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Membrane Channels: Mechanistic Insights
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Membrane Channels: Mechanistic Insights

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

Deadline for manuscript submissions: closed (30 December 2023) | Viewed by 13310

Special Issue Editors

Prof. Dr. Marco Colombini

E-Mail Website
Guest Editor
Department of Biology, University of Maryland, College Park, MD 20842, USA
Interests: biophysics of membrane channels and voltage-gated channels in bacteria; ceramide channels; VDAC channels; the function of the mitochondrial outer membrane
Dr. Sergey M. Bezrukov

E-Mail Website
Co-Guest Editor
Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
Interests: membrane channels

Special Issue Information

Dear Colleagues,

Membrane channels are amazing biological machines that work in a very complex environment that includes: at least 2 phases of matter, surface potentials, dipole potentials, strong electric fields, lateral pressures/tension, unphysiological values of pH and ionic strength, etc. Many of these factors influence or control the states of the channels and thus the flux of matter through the pores. The mechanisms by which membrane channels are regulated vary widely perhaps far more than other biological machines. This special issue will focus on research that proves insight into the molecular mechanisms responsible for the regulation of membrane channels. The contributions could be either original research papers or reviews that bring together recent advances in understanding the molecular mechanism used in a specific membrane channel that underlies the observed phenomenology. Although new insights into well-studied channels are welcome, even more desirable are contributions that provide mechanistic insights into unusual channel-formers. We would like to include as much as possible of the entire spectrum of molecular mechanisms that are known to exist in nature.

Prof. Dr. Marco Colombini
Dr. Sergey M. Bezrukov
Guest Editors

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Keywords

  • voltage gating mechanism
  • chemical gating mechanism
  • tension gating mechanism
  • channel forming antibiotic
  • pore forming mechanism
  • cochlear channel mechanism
  • sensory channel mechanism
  • porin gating mechanism
  • ion channel mechanism
  • metabolite channel mechanism
  • ATP channel mechanism
  • calcium channel gating mechanism
  • sodium channel gating mechanism
  • potassium channel gating mechanism
  • connexin gating mechanism
 
 

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Published Papers (8 papers)

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Research

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24 pages, 3596 KiB  
Article
Intrinsic Lipid Curvature and Bilayer Elasticity as Regulators of Channel Function: A Comparative Single-Molecule Study
by Mohammad Ashrafuzzaman, Roger E. Koeppe II and Olaf S. Andersen
Int. J. Mol. Sci. 2024, 25(5), 2758; https://doi.org/10.3390/ijms25052758 - 27 Feb 2024
Cited by 3 | Viewed by 1133
Abstract
Perturbations in bilayer material properties (thickness, lipid intrinsic curvature and elastic moduli) modulate the free energy difference between different membrane protein conformations, thereby leading to changes in the conformational preferences of bilayer-spanning proteins. To further explore the relative importance of curvature and elasticity [...] Read more.
Perturbations in bilayer material properties (thickness, lipid intrinsic curvature and elastic moduli) modulate the free energy difference between different membrane protein conformations, thereby leading to changes in the conformational preferences of bilayer-spanning proteins. To further explore the relative importance of curvature and elasticity in determining the changes in bilayer properties that underlie the modulation of channel function, we investigated how the micelle-forming amphiphiles Triton X-100, reduced Triton X-100 and the HII lipid phase promoter capsaicin modulate the function of alamethicin and gramicidin channels. Whether the amphiphile-induced changes in intrinsic curvature were negative or positive, amphiphile addition increased gramicidin channel appearance rates and lifetimes and stabilized the higher conductance states in alamethicin channels. When the intrinsic curvature was modulated by altering phospholipid head group interactions, however, maneuvers that promote a negative-going curvature stabilized the higher conductance states in alamethicin channels but destabilized gramicidin channels. Using gramicidin channels of different lengths to probe for changes in bilayer elasticity, we found that amphiphile adsorption increases bilayer elasticity, whereas altering head group interactions does not. We draw the following conclusions: first, confirming previous studies, both alamethicin and gramicidin channels are modulated by changes in lipid bilayer material properties, the changes occurring in parallel yet differing dependent on the property that is being changed; second, isolated, negative-going changes in curvature stabilize the higher current levels in alamethicin channels and destabilize gramicidin channels; third, increases in bilayer elasticity stabilize the higher current levels in alamethicin channels and stabilize gramicidin channels; and fourth, the energetic consequences of changes in elasticity tend to dominate over changes in curvature. Full article
(This article belongs to the Special Issue Membrane Channels: Mechanistic Insights)
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18 pages, 2909 KiB  
Article
Beta-Barrel Channel Response to High Electric Fields: Functional Gating or Reversible Denaturation?
by Ekaterina M. Nestorovich and Sergey M. Bezrukov
Int. J. Mol. Sci. 2023, 24(23), 16655; https://doi.org/10.3390/ijms242316655 - 23 Nov 2023
Cited by 1 | Viewed by 1232
Abstract
Ion channels exhibit gating behavior, fluctuating between open and closed states, with the transmembrane voltage serving as one of the essential regulators of this process. Voltage gating is a fundamental functional aspect underlying the regulation of ion-selective, mostly α-helical, channels primarily found in [...] Read more.
Ion channels exhibit gating behavior, fluctuating between open and closed states, with the transmembrane voltage serving as one of the essential regulators of this process. Voltage gating is a fundamental functional aspect underlying the regulation of ion-selective, mostly α-helical, channels primarily found in excitable cell membranes. In contrast, there exists another group of larger, and less selective, β-barrel channels of a different origin, which are not directly associated with cell excitability. Remarkably, these channels can also undergo closing, or “gating”, induced by sufficiently strong electric fields. Once the field is removed, the channels reopen, preserving a memory of the gating process. In this study, we explored the hypothesis that the voltage-induced closure of the β-barrel channels can be seen as a form of reversible protein denaturation by the high electric fields applied in model membranes experiments—typically exceeding twenty million volts per meter—rather than a manifestation of functional gating. Here, we focused on the bacterial outer membrane channel OmpF reconstituted into planar lipid bilayers and analyzed various characteristics of the closing-opening process that support this idea. Specifically, we considered the nearly symmetric response to voltages of both polarities, the presence of multiple closed states, the stabilization of the open conformation in channel clusters, the long-term gating memory, and the Hofmeister effects in closing kinetics. Furthermore, we contemplate the evolutionary aspect of the phenomenon, proposing that the field-induced denaturation of membrane proteins might have served as a starting point for their development into amazing molecular machines such as voltage-gated channels of nerve and muscle cells. Full article
(This article belongs to the Special Issue Membrane Channels: Mechanistic Insights)
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15 pages, 2071 KiB  
Article
Modulation of Voltage-Gating and Hysteresis of Lysenin Channels by Cu2+ Ions
by Andrew Bogard, Pangaea W. Finn, Aviana R. Smith, Ilinca M. Flacau, Rose Whiting and Daniel Fologea
Int. J. Mol. Sci. 2023, 24(16), 12996; https://doi.org/10.3390/ijms241612996 - 20 Aug 2023
Cited by 1 | Viewed by 1175
Abstract
The intricate voltage regulation presented by lysenin channels reconstituted in artificial lipid membranes leads to a strong hysteresis in conductance, bistability, and memory. Prior investigations on lysenin channels indicate that the hysteresis is modulated by multivalent cations which are also capable of eliciting [...] Read more.
The intricate voltage regulation presented by lysenin channels reconstituted in artificial lipid membranes leads to a strong hysteresis in conductance, bistability, and memory. Prior investigations on lysenin channels indicate that the hysteresis is modulated by multivalent cations which are also capable of eliciting single-step conformational changes and transitions to stable closed or sub-conducting states. However, the influence on voltage regulation of Cu2+ ions, capable of completely closing the lysenin channels in a two-step process, was not sufficiently addressed. In this respect, we employed electrophysiology approaches to investigate the response of lysenin channels to variable voltage stimuli in the presence of small concentrations of Cu2+ ions. Our experimental results showed that the hysteretic behavior, recorded in response to variable voltage ramps, is accentuated in the presence of Cu2+ ions. Using simultaneous AC/DC stimulation, we were able to determine that Cu2+ prevents the reopening of channels previously closed by depolarizing potentials and the channels remain in the closed state even in the absence of a transmembrane voltage. In addition, we showed that Cu2+ addition reinstates the voltage gating and hysteretic behavior of lysenin channels reconstituted in neutral lipid membranes in which lysenin channels lose their voltage-regulating properties. In the presence of Cu2+ ions, lysenin not only regained the voltage gating but also behaved like a long-term molecular memory controlled by electrical potentials. Full article
(This article belongs to the Special Issue Membrane Channels: Mechanistic Insights)
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13 pages, 2145 KiB  
Article
The Complex Proteolipidic Behavior of the SARS-CoV-2 Envelope Protein Channel: Weak Selectivity and Heterogeneous Oligomerization
by Wahyu Surya, Ernesto Tavares-Neto, Andrea Sanchis, María Queralt-Martín, Antonio Alcaraz, Jaume Torres and Vicente M. Aguilella
Int. J. Mol. Sci. 2023, 24(15), 12454; https://doi.org/10.3390/ijms241512454 - 5 Aug 2023
Cited by 5 | Viewed by 1558
Abstract
The envelope (E) protein is a small polypeptide that can form ion channels in coronaviruses. In SARS coronavirus 2 (SARS-CoV-2), the agent that caused the recent COVID-19 pandemic, and its predecessor SARS-CoV-1, E protein is found in the endoplasmic reticulum–Golgi intermediate compartment (ERGIC), [...] Read more.
The envelope (E) protein is a small polypeptide that can form ion channels in coronaviruses. In SARS coronavirus 2 (SARS-CoV-2), the agent that caused the recent COVID-19 pandemic, and its predecessor SARS-CoV-1, E protein is found in the endoplasmic reticulum–Golgi intermediate compartment (ERGIC), where virion budding takes place. Several reports claim that E protein promotes the formation of “cation-selective channels”. However, whether this term represents specificity to certain ions (e.g., potassium or calcium) or the partial or total exclusion of anions is debatable. Herein, we discuss this claim based on the available data for SARS-CoV-1 and -2 E and on new experiments performed using the untagged full-length E protein from SARS-CoV-2 in planar lipid membranes of different types, including those that closely mimic the ERGIC membrane composition. We provide evidence that the selectivity of the E-induced channels is very mild and depends strongly on lipid environment. Thus, despite past and recent claims, we found no indication that the E protein forms cation-selective channels that prevent anion transport, and even less that E protein forms bona fide specific calcium channels. In fact, the E channel maintains its multi-ionic non-specific neutral character even in concentrated solutions of Ca2+ ions. Also, in contrast to previous studies, we found no evidence that SARS-CoV-2 E channel activation requires a particular voltage, high calcium concentrations or low pH, in agreement with available data from SARS-CoV-1 E. In addition, sedimentation velocity experiments suggest that the E channel population is mostly pentameric, but very dynamic and probably heterogeneous, consistent with the broad distribution of conductance values typically found in electrophysiological experiments. The latter has been explained by the presence of proteolipidic channel structures. Full article
(This article belongs to the Special Issue Membrane Channels: Mechanistic Insights)
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14 pages, 1835 KiB  
Article
Triplin: Mechanistic Basis for Voltage Gating
by Marco Colombini, Patrick Liu and Chase Dee
Int. J. Mol. Sci. 2023, 24(14), 11473; https://doi.org/10.3390/ijms241411473 - 14 Jul 2023
Cited by 1 | Viewed by 1034
Abstract
The outer membrane of Gram-negative bacteria contains a variety of pore-forming structures collectively referred to as porins. Some of these are voltage dependent, but weakly so, closing at high voltages. Triplin, a novel bacterial pore-former, is a three-pore structure, highly voltage dependent, with [...] Read more.
The outer membrane of Gram-negative bacteria contains a variety of pore-forming structures collectively referred to as porins. Some of these are voltage dependent, but weakly so, closing at high voltages. Triplin, a novel bacterial pore-former, is a three-pore structure, highly voltage dependent, with a complex gating process. The three pores close sequentially: pore 1 at positive potentials, 2 at negative and 3 at positive. A positive domain containing 14 positive charges (the voltage sensor) translocates through the membrane during the closing process, and the translocation is proposed to take place by the domain entering the pore and thus blocking it, resulting in the closed conformation. This mechanism of pore closure is supported by kinetic measurements that show that in the closing process the voltage sensor travels through most of the transmembrane voltage before reaching the energy barrier. Voltage-dependent blockage of the pores by polyarginine, but not by a 500-fold higher concentrations of polylysine, is consistent with the model of pore closure, with the sensor consisting mainly of arginine residues, and with the presence, in each pore, of a complementary surface that serves as a binding site for the sensor. Full article
(This article belongs to the Special Issue Membrane Channels: Mechanistic Insights)
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Review

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17 pages, 2708 KiB  
Review
Counter-Intuitive Features of Particle Dynamics in Nanopores
by Alexander M. Berezhkovskii and Sergey M. Bezrukov
Int. J. Mol. Sci. 2023, 24(21), 15923; https://doi.org/10.3390/ijms242115923 - 3 Nov 2023
Cited by 1 | Viewed by 882
Abstract
Using the framework of a continuous diffusion model based on the Smoluchowski equation, we analyze particle dynamics in the confinement of a transmembrane nanopore. We briefly review existing analytical results to highlight consequences of interactions between the channel nanopore and the translocating particles. [...] Read more.
Using the framework of a continuous diffusion model based on the Smoluchowski equation, we analyze particle dynamics in the confinement of a transmembrane nanopore. We briefly review existing analytical results to highlight consequences of interactions between the channel nanopore and the translocating particles. These interactions are described within a minimalistic approach by lumping together multiple physical forces acting on the particle in the pore into a one-dimensional potential of mean force. Such radical simplification allows us to obtain transparent analytical results, often in a simple algebraic form. While most of our findings are quite intuitive, some of them may seem unexpected and even surprising at first glance. The focus is on five examples: (i) attractive interactions between the particles and the nanopore create a potential well and thus cause the particles to spend more time in the pore but, nevertheless, increase their net flux; (ii) if the potential well-describing particle-pore interaction occupies only a part of the pore length, the mean translocation time is a non-monotonic function of the well length, first increasing and then decreasing with the length; (iii) when a rectangular potential well occupies the entire nanopore, the mean particle residence time in the pore is independent of the particle diffusivity inside the pore and depends only on its diffusivity in the bulk; (iv) although in the presence of a potential bias applied to the nanopore the “downhill” particle flux is higher than the “uphill” one, the mean translocation times and their distributions are identical, i.e., independent of the translocation direction; and (v) fast spontaneous gating affects nanopore selectivity when its characteristic time is comparable to that of the particle transport through the pore. Full article
(This article belongs to the Special Issue Membrane Channels: Mechanistic Insights)
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12 pages, 1324 KiB  
Review
Mechanisms of PIEZO Channel Inactivation
by Zijing Zhou and Boris Martinac
Int. J. Mol. Sci. 2023, 24(18), 14113; https://doi.org/10.3390/ijms241814113 - 14 Sep 2023
Cited by 6 | Viewed by 3243
Abstract
PIEZO channels PIEZO1 and PIEZO2 are the newly identified mechanosensitive, non-selective cation channels permeable to Ca2+. In higher vertebrates, PIEZO1 is expressed ubiquitously in most tissues and cells while PIEZO2 is expressed more specifically in the peripheral sensory neurons. PIEZO channels [...] Read more.
PIEZO channels PIEZO1 and PIEZO2 are the newly identified mechanosensitive, non-selective cation channels permeable to Ca2+. In higher vertebrates, PIEZO1 is expressed ubiquitously in most tissues and cells while PIEZO2 is expressed more specifically in the peripheral sensory neurons. PIEZO channels contribute to a wide range of biological behaviors and developmental processes, therefore driving significant attention in the effort to understand their molecular properties. One prominent property of PIEZO channels is their rapid inactivation, which manifests itself as a decrease in channel open probability in the presence of a sustained mechanical stimulus. The lack of the PIEZO channel inactivation is linked to various mechanopathologies emphasizing the significance of studying this PIEZO channel property and the factors affecting it. In the present review, we discuss the mechanisms underlying the PIEZO channel inactivation, its modulation by the interaction of the channels with lipids and/or proteins, and how the changes in PIEZO inactivation by the channel mutations can cause a variety of diseases in animals and humans. Full article
(This article belongs to the Special Issue Membrane Channels: Mechanistic Insights)
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26 pages, 3737 KiB  
Review
Gating of β-Barrel Protein Pores, Porins, and Channels: An Old Problem with New Facets
by Lauren A. Mayse and Liviu Movileanu
Int. J. Mol. Sci. 2023, 24(15), 12095; https://doi.org/10.3390/ijms241512095 - 28 Jul 2023
Cited by 8 | Viewed by 2089
Abstract
β barrels are ubiquitous proteins in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These transmembrane proteins (TMPs) execute a wide variety of tasks. For example, they can serve as transporters, receptors, membrane-bound enzymes, as well as adhesion, structural, and signaling elements. [...] Read more.
β barrels are ubiquitous proteins in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These transmembrane proteins (TMPs) execute a wide variety of tasks. For example, they can serve as transporters, receptors, membrane-bound enzymes, as well as adhesion, structural, and signaling elements. In addition, multimeric β barrels are common structural scaffolds among many pore-forming toxins. Significant progress has been made in understanding the functional, structural, biochemical, and biophysical features of these robust and versatile proteins. One frequently encountered fundamental trait of all β barrels is their voltage-dependent gating. This process consists of reversible or permanent conformational transitions between a large-conductance, highly permeable open state and a low-conductance, solute-restrictive closed state. Several intrinsic molecular mechanisms and environmental factors modulate this universal property of β barrels. This review article outlines the typical signatures of voltage-dependent gating. Moreover, we discuss recent developments leading to a better qualitative understanding of the closure dynamics of these TMPs. Full article
(This article belongs to the Special Issue Membrane Channels: Mechanistic Insights)
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