Publications


Structure and assembly of calcium homeostasis modulator proteins.

Nat Struct Mol Biol 27 (2020) 150-159

JL Syrjanen, K Michalski, T-H Chou, T Grant, S Rao, N Simorowski, SJ Tucker, N Grigorieff, H Furukawa

The biological membranes of many cell types contain large-pore channels through which a wide variety of ions and metabolites permeate. Examples include connexin, innexin and pannexin, which form gap junctions and/or bona fide cell surface channels. The most recently identified large-pore channels are the calcium homeostasis modulators (CALHMs), through which ions and ATP permeate in a voltage-dependent manner to control neuronal excitability, taste signaling and pathologies of depression and Alzheimer's disease. Despite such critical biological roles, the structures and patterns of their oligomeric assembly remain unclear. Here, we reveal the structures of two CALHMs, chicken CALHM1 and human CALHM2, by single-particle cryo-electron microscopy (cryo-EM), which show novel assembly of the four transmembrane helices into channels of octamers and undecamers, respectively. Furthermore, molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1, demonstrating the potential correlation between pore size, lipid accommodation and channel activity.


A lower X-gate in TASK channels traps inhibitors within the vestibule

Nature (2020)

KEJ Rödström, AK Kiper, W Zhang, S Rinné, ACW Pike, M Goldstein, LJ Conrad, M Delbeck, MG Hahn, H Meier, M Platzk, A Quigley, D Speedman, L Shrestha, SMM Mukhopadhyay, NA Burgess-Brown, SJ Tucker, T Müller, N Decher, EP Carpenter

© 2020, The Author(s), under exclusive licence to Springer Nature Limited. TWIK-related acid-sensitive potassium (TASK) channels—members of the two pore domain potassium (K2P) channel family—are found in neurons1, cardiomyocytes2–4 and vascular smooth muscle cells5, where they are involved in the regulation of heart rate6, pulmonary artery tone5,7, sleep/wake cycles8 and responses to volatile anaesthetics8–11. K2P channels regulate the resting membrane potential, providing background K+ currents controlled by numerous physiological stimuli12–15. Unlike other K2P channels, TASK channels are able to bind inhibitors with high affinity, exceptional selectivity and very slow compound washout rates. As such, these channels are attractive drug targets, and TASK-1 inhibitors are currently in clinical trials for obstructive sleep apnoea and atrial fibrillation16. In general, potassium channels have an intramembrane vestibule with a selectivity filter situated above and a gate with four parallel helices located below; however, the K2P channels studied so far all lack a lower gate. Here we present the X-ray crystal structure of TASK-1, and show that it contains a lower gate—which we designate as an ‘X-gate’—created by interaction of the two crossed C-terminal M4 transmembrane helices at the vestibule entrance. This structure is formed by six residues (243VLRFMT248) that are essential for responses to volatile anaesthetics10, neurotransmitters13 and G-protein-coupled receptors13. Mutations within the X-gate and the surrounding regions markedly affect both the channel-open probability and the activation of the channel by anaesthetics. Structures of TASK-1 bound to two high-affinity inhibitors show that both compounds bind below the selectivity filter and are trapped in the vestibule by the X-gate, which explains their exceptionally low washout rates. The presence of the X-gate in TASK channels explains many aspects of their physiological and pharmacological behaviour, which will be beneficial for the future development and optimization of TASK modulators for the treatment of heart, lung and sleep disorders.


Induced Polarization in MD Simulations of the 5HT3 Receptor Channel

Journal of the American Chemical Society American Chemical Society (2020)

S Tucker, M Sansom

Ion channel proteins form water-filled nanoscale pores within lipid bilayers and their properties are dependent on the complex behavior of water in a nano-confined environment. Using a simplified model of the pore of the 5HT3 receptor (5HT3R) which restrains the backbone structure to that of the parent channel protein from which it is derived we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular Dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model, to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl- ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl- whilst it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties.


Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5-HT3 Receptor Channel

bioRxiv (2020)

G Klesse, S Tucker, MSP Sansom

Abstract In this study we examined the influence of a transmembrane voltage on the hydrophobic gating of nanopores using molecular dynamics simulations. We observed electric field induced wetting of a hydrophobic gate in a biologically inspired model nanopore based on the 5-HT 3 receptor in its closed state, with a field of at least ∼100 mV nm −1 was required to hydrate the pore. We also found an unequal distribution of charged residues can generate an electric field intrinsic to the nanopore which, depending on its orientation, can alter the effect of the external field, thus making the wetting response asymmetric. This wetting response could be described by a simple model based on water surface tension, the volumetric energy contribution of the electric field, and the influence of charged amino acids lining the pore. Finally, the electric field response was used to determine time constants characterising the phase transitions of water confined within the nanopore, revealing liquid-vapour oscillations on a time scale of ~5 ns. This time scale was largely independent of the water model employed and was similar for different sized pores representative of the open and closed states of the pore. Furthermore, our finding that the threshold voltage required for hydrating a hydrophobic gate depends on the orientation of the electric field provides an attractive perspective for the design of rectifying artificial nanopores. ToC/Abstract Graphic <jats:fig id="ufig1" position="float" orientation="portrait" fig-type="figure"><jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="114157v1_ufig1" position="float" orientation="portrait" />


Altered functional properties of a missense variant in the TRESK K+ channel (KCNK18) associated with migraine and intellectual disability.

Pflugers Archiv : European journal of physiology 472 (2020) 923-930

P Imbrici, E Nematian-Ardestani, S Hasan, M Pessia, SJ Tucker, MC D'Adamo

Mutations in the KCNK18 gene that encodes the TRESK K2P potassium channel have previously been linked with typical familial migraine with aura. Recently, an atypical clinical case has been reported in which a male individual carrying the p.Trp101Arg (W101R) missense mutation in the KCNK18 gene was diagnosed with intellectual disability and migraine with brainstem aura. Here we report the functional characterization of this new missense variant. This mutation is located in a highly conserved residue close to the selectivity filter, and our results show although these mutant channels retain their K+ selectivity and calcineurin-dependent regulation, the variant causes an overall dramatic loss of TRESK channel function as well as an initial dominant-negative effect when co-expressed with wild-type channels in Xenopus laevis oocytes. The dramatic functional consequences of this mutation thereby support a potentially pathogenic role for this variant and provide further insight into the relationship between the structure and function of this ion channel.


Publisher Correction: Structure and assembly of calcium homeostasis modulator proteins.

Nature structural & molecular biology 27 (2020) 305-

JL Syrjanen, K Michalski, T-H Chou, T Grant, S Rao, N Simorowski, SJ Tucker, N Grigorieff, H Furukawa

An amendment to this paper has been published and can be accessed via a link at the top of the paper.


Electric field induced wetting of a hydrophobic gate in a model nanopore based on the 5-HT3 receptor channel

ACS Nano American Chemical Society 14 (2020) 10480-10491

G Klesse, SJ Tucker, MSP Sansom

In this study we examined the influence of a transmembrane voltage on the hydrophobic gating of nanopores using molecular dynamics simulations. We observed electric field induced wetting of a hydrophobic gate in a biologically inspired model nanopore based on the 5-HT3 receptor in its closed state, with a field of at least ∼100 mV nm–1 (corresponding to a supra-physiological potential difference of ∼0.85 V across the membrane) required to hydrate the pore. We also found an unequal distribution of charged residues can generate an electric field intrinsic to the nanopore which, depending on its orientation, can alter the effect of the external field, thus making the wetting response asymmetric. This wetting response could be described by a simple model based on water surface tension, the volumetric energy contribution of the electric field, and the influence of charged amino acids lining the pore. Finally, the electric field response was used to determine time constants characterizing the phase transitions of water confined within the nanopore, revealing liquid–vapor oscillations on a time scale of ∼5 ns. This time scale was largely independent of the water model employed and was similar for different sized pores representative of the open and closed states of the pore. Furthermore, our finding that the threshold voltage required for hydrating a hydrophobic gate depends on the orientation of the electric field provides an attractive perspective for the design of rectifying artificial nanopores.


Selectivity filter instability dominates the low intrinsic activity of the TWIK-1 K2P K+ Channel.

The Journal of biological chemistry (2019)

E Nematian-Ardestani, MF Abd-Wahab, FC Chatelain, H Sun, M Schewe, T Baukrowitz, SJ Tucker

Two-pore domain (K2P) K+ channels have many important physiological functions. However, the functional properties of the TWIK-1 (K2P1.1/KCNK1) K2P channel remain poorly characterized because heterologous expression of this ion channel yields only very low levels of functional activity. Several underlying reasons have been proposed, including TWIK-1 retention in intracellular organelles, inhibition by post-translational sumoylation, a hydrophobic barrier within the pore, and a low open probability of the selectivity filter (SF) gate. By evaluating these various potential mechanisms, we found that the latter dominates the low intrinsic functional activity of TWIK-1. Investigating the underlying mechanism, we observed that the low activity of the SF gate appears to arise from the inefficiency of K+ in stabilizing an active (i.e. conductive) SF conformation. In contrast, other permeant ion species, such as Rb+, NH4+, and Cs+, strongly promoted a pH-dependent activated conformation. Furthermore, many K2P channels are activated by membrane depolarization via a SF-mediated gating mechanism, but we found here that only very strong, non-physiological depolarization produces voltage-dependent activation of heterologously expressed TWIK-1. Remarkably, we also observed that TWIK-1 Rb+ currents are potently inhibited by intracellular K+ (IC50 = 2.8 mM). We conclude that TWIK-1 displays unique SF gating properties among the family of K2P channels. In particular, the apparent instability of the conductive conformation of the TWIK-1 SF in the presence of K+ appears to dominate the low levels of intrinsic functional activity observed when the channel is expressed at the cell surface.


Induced Polarization in MD Simulations of the 5HT3 Receptor Channel

(2020)

G Klesse, S Rao, S Tucker, MSP Sansom

Abstract Ion channel proteins form water-filled nanoscale pores within lipid bilayers and their properties are dependent on the complex behavior of water in a nano-confined environment. Using the pore of the 5HT3 receptor (5HT3R) we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular Dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model, to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl− ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl− whilst it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties. ToC Graphic <jats:fig id="ufig1" position="float" fig-type="figure" orientation="portrait"><jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="971853v1_ufig1" position="float" orientation="portrait" />


Annotating Ion Channel Pores: Structures, Hydrophobicity and the Threshold for Permeation

BIOPHYSICAL JOURNAL 118 (2020) 272A-272A

S Rao, G Klesse, SJ Tucker, MSP Sansom


Induced Polarization in Molecular Dynamics Simulations of the 5-HT3 Receptor Channel.

J Am Chem Soc 142 (2020) 9415-9427

G Klesse, S Rao, SJ Tucker, MSP Sansom

Ion channel proteins form water-filled nanoscale pores within lipid bilayers, and their properties are dependent on the complex behavior of water in a nanoconfined environment. Using a simplified model of the pore of the 5-HT3 receptor (5HT3R) which restrains the backbone structure to that of the parent channel protein from which it is derived, we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl- ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl- while it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties.


A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates

Proceedings of the National Academy of Sciences National Academy of Sciences (2019)

S Rao, K Klesse, P Stansfeld, S Tucker, M Sansom

Ion channel proteins control ionic flux across biological membranes through conformational changes in their transmembrane pores. An exponentially increasing number of channel structures captured in different conformational states are now being determined; however, these newly resolved structures are commonly classified as either open or closed based solely on the physical dimensions of their pore, and it is now known that more accurate annotation of their conductive state requires additional assessment of the effect of pore hydrophobicity. A narrow hydrophobic gate region may disfavor liquid-phase water, leading to local dewetting, which will form an energetic barrier to water and ion permeation without steric occlusion of the pore. Here we quantify the combined influence of radius and hydrophobicity on pore dewetting by applying molecular dynamics simulations and machine learning to nearly 200 ion channel structures. This allows us to propose a simple simulation-free heuristic model that rapidly and accurately predicts the presence of hydrophobic gates. This not only enables the functional annotation of new channel structures as soon as they are determined, but also may facilitate the design of novel nanopores controlled by hydrophobic gates.


CHAP: A Versatile Tool for the Structural and Functional Annotation of Ion Channel Pores.

Journal of molecular biology (2019)

G Klesse, S Rao, MSP Sansom, SJ Tucker

The control of ion channel permeation requires the modulation of energetic barriers or "gates" within their pores. However, such barriers are often simply identified from the physical dimensions of the pore. Such approaches have worked well in the past,but there is now evidence that the unusual behaviour of water within narrow hydrophobic pores can produce an energetic barrier to permeation without requiring steric occlusion of the pathway. Many different ion channels have now been shown to exploit "hydrophobic gating" to regulate ion flow, and it is clear that new tools are required for more accurate functional annotation of the increasing number of ion channel structures becoming available. We have previously shown how molecular dynamics simulations of water can be used as a proxy to predict hydrophobic gates, and we now present a new and highly versatile computational tool, the Channel Annotation Package (CHAP) that implements this methodology.


A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels

Science American Association for the Advancement of Science 363 (2019) 875-880

M Schewe, H Sun, Ü Mert, A Mackenzie, ACW Pike, F Schulz, C Constantin, KS Vowinkel, LJ Conrad, AK Kiper, W Gonzalez, M Musinszki, M Tegtmeier, DC Pryde, H Belabed, M Nazare, BL De Groot, N Decher, B Fakler, EP Carpenter, S Tucker, T Baukrowitz

<jats:p>Potassium (K<jats:sup>+</jats:sup>) channels have been evolutionarily tuned for activation by diverse biological stimuli, and pharmacological activation is thought to target these specific gating mechanisms. Here we report a class of negatively charged activators (NCAs) that bypass the specific mechanisms but act as master keys to open K<jats:sup>+</jats:sup> channels gated at their selectivity filter (SF), including many two-pore domain K<jats:sup>+</jats:sup> (K<jats:sub>2P</jats:sub>) channels, voltage-gated hERG (human ether-à-go-go–related gene) channels and calcium (Ca<jats:sup>2+</jats:sup>)–activated big-conductance potassium (BK)–type channels. Functional analysis, x-ray crystallography, and molecular dynamics simulations revealed that the NCAs bind to similar sites below the SF, increase pore and SF K<jats:sup>+</jats:sup> occupancy, and open the filter gate. These results uncover an unrecognized polypharmacology among K<jats:sup>+</jats:sup> channel activators and highlight a filter gating machinery that is conserved across different families of K<jats:sup>+</jats:sup> channels with implications for rational drug design.</jats:p>


A Pharmacological Masterkey Mechanism to Unlock the Selectivity Filter Gate in K plus Channels

BIOPHYSICAL JOURNAL 116 (2019) 301A-302A

M Schewe, H Sun, A Mackenzie, ACW Pike, F Schulz, C Constantin, AK Kiper, LJ Conrad, W Gonzalez, BL de Groot, N Decher, B Fakler, EP Carpenter, SJ Tucker, T Baukrowitz


Insights into Selectivity Filter Gating of K2P Channels from Single Channel Recordings

BIOPHYSICAL JOURNAL 116 (2019) 248A-249A

LJ Conrad, SJ Tucker


Systematic Scanning Mutagenesis of the Pore Helices in the TREK-2 K2P Channel

BIOPHYSICAL JOURNAL 116 (2019) 398A-399A

M Arcangeletti, SJ Tucker


Functional Annotation of Ion Channel Structures: Predicting Pore Solvation States Based on Local Radius and Hydrophobicity

BIOPHYSICAL JOURNAL 116 (2019) 241A-241A

S Rao, G Klesse, PJ Stansfeld, SJ Tucker, MSP Sansom


Structure and assembly of calcium homeostasis modulator proteins

(2019)

J Syrjanen, K Michalski, T-H Chou, T Grant, S Rao, N Simorowski, S Tucker, N Grigorieff, H Furukawa

Abstract Biological membranes of many tissues and organs contain large-pore channels designed to permeate a wide variety of ions and metabolites. Examples include connexin, innexin, and pannexin, which form gap junctions and/or bona fide cell surface channels. The most recently identified large-pore channels are the calcium homeostasis modulators (CALHMs), which permeate ions and ATP in a voltage-dependent manner to control neuronal excitability, taste signaling, and pathologies of depression and Alzheimer’s disease. Despite such critical biological roles, the structures and patterns of oligomeric assembly remain unclear. Here, we reveal the first structures of two CALHMs, CALHM1 and CALHM2, by single particle cryo-electron microscopy, which show novel assembly of the four transmembrane helices into channels of 8-mers and 11-mers, respectively. Furthermore, molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1, demonstrating the potential correlation between pore-size, lipid accommodation, and channel activity.


Selectivity filter instability dominates the low intrinsic activity of the TWIK-1 K2P K+ Channel

(2019)

E Nematian-Ardestani, F Abd-Wahab, F Chatelain, H Sun, M Schewe, T Baukrowitz, S Tucker

ABSTRACT Two-pore domain (K2P) K + channels have many important physiological functions. However, the functional properties of the TWIK-1 (K2P1.1/ KCNK1 ) K2P channel remain poorly characterized because heterologous expression of this ion channel yields only very low levels of functional activity. Several underlying reasons have been proposed, including TWIK-1 retention in intracellular organelles, inhibition by post-translational sumoylation, a hydrophobic barrier within the pore, and a low open probability of the selectivity filter (SF) gate. By evaluating these various potential mechanisms, we found that the latter dominates the low intrinsic functional activity of TWIK-1. Investigating the underlying mechanism, we observed that the low activity of the SF gate appears to arise from the inefficiency of K + in stabilizing an active ( i.e. conductive) SF conformation. In contrast, other permeant ion species, such as Rb + , NH 4 + , and Cs + , strongly promoted a pH-dependent activated conformation. Furthermore, many K2P channels are activated by membrane depolarization via a SF-mediated gating mechanism, but we found here that only very strong, non-physiological depolarization produces voltage-dependent activation of heterologously expressed TWIK-1. Remarkably, we also observed that TWIK-1 Rb + currents are potently inhibited by intracellular K + (IC 50 = 2.8 mM). We conclude that TWIK-1 displays unique SF gating properties among the family of K2P channels. In particular, the apparent instability of the conductive conformation of the TWIK-1 SF in the presence of K + appears to dominate the low levels of intrinsic functional activity observed when the channel is expressed at the cell surface.

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