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Yuan Y, Yu L, Zhuang X, Wen D, He J, Hong J, Xie J, Ling S, Du X, Chen W, Wang X. Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures. Neural Regen Res 2025; 20:265-276. [PMID: 38767491 PMCID: PMC11246156 DOI: 10.4103/1673-5374.391302] [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: 04/25/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00034/figure1/v/2024-05-14T021156Z/r/image-tiff Certain amino acids changes in the human Na+/K+-ATPase pump, ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1), cause Charcot-Marie-Tooth disease type 2 (CMT2) disease and refractory seizures. To develop in vivo models to study the role of Na+/K+-ATPase in these diseases, we modified the Drosophila gene homolog, Atpα, to mimic the human ATP1A1 gene mutations that cause CMT2. Mutations located within the helical linker region of human ATP1A1 (I592T, A597T, P600T, and D601F) were simultaneously introduced into endogenous DrosophilaAtpα by CRISPR/Cas9-mediated genome editing, generating the AtpαTTTF model. In addition, the same strategy was used to generate the corresponding single point mutations in flies (AtpαI571T, AtpαA576T, AtpαP579T, and AtpαD580F). Moreover, a deletion mutation (Atpαmut) that causes premature termination of translation was generated as a positive control. Of these alleles, we found two that could be maintained as homozygotes (AtpαI571T and AtpαP579T). Three alleles (AtpαA576T, AtpαP579 and AtpαD580F) can form heterozygotes with the Atpαmut allele. We found that the Atpα allele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila. Flies heterozygous for AtpαTTTF mutations have motor performance defects, a reduced lifespan, seizures, and an abnormal neuronal morphology. These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.
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Affiliation(s)
- Yao Yuan
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Lingqi Yu
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xudong Zhuang
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian Province, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Dongjing Wen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Jin He
- Department of Neurology and Institute of Neurology of The First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jingmei Hong
- Department of Neurology and Institute of Neurology of The First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jiayu Xie
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Shengan Ling
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xiaoyue Du
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Wenfeng Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xinrui Wang
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian Province, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian Province, China
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Homma M, Wakabayashi T, Moriwaki Y, Shiotani N, Shigeta T, Isobe K, Okazawa A, Ohta D, Terada T, Shimizu K, Mizutani M, Takikawa H, Sugimoto Y. Insights into stereoselective ring formation in canonical strigolactone: Identification of a dirigent domain-containing enzyme catalyzing orobanchol synthesis. Proc Natl Acad Sci U S A 2024; 121:e2313683121. [PMID: 38905237 PMCID: PMC11214005 DOI: 10.1073/pnas.2313683121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/30/2024] [Indexed: 06/23/2024] Open
Abstract
Strigolactones (SLs) are plant apocarotenoids with diverse roles and structures. Canonical SLs, widespread and characterized by structural variations in their tricyclic lactone (ABC-ring), are classified into two types based on C-ring configurations. The steric C-ring configuration emerges during the BC-ring closure, downstream of the biosynthetic intermediate, carlactonoic acid (CLA). Most plants produce either type of canonical SLs stereoselectively, e.g., tomato (Solanum lycopersicum) yields orobanchol with an α-oriented C-ring. The mechanisms driving SL structural diversification are partially understood, with limited insight into functional implications. Furthermore, the exact molecular mechanism for the stereoselective BC-ring closure reaction is yet to be known. We identified an enzyme, the stereoselective BC-ring-forming factor (SRF), from the dirigent protein (DIR) family, specifically the DIR-f subfamily, whose biochemical function had not been characterized, making it a key enzyme in stereoselective canonical SL biosynthesis with the α-oriented C-ring. We first confirm the precise catalytic function of the tomato cytochrome P450 SlCYP722C, previously shown to be involved in orobanchol biosynthesis [T. Wakabayashi et al., Sci. Adv. 5, eaax9067 (2019)], to convert CLA to 18-oxocarlactonoic acid. We then show that SRF catalyzes the stereoselective BC-ring closure reaction of 18-oxocarlactonoic acid, forming orobanchol. Our methodology combines experimental and computational techniques, including SRF structure prediction and conducting molecular dynamics simulations, suggesting a catalytic mechanism based on the conrotatory 4π-electrocyclic reaction for the stereoselective BC-ring formation in orobanchol. This study sheds light on the molecular basis of how plants produce SLs with specific stereochemistry in a controlled manner.
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Affiliation(s)
- Masato Homma
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Takatoshi Wakabayashi
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Nanami Shiotani
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Takumi Shigeta
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Kazuki Isobe
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
| | - Atsushi Okazawa
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
- Department of Agricultural Biology, Graduate School of Agriculture, Osaka Metropolitan University, Sakai599-8531, Japan
| | - Daisaku Ohta
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
- Department of Agricultural Biology, Graduate School of Agriculture, Osaka Metropolitan University, Sakai599-8531, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Kentaro Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Masaharu Mizutani
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Hirosato Takikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Yukihiro Sugimoto
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
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3
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Champion C, Hünenberger PH, Riniker S. Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations. J Chem Theory Comput 2024; 20:4350-4362. [PMID: 38742760 PMCID: PMC11137823 DOI: 10.1021/acs.jctc.4c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
The majority of drug-like molecules contain at least one ionizable group, and many common drug scaffolds are subject to tautomeric equilibria. Thus, these compounds are found in a mixture of protonation and/or tautomeric states at physiological pH. Intrinsically, standard classical molecular dynamics (MD) simulations cannot describe such equilibria between states, which negatively impacts the prediction of key molecular properties in silico. Following the formalism described by de Oliveira and co-workers (J. Chem. Theory Comput. 2019, 15, 424-435) to consider the influence of all states on the binding process based on alchemical free-energy calculations, we demonstrate in this work that the multistate method replica-exchange enveloping distribution sampling (RE-EDS) is well suited to describe molecules with multiple protonation and/or tautomeric states in a single simulation. We apply our methodology to a series of eight inhibitors of factor Xa with two protonation states and a series of eight inhibitors of glycogen synthase kinase 3β (GSK3β) with two tautomeric states. In particular, we show that given a sufficient phase-space overlap between the states, RE-EDS is computationally more efficient than standard pairwise free-energy methods.
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Affiliation(s)
- Candide Champion
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Philippe H. Hünenberger
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Hołyst R, Bubak G, Kalwarczyk T, Kwapiszewska K, Michalski J, Pilz M. Living Cell as a Self-Synchronized Chemical Reactor. J Phys Chem Lett 2024; 15:3559-3570. [PMID: 38526849 PMCID: PMC11000238 DOI: 10.1021/acs.jpclett.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
Thermal fluctuations power all processes inside living cells. Therefore, these processes are inherently random. However, myriad multistep chemical reactions act in concerto inside a cell, finally leading to this chemical reactor's self-replication. We speculate that an underlying mechanism in nature must exist that allows all of these reactions to synchronize at multiple time and length scales, overcoming in this way the random nature of any single process in a cell. This Perspective discusses what type of research is needed to understand this undiscovered synchronization law.
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Affiliation(s)
- Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Grzegorz Bubak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Jarosław Michalski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marta Pilz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Panagiotakaki E, Tiziano FD, Mikati MA, Vijfhuizen LS, Nicole S, Lesca G, Abiusi E, Novelli A, Di Pietro L, Harder AVE, Walley NM, De Grandis E, Poulat AL, Portes VD, Lépine A, Nassogne MC, Arzimanoglou A, Vavassori R, Koenderink J, Thompson CH, George AL, Gurrieri F, van den Maagdenberg AMJM, Heinzen EL. Exome sequencing of ATP1A3-negative cases of alternating hemiplegia of childhood reveals SCN2A as a novel causative gene. Eur J Hum Genet 2024; 32:224-231. [PMID: 38097767 PMCID: PMC10853263 DOI: 10.1038/s41431-023-01489-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/25/2023] [Accepted: 10/18/2023] [Indexed: 02/10/2024] Open
Abstract
Alternating hemiplegia of childhood (AHC) is a rare neurodevelopment disorder that is typically characterized by debilitating episodic attacks of hemiplegia, seizures, and intellectual disability. Over 85% of individuals with AHC have a de novo missense variant in ATP1A3 encoding the catalytic α3 subunit of neuronal Na+/K+ ATPases. The remainder of the patients are genetically unexplained. Here, we used next-generation sequencing to search for the genetic cause of 26 ATP1A3-negative index patients with a clinical presentation of AHC or an AHC-like phenotype. Three patients had affected siblings. Using targeted sequencing of exonic, intronic, and flanking regions of ATP1A3 in 22 of the 26 index patients, we found no ultra-rare variants. Using exome sequencing, we identified the likely genetic diagnosis in 9 probands (35%) in five genes, including RHOBTB2 (n = 3), ATP1A2 (n = 3), ANK3 (n = 1), SCN2A (n = 1), and CHD2 (n = 1). In follow-up investigations, two additional ATP1A3-negative individuals were found to have rare missense SCN2A variants, including one de novo likely pathogenic variant and one likely pathogenic variant for which inheritance could not be determined. Functional evaluation of the variants identified in SCN2A and ATP1A2 supports the pathogenicity of the identified variants. Our data show that genetic variants in various neurodevelopmental genes, including SCN2A, lead to AHC or AHC-like presentation. Still, the majority of ATP1A3-negative AHC or AHC-like patients remain unexplained, suggesting that other mutational mechanisms may account for the phenotype or that cases may be explained by oligo- or polygenic risk factors.
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Affiliation(s)
- Eleni Panagiotakaki
- Department of Paediatric Clinical Epileptology, Sleep Disorders and Functional Neurology, Member of the ERN EpiCare, University Hospitals of Lyon (HCL), Lyon, France
| | - Francesco D Tiziano
- Institute of Genomic Medicine, Catholic University and Policlinico Gemelli, Fondazione Policlinico Universitario Agostino Gemelli IRCSS, Rome, Italy
| | - Mohamad A Mikati
- Division of Pediatric Neurology and Developmental Medicine, Duke University, Durham, NC, USA
| | - Lisanne S Vijfhuizen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sophie Nicole
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Gaetan Lesca
- Department of Medical Genetics, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon France - Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM U1315, Lyon, France
| | - Emanuela Abiusi
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Agnese Novelli
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Lorena Di Pietro
- Institute of Genomic Medicine, Catholic University and Policlinico Gemelli, Fondazione Policlinico Universitario Agostino Gemelli IRCSS, Rome, Italy
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Aster V E Harder
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nicole M Walley
- Department of Pediatrics, Division of Medical Genetics, Duke Health, Durham, NC, USA
| | - Elisa De Grandis
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- Child Neuropsychiatry Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Anne-Lise Poulat
- Pediatric Neurology Department, Member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France
| | - Vincent Des Portes
- Pediatric Neurology Department, Member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France
| | - Anne Lépine
- Service de neuropédiatrie, Centre hospitalo universitaire de la Timone, Marseille, France
| | - Marie-Cecile Nassogne
- Institut des Maladies Rares, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
- Service de Neurologie Pédiatrique, Member of the ERN MetabERN, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | - Alexis Arzimanoglou
- Department of Paediatric Clinical Epileptology, Sleep Disorders and Functional Neurology, Member of the ERN EpiCare, University Hospitals of Lyon (HCL), Lyon, France
- Department of Child Neurology and Epilepsy Research Unit, Member of the ERN EpiCARE, Hospital San Juan de Dios, Barcelona, Spain
| | - Rosaria Vavassori
- Euro-Mediterranean Institute for Science and Technology I.E.ME.S.T., Palermo, Italy
| | - Jan Koenderink
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christopher H Thompson
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Fiorella Gurrieri
- Department of Medicine, Research Unit of Medical Genetics, Università Campus Bio-Medico di Roma, Roma, Italy
- Operative Research Unit of Medical Genetics Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy
| | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Erin L Heinzen
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Madapally HV, Abe K, Dubey V, Khandelia H. Specific protonation of acidic residues confers K + selectivity to the gastric proton pump. J Biol Chem 2024; 300:105542. [PMID: 38072058 PMCID: PMC10825007 DOI: 10.1016/j.jbc.2023.105542] [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: 10/22/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024] Open
Abstract
The gastric proton pump (H+,K+-ATPase) transports a proton into the stomach lumen for every K+ ion exchanged in the opposite direction. In the lumen-facing state of the pump (E2), the pump selectively binds K+ despite the presence of a 10-fold higher concentration of Na+. The molecular basis for the ion selectivity of the pump is unknown. Using molecular dynamics simulations, free energy calculations, and Na+ and K+-dependent ATPase activity assays, we demonstrate that the K+ selectivity of the pump depends upon the simultaneous protonation of the acidic residues E343 and E795 in the ion-binding site. We also show that when E936 is protonated, the pump becomes Na+ sensitive. The protonation-mimetic mutant E936Q exhibits weak Na+-activated ATPase activity. A 2.5-Å resolution cryo-EM structure of the E936Q mutant in the K+-occluded E2-Pi form shows, however, no significant structural difference compared with wildtype except less-than-ideal coordination of K+ in the mutant. The selectivity toward a specific ion correlates with a more rigid and less fluctuating ion-binding site. Despite being exposed to a pH of 1, the fundamental principle driving the K+ ion selectivity of H+,K+-ATPase is similar to that of Na+,K+-ATPase: the ionization states of the acidic residues in the ion-binding sites determine ion selectivity. Unlike the Na+,K+-ATPase, however, protonation of an ion-binding glutamate residue (E936) confers Na+ sensitivity.
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Affiliation(s)
- Hridya Valia Madapally
- PHYLIFE, Physical Life Science, Department of Physics Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Kazuhiro Abe
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan; Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan
| | - Vikas Dubey
- PHYLIFE, Physical Life Science, Department of Physics Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Himanshu Khandelia
- PHYLIFE, Physical Life Science, Department of Physics Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark.
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7
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Artigas P, Meyer DJ, Young VC, Spontarelli K, Eastman J, Strandquist E, Rui H, Roux B, Birk MA, Nakanishi H, Abe K, Gatto C. A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities. Proc Natl Acad Sci U S A 2023; 120:e2313999120. [PMID: 38079564 PMCID: PMC10756188 DOI: 10.1073/pnas.2313999120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
Brine shrimp (Artemia) are the only animals to thrive at sodium concentrations above 4 M. Salt excretion is powered by the Na+,K+-ATPase (NKA), a heterodimeric (αβ) pump that usually exports 3Na+ in exchange for 2 K+ per hydrolyzed ATP. Artemia express several NKA catalytic α-subunit subtypes. High-salinity adaptation increases abundance of α2KK, an isoform that contains two lysines (Lys308 and Lys758 in transmembrane segments TM4 and TM5, respectively) at positions where canonical NKAs have asparagines (Xenopus α1's Asn333 and Asn785). Using de novo transcriptome assembly and qPCR, we found that Artemia express two salinity-independent canonical α subunits (α1NN and α3NN), as well as two β variants, in addition to the salinity-controlled α2KK. These β subunits permitted heterologous expression of the α2KK pump and determination of its CryoEM structure in a closed, ion-free conformation, showing Lys758 residing within the ion-binding cavity. We used electrophysiology to characterize the function of α2KK pumps and compared it to that of Xenopus α1 (and its α2KK-mimicking single- and double-lysine substitutions). The double substitution N333K/N785K confers α2KK-like characteristics to Xenopus α1, and mutant cycle analysis reveals energetic coupling between these two residues, illustrating how α2KK's Lys308 helps to maintain high affinity for external K+ when Lys758 occupies an ion-binding site. By measuring uptake under voltage clamp of the K+-congener 86Rb+, we prove that double-lysine-substituted pumps transport 2Na+ and 1 K+ per catalytic cycle. Our results show how the two lysines contribute to generate a pump with reduced stoichiometry allowing Artemia to maintain steeper Na+ gradients in hypersaline environments.
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Affiliation(s)
- Pablo Artigas
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX79430
| | - Dylan J. Meyer
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX79430
| | - Victoria C. Young
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX79430
| | - Kerri Spontarelli
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX79430
| | - Jessica Eastman
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX79430
| | - Evan Strandquist
- School of Biological Sciences, Illinois State University, Normal, IL61790
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL60637
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL60637
| | - Matthew A. Birk
- Department of Biology, Saint Francis University, Loretto, PA15940
| | - Hanayo Nakanishi
- Department of Basic Medical Sciences, Cellular and Structural Physiology Institute, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya464-8601, Japan
| | - Kazuhiro Abe
- Department of Basic Medical Sciences, Cellular and Structural Physiology Institute, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya464-8601, Japan
| | - Craig Gatto
- School of Biological Sciences, Illinois State University, Normal, IL61790
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8
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Jacobsen L, Lydersen L, Khandelia H. ATP-Bound State of the Uncoupling Protein 1 (UCP1) from Molecular Simulations. J Phys Chem B 2023; 127:9685-9696. [PMID: 37921649 DOI: 10.1021/acs.jpcb.3c03473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The uncoupling protein 1 (UCP1) dissipates the transmembrane (TM) proton gradient in the inner mitochondrial membrane (IMM) by leaking protons across the membrane and producing heat in the process. Such a nonshivering production of heat in the brown adipose tissue can combat obesity-related diseases. UCP1-associated proton leak is activated by free fatty acids and inhibited by purine nucleotides. The mechanism of proton leak and the binding sites of the activators (fatty acids) remain unknown, while the binding site of the inhibitors (nucleotides) was described recently. Using molecular dynamics simulations, we generated a conformational ensemble of UCP1. Using metadynamics-based free energy calculations, we obtained the most likely ATP-bound conformation of UCP1. Our conformational ensemble provides a molecular basis for a breadth of prior biochemical data available for UCP1. Based on the simulations, we make the following testable predictions about the mechanisms of activation of proton leak and proton leak inhibition by ATP: (1) R277 plays the dual role of stabilizing ATP at the binding site for inhibition and acting as a proton surrogate for D28 in the absence of a proton during proton transport, (2) the binding of ATP to UCP1 is mediated by residues R84, R92, R183, and S88, (3) R92 shuttles ATP from the E191-R92 gate in the intermembrane space to the nucleotide binding site and serves to increase ATP affinity, (4) ATP can inhibit proton leak by controlling the ionization states of matrix facing lysine residues such as K269 and K56, and (5) fatty acids can bind to UCP1 from the IMM either via the cavity between TM1 and TM2 or between TM5 and TM6. Our simulations set the platform for future investigations into the proton transport and inhibition mechanisms of UCP1.
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Affiliation(s)
- Luise Jacobsen
- PhyLife: Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Laura Lydersen
- PhyLife: Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Himanshu Khandelia
- PhyLife: Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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9
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Peluffo RD, Hernández JA. The Na +,K +-ATPase and its stoichiometric ratio: some thermodynamic speculations. Biophys Rev 2023; 15:539-552. [PMID: 37681108 PMCID: PMC10480117 DOI: 10.1007/s12551-023-01082-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/18/2023] [Indexed: 09/09/2023] Open
Abstract
Almost seventy years after its discovery, the sodium-potassium adenosine triphosphatase (the sodium pump) located in the cell plasma membrane remains a source of novel mechanistic and physiologic findings. A noteworthy feature of this enzyme/transporter is its robust stoichiometric ratio under physiological conditions: it sequentially counter-transports three sodium ions and two potassium ions against their electrochemical potential gradients per each hydrolyzed ATP molecule. Here we summarize some present knowledge about the sodium pump and its physiological roles, and speculate whether energetic constraints may have played a role in the evolutionary selection of its characteristic stoichiometric ratio.
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Affiliation(s)
- R. Daniel Peluffo
- Group of Biophysical Chemistry, Department of Biological Sciences, CENUR Litoral Norte, Universidad de La República, Rivera 1350, CP: 50000 Salto, Uruguay
| | - Julio A. Hernández
- Biophysics and Systems Biology Section, Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de La República, Iguá 4225, CP: 11400 Montevideo, Uruguay
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10
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Higgins JA, Ramos DS, Gili S, Spetea C, Kanoski S, Ha D, McDonough AA, Youn JH. Stable potassium isotopes (41K/39K) track transcellular and paracellular potassium transport in biological systems. Front Physiol 2022; 13:1016242. [PMID: 36388124 PMCID: PMC9644202 DOI: 10.3389/fphys.2022.1016242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/21/2022] [Indexed: 12/04/2022] Open
Abstract
As the most abundant cation in archaeal, bacterial, and eukaryotic cells, potassium (K+) is an essential element for life. While much is known about the machinery of transcellular and paracellular K transport–channels, pumps, co-transporters, and tight-junction proteins—many quantitative aspects of K homeostasis in biological systems remain poorly constrained. Here we present measurements of the stable isotope ratios of potassium (41K/39K) in three biological systems (algae, fish, and mammals). When considered in the context of our current understanding of plausible mechanisms of K isotope fractionation and K+ transport in these biological systems, our results provide evidence that the fractionation of K isotopes depends on transport pathway and transmembrane transport machinery. Specifically, we find that passive transport of K+ down its electrochemical potential through channels and pores in tight-junctions at favors 39K, a result which we attribute to a kinetic isotope effect associated with dehydration and/or size selectivity at the channel/pore entrance. In contrast, we find that transport of K+ against its electrochemical gradient via pumps and co-transporters is associated with less/no isotopic fractionation, a result that we attribute to small equilibrium isotope effects that are expressed in pumps/co-transporters due to their slower turnover rate and the relatively long residence time of K+ in the ion pocket. These results indicate that stable K isotopes may be able to provide quantitative constraints on transporter-specific K+ fluxes (e.g., the fraction of K efflux from a tissue by channels vs. co-transporters) and how these fluxes change in different physiological states. In addition, precise determination of K isotope effects associated with K+ transport via channels, pumps, and co-transporters may provide unique constraints on the mechanisms of K transport that could be tested with steered molecular dynamic simulations.
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Affiliation(s)
- John A. Higgins
- Department of Geosciences, Princeton University, Princeton, NJ, United States
- *Correspondence: John A. Higgins,
| | - Danielle Santiago Ramos
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
| | - Stefania Gili
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Scott Kanoski
- Department of Human and Evolutionary Biology, University of Southern California, Los Angeles, CA, United States
| | - Darren Ha
- Department of Physiology and Neuroscience, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
| | - Alicia A. McDonough
- Department of Physiology and Neuroscience, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
| | - Jang H. Youn
- Department of Physiology and Neuroscience, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
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11
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Kumar A, Satpati P. Structure-based thermodynamics of ion selectivity (Mg 2+versus Ca 2+ and K +versus Na +) in the active site of the eukaryotic lariat group II intron from algae Pylaiella littoralis. Phys Chem Chem Phys 2022; 24:24192-24202. [PMID: 36168989 DOI: 10.1039/d2cp03472g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Group II introns are metalloenzymes that can catalyze self-splicing. Recently, the crystal structures of the eukaryotic group IIB lariat intron from the brown algae Pylaiella littoralis have been reported for two intermediate states (pre-hydrolytic (2s) and post-hydrolytic) along the self-splicing pathway. Three characteristic metal-ion binding sites (M1 and M2 sites for catalytic Mg2+ ions, and K1 site for K+) in the catalytic pocket of the lariat intron have been identified and proposed to be crucial for self-splicing. Using the X-ray structures as a template, we quantitatively estimated the energetics of divalent (Mg2+versus Ca2+) and monovalent (K+versus Na+) ion selectivity and established a direct link between the energetics and structures of this lariat intron (bound to cognate and near-cognate metal ions). Molecular dynamics (MD) free energy simulations showed that the lariat intron was strongly selective between divalent metal ions. The strength of divalent metal-ion selectivity was noticeably high in the post-hydrolytic state (ΔΔG ≈ 20 kcal mol-1) relative to its pre-hydrolytic (2s) state (ΔΔG ≈ 13 kcal mol-1). Quantum chemical calculations ensured that the sign of the estimated divalent metal-ion selectivity was correct. The M1-binding pocket was less solvent-exposed in the case of the post-hydrolytic state relative to the pre-hydrolytic (2s) state, which boosted the metal-ion selectivity of the former. Surprisingly, in contrast to the bacterial linear group II intron, the lariat intron was found to be non-selective between monovalent ions (K+versus Na+). The interaction network in the first coordination shell of Ca2+ in the M1-binding pocket was different relative to Mg2+. Mg2+ substitution by Ca2+ resulted in the substitution of a single M1-RNA interaction by the M1-water interaction. In the pre-hydrolytic (2s) state, Ca2+ substitution completely disrupted the M1⋯5'-exon interaction; thus, the nature of the divalent metal ion is critical for catalysis. The interaction network in the M2 site was independent of the nature of the divalent metal ions (Mg2+ or Ca2+). The monovalent ion was loosely bound in the wet binding pocket (K1 site) of the lariat intron; thus, the substitution of K+ by Na+ could not significantly alter the free energy of the complex. The metal ion selectivity was dependent on the solvent accessibility of the metal-ion-binding-pocket, dry pocket enhanced the selectivity.
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Affiliation(s)
- Abhishek Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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12
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Structure and function of H +/K + pump mutants reveal Na +/K + pump mechanisms. Nat Commun 2022; 13:5270. [PMID: 36085139 PMCID: PMC9463140 DOI: 10.1038/s41467-022-32793-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022] Open
Abstract
Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na+ to H+ selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via P-type ATPases using functional and structural analyses to demonstrate that four simultaneous residue substitutions transform the non-gastric H+/K+ pump, a strict H+-dependent electroneutral P-type ATPase, into a bona fide Na+-dependent electrogenic Na+/K+ pump. Conversion of a H+-dependent primary-active transporter into a Na+-dependent one provides a prototype for similar studies of ion-transport proteins. Moreover, we solve the structures of the wild-type non-gastric H+/K+ pump, a suitable drug target to treat cystic fibrosis, and of its Na+/K+ pump-mimicking mutant in two major conformations, providing insight on how Na+ binding drives a concerted mechanism leading to Na+/K+ pump phosphorylation.
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13
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Seflova J, Habibi NR, Yap JQ, Cleary SR, Fang X, Kekenes-Huskey PM, Espinoza-Fonseca LM, Bossuyt JB, Robia SL. Fluorescence lifetime imaging microscopy reveals sodium pump dimers in live cells. J Biol Chem 2022; 298:101865. [PMID: 35339486 PMCID: PMC9048134 DOI: 10.1016/j.jbc.2022.101865] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/30/2022] Open
Abstract
The sodium-potassium ATPase (Na/K-ATPase, NKA) establishes ion gradients that facilitate many physiological functions including action potentials and secondary transport processes. NKA comprises a catalytic subunit (alpha) that interacts closely with an essential subunit (beta) and regulatory transmembrane micropeptides called FXYD proteins. In the heart, a key modulatory partner is the FXYD protein phospholemman (PLM, FXYD1), but the stoichiometry of the alpha-beta-PLM regulatory complex is unknown. Here, we used fluorescence lifetime imaging and spectroscopy to investigate the structure, stoichiometry, and affinity of the NKA-regulatory complex. We observed a concentration-dependent binding of the subunits of NKA-PLM regulatory complex, with avid association of the alpha subunit with the essential beta subunit as well as lower affinity alpha-alpha and alpha-PLM interactions. These data provide the first evidence that, in intact live cells, the regulatory complex is composed of two alpha subunits associated with two beta subunits, decorated with two PLM regulatory subunits. Docking and molecular dynamics (MD) simulations generated a structural model of the complex that is consistent with our experimental observations. We propose that alpha-alpha subunit interactions support conformational coupling of the catalytic subunits, which may enhance NKA turnover rate. These observations provide insight into the pathophysiology of heart failure, wherein low NKA expression may be insufficient to support formation of the complete regulatory complex with the stoichiometry (alpha-beta-PLM)2.
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Affiliation(s)
- Jaroslava Seflova
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA
| | - Nima R Habibi
- Department of Pharmacology, University of California Davis, Davis, California, USA
| | - John Q Yap
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA
| | - Sean R Cleary
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA
| | - Xuan Fang
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA
| | - L Michel Espinoza-Fonseca
- Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Julie B Bossuyt
- Department of Pharmacology, University of California Davis, Davis, California, USA.
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA.
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14
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Zimmermann MT. Molecular Modeling is an Enabling Approach to Complement and Enhance Channelopathy Research. Compr Physiol 2022; 12:3141-3166. [PMID: 35578963 DOI: 10.1002/cphy.c190047] [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
Hundreds of human membrane proteins form channels that transport necessary ions and compounds, including drugs and metabolites, yet details of their normal function or how function is altered by genetic variants to cause diseases are often unknown. Without this knowledge, researchers are less equipped to develop approaches to diagnose and treat channelopathies. High-resolution computational approaches such as molecular modeling enable researchers to investigate channelopathy protein function, facilitate detailed hypothesis generation, and produce data that is difficult to gather experimentally. Molecular modeling can be tailored to each physiologic context that a protein may act within, some of which may currently be difficult or impossible to assay experimentally. Because many genomic variants are observed in channelopathy proteins from high-throughput sequencing studies, methods with mechanistic value are needed to interpret their effects. The eminent field of structural bioinformatics integrates techniques from multiple disciplines including molecular modeling, computational chemistry, biophysics, and biochemistry, to develop mechanistic hypotheses and enhance the information available for understanding function. Molecular modeling and simulation access 3D and time-dependent information, not currently predictable from sequence. Thus, molecular modeling is valuable for increasing the resolution with which the natural function of protein channels can be investigated, and for interpreting how genomic variants alter them to produce physiologic changes that manifest as channelopathies. © 2022 American Physiological Society. Compr Physiol 12:3141-3166, 2022.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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15
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Grigoryan R, Costas-Rodríguez M, Van Wonterghem E, Vandenbroucke RE, Vanhaecke F. Effect of Endotoxemia Induced by Intraperitoneal Injection of Lipopolysaccharide on the Mg isotopic Composition of Biofluids and Tissues in Mice. Front Med (Lausanne) 2021; 8:664666. [PMID: 34368182 PMCID: PMC8342922 DOI: 10.3389/fmed.2021.664666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
Endotoxemia induced in vivo in mice by intraperitoneal injection of lipopolysaccharide (LPS) leads to (neuro)inflammation and sepsis. Also the homeostasis of mineral elements can be altered through mechanisms that still are poorly understood. The isotopic composition of Mg and the concentrations of the minor elements Ca, K, Mg, Na, P, and S were determined in biological fluids and tissues of young (14–28 weeks) and aged (40–65 weeks) LPS-injected mice and age-matched controls to reveal potential effects of the LPS-induced infection. Blood plasma of young and aged LPS-injected mice showed a heavy Mg isotopic composition, as well as elevated Mg and P concentrations, compared to matched controls. The plasma Mg isotopic composition was correlated with the P concentration in aged mice. Also the liver Mg isotopic composition was strongly affected in the young and aged LPS-injected mice, while for aged mice, an additional effect on the urine Mg isotopic composition was established. These observations were hypothetically associated with liver inflammation and/or hepatotoxicity, and reduced urinary Mg excretion, respectively. Also a regional endotoxin-induced difference was observed in the brain Mg isotopic composition for the aged mice only, and was attributed to potential disruption of the blood-brain barrier.
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Affiliation(s)
- Rosa Grigoryan
- Atomic & Mass Spectrometry - A&MS Research Unit, Department of Chemistry, Ghent University, Ghent, Belgium
| | - Marta Costas-Rodríguez
- Atomic & Mass Spectrometry - A&MS Research Unit, Department of Chemistry, Ghent University, Ghent, Belgium
| | - Elien Van Wonterghem
- Atomic & Mass Spectrometry - A&MS Research Unit, Department of Chemistry, Ghent University, Ghent, Belgium
| | - Roosmarijn E Vandenbroucke
- Vlaams Instituut voor Biotechnologie (VIB) Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Frank Vanhaecke
- Atomic & Mass Spectrometry - A&MS Research Unit, Department of Chemistry, Ghent University, Ghent, Belgium
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16
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Bejček J, Spiwok V, Kmoníčková E, Rimpelová S. Na +/K +-ATPase Revisited: On Its Mechanism of Action, Role in Cancer, and Activity Modulation. Molecules 2021; 26:molecules26071905. [PMID: 33800655 PMCID: PMC8061769 DOI: 10.3390/molecules26071905] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 01/08/2023] Open
Abstract
Maintenance of Na+ and K+ gradients across the cell plasma membrane is an essential process for mammalian cell survival. An enzyme responsible for this process, sodium-potassium ATPase (NKA), has been currently extensively studied as a potential anticancer target, especially in lung cancer and glioblastoma. To date, many NKA inhibitors, mainly of natural origin from the family of cardiac steroids (CSs), have been reported and extensively studied. Interestingly, upon CS binding to NKA at nontoxic doses, the role of NKA as a receptor is activated and intracellular signaling is triggered, upon which cancer cell death occurs, which lies in the expression of different NKA isoforms than in healthy cells. Two major CSs, digoxin and digitoxin, originally used for the treatment of cardiac arrhythmias, are also being tested for another indication—cancer. Such drug repositioning has a big advantage in smoother approval processes. Besides this, novel CS derivatives with improved performance are being developed and evaluated in combination therapy. This article deals with the NKA structure, mechanism of action, activity modulation, and its most important inhibitors, some of which could serve not only as a powerful tool to combat cancer, but also help to decipher the so-far poorly understood NKA regulation.
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Affiliation(s)
- Jiří Bejček
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic; (J.B.); (V.S.)
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic; (J.B.); (V.S.)
| | - Eva Kmoníčková
- Department of Pharmacology, Second Faculty of Medicine, Charles University, Plzeňská 311, 150 00 Prague, Czech Republic;
| | - Silvie Rimpelová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic; (J.B.); (V.S.)
- Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic
- Correspondence: ; Tel.: +420-220-444-360
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17
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Yap JQ, Seflova J, Sweazey R, Artigas P, Robia SL. FXYD proteins and sodium pump regulatory mechanisms. J Gen Physiol 2021; 153:211866. [PMID: 33688925 PMCID: PMC7953255 DOI: 10.1085/jgp.202012633] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
The sodium/potassium-ATPase (NKA) is the enzyme that establishes gradients of sodium and potassium across the plasma membrane. NKA activity is tightly regulated for different physiological contexts through interactions with single-span transmembrane peptides, the FXYD proteins. This diverse family of regulators has in common a domain containing a Phe-X-Tyr-Asp (FXYD) motif, two conserved glycines, and one serine residue. In humans, there are seven tissue-specific FXYD proteins that differentially modulate NKA kinetics as appropriate for each system, providing dynamic responsiveness to changing physiological conditions. Our understanding of how FXYD proteins contribute to homeostasis has benefitted from recent advances described in this review: biochemical and biophysical studies have provided insight into regulatory mechanisms, genetic models have uncovered remarkable complexity of FXYD function in integrated physiological systems, new posttranslational modifications have been identified, high-resolution structural studies have revealed new details of the regulatory interaction with NKA, and new clinical correlations have been uncovered. In this review, we address the structural determinants of diverse FXYD functions and the special roles of FXYDs in various physiological systems. We also discuss the possible roles of FXYDs in protein trafficking and regulation of non-NKA targets.
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Affiliation(s)
- John Q Yap
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL
| | - Jaroslava Seflova
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL
| | - Ryan Sweazey
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Pablo Artigas
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL
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18
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Ladefoged LK, Schiøtt B, Fedosova NU. Beneficent and Maleficent Effects of Cations on Bufadienolide Binding to Na +,K +-ATPase. J Chem Inf Model 2021; 61:976-986. [PMID: 33502848 DOI: 10.1021/acs.jcim.0c01396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic properties and crystal structures of the Na+,K+-ATPase in complex with cardiotonic steroids (CTS) revealed significant differences between CTS subfamilies (Laursen et al.). Thus, we found beneficial effects of K+ on bufadienolide binding, which strongly contrasted with the well-known antagonism between K+ and cardenolides. In order to understand this peculiarity of bufalin interactions, we used docking and molecular dynamics simulations of the complexes involving Na+,K+-ATPase, bufadienolides (bufalin, cinobufagin), and ions (K+, Na+, Mg2+). The results revealed that bufadienolide binding is affected by (i) electrostatic attraction of the lactone ring by a cation and (ii) the ability of a cation to stabilize and "shape" the site constituted by transmembrane helices of the α-subunit (αM1-6). The latter effect was due to varying coordination patterns involving amino acid residues from helix bundles αM1-4 and αM5-10. Substituents on the steroid core of a bufadienolide add to and modify the cation effects. The above rationale is fully consistent with the ion effects on the kinetics of Na+,K+-ATPase/bufadienolide interactions.
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Affiliation(s)
- Lucy Kate Ladefoged
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Natalya U Fedosova
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark
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19
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Dabravolski SA, Isayenkov SV. Evolution of Plant Na +-P-Type ATPases: From Saline Environments to Land Colonization. PLANTS 2021; 10:plants10020221. [PMID: 33498844 PMCID: PMC7911474 DOI: 10.3390/plants10020221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/17/2022]
Abstract
Soil salinity is one of the major factors obstructing the growth and development of agricultural crops. Eukaryotes have two main transport systems involved in active Na+ removal: cation/H+ antiporters and Na+-P-type ATPases. Key transport proteins, Na+/K+-P-ATPases, are widely distributed among the different taxa families of pumps which are responsible for keeping cytosolic Na+ concentrations below toxic levels. Na+/K+-P-ATPases are considered to be absent in flowering plants. The data presented here are a complete inventory of P-type Na+/K+-P-ATPases in the major branches of the plant kingdom. We also attempt to elucidate the evolution of these important membrane pumps in plants in comparison with other organisms. We were able to observe the gradual replacement of the Na+-binding site to the Ca2+-binding site, starting with cyanobacteria and moving to modern land plants. Our results show that the α-subunit likely evolved from one common ancestor to bacteria, fungi, plants, and mammals, whereas the β-subunit did not evolve in green algae. In conclusion, our results strongly suggest the significant differences in the domain architecture and subunit composition of plant Na+/K+-P-ATPases depending on plant taxa and the salinity of the environment. The obtained data clarified and broadened the current views on the evolution of Na+/K+-P-ATPases. The results of this work would be helpful for further research on P-type ATPase functionality and physiological roles.
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Affiliation(s)
- Siarhei A. Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], 21002 Vitebsk, Belarus;
| | - Stanislav V. Isayenkov
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics NAS of Ukraine, 04123 Kyiv, Ukraine
- Correspondence: author:
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20
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Yamamoto K, Dubey V, Irie K, Nakanishi H, Khandelia H, Fujiyoshi Y, Abe K. A single K +-binding site in the crystal structure of the gastric proton pump. eLife 2019; 8:47701. [PMID: 31436534 PMCID: PMC6706254 DOI: 10.7554/elife.47701] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/05/2019] [Indexed: 11/13/2022] Open
Abstract
The gastric proton pump (H+,K+-ATPase), a P-type ATPase responsible for gastric acidification, mediates electro-neutral exchange of H+ and K+ coupled with ATP hydrolysis, but with an as yet undetermined transport stoichiometry. Here we show crystal structures at a resolution of 2.5 Å of the pump in the E2-P transition state, in which the counter-transporting cation is occluded. We found a single K+ bound to the cation-binding site of the H+,K+-ATPase, indicating an exchange of 1H+/1K+ per hydrolysis of one ATP molecule. This fulfills the energy requirement for the generation of a six pH unit gradient across the membrane. The structural basis of K+ recognition is resolved and supported by molecular dynamics simulations, establishing how the H+,K+-ATPase overcomes the energetic challenge to generate an H+ gradient of more than a million-fold-one of the highest cation gradients known in mammalian tissue-across the membrane.
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Affiliation(s)
- Kenta Yamamoto
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Vikas Dubey
- Department of Physics, Chemistry and Pharmacy, PHYLIFE, University of Southern Denmark, Odense, Denmark
| | - Katsumasa Irie
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hanayo Nakanishi
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Himanshu Khandelia
- Department of Physics, Chemistry and Pharmacy, PHYLIFE, University of Southern Denmark, Odense, Denmark
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,CeSPIA Inc, Tokyo, Japan
| | - Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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21
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Pieńko T, Trylska J. Computational Methods Used to Explore Transport Events in Biological Systems. J Chem Inf Model 2019; 59:1772-1781. [DOI: 10.1021/acs.jcim.8b00974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tomasz Pieńko
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, S. Banacha 1a, 02-097 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
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22
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Grasso G, Morbiducci U, Massai D, Tuszynski JA, Danani A, Deriu MA. Destabilizing the AXH Tetramer by Mutations: Mechanisms and Potential Antiaggregation Strategies. Biophys J 2019; 114:323-330. [PMID: 29401430 DOI: 10.1016/j.bpj.2017.11.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/03/2017] [Accepted: 11/20/2017] [Indexed: 01/12/2023] Open
Abstract
The AXH domain of protein Ataxin 1 is thought to play a key role in the misfolding and aggregation pathway responsible for Spinocerebellar ataxia 1. For this reason, a molecular level understanding of AXH oligomerization pathway is crucial to elucidate the aggregation mechanism, which is thought to trigger the disease. This study employs classical and enhanced molecular dynamics to identify the structural and energetic basis of AXH tetramer stability. Results of this work elucidate molecular mechanisms behind the destabilizing effect of protein mutations, which consequently affect the AXH tetramer assembly. Moreover, results of the study draw attention for the first time, to our knowledge, to the R638 protein residue, which is shown to play a key role in AXH tetramer stability. Therefore, R638 might be also implicated in the AXH oligomerization pathway and stands out as a target for future experimental studies focused on self-association mechanisms and fibril formation of full-length ATX1.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Diana Massai
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Andrea Danani
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland
| | - Marco A Deriu
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland.
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23
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Rui H, Das A, Nakamoto R, Roux B. Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump. J Mol Biol 2018; 430:5050-5065. [PMID: 30539761 DOI: 10.1016/j.jmb.2018.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/25/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
Abstract
The calcium pump of the sarcoplasmic reticulum (SERCA) is an ATP-driven active transporter of Ca2+ ions that functions via an "alternating-access" cycle mechanism. In each cycle, SERCA transports two Ca2+ ions toward the lumen of the sarcoplasmic reticulum and two to three protons to the cytoplasm. How the latter conformational transition is coupled to cytoplasmic release of protons remains poorly understood. The present computational study shows how the mechanism of proton countertransport is coupled to the alternating access gating process in SERCA. Molecular dynamics simulation trajectories are generated starting from a series of configurations taken along the E2 to E1 transition pathway determined by the string method with swarms-of-trajectories. Simulations of different protonation configurations at the binding sites reveal how deprotonation events affect the opening of the cytoplasmic gate. The results show that there is a strong coupling between the chronological order of deprotonation, the entry of water molecules into the TM region, and the opening of the cytoplasmic gate. Deprotonation of E309 and E771 is sequential with E309 being the first to lose the proton. The deprotonation promotes the opening of the cytoplasmic gate but leads to a productive gating transition only if it occurs after the transmembrane domain has reached an intermediate conformation. Deprotonation of E309 and E771 is unproductive when it occurs too early because it causes the re-opening of the luminal gate.
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Affiliation(s)
- Huan Rui
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Avisek Das
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Robert Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, PO Box 800886, 480 Ray C. Hunt Drive, Charlottesville, VA 22908, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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24
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Dubey V, Han M, Kopec W, Solov'yov IA, Abe K, Khandelia H. K + binding and proton redistribution in the E 2P state of the H +, K +-ATPase. Sci Rep 2018; 8:12732. [PMID: 30143663 PMCID: PMC6109069 DOI: 10.1038/s41598-018-30885-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022] Open
Abstract
The H+, K+-ATPase (HKA) uses ATP to pump protons into the gastric lumen against a million-fold proton concentration gradient while counter-transporting K+ from the lumen. The mechanism of release of a proton into a highly acidic stomach environment, and the subsequent binding of a K+ ion necessitates a network of protonable residues and dynamically changing protonation states in the cation binding pocket dominated by five acidic amino acid residues E343, E795, E820, D824, and D942. We perform molecular dynamics simulations of spontaneous K+ binding to all possible protonation combinations of the acidic amino acids and carry out free energy calculations to determine the optimal protonation state of the luminal-open E2P state of the pump which is ready to bind luminal K+. A dynamic pKa correlation analysis reveals the likelihood of proton transfer events within the cation binding pocket. In agreement with in-vitro measurements, we find that E795 is likely to be protonated, and that E820 is at the center of the proton transfer network in the luminal-open E2P state. The acidic residues D942 and D824 are likely to remain protonated, and the proton redistribution occurs predominantly amongst the glutamate residues exposed to the lumen. The analysis also shows that a lower number of K+ ions bind at lower pH, modeled by a higher number of protons in the cation binding pocket, in agreement with the 'transport stoichiometry variation' hypothesis.
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Affiliation(s)
- Vikas Dubey
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230 M, Denmark
- MEMPHYS-Center for Biomembrane Physics, Odense, Denmark
| | - Minwoo Han
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230 M, Denmark
- MEMPHYS-Center for Biomembrane Physics, Odense, Denmark
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230 M, Denmark
| | - Kazuhiro Abe
- Cellular and Structural Physiology Institute and Department of Medicinal Science, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Himanshu Khandelia
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230 M, Denmark.
- MEMPHYS-Center for Biomembrane Physics, Odense, Denmark.
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25
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Vleeskens E, Clarke RJ. Kinetic contribution to extracellular Na +/K + selectivity in the Na +/K + pump. FEBS Open Bio 2018; 8:854-859. [PMID: 29744299 PMCID: PMC5929939 DOI: 10.1002/2211-5463.12418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/16/2018] [Accepted: 03/22/2018] [Indexed: 11/25/2022] Open
Abstract
The sodium potassium pump (Na+,K+‐ATPase) shows a high selectivity for K+ over Na+ binding from the extracellular medium. To understand the K+ selectivity in the presence of a high concentration of competing Na+ ions requires consideration of more than just ion binding affinities. Here, equilibrium‐based calculations of the extracellular occupation of the Na+,K+‐ATPase transport sites by Na+ and K+ are compared to fluxes through Na+ and K+ transport pathways. The results show that, under physiological conditions, there is a 332‐fold selectivity for pumping of K+ from the extracellular medium into the cytoplasm relative to Na+, whereas equilibrium calculations alone predict only a 7.5‐fold selectivity for K+. Thus, kinetic effects make a major contribution to the determination of extracellular K+ selectivity.
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Affiliation(s)
| | - Ronald J Clarke
- School of Chemistry University of Sydney Australia.,The University of Sydney Nano Institute Australia
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26
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Cornelius F, Tsunekawa N, Toyoshima C. Distinct pH dependencies of Na +/K + selectivity at the two faces of Na,K-ATPase. J Biol Chem 2017; 293:2195-2205. [PMID: 29247005 DOI: 10.1074/jbc.ra117.000700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/28/2017] [Indexed: 11/06/2022] Open
Abstract
The sodium pump (Na,K-ATPase) in animal cells is vital for actively maintaining ATP hydrolysis-powered Na+ and K+ electrochemical gradients across the cell membrane. These ion gradients drive co- and countertransport and are critical for establishing the membrane potential. It has been an enigma how Na,K-ATPase discriminates between Na+ and K+, despite the pumped ion on each side being at a lower concentration than the other ion. Recent crystal structures of analogs of the intermediate conformations E2·Pi·2K+ and Na+-bound E1∼P·ADP suggest that the dimensions of the respective binding sites in Na,K-ATPase are crucial in determining its selectivity. Here, we found that the selectivity at each membrane face is pH-dependent and that this dependence is unique for each face. Most notable was a strong increase in the specific affinity for K+ at the extracellular face (i.e. E2 conformation) as the pH is lowered from 7.5 to 5. We also observed a smaller increase in affinity for K+ on the cytoplasmic side (E1 conformation), which reduced the selectivity for Na+ Theoretical analysis of the pKa values of ion-coordinating acidic amino acid residues suggested that the face-specific pH dependences and Na+/K+ selectivities may arise from the protonation or ionization of key residues. The increase in K+ selectivity at low pH on the cytoplasmic face, for instance, appeared to be associated with Asp808 protonation. We conclude that changes in the ionization state of coordinating residues in Na,K-ATPase could contribute to altering face-specific ion selectivity.
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Affiliation(s)
- Flemming Cornelius
- From the Department of Biomedicine, University of Aarhus, Ole Worms Allé 6, 8000 Aarhus C, Denmark and
| | - Naoki Tsunekawa
- the Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032
| | - Chikashi Toyoshima
- the Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032
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27
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Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:909-926. [PMID: 29113819 DOI: 10.1016/j.bbamem.2017.10.033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/24/2017] [Accepted: 10/28/2017] [Indexed: 11/22/2022]
Abstract
The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables.
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28
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Razavi AM, Delemotte L, Berlin JR, Carnevale V, Voelz VA. Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na +/K +-ATPase ion selectivity. J Biol Chem 2017; 292:12412-12423. [PMID: 28588025 DOI: 10.1074/jbc.m117.779090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/05/2017] [Indexed: 12/14/2022] Open
Abstract
Na+/K+-ATPase transports Na+ and K+ ions across the cell membrane via an ion-binding site becoming alternatively accessible to the intra- and extracellular milieu by conformational transitions that confer marked changes in ion-binding stoichiometry and selectivity. To probe the mechanism of these changes, we used molecular simulation and free-energy perturbation approaches to identify probable protonation states of Na+- and K+-coordinating residues in E1P and E2P conformations of Na+/K+-ATPase. Analysis of these simulations revealed a molecular mechanism responsible for the change in protonation state: the conformation-dependent binding of an anion (a chloride ion in our simulations) to a previously unrecognized cytoplasmic site in the loop between transmembrane helices 8 and 9, which influences the electrostatic potential of the crucial Na+-coordinating residue Asp926 This mechanistic model is consistent with experimental observations and provides a molecular-level picture of how E1P to E2P enzyme conformational transitions are coupled to changes in ion-binding stoichiometry and selectivity.
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Affiliation(s)
- Asghar M Razavi
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Lucie Delemotte
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122; Science for Life Laboratory, Department of Theoretical Physics, KTH Royal Institute of Technology, Stockholm 11428, Sweden
| | - Joshua R Berlin
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Vincenzo Carnevale
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122; Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122.
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122; Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122.
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29
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Ion channels and ion selectivity. Essays Biochem 2017; 61:201-209. [PMID: 28487397 DOI: 10.1042/ebc20160074] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/16/2017] [Accepted: 03/01/2017] [Indexed: 12/26/2022]
Abstract
Specific macromolecular transport systems, ion channels and pumps, provide the pathways to facilitate and control the passage of ions across the lipid membrane. Ion channels provide energetically favourable passage for ions to diffuse rapidly and passively according to their electrochemical potential. Selective ion channels are essential for the excitability of biological membranes: the action potential is a transient phenomenon that reflects the rapid opening and closing of voltage-dependent Na+-selective and K+-selective channels. One of the most critical functional aspects of K+ channels is their ability to remain highly selective for K+ over Na+ while allowing high-throughput ion conduction at a rate close to the diffusion limit. Permeation through the K+ channel selectivity filter is believed to proceed as a 'knockon' mechanism, in which 2-3 K+ ions interspersed by water molecules move in a single file. Permeation through the comparatively wider and less selective Na+ channels also proceeds via a loosely coupled knockon mechanism, although the ions do not need to be fully dehydrated. While simple structural concepts are often invoked to rationalize the mechanism of ion selectivity, a deeper analysis shows that subtle effects play an important role in these flexible dynamical structures.
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30
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Han M, Kopec W, Solov’yov IA, Khandelia H. Glutamate Water Gates in the Ion Binding Pocket of Na + Bound Na +, K +-ATPase. Sci Rep 2017; 7:39829. [PMID: 28084301 PMCID: PMC5233988 DOI: 10.1038/srep39829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/25/2016] [Indexed: 11/15/2022] Open
Abstract
The dynamically changing protonation states of the six acidic amino acid residues in the ion binding pocket of the Na+, K+ -ATPase (NKA) during the ion transport cycle are proposed to drive ion binding, release and possibly determine Na+ or K+ selectivity. We use molecular dynamics (MD) and density functional theory (DFT) simulations to determine the protonation scheme of the Na+ bound conformation of NKA. MD simulations of all possible protonation schemes show that the bound Na+ ions are most stably bound when three or four protons reside in the binding sites, and that Glu954 in site III is always protonated. Glutamic acid residues in the three binding sites act as water gates, and their deprotonation triggers water entry to the binding sites. From DFT calculations of Na+ binding energies, we conclude that three protons in the binding site are needed to effectively bind Na+ from water and four are needed to release them in the next step. Protonation of Asp926 in site III will induce Na+ release, and Glu327, Glu954 and Glu779 are all likely to be protonated in the Na+ bound occluded conformation. Our data provides key insights into the role of protons in the Na+ binding and release mechanism of NKA.
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Affiliation(s)
- Minwoo Han
- MEMPHYS−Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Wojciech Kopec
- MEMPHYS−Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ilia A. Solov’yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Himanshu Khandelia
- MEMPHYS−Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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