conformational and steric features led to the identification of the molecular volume required for selective NCX1 activation for mixed NCX1/NCX3 activation or for NCX1 inhibition, providing the first prototypal model for the design of optimized isoform modulators.
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Affiliation(s)
- Elisa Magli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Marco Persico
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Angela Corvino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Gianluca Esposito
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Ferdinando Fiorino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Paolo Luciano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Elisa Perissutti
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Vincenzo Santagada
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Beatrice Severino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Valentina Tedeschi
- Department of Neuroscience, Division of Pharmacology, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Anna Pannaccione
- Department of Neuroscience, Division of Pharmacology, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Giuseppe Pignataro
- Department of Neuroscience, Division of Pharmacology, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Giuseppe Caliendo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | | | - Agnese Secondo
- Department of Neuroscience, Division of Pharmacology, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Francesco Frecentese
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
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Pan-phylum genome-wide identification of sodium calcium exchangers reveal heterogeneous expansions and possible roles in nematode parasitism. Gene 2021; 810:146052. [PMID: 34756961 DOI: 10.1016/j.gene.2021.146052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
Calcium signaling is ubiquitous in nematode development from fertilization to cell specification to apoptosis. Calcium also regulates dauer entry in Caenorhabditis elegans, which corresponds to the infective stage of parasitic nematodes. In diverse parasites such as Trypanosoma cruzi and Toxoplasma gondii calcium has been shown to regulate host cell entry and egress, and perturbing calcium signaling represents a possible route to inhibit infection and parasitism in these species. Sodium calcium exchangers are considered the most important mechanism of calcium efflux, and our lab has previously characterized the sodium calcium exchanger gene family in C. elegans and studied the diversity of this family across a subset of specific nematode species. Here we build upon these data and explore sodium calcium exchangers across 108 species of nematodes. Our data reveal substantial differences in sodium calcium exchanger counts across the Phylum and detail expansions and contractions of specific exchanger subtypes within certain nematode clades. Finally, we also provide evidence for a role of sodium calcium exchangers in parasite activation by examining differentially expressed genes in non-activated versus activated infective stage larvae. Taken together our findings paint a heterogeneous picture of sodium calcium exchanger evolution across the Phylum Nematoda that may reflect unique adaptations to free-living and parasitic lifestyles.
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A Unique Reverse Adaptation Mechanism Assists Bordetella pertussis in Resistance to Both Scarcity and Toxicity of Manganese. mBio 2021; 12:e0190221. [PMID: 34700381 PMCID: PMC8546581 DOI: 10.1128/mbio.01902-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The ability of bacterial pathogens to acquire essential micronutrients is critical for their survival in the host environment. Manganese plays a complex role in the virulence of a variety of pathogens due to its function as an antioxidant and enzymatic cofactor. Therefore, host cells deprive pathogens of manganese to prevent or attenuate infection. Here, we show that evolution of the human-restricted pathogen Bordetella pertussis has selected for an inhibitory duplication within a manganese exporter of the calcium:cation antiporter superfamily. Intriguingly, upon exposure to toxic levels of manganese, the nonfunctional exporter becomes operative in resister cells due to a unique reverse adaptation mechanism. However, compared with wild-type (wt) cells, the resisters carrying a functional copy of the exporter displayed strongly reduced intracellular levels of manganese and impaired growth under oxidative stress. Apparently, inactivation of the manganese exporter and the resulting accumulation of manganese in the cytosol benefited the pathogen by improving its survival under stress conditions. The inhibitory duplication within the exporter gene is highly conserved among B. pertussis strains, absent from all other Bordetella species and from a vast majority of organisms across all kingdoms of life. Therefore, we conclude that inactivation of the exporter gene represents an exceptional example of a flexible genome decay strategy employed by a human pathogen to adapt to its exclusive host.
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Abstract
The uptake of calcium into and extrusion of calcium from the mitochondrial matrix is a fundamental biological process that has critical effects on cellular metabolism, signaling, and survival. Disruption of mitochondrial calcium (mCa2+) cycling is implicated in numerous acquired diseases such as heart failure, stroke, neurodegeneration, diabetes, and cancer, and is genetically linked to several inherited neuromuscular disorders. Understanding the mechanisms responsible for mCa2+ exchange therefore holds great promise for the treatment of these diseases. The past decade has seen the genetic identification of many of the key proteins that mediate mitochondrial calcium uptake and efflux. Here, we present an overview of the phenomenon of mCa2+ transport, and a comprehensive examination of the molecular machinery that mediates calcium flux across the inner mitochondrial membrane: the mitochondrial uniporter complex (consisting of MCU, EMRE, MICU1, MICU2, MICU3, MCUB, and MCUR1), NCLX, LETM1, the mitochondrial ryanodine receptor, and the mitochondrial permeability transition pore. We then consider the physiological implications of mCa2+ flux and evaluate how alterations in mCa2+ homeostasis contribute to human disease. This review concludes by highlighting opportunities and challenges for therapeutic intervention in pathologies characterized by aberrant mCa2+ handling and by summarizing critical unanswered questions regarding the biology of mCa2+ flux.
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Affiliation(s)
- Joanne F Garbincius
- Center for Translational Medicine, Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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32
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Proton-modulated interactions of ions with transport sites of prokaryotic and eukaryotic NCX prototypes. Cell Calcium 2021; 99:102476. [PMID: 34564055 DOI: 10.1016/j.ceca.2021.102476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/23/2022]
Abstract
The cytosolic pH decline from 7.2 to 6.9 results in 90% inactivation of mammalian Na+/Ca2+ exchangers (NCXs) due to protons interactions with regulatory and transport domains ("proton block"). Remarkably, the pH titration curves of mammalian and prokaryotic NCXs significantly differ, even after excluding the allosteric effects through regulatory domains. This is fascinating since "only" three (out of twelve) ion-coordinating residues (T50S, E213D, and D240N) differ between the archaeal NCX_Mj and mammalian NCXs although they contain either three or two carboxylates, respectively. To resolve the underlying mechanisms of pH-dependent regulation, the ion-coordinating residues of NCX_Mj were mutated to imitate the ion ligation arrays of mammalian NCXs; the mutational effects were tested on the ion binding/transport by using ion-flux assays and two-dimensional infrared (2D IR) spectroscopy. Our analyses revealed that two deprotonated carboxylates ligate 3Na+ or 1Ca2+ in NCX prototypes with three or two carboxylates. The Na+/Ca2+ exchange rates of NCX_Mj reach saturation at pH 5.0, whereas the Na+/Ca2+ exchange rates of the cardiac NCX1.1 gradually increase even at alkaline pHs. The T50S replacement in NCX_Mj "recapitulates" the pH titration curves of mammalian NCX by instigating an alkaline shift. Proteolytic shaving of regulatory CBD domains activates NCX1.1, although the normalized pH-titration curves are comparable in trypsin treated and untreated NCX1.1. Thus, the T50S-dependent alkaline shift sets a dynamic range for "proton block" function at physiological pH, whereas the CBDs (and other regulatory modes) modulate incremental changes in the transport rates rather than affect the shape of pH dependent curves.
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33
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Zhang QW, Baig MMFA, Zhang TQ, Zhai TT, Qin X, Xia XH. RETRACTED: Liposomal valinomycin mediated cellular K + leak promoting apoptosis of liver cancer cells. J Control Release 2021; 337:317-328. [PMID: 34311027 DOI: 10.1016/j.jconrel.2021.07.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 01/18/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the corresponding author. It has been found that Fig 2B contains manipulated components, and Fig 5A partially overlaps with Fig 6 of a published paper authored by Mirza Muhammad Faran Ashraf Baig, et, al., The effective transfection of a low dose of negatively charged drug-loaded DNA-nanocarriers into cancer cells via scavenger receptors, J. Pharm. Anal. 11 (2021) 174-182, https://doi.org/10.1016/j.jpha.2020.10.003. The corresponding author indicated that they cannot guarantee the integrity of the images in the manuscript, as well as the conclusions of the paper. As a result, the Editor-in-Chief has decided to retract the paper. The corresponding author deeply regrets the circumstances and apologizes to the scientific community for not having detected this prior to publication.
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Affiliation(s)
- Qian-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mirza Muhammad Faran Ashraf Baig
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tian-Qi Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ting-Ting Zhai
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiang Qin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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34
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Khananshvili D. The Archaeal Na +/Ca 2+ Exchanger (NCX_Mj) as a Model of Ion Transport for the Superfamily of Ca 2+/CA Antiporters. Front Chem 2021; 9:722336. [PMID: 34409017 PMCID: PMC8366772 DOI: 10.3389/fchem.2021.722336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The superfamily of Calcium/Cation (Ca2+/CA) antiporters extrude Ca2+ from the cytosol or subcellular compartments in exchange with Na+, K+, H+, Li+, or Mg2+ and thereby provide a key mechanism for Ca2+ signaling and ion homeostasis in biological systems ranging from bacteria to humans. The structure-dynamic determinants of ion selectivity and transport rates remain unclear, although this is of primary physiological significance. Despite wide variances in the ion selectivity and transport rates, the Ca2+/CA proteins share structural motifs, although it remains unclear how the ion recognition/binding is coupled to the ion translocation events. Here, the archaeal Na+/Ca2+ exchanger (NCX_Mj) is considered as a structure-based model that can help to resolve the ion transport mechanisms by using X-ray, HDX-MS, ATR-FTIR, and computational approaches in conjunction with functional analyses of mutants. Accumulating data reveal that the local backbone dynamics at ion-coordinating residues is characteristically constrained in apo NCX_Mj, which may predefine the affinity and stability of ion-bound species in the ground and transition states. The 3Na+ or 1Ca2+ binding to respective sites of NCX_Mj rigidify the backbone dynamics at specific segments, where the ion-dependent compression of the ion-permeating four-helix bundle (TM2, TM3, TM7, and TM8) induces the sliding of the two-helix cluster (TM1/TM6) on the protein surface to switch the OF (outward-facing) and IF (inward-facing) conformations. Taking into account the common structural elements shared by Ca2+/CAs, NCX_Mj may serve as a model for studying the structure-dynamic and functional determinants of ion-coupled alternating access, transport catalysis, and ion selectivity in Ca2+/CA proteins.
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Affiliation(s)
- Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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35
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Cross-Talk between Mechanosensitive Ion Channels and Calcium Regulatory Proteins in Cardiovascular Health and Disease. Int J Mol Sci 2021; 22:ijms22168782. [PMID: 34445487 PMCID: PMC8395829 DOI: 10.3390/ijms22168782] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/12/2022] Open
Abstract
Mechanosensitive ion channels are widely expressed in the cardiovascular system. They translate mechanical forces including shear stress and stretch into biological signals. The most prominent biological signal through which the cardiovascular physiological activity is initiated or maintained are intracellular calcium ions (Ca2+). Growing evidence show that the Ca2+ entry mediated by mechanosensitive ion channels is also precisely regulated by a variety of key proteins which are distributed in the cell membrane or endoplasmic reticulum. Recent studies have revealed that mechanosensitive ion channels can even physically interact with Ca2+ regulatory proteins and these interactions have wide implications for physiology and pathophysiology. Therefore, this paper reviews the cross-talk between mechanosensitive ion channels and some key Ca2+ regulatory proteins in the maintenance of calcium homeostasis and its relevance to cardiovascular health and disease.
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36
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Chandra Rajan K, Meng Y, Yu Z, Roberts SB, Vengatesen T. Oyster biomineralization under ocean acidification: From genes to shell. GLOBAL CHANGE BIOLOGY 2021; 27:3779-3797. [PMID: 33964098 DOI: 10.1111/gcb.15675] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/02/2021] [Indexed: 05/27/2023]
Abstract
Biomineralization is one of the key processes that is notably affected in marine calcifiers such as oysters under ocean acidification (OA). Understanding molecular changes in the biomineralization process under OA and its heritability, therefore, is key to developing conservation strategies for protecting ecologically and economically important oyster species. To do this, in this study, we have explicitly chosen the tissue involved in biomineralization (mantle) of an estuarine commercial oyster species, Crassostrea hongkongensis. The primary aim of this study is to understand the influence of DNA methylation over gene expression of mantle tissue under decreased ~pH 7.4, a proxy of OA, and to extrapolate if these molecular changes can be observed in the product of biomineralization-the shell. We grew early juvenile C. hongkongensis, under decreased ~pH 7.4 and control ~pH 8.0 over 4.5 months and studied OA-induced DNA methylation and gene expression patterns along with shell properties such as microstructure, crystal orientation and hardness. The population of oysters used in this study was found to be moderately resilient to OA at the end of the experiment. The expression of key biomineralization-related genes such as carbonic anhydrase and alkaline phosphatase remained unaffected; thus, the mechanical properties of the shell (shell growth rate, hardness and crystal orientation) were also maintained without any significant difference between control and OA conditions with signs of severe dissolution. In addition, this study makes three major conclusions: (1) higher expression of Ca2+ binding/signalling-related genes in the mantle plays a key role in maintaining biomineralization under OA; (2) DNA methylation changes occur in response to OA; however, these methylation changes do not directly control gene expression; and (3) OA would be more of a 'dissolution problem' rather than a 'biomineralization problem' for resilient species that maintain calcification rate with normal shell growth and mechanical properties.
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Affiliation(s)
- Kanmani Chandra Rajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Yuan Meng
- State Key Laboratory of Respiratory Disease, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ziniu Yu
- South China Sea Institute of Oceanology, Guangzhou, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Thiyagarajan Vengatesen
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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37
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Boo MV, Chew SF, Ip YK. Basolateral Na +/Ca 2+ exchanger 1 and Na +/K +-ATPase, which display light-enhanced gene and protein expression levels, could be involved in the absorption of exogenous Ca 2+ through the ctenidium of the giant clam, Tridacna squamosa. Comp Biochem Physiol A Mol Integr Physiol 2021; 259:110997. [PMID: 34051370 DOI: 10.1016/j.cbpa.2021.110997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
Giant clams perform light-enhanced shell formation (calcification) and therefore need to increase the uptake of exogenous Ca2+ during illumination. The ctenidium of the fluted giant clam, Tridacna squamosa, is involved in light-enhanced Ca2+ uptake. It expresses the pore-forming voltage-gated calcium channel (VGCC) subunit alpha 1 (CACNA1) in the apical membrane of the epithelial cells, and the protein expression level of CACNA1 is upregulated in the ctenidium during illumination. This study aimed to elucidate the mechanism involved in the transport of the absorbed Ca2+ across the basolateral membrane of the ctenidial epithelial cells into the hemolymph. We obtained a homolog of Na+/Ca2+exchanger 1 (NCX1-like) from the ctenidium of T. squamosa, which comprised 2418 bp, encoding a protein of 806 amino acids (88.9 kDa). NCX1-like had a basolateral localization in the epithelial cells of the ctenidial filaments and tertiary water channels. Illumination resulted in significant increases in the transcript and protein levels of NCX1-like/NCX1-like in the ctenidium. Hence, NCX1-like could operate in conjunction with VGCC to increase the transport of Ca2+ from the ambient seawater into the hemolymph during illumination. Illumination also resulted in the upregulation of the gene and protein expression levels of Na+/K+-ATPase (NKA) α-subunit (NKAα/NKAα) in the ctenidium of T. squamosa. As light-enhanced extrusion of Ca2+ into the hemolymph through NCX1-like would lead to a greater influx of extracellular Na+, the increased expression of the basolateral NKA was required to augment the capacity of intracellular Na+ homeostasis.
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Affiliation(s)
- Mel V Boo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Shit F Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
| | - Yuen K Ip
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore.
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Gök C, Plain F, Robertson AD, Howie J, Baillie GS, Fraser NJ, Fuller W. Dynamic Palmitoylation of the Sodium-Calcium Exchanger Modulates Its Structure, Affinity for Lipid-Ordered Domains, and Inhibition by XIP. Cell Rep 2021; 31:107697. [PMID: 32521252 PMCID: PMC7296346 DOI: 10.1016/j.celrep.2020.107697] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/07/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
The transmembrane sodium-calcium (Na-Ca) exchanger 1 (NCX1) regulates cytoplasmic Ca levels by facilitating electrogenic exchange of Ca for Na. Palmitoylation, the only reversible post-translational modification known to modulate NCX1 activity, controls NCX1 inactivation. Here, we show that palmitoylation of NCX1 modifies the structural arrangement of the NCX1 dimer and controls its affinity for lipid-ordered membrane domains. NCX1 palmitoylation occurs dynamically at the cell surface under the control of the enzymes zDHHC5 and APT1. We identify the position of the endogenous exchange inhibitory peptide (XIP) binding site within the NCX1 regulatory intracellular loop and demonstrate that palmitoylation controls the ability of XIP to bind this site. We also show that changes in NCX1 palmitoylation change cytosolic Ca. Our results thus demonstrate the broad molecular consequences of NCX1 palmitoylation and highlight a means to manipulate the inactivation of this ubiquitous ion transporter that could ameliorate pathologies linked to Ca overload via NCX1. NCX1 is dynamically palmitoylated at the cell surface by zDHHC5 and APT1 Palmitoylation modifies the NCX1 dimer’s structure and affinity for lipid rafts We identify the binding site of the endogenous XIP domain in NCX1’s regulatory loop Palmitoylation modifies NCX1 XIP affinity and hence regulates intracellular Ca
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Affiliation(s)
- Caglar Gök
- Institute of Cardiovascular & Medical Sciences, Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Fiona Plain
- School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, UK
| | - Alan D Robertson
- Institute of Cardiovascular & Medical Sciences, Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Jacqueline Howie
- Institute of Cardiovascular & Medical Sciences, Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - George S Baillie
- Institute of Cardiovascular & Medical Sciences, Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Niall J Fraser
- School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, UK
| | - William Fuller
- Institute of Cardiovascular & Medical Sciences, Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
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Datta S, Jaiswal M. Mitochondrial calcium at the synapse. Mitochondrion 2021; 59:135-153. [PMID: 33895346 DOI: 10.1016/j.mito.2021.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/28/2021] [Accepted: 04/13/2021] [Indexed: 12/15/2022]
Abstract
Mitochondria are dynamic organelles, which serve various purposes, including but not limited to the production of ATP and various metabolites, buffering ions, acting as a signaling hub, etc. In recent years, mitochondria are being seen as the central regulators of cellular growth, development, and death. Since neurons are highly specialized cells with a heavy metabolic demand, it is not surprising that neurons are one of the most mitochondria-rich cells in an animal. At synapses, mitochondrial function and dynamics is tightly regulated by synaptic calcium. Calcium influx during synaptic activity causes increased mitochondrial calcium influx leading to an increased ATP production as well as buffering of synaptic calcium. While increased ATP production is required during synaptic transmission, calcium buffering by mitochondria is crucial to prevent faulty neurotransmission and excitotoxicity. Interestingly, mitochondrial calcium also regulates the mobility of mitochondria within synapses causing mitochondria to halt at the synapse during synaptic transmission. In this review, we summarize the various roles of mitochondrial calcium at the synapse.
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Affiliation(s)
- Sayantan Datta
- Tata Institute of Fundamental Research, Hyderabad, India
| | - Manish Jaiswal
- Tata Institute of Fundamental Research, Hyderabad, India.
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Ottolini M, Sonkusare SK. The Calcium Signaling Mechanisms in Arterial Smooth Muscle and Endothelial Cells. Compr Physiol 2021; 11:1831-1869. [PMID: 33792900 PMCID: PMC10388069 DOI: 10.1002/cphy.c200030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The contractile state of resistance arteries and arterioles is a crucial determinant of blood pressure and blood flow. Physiological regulation of arterial contractility requires constant communication between endothelial and smooth muscle cells. Various Ca2+ signals and Ca2+ -sensitive targets ensure dynamic control of intercellular communications in the vascular wall. The functional effect of a Ca2+ signal on arterial contractility depends on the type of Ca2+ -sensitive target engaged by that signal. Recent studies using advanced imaging methods have identified the spatiotemporal signatures of individual Ca2+ signals that control arterial and arteriolar contractility. Broadly speaking, intracellular Ca2+ is increased by ion channels and transporters on the plasma membrane and endoplasmic reticular membrane. Physiological roles for many vascular Ca2+ signals have already been confirmed, while further investigation is needed for other Ca2+ signals. This article focuses on endothelial and smooth muscle Ca2+ signaling mechanisms in resistance arteries and arterioles. We discuss the Ca2+ entry pathways at the plasma membrane, Ca2+ release signals from the intracellular stores, the functional and physiological relevance of Ca2+ signals, and their regulatory mechanisms. Finally, we describe the contribution of abnormal endothelial and smooth muscle Ca2+ signals to the pathogenesis of vascular disorders. © 2021 American Physiological Society. Compr Physiol 11:1831-1869, 2021.
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Affiliation(s)
- Matteo Ottolini
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia, USA
| | - Swapnil K Sonkusare
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia, USA.,Department of Molecular Physiology & Biological Physics, University of Virginia, Charlottesville, Virginia, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
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41
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Wallace MJ, El Refaey M, Mesirca P, Hund TJ, Mangoni ME, Mohler PJ. Genetic Complexity of Sinoatrial Node Dysfunction. Front Genet 2021; 12:654925. [PMID: 33868385 PMCID: PMC8047474 DOI: 10.3389/fgene.2021.654925] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
The pacemaker cells of the cardiac sinoatrial node (SAN) are essential for normal cardiac automaticity. Dysfunction in cardiac pacemaking results in human sinoatrial node dysfunction (SND). SND more generally occurs in the elderly population and is associated with impaired pacemaker function causing abnormal heart rhythm. Individuals with SND have a variety of symptoms including sinus bradycardia, sinus arrest, SAN block, bradycardia/tachycardia syndrome, and syncope. Importantly, individuals with SND report chronotropic incompetence in response to stress and/or exercise. SND may be genetic or secondary to systemic or cardiovascular conditions. Current management of patients with SND is limited to the relief of arrhythmia symptoms and pacemaker implantation if indicated. Lack of effective therapeutic measures that target the underlying causes of SND renders management of these patients challenging due to its progressive nature and has highlighted a critical need to improve our understanding of its underlying mechanistic basis of SND. This review focuses on current information on the genetics underlying SND, followed by future implications of this knowledge in the management of individuals with SND.
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Affiliation(s)
- Michael J. Wallace
- Frick Center for Heart Failure and Arrhythmia Research, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Mona El Refaey
- Frick Center for Heart Failure and Arrhythmia Research, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Pietro Mesirca
- CNRS, INSERM, Institut de Génomique Fonctionnelle, Université de Montpellier, Montpellier, France
- Laboratory of Excellence ICST, Montpellier, France
| | - Thomas J. Hund
- Frick Center for Heart Failure and Arrhythmia Research, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH, United States
| | - Matteo E. Mangoni
- CNRS, INSERM, Institut de Génomique Fonctionnelle, Université de Montpellier, Montpellier, France
- Laboratory of Excellence ICST, Montpellier, France
| | - Peter J. Mohler
- Frick Center for Heart Failure and Arrhythmia Research, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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Huang Y, Jin F, Funato Y, Xu Z, Zhu W, Wang J, Sun M, Zhao Y, Yu Y, Miki H, Hattori M. Structural basis for the Mg 2+ recognition and regulation of the CorC Mg 2+ transporter. SCIENCE ADVANCES 2021; 7:7/7/eabe6140. [PMID: 33568487 PMCID: PMC7875539 DOI: 10.1126/sciadv.abe6140] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/23/2020] [Indexed: 05/05/2023]
Abstract
The CNNM/CorC family proteins are Mg2+ transporters that are widely distributed in all domains of life. In bacteria, CorC has been implicated in the survival of pathogenic microorganisms. In humans, CNNM proteins are involved in various biological events, such as body absorption/reabsorption of Mg2+ and genetic disorders. Here, we determined the crystal structure of the Mg2+-bound CorC TM domain dimer. Each protomer has a single Mg2+ binding site with a fully dehydrated Mg2+ ion. The residues at the Mg2+ binding site are strictly conserved in both human CNNM2 and CNNM4, and many of these residues are associated with genetic diseases. Furthermore, we determined the structures of the CorC cytoplasmic region containing its regulatory ATP-binding domain. A combination of structural and functional analyses not only revealed the potential interface between the TM and cytoplasmic domains but also showed that ATP binding is important for the Mg2+ export activity of CorC.
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Affiliation(s)
- Yichen Huang
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Fei Jin
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research and Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong New Area, Shanghai 201203, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research and Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong New Area, Shanghai 201203, China
| | - Jing Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Medical Building, Room 128, 639 Long-Mian Road, Nanjing 200098, China
| | - Minxuan Sun
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yimeng Zhao
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Ye Yu
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Medical Building, Room 128, 639 Long-Mian Road, Nanjing 200098, China
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China.
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Liu G, Fu D, Tian H, Dai A. The mechanism of ions in pulmonary hypertension. Pulm Circ 2021; 11:2045894020987948. [PMID: 33614016 PMCID: PMC7869166 DOI: 10.1177/2045894020987948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022] Open
Abstract
Pulmonary hypertension(PH)is a kind of hemodynamic and pathophysiological state, in which the pulmonary artery pressure (PAP) rises above a certain threshold. The main pathological manifestation is pulmonary vasoconstriction and remodelling progressively. More and more studies have found that ions play a major role in the pathogenesis of PH. Many vasoactive substances, inflammatory mediators, transcription-inducing factors, apoptosis mediators, redox substances and translation modifiers can control the concentration of ions inside and outside the cell by regulating the activity of ion channels, which can regulate vascular contraction, cell proliferation, migration, apoptosis, inflammation and other functions. We all know that there are no effective drugs to treat PH. Ions are involved in the occurrence and development of PH, so it is necessary to clarify the mechanism of ions in PH as a therapeutic target for PH. The main ions involved in PH are calcium ion (Ca2+), potassium ion (K+), sodium ion (Na+) and chloride ion (Cl-). Here, we mainly discuss the distribution of these ions and their channels in pulmonary arteries and their role in the pathogenesis of PH.
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Affiliation(s)
- Guogu Liu
- Department of Graduate School, University of South China,
Hengyang, China
- Department of Respiratory Medicine, Hunan Provincial People’s
Hospital, Changsha, China
| | - Daiyan Fu
- Department of Respiratory Medicine, Hunan Provincial People’s
Hospital, Changsha, China
| | - Heshen Tian
- Department of Graduate School, University of South China,
Hengyang, China
- Department of Respiratory Medicine, Hunan Provincial People’s
Hospital, Changsha, China
| | - Aiguo Dai
- Department of Respiratory Diseases, Hunan University of Chinese
Medicine, Changsha, China
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44
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Gyimesi G, Hediger MA. Sequence Features of Mitochondrial Transporter Protein Families. Biomolecules 2020; 10:E1611. [PMID: 33260588 PMCID: PMC7761412 DOI: 10.3390/biom10121611] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 02/08/2023] Open
Abstract
Mitochondrial carriers facilitate the transfer of small molecules across the inner mitochondrial membrane (IMM) to support mitochondrial function and core cellular processes. In addition to the classical SLC25 (solute carrier family 25) mitochondrial carriers, the past decade has led to the discovery of additional protein families with numerous members that exhibit IMM localization and transporter-like properties. These include mitochondrial pyruvate carriers, sideroflexins, and mitochondrial cation/H+ exchangers. These transport proteins were linked to vital physiological functions and disease. Their structures and transport mechanisms are, however, still largely unknown and understudied. Protein sequence analysis per se can often pinpoint hotspots that are of functional or structural importance. In this review, we summarize current knowledge about the sequence features of mitochondrial transporters with a special focus on the newly included SLC54, SLC55 and SLC56 families of the SLC solute carrier superfamily. Taking a step further, we combine sequence conservation analysis with transmembrane segment and secondary structure prediction methods to extract residue positions and sequence motifs that likely play a role in substrate binding, binding site gating or structural stability. We hope that our review will help guide future experimental efforts by the scientific community to unravel the transport mechanisms and structures of these novel mitochondrial carriers.
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Affiliation(s)
- Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, CH-3010 Bern, Switzerland;
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45
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Wu Y, Liu H, Wang X. Cardioprotection of pharmacological postconditioning on myocardial ischemia/reperfusion injury. Life Sci 2020; 264:118628. [PMID: 33131670 DOI: 10.1016/j.lfs.2020.118628] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/08/2020] [Accepted: 10/16/2020] [Indexed: 12/26/2022]
Abstract
Acute myocardial infarction is associated with high rates of morbidity and mortality and can cause irreversible myocardial damage. Timely reperfusion is critical to limit infarct size and salvage the ischemic myocardium. However, reperfusion may exacerbate lethal tissue injury, a phenomenon known as myocardial ischemia/reperfusion (I/R) injury. Pharmacological postconditioning (PPC), a strategy involving medication administration before or during the early minutes of reperfusion, is more efficient and flexible than preconditioning or ischemic conditioning. Previous studies have shown that various mechanisms are involved in the effects of PPC. In this review, we summarize the relative effects and potential underlying mechanisms of PPC to provide a foundation for future research attempting to develop novel treatments against myocardial I/R injury.
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Affiliation(s)
- Yushi Wu
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, NO. 253, Gongye Avenue, 510282 Guangzhou, China; Guangdong Provincial Biomedical Engineering Technology Research Center for cardiovascular Disease, 510282 Guangzhou, China; Sino-Japanese cooperation Platform for Translational Research in Heart Failure, 510282 Guangzhou, China; Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, 510282 Guangzhou, China
| | - Haiqiong Liu
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, NO. 253, Gongye Avenue, 510282 Guangzhou, China; Guangdong Provincial Biomedical Engineering Technology Research Center for cardiovascular Disease, 510282 Guangzhou, China; Sino-Japanese cooperation Platform for Translational Research in Heart Failure, 510282 Guangzhou, China; Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, 510282 Guangzhou, China
| | - Xianbao Wang
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, NO. 253, Gongye Avenue, 510282 Guangzhou, China; Guangdong Provincial Biomedical Engineering Technology Research Center for cardiovascular Disease, 510282 Guangzhou, China; Sino-Japanese cooperation Platform for Translational Research in Heart Failure, 510282 Guangzhou, China; Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, 510282 Guangzhou, China.
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46
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Ion-exchange coupled crystallization for the removal of calcium ions from dicyandiamide. KOREAN J CHEM ENG 2020. [DOI: 10.1007/s11814-020-0572-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Otsomaa L, Levijoki J, Wohlfahrt G, Chapman H, Koivisto AP, Syrjänen K, Koskelainen T, Peltokorpi SE, Finckenberg P, Heikkilä A, Abi-Gerges N, Ghetti A, Miller PE, Page G, Mervaala E, Nagy N, Kohajda Z, Jost N, Virág L, Varró A, Papp JG. Discovery and characterization of ORM-11372, a novel inhibitor of the sodium-calcium exchanger with positive inotropic activity. Br J Pharmacol 2020; 177:5534-5554. [PMID: 32959887 PMCID: PMC7707092 DOI: 10.1111/bph.15257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 11/29/2022] Open
Abstract
Background and Purpose The lack of selective sodium–calcium exchanger (NCX) inhibitors has hampered the exploration of physiological and pathophysiological roles of cardiac NCX 1.1. We aimed to discover more potent and selective drug like NCX 1.1 inhibitor. Experimental Approach A flavan series‐based pharmacophore model was constructed. Virtual screening helped us identify a novel scaffold for NCX inhibition. A distinctively different NCX 1.1 inhibitor, ORM‐11372, was discovered after lead optimization. Its potency against human and rat NCX 1.1 and selectivity against other ion channels was assessed. The cardiovascular effects of ORM‐11372 were studied in normal and infarcted rats and rabbits. Human cardiac safety was studied ex vivo using human ventricular trabeculae. Key Results ORM‐11372 inhibited human NCX 1.1 reverse and forward currents; IC50 values were 5 and 6 nM respectively. ORM‐11372 inhibited human cardiac sodium 1.5 (INa) and hERG KV11.1 currents (IhERG) in a concentration‐dependent manner; IC50 values were 23.2 and 10.0 μM. ORM‐11372 caused no changes in action potential duration; short‐term variability and triangulation were observed for concentrations of up to 10 μM. ORM‐11372 induced positive inotropic effects of 18 ± 6% and 35 ± 8% in anaesthetized rats with myocardial infarctions and in healthy rabbits respectively; no other haemodynamic effects were observed, except improved relaxation at the lowest dose. Conclusion and Implications ORM‐11372, a unique, novel, and potent inhibitor of human and rat NCX 1.1, is a positive inotropic compound. NCX inhibition can induce clinically relevant improvements in left ventricular contractions without affecting relaxation, heart rate, or BP, without pro‐arrhythmic risk.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Piet Finckenberg
- Department of Pharmacology, Faculty of Medicine, Helsinki, Finland
| | | | | | | | | | - Guy Page
- R&D, AnaBios Corporation, San Diego, CA, USA
| | - Eero Mervaala
- Department of Pharmacology, Faculty of Medicine, Helsinki, Finland
| | - Norbert Nagy
- MTA-SZTE Research Group of Cardiovascular Pharmacology, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Pharmacology and Pharmacotherapy, Interdisciplinary Excellence Centre, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsófia Kohajda
- MTA-SZTE Research Group of Cardiovascular Pharmacology, Hungarian Academy of Sciences, Szeged, Hungary
| | - Norbert Jost
- MTA-SZTE Research Group of Cardiovascular Pharmacology, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Pharmacology and Pharmacotherapy, Interdisciplinary Excellence Centre, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - László Virág
- Department of Pharmacology and Pharmacotherapy, Interdisciplinary Excellence Centre, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - András Varró
- MTA-SZTE Research Group of Cardiovascular Pharmacology, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Pharmacology and Pharmacotherapy, Interdisciplinary Excellence Centre, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Julius Gy Papp
- MTA-SZTE Research Group of Cardiovascular Pharmacology, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Pharmacology and Pharmacotherapy, Interdisciplinary Excellence Centre, Faculty of Medicine, University of Szeged, Szeged, Hungary
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48
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Noble M, Lin QT, Sirko C, Houpt JA, Novello MJ, Stathopulos PB. Structural Mechanisms of Store-Operated and Mitochondrial Calcium Regulation: Initiation Points for Drug Discovery. Int J Mol Sci 2020; 21:E3642. [PMID: 32455637 PMCID: PMC7279490 DOI: 10.3390/ijms21103642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/11/2020] [Accepted: 05/17/2020] [Indexed: 12/18/2022] Open
Abstract
Calcium (Ca2+) is a universal signaling ion that is essential for the life and death processes of all eukaryotes. In humans, numerous cell stimulation pathways lead to the mobilization of sarco/endoplasmic reticulum (S/ER) stored Ca2+, resulting in the propagation of Ca2+ signals through the activation of processes, such as store-operated Ca2+ entry (SOCE). SOCE provides a sustained Ca2+ entry into the cytosol; moreover, the uptake of SOCE-mediated Ca2+ by mitochondria can shape cytosolic Ca2+ signals, function as a feedback signal for the SOCE molecular machinery, and drive numerous mitochondrial processes, including adenosine triphosphate (ATP) production and distinct cell death pathways. In recent years, tremendous progress has been made in identifying the proteins mediating these signaling pathways and elucidating molecular structures, invaluable for understanding the underlying mechanisms of function. Nevertheless, there remains a disconnect between using this accumulating protein structural knowledge and the design of new research tools and therapies. In this review, we provide an overview of the Ca2+ signaling pathways that are involved in mediating S/ER stored Ca2+ release, SOCE, and mitochondrial Ca2+ uptake, as well as pinpoint multiple levels of crosstalk between these pathways. Further, we highlight the significant protein structures elucidated in recent years controlling these Ca2+ signaling pathways. Finally, we describe a simple strategy that aimed at applying the protein structural data to initiating drug design.
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Affiliation(s)
- Megan Noble
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A5C1, Canada; (M.N.); (Q.-T.L.); (C.S.); (M.J.N.)
| | - Qi-Tong Lin
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A5C1, Canada; (M.N.); (Q.-T.L.); (C.S.); (M.J.N.)
| | - Christian Sirko
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A5C1, Canada; (M.N.); (Q.-T.L.); (C.S.); (M.J.N.)
| | - Jacob A. Houpt
- Department of Medicine, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A5C1, Canada;
| | - Matthew J. Novello
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A5C1, Canada; (M.N.); (Q.-T.L.); (C.S.); (M.J.N.)
| | - Peter B. Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A5C1, Canada; (M.N.); (Q.-T.L.); (C.S.); (M.J.N.)
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Molecular Mean-Field Theory of Ionic Solutions: A Poisson-Nernst-Planck-Bikerman Model. ENTROPY 2020; 22:e22050550. [PMID: 33286322 PMCID: PMC7517072 DOI: 10.3390/e22050550] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022]
Abstract
We have developed a molecular mean-field theory—fourth-order Poisson–Nernst–Planck–Bikerman theory—for modeling ionic and water flows in biological ion channels by treating ions and water molecules of any volume and shape with interstitial voids, polarization of water, and ion-ion and ion-water correlations. The theory can also be used to study thermodynamic and electrokinetic properties of electrolyte solutions in batteries, fuel cells, nanopores, porous media including cement, geothermal brines, the oceanic system, etc. The theory can compute electric and steric energies from all atoms in a protein and all ions and water molecules in a channel pore while keeping electrolyte solutions in the extra- and intracellular baths as a continuum dielectric medium with complex properties that mimic experimental data. The theory has been verified with experiments and molecular dynamics data from the gramicidin A channel, L-type calcium channel, potassium channel, and sodium/calcium exchanger with real structures from the Protein Data Bank. It was also verified with the experimental or Monte Carlo data of electric double-layer differential capacitance and ion activities in aqueous electrolyte solutions. We give an in-depth review of the literature about the most novel properties of the theory, namely Fermi distributions of water and ions as classical particles with excluded volumes and dynamic correlations that depend on salt concentration, composition, temperature, pressure, far-field boundary conditions etc. in a complex and complicated way as reported in a wide range of experiments. The dynamic correlations are self-consistent output functions from a fourth-order differential operator that describes ion-ion and ion-water correlations, the dielectric response (permittivity) of ionic solutions, and the polarization of water molecules with a single correlation length parameter.
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Intracellular Ca 2+ regulation of H +/Ca 2+ antiporter YfkE mediated by a Ca 2+ mini-sensor. Proc Natl Acad Sci U S A 2020; 117:10313-10321. [PMID: 32341169 DOI: 10.1073/pnas.1918604117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The H+/Ca2+ (calcium ion) antiporter (CAX) plays an important role in maintaining cellular Ca2+ homeostasis in bacteria, yeast, and plants by promoting Ca2+ efflux across the cell membranes. However, how CAX facilitates Ca2+ balance in response to dynamic cytosolic Ca2+ perturbations is unknown. Here, we identified a type of Ca2+ "mini-sensor" in YfkE, a bacterial CAX homolog from Bacillus subtilis. The mini-sensor is formed by six tandem carboxylate residues within the transmembrane (TM)5-6 loop on the intracellular membrane surface. Ca2+ binding to the mini-sensor triggers the transition of the transport mode of YfkE from a high-affinity to a low-affinity state. Molecular dynamics simulation and fluorescence resonance energy transfer analysis suggest that Ca2+ binding to the mini-sensor causes an adjacent segment, namely, the exchanger inhibitory peptide (XIP), to move toward the Ca2+ translocation pathway to interact with TM2a in an inward-open cavity. The specific interaction was demonstrated with a synthetic peptide of the XIP, which inhibits YfkE transport and interrupts conformational changes mediated by the mini-sensor. By comparing the apo and Ca2+-bound CAX structures, we propose the following Ca2+ transport regulatory mechanism of YfkE: Ca2+ binding to the mini-sensor induces allosteric conformational changes in the Ca2+ translocation pathway via the XIP, resulting in a rearrangement of the Ca2+-binding transport site in the midmembrane. Since the Ca2+ mini-sensor and XIP sequences are also identified in other CAX homologs and/or Ca2+ transporters, including the mammalian Na+/Ca2+ exchanger (NCX), our study provides a regulatory mechanism for the Ca2+/cation transporter superfamily.
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