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Ion Pumps: Molecular Mechanisms, Structure, Physiology
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Ion Pumps: Molecular Mechanisms, Structure, Physiology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 30 August 2024 | Viewed by 5431

Special Issue Editor

Prof. Dr. Sergey Siletsky

E-Mail Website
Guest Editor
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
Interests: biophysics; biochemistry; molecular bioenergetics; mechanisms of enzyme action; membrane proteins; terminal oxidases; cytochrome oxidase; cytochromes; retinal proteins; photosystem 2; proton pump; electrogenic mechanisms of membrane potential generation; reactive oxygen species; fast kinetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ion pumps are integrated membrane proteins that directly convert energy from various sources, including ATP, sunlight, and redox reactions, into potential energy by pumping an ion up its electrochemical concentration gradient. This potential energy can then be used by secondary transporters, including ion carriers and ion channels, to control cellular processes, including ATP synthesis. Ion pumps are divided into various large classes, which differ in their ion specificity, use of different energy sources, polypeptide composition and evolutionary origin. Examples of the primary ion transporters that use the energy of ATP to transport ions across cell membranes are the transporting caution pumps (P-type ATPases, including Na+/K+-ATPase, H+/K+ ATPase, Ca2+ATPase, etc.) and anionic pumps (A-type ATPases). Ion pumps can be electrogenic, including sodium–potassium pumps, which are universal to all animals and maintain the membrane potential by moving three Na+ ions out of the cell for every two K+ ions moved into the cell.  However, there are also non-electrogenic ion pumps, such as f.e., hydrogen–potassium ATPase or H+/K+ ATPase of the gastric mucosa, which are primarily responsible for the acidification of the stomach contents and can be attributed to the proton pumps. Proton pumps, as a special case of ion pumps, are proteins that create and maintain an electrochemical gradient of protons in biological membranes by driving protons through the membrane. Proton pumping driven by the chemical energy of energy-rich metabolites is exemplified by proton ATPases (ATP synthases), proton-pumping pyrophosphatase, proton-translocating transhydrogenase, etc. The redox energy of electron transfer from NADH to oxygen is used in the electron transfer complexes of the respiratory chain to move protons across the inner mitochondrial membrane against their concentration gradient. Among them, the mechanisms of NADH dehydrogenase and cytochrome oxidase proton pumping deserve attention. The source of free energy for the pumping of ions (H+, Cl-, Na+ and other ions) in pumps of procariotes can be light energy (f.e., bacteriorhodopsin, halorhodopsin and other retinal-based ion pumps). Electron- and proton-coupled reactions are used in the membrane proteins involved in the photosynthesis of higher plants, where the light energy of photons is used to create a proton gradient across the thylakoid membrane and reduction power in the form of NADPH. The study of the mechanisms of functioning of such natural nanoscale devices as ion pumping proteins and associated membrane structures should contribute to the creation of artificial efficient energy converters, the rational use of biomimetic technologies, the regulation of cellular processes in norm and pathology, the creation of specific drugs and pharmaceuticals and the development of new tools in optogenetics, neurobiology and new approaches in medicine. We welcome studies that contribute to our understanding of the molecular mechanisms, structure and functional properties of ion pumps and related enzymes, their physiological roles, mechanisms of inhibition and activation, ways of assembly and maturation and biotechnological and medical applications. Original research articles and up-to-date reviews on these and related topics are also welcome in this Special Issue.

Prof. Dr. Sergey Siletsky
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • ion pump
  • proton pump
  • electrogenic
  • Na+/K+ ATPase
  • Ca2+ ATPase
  • P-type ATPase
  • A-type ATPases
  • H+/K+ ATPase
  • gastric proton pump
  • proton pump inhibitor
  • photosynthesis
  • respiratory chain
  • complex I
  • NADH dehydrogenase
  • quinol oxidase
  • complex IV
  • cytochrome oxidase
  • cytochrome
  • pyrophosphatase
  • transhydrogenase
  • proton-translocating ATPase
  • ATP synthase
  • retinal
  • bacteriorhodopsin
  • halorhodopsin

Published Papers (5 papers)

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Research

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16 pages, 19129 KiB  
Article
Atp6v1h Deficiency Blocks Bone Loss in Simulated Microgravity Mice through the Fos-Jun-Src-Integrin Pathway
by Zanyan Zhao, Xiangpu Wang, Yu Ma and Xiaohong Duan
Int. J. Mol. Sci. 2024, 25(1), 637; https://doi.org/10.3390/ijms25010637 - 04 Jan 2024
Viewed by 802
Abstract
The microgravity conditions in outer space are widely acknowledged to induce significant bone loss. Recent studies have implicated the close relationship between Atp6v1h gene and bone loss. Despite this, the role of Atp6v1h in bone remodeling and its molecular mechanisms in microgravity have [...] Read more.
The microgravity conditions in outer space are widely acknowledged to induce significant bone loss. Recent studies have implicated the close relationship between Atp6v1h gene and bone loss. Despite this, the role of Atp6v1h in bone remodeling and its molecular mechanisms in microgravity have not been fully elucidated. To address this, we used a mouse tail suspension model to simulate microgravity. We categorized both wild-type and Atp6v1h knockout (Atp6v1h+/-) mice into two groups: regular feeding and tail-suspension feeding, ensuring uniform feeding conditions across all cohorts. Analysis via micro-CT scanning, hematoxylin-eosin staining, and tartrate-resistant acid phosphatase assays indicated that wild-type mice underwent bone loss under simulated microgravity. Atp6v1h+/- mice exhibited bone loss due to Atp6v1h deficiency but did not present aggravated bone loss under the same simulated microgravity. Transcriptomic sequencing revealed the upregulation of genes, such as Fos, Src, Jun, and various integrin subunits in the context of simulated microgravity and Atp6v1h knockout. Real-time quantitative polymerase chain reaction (RT-qPCR) further validated the modulation of downstream osteoclast-related genes in response to interactions with ATP6V1H overexpression cell lines. Co-immunoprecipitation indicated potential interactions between ATP6V1H and integrin beta 1, beta 3, beta 5, alpha 2b, and alpha 5. Our results indicate that Atp6v1h level influences bone loss in simulated microgravity by modulating the Fos-Jun-Src-Integrin pathway, which, in turn, affects osteoclast activity and bone resorption, with implications for osteoporosis. Therefore, modulating Atp6v1h expression could mitigate bone loss in microgravity conditions. This study elucidates the molecular mechanism of Atp6v1h’s role in osteoporosis and positions it as a potential therapeutic target against environmental bone loss. These findings open new possibilities for the treatment of multifactorial osteoporosis. Full article
(This article belongs to the Special Issue Ion Pumps: Molecular Mechanisms, Structure, Physiology)
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21 pages, 5436 KiB  
Article
Anionic Phospholipids Stimulate the Proton Pumping Activity of the Plant Plasma Membrane P-Type H+-ATPase
by Laura C. Paweletz, Simon L. Holtbrügge, Malina Löb, Dario De Vecchis, Lars V. Schäfer, Thomas Günther Pomorski and Bo Højen Justesen
Int. J. Mol. Sci. 2023, 24(17), 13106; https://doi.org/10.3390/ijms241713106 - 23 Aug 2023
Cited by 1 | Viewed by 822
Abstract
The activity of membrane proteins depends strongly on the surrounding lipid environment. Here, we characterize the lipid stimulation of the plant plasma membrane H+-ATPase Arabidopsis thaliana H+-ATPase isoform 2 (AHA2) upon purification and reconstitution into liposomes of defined lipid [...] Read more.
The activity of membrane proteins depends strongly on the surrounding lipid environment. Here, we characterize the lipid stimulation of the plant plasma membrane H+-ATPase Arabidopsis thaliana H+-ATPase isoform 2 (AHA2) upon purification and reconstitution into liposomes of defined lipid compositions. We show that the proton pumping activity of AHA2 is stimulated by anionic phospholipids, especially by phosphatidylserine. This activation was independent of the cytoplasmic C-terminal regulatory domain of the pump. Molecular dynamics simulations revealed several preferential contact sites for anionic phospholipids in the transmembrane domain of AHA2. These contact sites are partially conserved in functionally different P-type ATPases from different organisms, suggesting a general regulation mechanism by the membrane lipid environment. Our findings highlight the fact that anionic lipids play an important role in the control of H+-ATPase activity. Full article
(This article belongs to the Special Issue Ion Pumps: Molecular Mechanisms, Structure, Physiology)
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32 pages, 22302 KiB  
Article
Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase
by Rene F. Gorriz, Senta Volkenandt and Petra Imhof
Int. J. Mol. Sci. 2023, 24(13), 10464; https://doi.org/10.3390/ijms241310464 - 21 Jun 2023
Viewed by 785
Abstract
Cytochrome c Oxidase (CcO), a membrane protein of the respiratory chain, pumps protons against an electrochemical gradient by using the energy of oxygen reduction to water. The (“chemical”) protons required for this reaction and those pumped are taken up via two distinct channels, [...] Read more.
Cytochrome c Oxidase (CcO), a membrane protein of the respiratory chain, pumps protons against an electrochemical gradient by using the energy of oxygen reduction to water. The (“chemical”) protons required for this reaction and those pumped are taken up via two distinct channels, named D-channel and K-channel, in a step-wise and highly regulated fashion. In the reductive phase of the catalytic cycle, both channels transport protons so that the pumped proton passes the D-channel before the “chemical” proton has crossed the K-channel. By performing molecular dynamics simulations of CcO in the O→E redox state (after the arrival of the first reducing electron) with various combinations of protonation states of the D- and K-channels, we analysed the effect of protonation on the two channels. In agreement with previous work, the amount of water observed in the D-channel was significantly higher when the terminal residue E286 was not (yet) protonated than when the proton arrived at this end of the D-channel and E286 was neutral. Since a sufficient number of water molecules in the channel is necessary for proton transport, this can be understood as E286 facilitating its own protonation. K-channel hydration shows an even higher dependence on the location of the excess proton in the K-channel. Also in agreement with previous work, the K-channel exhibits a very low hydration level that likely hinders proton transfer when the excess proton is located in the lower part of the K-channel, that is, on the N-side of S365. Once the proton has passed S365 (towards the reaction site, the bi-nuclear centre (BNC)), the amount of water in the K-channel provides hydrogen-bond connectivity that renders proton transfer up to Y288 at the BNC feasible. No significant direct effect of the protonation state of one channel on the hydration level, hydrogen-bond connectivity, or interactions between protein residues in the other channel could be observed, rendering proton conductivity in the two channels independent of each other. Regulation of the order of proton uptake and proton passage in the two channels such that the “chemical” proton leaves its channel last must, therefore, be achieved by other means of communication, such as the location of the reducing electron. Full article
(This article belongs to the Special Issue Ion Pumps: Molecular Mechanisms, Structure, Physiology)
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18 pages, 3583 KiB  
Article
Oriented Insertion of ESR-Containing Hybrid Proteins in Proteoliposomes
by Lada E. Petrovskaya, Evgeniy P. Lukashev, Mahir D. Mamedov, Elena A. Kryukova, Sergei P. Balashov, Dmitry A. Dolgikh, Andrei B. Rubin, Mikhail P. Kirpichnikov and Sergey A. Siletsky
Int. J. Mol. Sci. 2023, 24(8), 7369; https://doi.org/10.3390/ijms24087369 - 17 Apr 2023
Viewed by 1324
Abstract
Microbial rhodopsins comprise a diverse family of retinal-containing membrane proteins that convert absorbed light energy to transmembrane ion transport or sensory signals. Incorporation of these proteins in proteoliposomes allows their properties to be studied in a native-like environment; however, unidirectional protein orientation in [...] Read more.
Microbial rhodopsins comprise a diverse family of retinal-containing membrane proteins that convert absorbed light energy to transmembrane ion transport or sensory signals. Incorporation of these proteins in proteoliposomes allows their properties to be studied in a native-like environment; however, unidirectional protein orientation in the artificial membranes is rarely observed. We aimed to obtain proteoliposomes with unidirectional orientation using a proton-pumping retinal protein from Exiguobacterium sibiricum, ESR, as a model. Three ESR hybrids with soluble protein domains (mCherry or thioredoxin at the C-terminus and Caf1M chaperone at the N-terminus) were obtained and characterized. The photocycle of the hybrid proteins incorporated in proteoliposomes demonstrated a higher pKa of the M state accumulation compared to that of the wild-type ESR. Large negative electrogenic phases and an increase in the relative amplitude of kinetic components in the microsecond time range in the kinetics of membrane potential generation of ESR-Cherry and ESR-Trx indicate a decrease in the efficiency of transmembrane proton transport. On the contrary, Caf-ESR demonstrates a native-like kinetics of membrane potential generation and the corresponding electrogenic stages. Our experiments show that the hybrid with Caf1M promotes the unidirectional orientation of ESR in proteoliposomes. Full article
(This article belongs to the Special Issue Ion Pumps: Molecular Mechanisms, Structure, Physiology)
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Review

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27 pages, 2171 KiB  
Review
Potential Theranostic Roles of SLC4 Molecules in Human Diseases
by Jingwen Zhong, Jing Dong, Wenyan Ruan and Xiaohong Duan
Int. J. Mol. Sci. 2023, 24(20), 15166; https://doi.org/10.3390/ijms242015166 - 13 Oct 2023
Viewed by 1218
Abstract
The solute carrier family 4 (SLC4) is an important protein responsible for the transport of various ions across the cell membrane and mediating diverse physiological functions, such as the ion transporting function, protein-to-protein interactions, and molecular transduction. The deficiencies in SLC4 molecules may [...] Read more.
The solute carrier family 4 (SLC4) is an important protein responsible for the transport of various ions across the cell membrane and mediating diverse physiological functions, such as the ion transporting function, protein-to-protein interactions, and molecular transduction. The deficiencies in SLC4 molecules may cause multisystem disease involving, particularly, the respiratory system, digestive, urinary, endocrine, hematopoietic, and central nervous systems. Currently, there are no effective strategies to treat these diseases. SLC4 proteins are also found to contribute to tumorigenesis and development, and some of them are regarded as therapeutic targets in quite a few clinical trials. This indicates that SLC4 proteins have potential clinical prospects. In view of their functional characteristics, there is a critical need to review the specific functions of bicarbonate transporters, their related diseases, and the involved pathological mechanisms. We summarize the diseases caused by the mutations in SLC4 family genes and briefly introduce the clinical manifestations of these diseases as well as the current treatment strategies. Additionally, we illustrate their roles in terms of the physiology and pathogenesis that has been currently researched, which might be the future therapeutic and diagnostic targets of diseases and a new direction for drug research and development. Full article
(This article belongs to the Special Issue Ion Pumps: Molecular Mechanisms, Structure, Physiology)
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