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The Journal of Membrane Biology Jun 2018The dependency of current-voltage characteristics of the α-hemolysin channel on the channel position within the membrane was studied using Poisson-Nernst-Planck theory...
The dependency of current-voltage characteristics of the α-hemolysin channel on the channel position within the membrane was studied using Poisson-Nernst-Planck theory of ion conductivity with soft repulsion between mobile ions and protein atoms (SP-PNP). The presence of the membrane environment also influences the protonation state of the residues at the boundary of the water-lipid interface. In this work, we predict that Asp and Lys residues at the protein rim change their protonation state upon penetration to the lipid environment. Free energies of protein insertion in the membrane for different penetration depths were estimated using the Poisson-Boltzmann/solvent-accessible surface area (PB/SASA) model. The results show that rectification and reversal potentials are very sensitive to the relative position of channel in the membrane, which in turn contributes to alternative protonation states of lipid-penetrating ionizable groups. The prediction of channel position based on the matching of calculated rectification with experimentally determined rectification is in good agreement with recent neutron reflection experiments. Based on the results, we conclude that α-hemolysin membrane position is determined by a combination of factors and not only by the pattern of the surface hydrophobicity as is typically assumed.
Topics: Hemolysin Proteins; Hydrophobic and Hydrophilic Interactions; Ion Channels; Membrane Potentials; Models, Molecular; Models, Theoretical
PubMed: 29340712
DOI: 10.1007/s00232-018-0013-3 -
Nature Communications Feb 2023Inorganic polyphosphate (polyP) is an ancient energy metabolite and phosphate store that occurs ubiquitously in all organisms. The vacuolar transporter chaperone (VTC)...
Inorganic polyphosphate (polyP) is an ancient energy metabolite and phosphate store that occurs ubiquitously in all organisms. The vacuolar transporter chaperone (VTC) complex integrates cytosolic polyP synthesis from ATP and polyP membrane translocation into the vacuolar lumen. In yeast and in other eukaryotes, polyP synthesis is regulated by inositol pyrophosphate (PP-InsP) nutrient messengers, directly sensed by the VTC complex. Here, we report the cryo-electron microscopy structure of signal-activated VTC complex at 3.0 Å resolution. Baker's yeast VTC subunits Vtc1, Vtc3, and Vtc4 assemble into a 3:1:1 complex. Fifteen trans-membrane helices form a novel membrane channel enabling the transport of newly synthesized polyP into the vacuolar lumen. PP-InsP binding orients the catalytic polymerase domain at the entrance of the trans-membrane channel, both activating the enzyme and coupling polyP synthesis and membrane translocation. Together with biochemical and cellular studies, our work provides mechanistic insights into the biogenesis of an ancient energy metabolite.
Topics: Polyphosphates; Cryoelectron Microscopy; Saccharomyces cerevisiae; Cytosol; Ion Channels
PubMed: 36759618
DOI: 10.1038/s41467-023-36466-4 -
The Journal of Membrane Biology Feb 2021The voltage-gated proton channel Hv1 mediates efflux of protons from the cell. Hv1 integrally contributes to various physiological processes including pH homeostasis and...
The voltage-gated proton channel Hv1 mediates efflux of protons from the cell. Hv1 integrally contributes to various physiological processes including pH homeostasis and the respiratory burst of phagocytes. Inhibition of Hv1 may provide therapeutic avenues for the treatment of inflammatory diseases, breast cancer, and ischemic brain damage. In this work, we investigate two prototypical Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI), and 5-chloro-2-guanidinobenzimidazole (GBIC), from an experimentally screened class of guanidine derivatives. Both compounds block proton conduction by binding the same site located on the intracellular side of the channel. However, when added to the extracellular medium, the compounds strongly differ in their ability to inhibit proton conduction, suggesting substantial differences in membrane permeability. Here, we compute the potential of mean force for each compound to permeate through the membrane using atomistic molecular dynamics simulations with the adaptive biasing force method. Our results rationalize the putative distinction between these two blockers with respect to their abilities to permeate the cellular membrane.
Topics: Cell Membrane Permeability; Ion Channels; Molecular Dynamics Simulation; Protons; Thermodynamics
PubMed: 33196887
DOI: 10.1007/s00232-020-00149-8 -
Channels (Austin, Tex.) Dec 2019Cannabidiol (CBD), the non-psychoactive component of Cannabis sativa, acts on a diverse selection of membrane proteins with promising therapeutic potential in epilepsy... (Review)
Review
Cannabidiol (CBD), the non-psychoactive component of Cannabis sativa, acts on a diverse selection of membrane proteins with promising therapeutic potential in epilepsy and chronic pain. One such protein is the voltage-gated sodium channel (Na). CBD shows a lack of specificity for sodium channels; however, the method of interaction is still unknown. In this review, we will outline the studies that report reproducible results of CBD and other cannabinoids changing membrane channel function, with particular interest on Na. Na are implicated in fatal forms of epilepsy and are also associated with chronic pain. This makes Na potential targets for CBD interaction since it has been reported to reduce pain and seizures. One potential method of interaction that is of interest in this review is whether CBD affects channel function by altering lipid bilayer properties, independent of any possible direct interaction with membrane channels. CBD's ability to interact with its targets is a novel and important discovery. This discovery will not only prompt further research towards CBD's characterization, but also promotes the application of cannabinoids as potentially therapeutic compounds for diseases like epilepsy and pain.
Topics: Animals; Brain; Cannabidiol; Cannabinoids; Epilepsy; Humans; Protein Binding; Voltage-Gated Sodium Channels
PubMed: 31088312
DOI: 10.1080/19336950.2019.1615824 -
Biochimica Et Biophysica Acta May 2015The past decade, membrane signaling lipids emerged as major regulators of ion channel function. However, the molecular nature of lipid binding to ion channels remained... (Review)
Review
The past decade, membrane signaling lipids emerged as major regulators of ion channel function. However, the molecular nature of lipid binding to ion channels remained poorly described due to a lack of structural information and assays to quantify and measure lipid binding in a membrane. How does a lipid-ligand bind to a membrane protein in the plasma membrane, and what does it mean for a lipid to activate or regulate an ion channel? How does lipid binding compare to activation by soluble neurotransmitter? And how does the cell control lipid agonism? This review focuses on lipids and their interactions with membrane proteins, in particular, ion channels. I discuss the intersection of membrane lipid biology and ion channel biophysics. A picture emerges of membrane lipids as bona fide agonists of ligand-gated ion channels. These freely diffusing signals reside in the plasma membrane, bind to the transmembrane domain of protein, and cause a conformational change that allosterically gates an ion channel. The system employs a catalog of diverse signaling lipids ultimately controlled by lipid enzymes and raft localization. I draw upon pharmacology, recent protein structure, and electrophysiological data to understand lipid regulation and define inward rectifying potassium channels (Kir) as a new class of PIP2 lipid-gated ion channels.
Topics: Animals; Humans; Ion Channel Gating; Ligand-Gated Ion Channels; Ligands; Membrane Microdomains; Membrane Potentials; Models, Molecular; Phosphatidylinositol 4,5-Diphosphate; Potassium Channels, Inwardly Rectifying; Protein Conformation; Structure-Activity Relationship
PubMed: 25633344
DOI: 10.1016/j.bbalip.2015.01.011 -
Pflugers Archiv : European Journal of... Jan 2015Mechanosensitive channels are integral components for the response of bacteria to osmotic shock. The mechanosensitive channel of large conductance (MscL) responds to... (Review)
Review
Mechanosensitive channels are integral components for the response of bacteria to osmotic shock. The mechanosensitive channel of large conductance (MscL) responds to extreme turgor pressure increase that would otherwise lyse the cellular membrane. MscL has been studied as a model mechanosensitive channel using both structural and functional approaches. We will summarize the structural data and discuss outstanding questions surrounding the gating mechanism of this homo-oligomeric channel that has ~3 nS conductance. Specifically, we will explore the following: (1) the variability in oligomeric state that has been observed, (2) the open pore size measurements, and (3) the role of the C-terminal coiled coil domain for channel function. The oligomeric state of MscL has been characterized using various techniques, with a pentamer being the predominant form; however, the presence of mixtures of oligomers in the membrane is still uncertain. In the absence of structural data for the open state of MscL, the diameter of the open state pore has been estimated by several different approaches, leading to a current estimate between 25 and 30 Å. While the C-terminal domain is highly conserved among MscL homologues, it is not required for activity in vivo or in vitro. This domain is likely to remain intact during the gating transition and perform a filtering function that retains valuable osmolytes in the cytosol. Overall, studies of MscL have provided significant insight to the field, and serve as a paradigm for the analysis of non-homologous, eukaryotic mechanosensitive channel proteins.
Topics: Cell Membrane; Computer Simulation; Escherichia coli Proteins; Ion Channel Gating; Ion Channels; Mechanotransduction, Cellular; Membrane Fluidity; Models, Chemical; Models, Molecular; Osmoregulation; Porosity; Structure-Activity Relationship
PubMed: 24859800
DOI: 10.1007/s00424-014-1535-x -
Current Opinion in Structural Biology Aug 1997Channel-forming bacterial toxins undergo a series of remarkable changes in solubility, oligomerization state, structure and dynamics during the processes of membrane... (Review)
Review
Channel-forming bacterial toxins undergo a series of remarkable changes in solubility, oligomerization state, structure and dynamics during the processes of membrane binding, assembly, membrane insertion and channel formation. Recent high-resolution crystal structures of channel-forming toxins, in both water-soluble and membrane-bound, channel-formed states, have brought a wealth of new information to bear on issues of structure, mechanism and function.
Topics: Bacterial Toxins; Ion Channels; Protein Conformation
PubMed: 9266180
DOI: 10.1016/s0959-440x(97)80123-6 -
Channels (Austin, Tex.) 2015A prerequisite for a successful target-based drug discovery program is a robust data set that increases confidence in the validation of the molecular target and the... (Review)
Review
A prerequisite for a successful target-based drug discovery program is a robust data set that increases confidence in the validation of the molecular target and the therapeutic approach. Given the significant time and resource investment required to carry a drug to market, early selection of targets that can be modulated safely and effectively forms the basis for a strong portfolio and pipeline. In this article we present some of the more useful scientific approaches that can be applied toward the validation of ion channel targets, a molecular family with a history of clinical success in therapeutic areas such as cardiovascular, respiratory, pain and neuroscience.
Topics: Animals; Drug Discovery; Genome, Human; Humans; Ion Channels; Membrane Transport Modulators; Validation Studies as Topic
PubMed: 26556675
DOI: 10.1080/19336950.2015.1081725 -
Microbiology and Molecular Biology... Feb 2020General principles in biology have often been elucidated from the study of bacteria. This is true for the bacterial mechanosensitive channel of large conductance, MscL,... (Review)
Review
General principles in biology have often been elucidated from the study of bacteria. This is true for the bacterial mechanosensitive channel of large conductance, MscL, the channel highlighted in this review. This channel functions as a last-ditch emergency release valve discharging cytoplasmic solutes upon decreases in osmotic environment. Opening the largest gated pore, MscL passes molecules up to 30 Å in diameter; exaggerated conformational changes yield advantages for study, including assays. MscL contains structural/functional themes that recur in higher organisms and help elucidate how other, structurally more complex, channels function. These features of MscL include (i) the ability to directly sense, and respond to, biophysical changes in the membrane, (ii) an α helix ("slide helix") or series of charges ("knot in a rope") at the cytoplasmic membrane boundary to guide transmembrane movements, and (iii) important subunit interfaces that, when disrupted, appear to cause the channel to gate inappropriately. MscL may also have medical applications: the modality of the MscL channel can be changed, suggesting its use as a triggered nanovalve in nanodevices, including those for drug targeting. In addition, recent studies have shown that the antibiotic streptomycin opens MscL and uses it as one of the primary paths to the cytoplasm. Moreover, the recent identification and study of novel specific agonist compounds demonstrate that the channel is a valid drug target. Such compounds may serve as novel-acting antibiotics and adjuvants, a way of permeabilizing the bacterial cell membrane and, thus, increasing the potency of commonly used antibiotics.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Physiological Phenomena; Cell Membrane; Escherichia coli; Escherichia coli Proteins; Ion Channels; Osmoregulation
PubMed: 31941768
DOI: 10.1128/MMBR.00055-19 -
Current Biology : CB Apr 2018The sensations of sound, touch and pressure are mediated by mechanotransduction channels - transmembrane proteins whose ionic permeabilities are gated by mechanical... (Review)
Review
The sensations of sound, touch and pressure are mediated by mechanotransduction channels - transmembrane proteins whose ionic permeabilities are gated by mechanical forces. New structures of Piezo1 by cryoEM lead to the suggestion that this channel might sense membrane tension through changes in the local curvature of the membrane.
Topics: Animals; Cytoskeleton; Hearing; Humans; Ion Channels; Mechanical Phenomena; Mechanotransduction, Cellular; Mice; Molecular Biology; Pressure; Touch
PubMed: 29689211
DOI: 10.1016/j.cub.2018.02.078