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2024 – Nanopore analysis of cis-diols in fruits
Orbit mini Publication in Nature communications (2024) Authors: Fan P., Cao Z., Zhang S., Wang Y., Xiao Y., Jia W:, Zhang P., Huang S.

Natural fruits contain a large variety of cis-diols. However, due to the lack of a high-resolution sensor that can simultaneously identify all cis-diols without a need of complex sample pretreatment, direct and rapid analysis of fruits in a hand-held device has never been previously reported. Nanopore, a versatile single molecule sensor, can be specially engineered to perform this task. A hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore modified with a sole phenylboronic acid (PBA) adapter is prepared. This engineered MspA accurately recognizes 1,2-diphenols, alditols, α-hydroxy acids and saccharides in prune, grape, lemon, different varieties of kiwifruits and commercial juice products. Assisted with a custom machine learning program, an accuracy of 99.3% is reported and the sample pretreatment is significantly simplified. Enantiomers such as DL-malic acids can also be directly identified, enabling sensing of synthetic food additives. Though demonstrated with fruits, these results suggest wide applications of nanopore in food and drug administration uses.

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Mitochondrial Membrane Research
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2024 – A dynamically gated triangular DNA nanopore for molecular sensing and cross-membrane transport
Vesicle Prep Pro and Orbit mini Preprint Publication in Research Square (2024) Authors: Liu X., Liu F., Chhabra H., Maffeo C., Huang Q., Aksimentiev A., Arai T.

Synthetic membrane nanopores made of DNA are promising systems to sense and control molecular transport in biosensing, sequencing, and synthetic cells. Dynamically gating cargo transport like the natural ion channels and systematically increasing the lumen size have become long-standing desires in developing nanopores. Here, we design a triangular DNA nanopore with a large dynamically-gated lumen. It can switch between expanded and contracted states without changing its stable triangular shape, whereby specific DNA bindings as stimuli mechanically pinch and release the three corners of the triangular frame. Transmission electron microscopy images and molecular dynamics simulations illustrated the large lumen up to 539 nm2, the stable architectures, and the high shape retention. Single channel current recordings and fluorescence influx studies demonstrated the low-noise repeatable readouts and the controllable cross-membrane macromolecular transport. We envision that the proposed DNA nanopores could offer powerful tools in molecular sensing, drug delivery, and the creation of synthetic cells.

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2024 – Dissecting the membrane association mechanism of aerolysin pore at femtomolar concentrations using water as a probe
Orbit mini Pre-print in bioRxiv (2024) Authors: Roesel T., Cao C., Bada J., Dal Peraro M., Roke S.

Aerolysin is a bacterial pore-forming toxin able to form transmembrane pores at the host plasma membrane of narrow internal diameter and great stability. These assets make it a highly promising nanopore for the detection of biopolymers such as nucleic acids and
peptides. While much is known about aerolysin from a microbiological and structural side, its membrane association and pore-formation mechanism are not yet fully disclosed. Here, we studied the interaction of femtomolar concentrations of aerolysin and its mutants with
liposomes in aqueous solution using angle-resolved second harmonic scattering (AR-SHS), in combination with single-channel current measurements. The measurements were so sensitive to detect electrostatic changes on the membrane-bound aerolysin induced by pH
variation induced by the changes in the hydration shell of aerolysin. We reported for the first time the membrane binding affinity of aerolysin at different stages of the pore formation mechanism: while wt aerolysin has a binding affinity as high as 20 fM, the quasi-pore state
and the prepore state show gradually decreasing membrane affinities, incomplete insertion and pore opening signature. Moreover, we quantitatively characterized the membrane affinity of mutants relevant for applications to nanopore sensing. This approach opens new
possibilities to efficiently screen biological pores suitable for conducting molecular sensing and sequencing measurements, as well as to probe pore forming processes.

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2024 – Propofol directly binds and inhibits skeletal muscle ryanodine receptor 1 (RyR1)
Orbit mini Pre-Print in bioRxiv. (2024) Authors: Joseph T., Bu W., Haji-Ghassemi O., Chen Y., Woll K., Allen P., Brannigan G., van Petegem F., Eckenhoff R.

As the primary Ca2+ release channel in skeletal muscle sarcoplasmic reticulum (SR), mutations in the type 1 ryanodine receptor (RyR1) or its binding partners underlie a constellation of muscle disorders, including malignant hyperthermia (MH). In patients with MH mutations, exposure to triggering drugs such as the
halogenated volatile anesthetics biases RyR1 to an open state, resulting in uncontrolled Ca2+ release, sarcomere tension and heat production. Restoration of Ca2+ into the SR also consumes ATP, generating a further untenable metabolic load. When anesthetizing patients with known MH mutations, the non-triggering intravenous general anesthetic propofol is commonly substituted for triggering anesthetics. Evidence of direct binding of anesthetic agents to RyR1 or its binding partners is scant, and the atomic-level interactions of propofol with RyR1 are entirely unknown. Here, we show that propofol decreases RyR1 opening in heavy SR vesicles and planar lipid bilayers, and that it inhibits activator-induced Ca2+ release from SR in human skeletal muscle. In addition to confirming direct binding, photoaffinity labeling using m-azipropofol (AziPm) revealed several putative propofol binding sites on RyR1. Prediction of binding affinity by molecular dynamics simulation suggests that propofol binds at least one of these sites at clinical concentrations. These findings invite the hypothesis that in addition to propofol not triggering MH, it may also be protective against MH by inhibiting induced Ca2+ flux through RyR1.

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2023 – Nanopore Signatures of Nucleoside Drugs
Orbit mini Publication in Nano Lett. (2023) Authors: Jia W., Ouyang Y., Zhang S., Du X., Zhang P., Huang S.

Nucleoside drugs, which are analogues of natural nucleosides, have been widely applied in the clinical treatment of viral infections and cancers. The development of nucleoside drugs, repurposing of existing drugs, and combined use of multiple drug types have made the rapid sensing of nucleoside drugs urgently needed. Nanopores are emerging single-molecule sensors that have high resolution to resolve even minor structural differences between chemical compounds. Here, an engineered Mycobacterium smegmatis porin A hetero-octamer was used to perform general nucleoside drug analysis. Ten nucleoside drugs were simultaneously detected and fully discriminated. An accuracy of >99.9% was consequently reported. This sensing capacity was further demonstrated in direct nanopore analysis of ribavirin buccal tablets, confirming its sensing reliability against complex samples and environments. No sample separation is needed, however, significantly minimizing the complexity of the measurement. This technique may inspire nanopore applications in pharmaceutical production and pharmacokinetics measurements.

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2023 – Deep Learning-Assisted Single-Molecule Detection of Protein Post-translational Modifications with a Biological Nanopore
Orbit mini Publication in ACS Nano (2023) Authors: Cao C.,MagalhaesP., Krapp L.F.,Bada J.F.J, Mayer S.F., Rukes V., Chiki A., Lashuel H.A., Dal Peraro M.

Protein post-translational modifications (PTMs) play a crucial role in countless biological processes, profoundly modulating protein properties on both spatial and temporal scales. Protein PTMs have also emerged as reliable biomarkers for several diseases. However, only a handful of techniques are available to accurately measure their levels, capture their complexity at a single molecule level, and characterize their multifaceted roles in health and disease. Nanopore sensing provides high sensitivity for the detection of low-abundance proteins, holding the potential to impact single-molecule proteomics and PTM detection, in particular. Here, we demonstrate the ability of a biological nanopore, the pore-forming toxin aerolysin, to detect and distinguish α-synuclein-derived peptides bearing single or multiple PTMs, namely, phosphorylation, nitration, and oxidation occurring at different positions and in various combinations. The characteristic current signatures of the α-synuclein peptide and its PTM variants could be confidently identified by using a deep learning model for signal processing. We further demonstrate that this framework can quantify α-synuclein peptides at picomolar concentrations and detect the C-terminal peptides generated by digestion of full-length α-synuclein. Collectively, our work highlights the advantage of using nanopores as a tool for simultaneous detection of multiple PTMs and facilitates their use in biomarker discovery and diagnostics.

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2023 – Confirming Silent Translocation through Nanopores with Simultaneous Single-Molecule Fluorescence and Single-Channel Electrical Recordings
Orbit mini Publication in Anal. Chem. (2023) Authors: Burden D.L., Meyer J.J., Michael R.D., Anderson S.C., Burden H.M., Pena S.M., Leong-Fern K.J., Ye L.A.V., Meyer E.C, Keranen-Burden L.M.

Most of what is known concerning the luminal passage of materials through nanopores arises from electrical measurements. Whether nanopores are biological, solid-state, synthetic, hybrid, glass-capillary-based, or protein ion channels in cells and tissues, characteristic signatures embedded in the flow of ionic current are foundational to understanding functional behavior. In contrast, this work describes passage through a nanopore that occurs without producing an electrical signature. We refer to the phenomenon as “silent translocation.” By definition, silent translocations are invisible to the standard tools of electrophysiology and fundamentally require a simultaneous ancillary measurement technique for positive identification. As a result, this phenomenon has been largely unexplored in the literature. Here, we report on a derivative of Cyanine 5 (sCy5a) that passes through the α-hemolysin (αHL) nanopore silently. Simultaneously acquired single-molecule fluorescence and single-channel electrical recordings from bilayers formed over a closed microcavity demonstrate that translocation does indeed take place, albeit infrequently. We report observations of silent translocation as a function of time, dye concentration, and nanopore population in the bilayer. Lastly, measurement of the translocation rate as a function of applied potential permits estimation of an effective energy barrier for transport through the pore as well as the effective charge on the dye, all in the absence of an information-containing electrical signature.

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2023 – Encoding extracellular modification of artificial cell membranes using engineered self-translocating proteins
Orbit mini Pre-Print Publication in BioRxiv (2023) Authors: Harjung A., Fracassi A., Devaraj N.

A common method of generating artificial cells is to encapsulate protein expression systems within lipid vesicles. However, to communicate with the external environment, protein translocation across lipid membranes must take place. In living cells, protein transport across membranes is achieved with the aid of complex translocase systems which are difficult to reconstitute into artificial cells. Thus, there is need for simple mechanisms by which proteins can be encoded and expressed inside synthetic compartments yet still be externally displayed. Here we present a genetically encodable membrane functionalization system based on mutants of pore-forming proteins. We show that the membrane translocating loop of α-hemolysin can be engineered to translocate functional peptides up to 52 amino acids across lipid membranes. Engineered hemolysins can be used for genetically programming artificial cells to display interacting peptide pairs, enabling their assembly into artificial tissue-like structures capable of signal transduction.

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2023 – Cryo-EM analysis of scorpion toxin binding to Ryanodine Receptors reveals subconductance that is abolished by PKA phosphorylation
Orbit mini Publication in Science Advances (2023) Authors: Haji-Ghassemi O., Seby Chen Y., Woll K., Gurrola G., Valdivia C., Cai W., Li S., Valdivia H., Van Petegem F.

Calcins are peptides from scorpion venom with the unique ability to cross cell membranes, gaining access to intracellular targets. Ryanodine Receptors (RyR) are intracellular ion channels that control release of Ca2+ from the endoplasmic and sarcoplasmic reticulum. Calcins target RyRs and induce long-lived subconductance states, whereby single-channel currents are decreased. We used cryo–electron microscopy to reveal the binding and structural effects of imperacalcin, showing that it opens the channel pore and causes large asymmetry throughout the cytosolic assembly of the tetrameric RyR. This also creates multiple extended ion conduction pathways beyond the transmembrane region, resulting in subconductance. Phosphorylation of imperacalcin by protein kinase A prevents its binding to RyR through direct steric hindrance, showing how posttranslational modifications made by the host organism can determine the fate of a natural toxin. The structure provides a direct template for developing calcin analogs that result in full channel block, with potential to treat RyR-related disorder

Read more in the publication here.

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2023 – Structural mechanisms of TRPM7 activation and inhibition
Orbit mini Publication in Nature Communications (2023) Authors: Nadezhdin K., Correia L., Narangoda C., Patel D., Neuberger A., Gudermann T., Kurnikova M., Chubanov V., Sobolevsky A.

The transient receptor potential channel TRPM7 is a master regulator of the organismal balance of divalent cations that plays an essential role in embryonic development, immune responses, cell mobility, proliferation, and differentiation. TRPM7 is implicated in neuronal and cardiovascular disorders, tumor progression and has emerged as a new drug target. Here we use cryo-EM, functional analysis, and molecular dynamics simulations to uncover two distinct structural mechanisms of TRPM7 activation by a gain-of-function mutation and by the agonist naltriben, which show different conformational dynamics and domain involvement. We identify a binding site for highly potent and selective inhibitors and show that they act by stabilizing the TRPM7 closed state. The discovered structural mechanisms provide foundations for understanding the molecular basis of TRPM7 channelopathies and drug development.

Read more in the publication here.

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2023 – Activation energy for pore opening in lipid membranes under an electric field
Orbit mini Publication in PNAS (2023) Authors: Lafarge E., Muller P., Schroder A., Zaitseva E., Behrends J., Marques C.

The standard model of pore formation was introduced more than fifty years ago, and it has been since, despite some refinements, the cornerstone for interpreting experiments related to pores in membranes. A central prediction of the model concerning pore opening under an electric field is that the activation barrier for pore formation is lowered proportionally to the square of the electric potential. However, this has only been scarcely and inconclusively confronted to experiments. In this paper, we study the electropermeability of model lipid membranes composed of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) containing different fractions of POPC-OOH, the hydroperoxidized form of POPC, in the range 0 to 100 mol %. By measuring ion currents across a 50-μm-diameter black lipid membrane (BLM) with picoampere and millisecond resolution, we detect hydroperoxidation-induced changes to the intrinsic bilayer electropermeability and to the probability of opening angstrom-size or larger pores. Our results over the full range of lipid compositions show that the energy barrier to pore formation is lowered linearly by the absolute value of the electric field, in contradiction with the predictions of the standard model.

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2023 – Biological fractionation of lithium isotopes by cellular Na+/H+ exchangers unravels fundamental transport mechanisms
Orbit mini Publication in iScience (2023) Authors: Poet M., Vigier N., Bouret Y., Jarretou G., Gautier R., Bendahhou S., Balter V., Montanes M., Thibon F., Counillon L.

Lithium (Li) has a wide range of uses in science, medicine, and industry, but its isotopy is underexplored, except in nuclear science and in geoscience. 6Li and 7Li isotopic ratio exhibits the second largest variation on earth’s surface and constitutes a widely used tool for reconstructing past oceans and climates. As large variations have been measured in mammalian organs, plants or marine species, and as 6Li elicits stronger effects than natural Li (∼95% 7Li), a central issue is the identification and quantification of biological influence of Li isotopes distribution. We show that membrane ion channels and Na+-Li+/H+ exchangers (NHEs) fractionate Li isotopes. This systematic 6Li enrichment is driven by membrane potential for channels, and by intracellular pH for NHEs, where it displays cooperativity, a hallmark of dimeric transport. Evidencing that transport proteins discriminate between isotopes differing by one neutron opens new avenues for transport mechanisms, Li physiology, and paleoenvironments.

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2023 – G-Quadruplex-Filtered Selective Ion-to-Ion Current Amplification for Non-Invasive Ion Monitoring in Real Time
Orbit mini Publication in Advanced Materials (2023) Authors: Yoo H., Lee H-R, Kang S-B, Lee J., Park K., Yoo H., Kim J., Chung T.D., Lee K-M., Lim H-H., Son C.Y., Sun J-Y, Oh S.S.

Living cells efflux intracellular ions for maintaining cellular life, so intravital measurements of specific ion signals are of significant importance for studying cellular functions and pharmacokinetics. In this work, de novo synthesis of artificial K+-selective membrane and its integration with polyelectrolyte hydrogel-based open-junction ionic diode (OJID) is demonstrated, achieving a real-time K+-selective ion-to-ion current amplification in complex bioenvironments. By mimicking biological K+ channels and nerve impulse transmitters, in-line K+-binding G-quartets are introduced across freestanding lipid bilayers by G-specific hexylation of monolithic G-quadruplex, and the pre-filtered K+ flow is directly converted to amplified ionic currents by the OJID with a fast response time at 100 ms intervals. By the synergistic combination of charge repulsion, sieving, and ion recognition, the synthetic membrane allows K+ transport exclusively without water leakage; it is 250× and 17× more permeable toward K+ than monovalent anion, Cl, and polyatomic cation, N-methyl-d-glucamine+, respectively. The molecular recognition-mediated ion channeling provides a 500% larger signal for K+ as compared to Li+ (0.6× smaller than K+) despite the same valence. Using the miniaturized device, non-invasive, direct, and real-time K+ efflux monitoring from living cell spheroids is achieved with minimal crosstalk, specifically in identifying osmotic shock-induced necrosis and drug-antidote dynamics.

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2023 – Dimerization mechanism of an inverted-topology ion channel in membranes
Orbit mini Pre-Print Publication in BioRxiv (2023) Authors: Ernst M., Orabi E.A., Stockbridge R.B., Faraldo-Gómez J.D., Robertson J.L.

Many ion channels are multi-subunit complexes with a polar permeation pathway at the oligomeric interface, but their mechanisms of assembly into functional, thermodynamically stable units within the membrane are largely unknown. Here we characterize the assembly of the inverted-topology, homodimeric fluoride channel Fluc, leveraging a known mutation, N43S, that weakens Na+ binding to the dimer interface, thereby unlocking the complex. While single-channel recordings show Na+ is required for activation, single-molecule photobleaching and bulk Förster Resonance Energy Transfer experiments in lipid bilayers demonstrate that N43S Fluc monomers and dimers exist in dynamic equilibrium, even without Na+. Molecular dynamics simulations indicate this equilibrium is dominated by a differential in the lipid-solvation energetics of monomer and dimer, which stems from hydrophobic exposure of the polar ion pathway in the monomer. These results suggest a model wherein membrane-associated forces induce channel assembly while subsequent factors, in this case Na+ binding, result in channel activation.

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2023 – TolC-AcrA complex formation monitored by time dependent single-channel electrophysiology
Orbit mini Publication in Biochimie (2023) Authors: Bodrenko I.V., Zewdie T.A., Wang J., Paul E., Witt S., Winterhalter M.

Characterizing protein-protein interaction on a single molecular level is a challenge, experimentally as well as interpretation of the data. For example, Gram-negative bacteria contain protein complexes spanning the outer and inner cell wall devoted to efflux effectively cell toxic substances. Recent seminal work revealed the high-resolution structure of such a tripartic composition TolC-AcrA-AcrB suggesting to design inhibitors preventing efflux of antibiotics. To show that electrophysiology can provide supporting information here, we reconstitute single TolC homotrimer into a planar lipid membrane, apply a transmembrane voltage and follow the assembly of AcrA to TolC using the modulation of the ion current through TolC channel during binding. In particular, the presence of AcrA in solution increases the average ionic current through TolC and, moreover, reduces the ion-current fluctuations caused by flickering of TolC. Here, we show that statistical properties of ion-current fluctuations (the power spectral density) provide a complementary measure of the interaction of the TolC-AcrA complex in presence of putative efflux pump inhibitors. Both characteristics, the average ion current across TolC and the current noise, taken into consideration together, point to a stiffening of the tip of TolC which might reduce the formation of the complex.

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2023 – Evaluation of Cell-Free Synthesized Human Channel Proteins for In Vitro Channel Research
Orbit mini Publication in Membranes (2023) Authors: Nishiguchi R., Tanaka T., Hayashida J., Nakagita T., Zhou W., Takeda H.

Despite channel proteins being important drug targets, studies on channel proteins remain limited, as the proteins are difficult to express and require correct complex formation within membranes. Although several in vitro synthesized recombinant channels have been reported, considering the vast diversity of the structures and functions of channel proteins, it remains unclear which classes of channels cell-free synthesis can be applied to. In this study, we synthesized 250 clones of human channels, including ion channel pore-forming subunits, gap junction proteins, porins, and regulatory subunits, using a wheat cell-free membrane protein production system, and evaluated their synthetic efficiency and function. Western blotting confirmed that 95% of the channels were successfully synthesized, including very large channels with molecular weights of over 200 kDa. A subset of 47 voltage-gated potassium ion channels was further analyzed using a planar lipid bilayer assay, out of which 80% displayed a voltage-dependent opening in the assay. We co-synthesized KCNB1 and KCNS3, a known heteromeric complex pair, and demonstrated that these channels interact on a liposome. These results indicate that cell-free protein synthesis provides a promising solution for channel studies to overcome the bottleneck of in vitro protein production.

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2023 – Multi-Stimuli-Responsive and Mechano-Actuated Biomimetic Membrane Nanopores Self-Assembled from DNA
Orbit mini Publication in Advanced Materials (2023) Authors: Xing Y., Dorey A., Howorka S.

In bioinspired design, biological templates are mimicked in structure and function by highly controllable synthetic means. Of interest are static barrel-like nanopores that enable molecular transport across membranes for use in biosensing, sequencing, and biotechnology. However, biological ion channels offer additional functions such as dynamic changes of the entire pore shape between open and closed states, and triggering of dynamic processes with biochemical and physical stimuli. To better capture this complexity, this report presents multi-stimuli and mechano-responsive biomimetic nanopores which are created with DNA nanotechnology. The nanopores switch between open and closed states, whereby specific binding of DNA and protein molecules as stimuli locks the pores in the open state. Furthermore, the physical stimulus of high transmembrane voltage switches the pores into a closed state. In addition, the pore diameters are larger and more tunable than those of natural templates. These multi-stimuli-responsive and mechanically actuated nanopores mimic several aspects of complex biological channels yet offer easier control over pore size, shape and stimulus response. The designer pores are expected to be applied in biosensing and synthetic biology.

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2016 – Next level toxicity screening: From single channel to overall cell behavior
Orbit mini, CardioExcyte 96 and SyncroPatch 384PE (a predecessor model of the SyncroPatch 384) poster, Meeting of the French Society of Toxinology (SFET) 2015 
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2020 – Electrophysiological characterization of transport across outer membrane channels from Gram‐negative bacteria in presence of lipopolysaccharides (LPS)
Port-a-Patch, Vesicle Prep Pro and Orbit mini Publication in Angewandte Chemie International Edition (2020) Authors: Wang J., Terrasse R., Bafna J.A., Benier L., Winterhalter M.

Multi‐drug resistance in Gram‐negative bacteria is often associated with low permeability of the outer membrane. To investigate the role of membrane channels in the uptake of antibiotics here, we show a robust approach using fusion of native outer membrane vesicles (OMV) into planar lipid bilayer, which moreover allows also characterization of membrane protein channels in their native environment. Two major membrane channels from E. coli , OmpF and OmpC, were overexpressed from the host and the corresponding OMVs were collected. Each OMV fusion revealed surprisingly single or only a few channel activities. The asymmetry of the OMV´s translates after fusion into the lipid membrane with the LPS dominantly present at the side of OMV addition. Compared to conventional reconstitution method, the channels fused from OMVs containing LPS have similar conductance but a much broader distribution and significantly lower permeation. We suggest using outer membrane vesicles as a fast and easy approach for functional and structural studies of membrane channels in the native membrane.

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2019 – Structure of the human ClC-1 chloride channel
Port-a-Patch, Vesicle Prep Pro and Orbit mini Publication in PLOS Biology (2019) Authors: Wang K., Preisler, SS, Zhang, L., Cui, Y., Missel, JW., Grønberg C., Gotfryd, K., Lindahl E., Andersson, M., Calloe, K., Egea P.F., Klaerke D.A., Pusch M., Pedersen P.A., Zhou, Z.H., Gourdon, P.

ClC-1 protein channels facilitate rapid passage of chloride ions across cellular membranes, thereby orchestrating skeletal muscle excitability. Malfunction of ClC-1 is associated with myotonia congenita, a disease impairing muscle relaxation. Here, we present the cryo-electron microscopy (cryo-EM) structure of human ClC-1, uncovering an architecture reminiscent of that of bovine ClC-K and CLC transporters. The chloride conducting pathway exhibits distinct features, including a central glutamate residue (“fast gate”) known to confer voltage-dependence (a mechanistic feature not present in ClC-K), linked to a somewhat rearranged central tyrosine and a narrower aperture of the pore toward the extracellular vestibule. These characteristics agree with the lower chloride flux of ClC-1 compared with ClCK and enable us to propose a model for chloride passage in voltage-dependent CLC channels. Comparison of structures derived from protein studied in different experimental conditions supports the notion that pH and adenine nucleotides regulate ClC-1 through interactions between the so-called cystathionine-β-synthase (CBS) domains and the intracellular vestibule (“slow gating”). The structure also provides a framework for analysis of mutations causing myotonia congenita and reveals a striking correlation between mutated residues and the phenotypic effect on voltage gating, opening avenues for rational design of therapies against ClC-1–related diseases. Author summary Chloride transporting CLC proteins are expressed in a wide range of organisms, and the family encompasses several members with numerous roles in human health and disease by allowing movement of chloride ions across the membranes that encapsulate cells and cellular organelles. Structurally, CLCs form dimers possessing a separate ion translocation pathway in each monomer, and they can operate as either channels or transporters that exchange chloride for protons. The CLC channel ClC-1 is critical to skeletal muscle excitability and has been proposed as a target to alleviate neuromuscular disorders. Here, we have analyzed the structure of human ClC-1 and revealed the high similarity of its ion conducting pathway to those observed in other CLC members, including prokaryotic and algal transporters. Our data suggest how ClC-1 is regulated by environmental cues to allow opening and closure, thereby permitting attenuation of muscle function. Our results help with understanding the principal determinants that govern CLC proteins and may guide downstream translational applications to combat muscle pathologies.

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2018 – Functional Analysis of Membrane Proteins Produced by Cell-Free Translation
Port-a-Patch and Orbit mini article in Protein Engineering (2018)   Authors: Dondapati S.K., Wüstenhagen D.A., Kubick S.

Cell-free production is a valuable and alternative method for the synthesis of membrane proteins. This system offers openness allowing the researchers to modify the reaction conditions without any boundaries. Additionally, the cell-free reactions are scalable from 20 μL up to several mL, faster and suitable for the high-throughput protein production. Here, we present two cell-free systems derived from Escherichia coli (E. coli) and Spodoptera frugiperda (Sf21) lysates. In the case of the E. coli cell-free system, nanodiscs are used for the solubilization and purification of membrane proteins. In the case of the Sf21 system, endogenous microsomes with an active translocon complex are present within the lysates which facilitate the incorporation of the bacterial potassium channel KcsA within the microsomal membranes. Following cell-free synthesis, these microsomes are directly used for the functional analysis of membrane proteins.

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2020 – Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity
Orbit mini and Vesicle Prep Pro Publication in Science Advances (2020)   Authors: Ni T., Jiao F., Yu X., Aden S., Ginger L., Williams S.I., Bai F., Pražák V., Karia D., Stansfeld P., Zhang P., Munson G., Anderluh G.,Scheuring S., Gilbert R.J.C.

Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual phagocytes and whole organisms significantly more susceptible to bacterial pathogens. Here, we reveal the mechanism of perforin-2 activation and activity using atomic structures of pre-pore and pore assemblies, high-speed atomic force microscopy, and functional assays. Perforin-2 forms a pre-pore assembly in which its pore-forming domain points in the opposite direction to its membrane-targeting domain. Acidification then triggers pore formation, via a 180° conformational change. This novel and unexpected mechanism prevents premature bactericidal attack and may have played a key role in the evolution of all perforin family proteins.

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2022 – An oomycete NLP cytolysin forms transient small pores in lipid membranes
Orbit mini and Vesicle Prep Pro Publication in Science Advances (2022)  Authors: Pirc K., Clifton L.A., Yilmaz N., Saltalmacchiamo A., Mally M., Snoj T., Žnidaršič N., Srnko M., Borišek J., Parkkila P., Albert I., Podobnik M., Numata K., Nürnberger T., Viitala T., Derganac J., Magistrato A., Lakey J.H., Anderluh G.

Microbial plant pathogens secrete a range of effector proteins that damage host plants and consequently constrain global food production. Necrosis and ethylene-inducing peptide 1–like proteins (NLPs) are produced by numerous phytopathogenic microbes that cause important crop diseases. Many NLPs are cytolytic, causing cell death and tissue necrosis by disrupting the plant plasma membrane. Here, we reveal the unique molecular mechanism underlying the membrane damage induced by the cytotoxic model NLP. This membrane disruption is a multistep process that includes electrostatic-driven, plant-specific lipid recognition, shallow membrane binding, protein aggregation, and transient pore formation. The NLP-induced damage is not caused by membrane reorganization or large-scale defects but by small membrane ruptures. This distinct mechanism of lipid membrane disruption is highly adapted to effectively damage plant cells.

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2017 – Engineering a pH responsive pore forming protein
Orbit mini and Vesicle Prep Pro Publication in Scientific Reports (2017)    Authors: Kisovec M., Rezelj S., Knap P., Cajnko M.M., Caserman S., Flašker A., Žnidaršič N., Repič M., Mavri J., Ruan Y., Scheuring S., Podobnik M., Anderluh G.

Listeriolysin O (LLO) is a cytolysin capable of forming pores in cholesterol-rich lipid membranes of host cells. It is conveniently suited for engineering a pH-governed responsiveness, due to a pH sensor identified in its structure that was shown before to affect its stability. Here we introduced a new level of control of its hemolytic activity by making a variant with hemolytic activity that was pH-dependent. Based on detailed structural analysis coupled with molecular dynamics and mutational analysis, we found that the bulky side chain of Tyr406 allosterically affects the pH sensor. Molecular dynamics simulation further suggested which other amino acid residues may also allosterically influence the pH-sensor. LLO was engineered to the point where it can, in a pH-regulated manner, perforate artificial and cellular membranes. The single mutant Tyr406Ala bound to membranes and oligomerized similarly to the wild-type LLO, however, the final membrane insertion step was pH-affected by the introduced mutation. We show that the mutant toxin can be activated at the surface of artificial membranes or living cells by a single wash with slightly acidic pH buffer. Y406A mutant has a high potential in development of novel nanobiotechnological applications such as controlled release of substances or as a sensor of environmental pH.

Webinar
29.06.2021 | Webinar: Channelopathies resolved via cryo-EM and X-ray crystallography: an investigation of muscle excitation-contraction coupling
Speakers:
Dr. Conrad Weichbrodt (Senior Scientist / Product Manager Orbit family; Nanion Technologies)
Dr. Filip Van Petegem (Professor, Biochemistry and Molecular Biology - University of British Columbia)

Muscle contraction requires a tight communication between Ca2+-permeable ion channels located in the plasma membrane (L-type calcium channels, CaVs ) and in the Sarcoplasmic Reticulum (Ryanodine Receptors, RyRs). In cardiac muscle, Ca2+ entering through CaV1.2 can stimulate the nearby RyR2 isoform, through a process of Ca2+-induced Ca2+ release. In skeletal muscle, however, the coupling is thought to occur mechanically, with voltage-dependent conformational changes in CaV1.1 being transmitted to RyR1, either through direct or indirect interactions. Mutations in RyR1 (as well as CaV1.1) can give rise to malignant hyperthermia (MH), a potentially lethal condition typically triggered by volatile anaesthetics. Other mutations cause central core disease (CCD), whereas some are linked to both MH and CCD. Similarly, mutations in RyR2 are linked to a form of stress-induced cardiac arrhythmia, known as CPVT (catecholaminergic polymorphic ventricular tachycardia). Our lab has been solving crystal structures of isolated RyR domains in WT and disease mutant forms, which show that many mutations cause conformational changes. More recently, we solved cryo-EM structures of RyR1 carrying the founding mutation (R615C) that links RyR1 to malignant hyperthermia. The structures show how many mutations can destabilize the closed state, leading to facilitated channel opening.

In addition, RyRs are heavily regulated by kinases (PKA, CaMKII) that can also facilitate channel opening. Excessive phosphorylation of RyRs has been linked to a range of acquired disorders, including atrial fibrillation and arrhythmias during heart failure. We elucidated how PKA recognizes the cardiac RyR2 via an unusual interface and show that phosphorylation may induce the formation of extra secondary structure elements.

Finally, I will discuss our efforts to understand the mechanical coupling between CaV1.1 and RyR1 in skeletal muscle. STAC3 is a small protein recently shown to be essential for the coupling. We found this protein to interact with a cytosolic loop of CaV1.1 and found that several mutations in STAC3, linked to myopathy, directly affect this interaction and the mechanical coupling.

Webinar
17.09.2020 | Webinar: Electrophysiological investigation of integral membrane proteins using the Orbit mini
Speakers:
Dr. Conrad Weichbrodt (Senior Scientist / Product Manager Orbit family; Nanion Technologies)

A free standing lipid bilayer separating two aqueous compartments represents a fundamental prerequisite for the investigation of electrophysiological features of membrane spanning proteins like ion channels, porins or certain membrane active toxins. The convenient and reproducible preparation of these model bilayers and the often tedious workflow of conducting such an experiment on classic one channel setups, however, still remain an obstacle for easy and fast data generation.

Here we present Nanion’s Orbit mini device which is explicitly designed to meet the special requirements of experiments on artificial lipid bilayers: use of Ionera’s MECA (micro electrode cavity array) chip technology combined with state of the art low noise amplifiers (Elements S.R.L.) enable the fully parallel low-noise recording of four separate lipid bilayers at bandwidths up to 100 kHz. Today’s webinar consists of a general introduction of the system and a brief overview of it features, applications and optional add ons. We then demonstrate how to actually perform an experiment on the device showcasing translocation of Polyethylene glycol (PEG) polymers through the well established and commercially available porin alpha-Hemolysin.

Webinar
28.06.2018 | Webinar: Artificial Lipid Bilayers in focus: Hand-held DNA-sequencing and biosensing with nanopores
Speakers:
Dr. Conrad Weichbrodt, Nanion Technologies Germany
Webinar
28.06.2018 | Webinar: Artificial Lipid Bilayers in focus: Hand-held DNA-sequencing and biosensing with nanopores
Speaker:
Prof. Dr. Stefan Howorka, University College London, Department of Chemistry

Portable DNA sequencing and biosensing can advance research, bedside-diagnostics, and homeland security. I describe how label-free sensing is achieved with atom-scale designed membrane nanopores. In this strategy, nanopores act as electronic sensors that detect when individual molecules pass the pores’ nanoscale hole. The temporary blockages cause changes in ionic pore current. The approach has helped pioneer portable DNA sequencing with protein pores(1) to discriminate individual bases. More recently, synthetic pores have been built by folding DNA strands into defined channels(2). The DNA nanopores are relevant as they overcome the narrow size range of protein pores and thereby accommodate folded protein analytes. The DNA nanostructures are also easier to rationally design than proteins(3) and thereby enable new applications, also in synthetic biology(4).

(1) Nature 2014 516 250;
(2) Nat. Nanotechnol. 2016 11 152;
(3) Nat. Nanotechnol. 2017 12 619;
(4) Science 2016 352 890; Nat. Chem. 2017 9 611

Webinar
27.01.2016 | Webinar: Instant bilayers – just add protein.
Speakers: Dr. Gerhard Baaken, Ionera GmbH and Dr. Mohamed Kreir, Application Scientist, Nanion Technologies

This webinar covers the use of the lipid bilayer platforms from Nanion: the Orbit16 and the Orbit mini for characterization of membrane proteins like ion channels, bacterial porins and biological nanopores. Both bilayer systems support high quality low noise recordings, but differ in throughput capabilities and experimental features. The Orbit16, introduced in 2012 is a device for efficient formation of 16 lipid bilayers simultaneously, allowing for parallel bilayer-reconstitution of ion channels and nanopores

Webinar
27.01.2016 | Webinar: Instant bilayers – just add protein.
This webinar covers the use of the lipid bilayer platforms from Nanion: the Orbit16 and the Orbit mini for characterization of membrane proteins like ion channels, bacterial porins and biological nanopores. Both bilayer systems support high quality low noise recordings, but differ in throughput capabilities and experimental features. The Orbit16, introduced in 2012 is a device for efficient formation of 16 lipid bilayers simultaneously, allowing for parallel bilayer-reconstitution of ion channels and nanopores.

Lipid bilayer arrays are automatically formed by remotely actuated painting. Orbit 16 has proven to be a versatile device for research and scientific applications which is reflected by numerous publication in high rank journals such as Science, Nature, Nano Letters, ACS Nano etc. The Orbit mini, introduced in 2015, is a smaller system, allowing low noise, high bandwidth recordings from 4 bilayers simultaneously. Orbit mini supports temperature-controlled experiments, allowing both active cooling and heating, a benefit when investigating thermo-sensitive channels such as TRPA1 or TRPV1, which will be shown in this webinar. Micro Electrode Cavity Array chips (MECA chips, Ionera Technologies GmbH, Freiburg) are the core of both devices. The MECA chips have successfully been validated with a wide variety of different ion channels and pores including KcsA, gramicidin, α-hemolysin, Kv- and Nav-channels etc. In this webinar the basics of the MECA technology will be explained and its applications will be shown in detail. Join this webinar and see how these outstanding platforms can add up to your work: Orbit 16 and Orbit mini!

Application Note PDF
TRPV1 – “Temperature activation of TRPV1 reconstituted into planar lipid bilayers and recorded using the Orbit mini platform”
Orbit mini application note:   

The transient receptor potential cation channel, subfamily V, member 1 (TRPV1), is a ligand-gated, non-selective cation channel widely expressed in the peripheral and central nervous system. The TRPV1 channel can be activated by a number of physical and chemical stimuli, including capsaicin (the active ingredient in chili peppers), noxious heat (typically >42˚C) and low pH. The TRPV1 channel is putatively involved in the perception and transmission of painful stimuli. Importantly, this channel is proposed to underlie many chronic pain states including inflammation, neuropathic pain and cancer pain, amongst others (1). These types of pain states are currently poorly managed by the pain medications available and this has led the pharmaceutical industry to seek novel targets for pain management, such as TRPV1. However, TRPV1 antagonists have so far failed in clinical trials due to an undesirable increase in core body temperature (2) resulting in hyperthermia. From these studies, it is proposed that tonically active TRPV1 channels are involved in maintaining normal body temperature and this could have significant influences on drug design. Finding novel compounds with differing effects on capsaicin activation and heat activation may be crucial in the discovery of lead compounds for the treatment of pain and other disease states.Here we present data collected on the 4-channel Orbit mini with temperature control showing the potential use of the Orbit mini to record heat activation of single channel TRPV1. 

Tutorial video
2015 – Orbit mini Tutorial Video
Short introduction on the Orbit mini

"The functionality of the Orbit mini is just incredible! Learning to use it takes only a few moments. Setting up an experiment, painting 4 individual bilayers and getting data so quickly, makes me feel almost sad. As I cannot deny the notion wasting a lot of time as PhD student working with different technology"
Tom Götze, Nanion Technologies

Product Sheet PDF
Orbit mini – Product Sheet
Tutorial video
2015 – Orbit mini Membrane Preparation Tutorial Video
Short introduction how to prepare membranes on the Orbit mini

Simultaneous recording from four lipid bilayers

Flyer PDF
Orbit mini Product Flyer – OPTO- INV
Flyer PDF
Orbit mini Product Flyer – Temperature Control
Publication link
2022 – Triggered Assembly of a DNA-Based Membrane Channel
Orbit Mini Publication in American Chemical Society (2022) Authors: Lanphere C., Ciccone J., Dorey A., Hagleitner-Ertuğrul N., Knyazev D., Haider S., Howorka S.

Chemistry is in a powerful position to synthetically replicate biomolecular structures. Adding functional complexity is key to increase the biomimetics’ value for science and technology yet is difficult to achieve with poorly controlled building materials. Here, we use defined DNA blocks to rationally design a triggerable synthetic nanopore that integrates multiple functions of biological membrane proteins. Soluble triggers bind via molecular recognition to the nanopore components changing their structure and membrane position, which controls the assembly into a defined channel for efficient transmembrane cargo transport. Using ensemble, single-molecule, and simulation analysis, our activatable pore provides insight into the kinetics and structural dynamics of DNA assembly at the membrane interface. The triggered channel advances functional DNA nanotechnology and synthetic biology and will guide the design of controlled nanodevices for sensing, cell biological research, and drug delivery.

Flyer PDF
Orbit mini – Quickstart Guide “Getting Started”
Publication link
2022 – Photoactivation of a Mechanosensitive Channel
Orbit mini Publication in Frontiers in Molecular Biosciences (2022) Authors: Crea F., Vorkas A., Redlich A., Cruz R., Shi C., Trauner D., Lange A., Schlesinger R., Heberle J.

Optogenetics in the conventional sense, i.e. the use of engineered proteins that gain their light sensitivity from naturally abundant chromophores, represents an exciting means to trigger and control biological activity by light. As an alternate approach, photopharmacology controls biological activity with the help of synthetic photoswitches. Here, we used an azobenzene-derived lipid analogue to optically activate the transmembrane mechanosensitive channel MscL which responds to changes in the lateral pressure of the lipid bilayer. In this work, MscL has been reconstituted in nanodiscs, which provide a native-like environment to the protein and a physical constraint to membrane expansion. We characterized this photomechanical system by FTIR spectroscopy and assigned the vibrational bands of the light-induced FTIR difference spectra of the trans and cis states of the azobenzene photolipid by DFT calculations. Differences in the amide I range indicated reversible conformational changes in MscL as a direct consequence of light switching. With the mediation of nanodiscs, we inserted the transmembrane protein in a free standing photoswitchable lipid bilayer, where electrophysiological recordings confirmed that the ion channel could be set to one of its sub-conducting states upon light illumination. In conclusion, a novel approach is presented to photoactivate and control cellular processes as complex and intricate as gravitropism and turgor sensing in plants, contractility of the heart, as well as sensing pain, hearing, and touch in animals.

Publication link
2022 – Pore-forming moss protein bryoporin is structurally and mechanistically related to actinoporins from evolutionarily distant cnidarians
Orbit mini Publication in Journal of Biological Chemistry (2022) Authors: Šolinc G., Švigelj T., Omersa N., Snoj T., Pirc K., Znidaršič N.,  Yamaji-Hasegawa A., Kobayashi T., Anderluh G., Podobnik M.

Pore-forming proteins perforate lipid membranes and consequently affect their integrity and cell fitness. Therefore, it is not surprising that many of these proteins from bacteria, fungi, or certain animals act as toxins. While pore-forming proteins have also been found in plants, there is little information on their molecular structure and mode of action. Bryoporin is a protein from the moss Physcomitrium patens, and its corresponding gene was found to be upregulated by various abiotic stresses, especially dehydration, as well as upon fungal infection. Based on the amino acid sequence, it was suggested that bryoporin was related to the actinoporin family of pore-forming proteins, originally discovered in sea anemones. Here, we provide the first detailed structural and functional analysis of this plant cytolysin. The crystal structure of the monomeric bryoporin is highly similar to those of actinoporins. Our cryo-EM analysis of its pores showed an actinoporin-like octameric structure, thereby revealing a close kinship of proteins from evolutionarily distant organisms. This was further confirmed by our observation of bryoporin‘s preferential binding to and formation of pores in membranes containing animal sphingolipids, such as sphingomyelin and ceramide phosphoethanolamine; however, its binding affinity was weaker than that of actinoporin equinatoxin II. We determined bryoporin did not bind to major sphingolipids found in fungi or plants, and its membrane-binding and pore-forming activity were enhanced by various sterols. Our results suggest that bryoporin could represent a part of the moss defense arsenal, acting as a pore-forming toxin against membranes of potential animal pathogens, parasites, or predators.

Publication link
2022 – Integrative Study of the Structural and Dynamical Properties of a KirBac3.1 Mutant: Functional Implication of a Highly Conserved Tryptophan in the Transmembrane Domain
Orbit Mini Publication in Molecular Biophysics (2022) Authors: Fagnen C., Bannwarth L., Oubella I., Zuniga D., Haouz A., Forest E., Scala R., Bendahhou S., De Zorzi R., Perahia D., Vénien-Bryan C.

ATP-sensitive potassium (K-ATP) channels are ubiquitously expressed on the plasma membrane of cells in several organs, including the heart, pancreas, and brain, and they govern a wide range of physiological processes. In pancreatic β-cells, K-ATP channels composed of Kir6.2 and SUR1 play a key role in coupling blood glucose and insulin secretion. A tryptophan residue located at the cytosolic end of the transmembrane helix is highly conserved in eukaryote and prokaryote Kir channels. Any mutation on this amino acid causes a gain of function and neonatal diabetes mellitus. In this study, we have investigated the effect of mutation on this highly conserved residue on a KirBac channel (prokaryotic homolog of mammalian Kir6.2). We provide the crystal structure of the mutant KirBac3.1 W46R (equivalent to W68R in Kir6.2) and its conformational flexibility properties using HDX-MS. In addition, the detailed dynamical view of the mutant during the gating was investigated using the in silico method. Finally, functional assays have been performed. A comparison of important structural determinants for the gating mechanism between the wild type KirBac and the mutant W46R suggests interesting structural and dynamical clues and a mechanism of action of the mutation that leads to the gain of function.

Publication link
2022 – Opening of glutamate receptor channel to subconductance levels
Orbit Mini Publication in Nature (2022) Authors: Yelshanskaya M.V., Patel D.S., Kottke C.M., Kurnikova M.G., & Sobolevsky A.I.

Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that open their pores in response to binding of the agonist glutamate. An ionic current through a single iGluR channel shows up to four discrete conductance levels (O1–O4). Higher conductance levels have been associated with an increased number of agonist molecules bound to four individual ligand-binding domains (LBDs). Here we determine structures of a synaptic complex of AMPA-subtype iGluR and the auxiliary subunit γ2 in non-desensitizing conditions with various occupancy of the LBDs by glutamate. We show that glutamate binds to LBDs of subunits B and D only after it is already bound to at least the same number of LBDs that belong to subunits A and C. Our structures combined with single-channel recordings, molecular dynamics simulations and machine-learning analysis suggest that channel opening requires agonist binding to at least two LBDs. Conversely, agonist binding to all four LBDs does not guarantee maximal channel conductance and favours subconductance states O1 and O2, with O3 and O4 being rare and not captured structurally. The lack of subunit independence and low efficiency coupling of glutamate binding to channel opening underlie the gating of synaptic complexes to submaximal conductance levels, which provide a potential for upregulation of synaptic activity.

Publication link
2022 – Cryo–electron microscopy unveils unique structural features of the human Kir2.1 channel
Orbit Mini Publication in Science Advances (2022) Authors: Fernandes C., Zuniga D., Fagnen C., Kugler V., Scala R., Péhau-Arnaudet G., Wagner R., Perahia D., Bendahhou S., Vénien-Bryan C.

We present the first structure of the human Kir2.1 channel containing both transmembrane domain (TMD) and cytoplasmic domain (CTD). Kir2.1 channels are strongly inward-rectifying potassium channels that play a key role in maintaining resting membrane potential. Their gating is modulated by phosphatidylinositol 4,5-bisphosphate (PIP2). Genetically inherited defects in Kir2.1 channels are responsible for several rare human diseases, including Andersen’s syndrome. The structural analysis (cryo–electron microscopy), surface plasmon resonance, and electrophysiological experiments revealed a well-connected network of interactions between the PIP2-binding site and the G-loop through residues R312 and H221. In addition, molecular dynamics simulations and normal mode analysis showed the intrinsic tendency of the CTD to tether to the TMD and a movement of the secondary anionic binding site to the membrane even without PIP2. Our results revealed structural features unique to human Kir2.1 and provided insights into the connection between G-loop and gating and the pathological mechanisms associated with this channel.

Publication link
2022 – Emerging enterococcus pore-forming toxins with MHC/HLA-I as receptors
Orbit Mini Publication in Cell (2022) Authors: Xiong X., Songhai Tian S., Yang P., Lebreton F., Bao H.,Sheng K., Yin L., Chen P., Zhang J., Qi W., Ruan J., Wu H., Chen H., Breault D.T., Wu H., Earl A.M., Gilmore M.S., Abraham J., Dong M. 

Enterococci are a part of human microbiota and a leading cause of multidrug resistant infections. Here, we identify a family of Enterococcus pore-forming toxins (Epxs) in E. faecalis, E. faecium, and E. hirae strains isolated across the globe. Structural studies reveal that Epxs form a branch of β-barrel pore-forming toxins with a β-barrel protrusion (designated the top domain) sitting atop the cap domain. Through a genome-wide CRISPR-Cas9 screen, we identify human leukocyte antigen class I (HLA-I) complex as a receptor for two members (Epx2 and Epx3), which preferentially recognize human HLA-I and homologous MHC-I of equine, bovine, and porcine, but not murine, origin. Interferon exposure, which stimulates MHC-I expression, sensitizes human cells and intestinal organoids to Epx2 and Epx3 toxicity. Co-culture with Epx2-harboring E. faecium damages human peripheral blood mononuclear cells and intestinal organoids, and this toxicity is neutralized by an Epx2 antibody, demonstrating the toxin-mediated virulence of Epx-carrying Enterococcus.

Publication link
2022 – A chip-based array for high-resolution fluorescence characterization of free-standing horizontal lipid membranes under voltage clamp
Orbit mini OPTO-INV Publication in Lab on a Chip (2022) Authors: Ensslen T., Behrends J.C.

Optical techniques, such as fluorescence microscopy, are of great value in characterizing the structural dynamics of membranes and membrane proteins. A particular challenge is to combine high-resolution optical measurements with high-resolution voltage clamp electrical recordings providing direct information on e.g. single ion channel gating and/or membrane capacitance. Here, we report on a novel chip-based array device which facilitates optical access with water or oil-immersion objectives of high numerical aperture to horizontal free-standing lipid membranes while controlling membrane voltage and recording currents using micropatterned Ag/AgCl-electrodes. We demonstrate both wide-field and confocal imaging, as well as time-resolved single photon counting on free-standing membranes spanning sub-picoliter CaVities are demonstrated while electrical signals, including single channel activity, are simultaneously acquired. This optically addressable microelectrode CaVity array will allow combined electrical-optical studies of membranes and membrane proteins to be performed as a routine experiment.

Publication link
2022 – Circularized fluorescent nanodiscs for probing protein–lipid interactions
Orbit mini Publication in Communications Biology (2022) Authors: Ren Q., Zhang S., Bao H.

Protein–lipid interactions are vital for numerous transmembrane signaling pathways. However, simple tools to characterize these interactions remain scarce and are much needed to advance our understanding of signal transduction across lipid bilayers. To tackle this challenge, we herein engineer nanodisc as a robust fluorescent sensor for reporting membrane biochemical reactions. We circularize nanodiscs via split GFP and thereby create an intensity-based fluorescent sensor (isenND) for detecting membrane binding and remodeling events. We show that isenND responds robustly and specifically to the action of a diverse array of membrane-interacting proteins and peptides, ranging from synaptotagmin and synuclein involved in neurotransmission to viral fusion peptides of HIV-1 and SARS-CoV-2. Together, isenND can serve as a versatile biochemical reagent useful for basic and translational research of membrane biology.

Publication link
2021 – Saccharomyces cerevisiae as a superior host for overproduction of prokaryotic integral membrane proteins
Orbit Mini Publication in Current Research in Structural Biology (2021) Authors: Spruce Preisler S., Wiuf A.D., Friss M., Kjaergaard L., Hurd M., Ramos Becares E., Nurup C.N., Bjoerkskov F.B., Szathmary Z., Gourson P.E., Calloe K., Klaerke D.A., Gotfryd K., Pedersen P.A.

Integral membrane proteins (IMPs) constitute ~30% of all proteins encoded by the genome of any organism and Escherichia coli remains the first-choice host for recombinant production of prokaryotic IMPs. However, the expression levels of prokaryotic IMPs delivered by this bacterium are often low and overproduced targets often accumulate in inclusion bodies. The targets are therefore often discarded to avoid an additional and inconvenient refolding step in the purification protocol. Here we compared expression of five prokaryotic (bacterial and archaeal) IMP families in E. coli and Saccharomyces cerevisiae. We demonstrate that our S. cerevisiae-based production platform is superior in expression of four investigated IMPs, overall being able to deliver high quantities of active target proteins. Surprisingly, in case of the family of zinc transporters (Zrt/Irt-like proteins, ZIPs), S. cerevisiae rescued protein expression that was undetectable in E. coli. We also demonstrate the effect of localization of the fusion tag on expression yield and sample quality in detergent micelles. Lastly, we present a road map to achieve the most efficient expression of prokaryotic IMPs in our yeast platform. Our findings demonstrate the great potential of S. cerevisiae as host for high-throughput recombinant overproduction of bacterial and archaeal IMPs for downstream biophysical characterization.

Publication link
2021 – Structure and desensitization of AMPA receptor complexes with type II TARP γ5 and GSG1L
Orbit Mini Publication in Molecular Cell (2021) Authors: Klykov O., Gangwar S. P., Yelshanskaya M. V., Laura Yen., Sobolevsky A. I.

AMPA receptors (AMPARs) mediate the majority of excitatory neurotransmission. Their surface expression, trafficking, gating, and pharmacology are regulated by auxiliary subunits. Of the two types of TARP auxiliary subunits, type I TARPs assume activating roles, while type II TARPs serve suppressive functions. We present cryo-EM structures of GluA2 AMPAR in complex with type II TARP γ5, which reduces steady-state currents, increases single-channel conductance, and slows recovery from desensitization. Regulation of AMPAR function depends on its ligand-binding domain (LBD) interaction with the γ5 head domain. GluA2-γ5 complex shows maximum stoichiometry of two TARPs per AMPAR tetramer, being different from type I TARPs but reminiscent of the auxiliary subunit GSG1L. Desensitization of both GluA2-GSG1L and GluA2-γ5 complexes is accompanied by rupture of LBD dimer interface, while GluA2-γ5 but not GluA2-GSG1L LBD dimers remain two-fold symmetric. Different structural architectures and desensitization mechanisms of complexes with auxiliary subunits endow AMPARs with broad functional capabilities.

Publication link
2021 – Pathological conformations of disease mutant Ryanodine Receptors revealed by cryo-EM
Orbit mini Publication in Nature Communications (2021) Authors: Woll K.A., Haji-Ghassemi O., Van Petegem F.

Ryanodine Receptors (RyRs) are massive channels that release Ca2+ from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and arrhythmias. Here, we explore the first MH mutation identified in humans by providing cryo-EM snapshots of the pig homolog, R615C, showing that it affects an interface between three solenoid regions. We also show the impact of apo-calmodulin (apoCaM) and how it can induce opening by bending of the bridging solenoid, mediated by its N-terminal lobe. For R615C RyR1, apoCaM binding abolishes a pathological ‘intermediate’ conformation, distributing the population to a mixture of open and closed channels, both different from the structure without apoCaM. Comparisons show that the mutation primarily affects the closed state, inducing partial movements linked to channel activation. This shows that disease mutations can cause distinct pathological conformations of the RyR and facilitate channel opening by disrupting interactions between different solenoid regions.

Publication link
2021 – Rapid and multiplex preparation of engineered Mycobacterium smegmatis porin A (MspA) nanopores for single molecule sensing and sequencing
Orbit Mini Publication in Chemical Science (2021) Authors: Yan S., Wang L., Du X., Zhang S., Wang S., Cao J., Zhang J., Jia W., Wang Y., Zhang P., Chen H-Y., Huang S.

Acknowledging its unique conical lumen structure, Mycobacterium smegmatis porin A (MspA) was the first type of nanopore that has successfully sequenced DNA. Recent developments of nanopore single molecule chemistry have also suggested MspA to be an optimum single molecule reactor. However, further investigations with this approach require heavy mutagenesis which is labor intensive and requires high end instruments for purifications. We here demonstrate an efficient and economic protocol which performs rapid and multiplex preparation of a variety of MspA mutants. The prepared MspA mutants were demonstrated in operations such as nanopore insertion, sequencing, optical single channel recording (oSCR), nanopore single molecule chemistry and nanopore rectification. The performance is no different from that of pores however prepared by other means. The time of all human operations and the cost for a single batch of preparation have been minimized to 40 min and 0.4$, respectively. This method is extremely useful in the screening of new MspA mutants, which has an urgent requirement in further investigations of new MspA nanoreactors. Its low cost and simplicity also enable efficient preparations of MspA nanopores for both industrial manufacturing and academic research.

Publication link
2020 – Small Molecule Permeation Across Membrane Channels: Chemical Modification to Quantify Transport Across OmpF
Orbit mini Publication in Angewandte Chemie (2020) Authors: Wang J., Bafna J.A., Bhamidimarri S.P., Winterhalter M.

Biological channels facilitate the exchange of small molecules across membranes, but surprisingly there is a lack of general tools for the identification and quantification of transport (i.e., translocation and binding). Analyzing the ion current fluctuation of a typical channel with its constriction region in the middle does not allow a direct conclusion on successful transport. For this, we created an additional barrier acting as a molecular counter at the exit of the channel. To identify permeation, we mainly read the molecule residence time in the channel lumen as the indicator whether the molecule reached the exit of the channel. As an example, here we use the well-studied porin, OmpF, an outer membrane channel from E. coli. Inspection of the channel structure suggests that aspartic acid at position 181 is located below the constriction region (CR) and we subsequently mutated this residue to cysteine, where else cysteine free and functionalized it by covalent binding with 2-sulfonatoethyl methanethiosulfonate (MTSES) or the larger glutathione (GLT) blockers. Using the dwell time as the signal for transport, we found that both mono-arginine and tri-arginine permeation process is prolonged by 20% and 50% respectively through OmpFE181CMTSES, while the larger sized blocker modification OmpFE181CGLT drastically decreased the permeation of mono-arginine by 9-fold and even blocked the pathway of the tri-arginine. In case of the hepta-arginine as substrate, both chemical modifications led to an identical ‘blocked’ pattern observed by the dwell time of ion current fluctuation of the OmpFwt. As an instance for antibiotic permeation, we analyzed norfloxacin, a fluoroquinolone antimicrobial agent. The modulation of the interaction dwell time suggests possible successful permeation of norfloxacin across OmpFwt. This approach may discriminate blockages from translocation events for a wide range of substrates. A potential application could be screening for scaffolds to improve the permeability of antibiotics.

Publication link
2021 – ATP and large signaling metabolites flux through caspase-activated Pannexin 1 channels
Orbit mini Publication in eLife (2021) Authors: Narahari A.K., Kreutzberger A JB., Gaete P.S., Chiu Yu-Hsin, Leonhardt S.A., Medina C.B., Jin X., Oleniacz P.W., Kiessling V., Barrett P.Q., Ravichandran K.S., Yeager M., Contreras J.E., Tamm L.K., Bayliss D.A.

Pannexin 1 (Panx1) is a membrane channel implicated in numerous physiological and pathophysiological processes via its ability to support release of ATP and other cellular metabolites for local intercellular signaling. However, to date, there has been no direct demonstration of large molecule permeation via the Panx1 channel itself, and thus the permselectivity of Panx1 for different molecules remains unknown. To address this, we expressed, purified, and reconstituted Panx1 into proteoliposomes and demonstrated that channel activation by caspase cleavage yields a dye-permeable pore that favors flux of anionic, large-molecule permeants (up to ~1 kDa). Large cationic molecules can also permeate the channel, albeit at a much lower rate. We further show that Panx1 channels provide a molecular pathway for flux of ATP and other anionic (glutamate) and cationic signaling metabolites (spermidine). These results verify large molecule permeation directly through caspase-activated Panx1 channels that can support their many physiological roles.

Publication link
2020 – Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel
Orbit mini Publication in Science Advances (2020) Authors: Lee H.J., Jeong H., Hyun J., Ryu B., Park K., Lim H.H., Yoo J., Woo J.S.

Connexin family proteins assemble into hexameric channels called hemichannels/connexons, which function as transmembrane channels or dock together to form gap junction intercellular channels (GJIChs). We determined the cryo–electron microscopy structures of human connexin 31.3 (Cx31.3)/GJC3 hemichannels in the presence and absence of calcium ions and with a hearing-loss mutation R15G at 2.3-, 2.5-, and 2.6-Å resolutions, respectively. Compared with available structures of GJICh in open conformation, Cx31.3 hemichannel shows substantial structural changes of highly conserved regions in the connexin family, including opening of calcium ion–binding tunnels, reorganization of salt-bridge networks, exposure of lipid-binding sites, and collocation of amino-terminal helices at the cytoplasmic entrance. We also found that the hemichannel has a pore with a diameter of ~8 Å and selectively transports chloride ions. Our study provides structural insights into the permeant selectivity of Cx31.3 hemichannel.

Publication link
2020 – New Structural insights into Kir channel gating from molecular simulations, HDX-MS and functional studies
Orbit mini Publication in Nature Scientific Reports (2020) Authors: Fagnen C., Bannwarth L, Oubella I., Forest E., De Zorzi R., de Araujo A., Mhoumadi Y., Bendahhou S., Perahia D., Vénien-Bryan C.

Inward rectifer potassium (Kir) channels play diverse and important roles in shaping action potentials in biological membranes. An increasing number of diseases are now known to be directly associated with abnormal Kir function. However, the gating of Kir still remains unknown. To increase our understanding of its gating mechanism, a dynamical view of the entire channel is essential. Here the gating activation was studied using a recent developped in silico method, MDeNM, which combines normal mode analysis and molecular dynamics simulations that showed for the very frst time the importance of interrelated collective and localized conformational movements. In particular, we highlighted the role played by concerted movements of the diferent regions throughout the entire protein, such as the cytoplasmic and transmembrane domains and the slide helices. In addition, the HDX-MS analysis achieved in these studies provided a comprehensive and detailed view of the dynamics associated with open/closed transition of the Kir channel in coherence with the theoretical results. MDeNM gives access to the probability of the diferent opening states that are in agreement with our electrophysiological experiments. The investigations presented in this article are important to remedy dysfunctional channels and are of interest for designing new pharmacological compounds.

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2020 – Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Orbit mini Publication in Science Advances (2020) Authors: Cao C., Krapp L.F., Al Ouahabi A., König N.F., Cirauqui N., Radenovic A., Lutz J.F. Dal Peraro M.

Digital data storage is a growing need for our society and finding alternative solutions than those based on silicon or magnetic tapes is a challenge in the era of “big data.” The recent development of polymers that can store information at the molecular level has opened up new opportunities for ultrahigh density data storage, long-term archival, anticounterfeiting systems, and molecular cryptography. However, synthetic informational polymers are so far only deciphered by tandem mass spectrometry. In comparison, nanopore technology can be faster, cheaper, nondestructive and provide detection at the single-molecule level; moreover, it can be massively parallelized and miniaturized in portable devices. Here, we demonstrate the ability of engineered aerolysin nanopores to accurately read, with single-bit resolution, the digital information encoded in tailored informational polymers alone and in mixed samples, without compromising information density. These findings open promising possibilities to develop writing-reading technologies to process digital data using a biological-inspired platform.

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2020 – Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field
Orbit mini Publication in Journal of Chemical Information and Modeling (2020) Authors: Prajapati J.D., Mele C., Alphan Aksoyoglu M.A., Winterhalter M., Kleinekathöfer U.

In the past two decades, molecular dynamics simulations have become the method of choice for elucidating the transport mechanisms of ions through various membrane channels. Often, these simulations heavily rely on classical nonpolarizable force fields (FFs), which lack electronic polarizability in the treatment of the electrostatics. The recent advancements in the Drude polarizable FF lead to a complete set of parameters for water, ions, protein, and lipids, allowing for a more realistic modeling of membrane proteins. However, the quality of these Drude FFs remains untested for such systems. Here, we examine the quality of this FF set in two ways, i.e., (i) in simple ionic aqueous solution simulations and (ii) in more complex membrane channel simulations. First, the aqueous solutions of KCl, NaCl, MgCl2, and CaCl2 salts are simulated using the polarizable Drude and the nonpolarizable CHARMM36 FFs. The bulk conductivity has been estimated for both FF sets using applied-field simulations for several concentrations and temperatures in the case of all investigated salts and compared to experimental findings. An excellent improvement in the ability of the Drude FF to reproduce the experimental bulk conductivities for KCl, NaCl, and MgCl2 solutions can be observed but not in the case of CaCl2. Moreover, the outer membrane channel OmpC from the bacterium Escherichia coli has been employed to examine the ability of the polarizable and nonpolarizable FFs to reproduce ion transport-related quantities known from experiment. Unbiased and applied-field simulations have been performed in the presence of KCl using both FF sets. Unlike for the bulk systems of aqueous salt solutions, it has been found that the Drude FF is not accurate in modeling KCl transport properties across the OmpC porin.

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2019 – Revisiting an old antibiotic: bacitracin neutralizes binary bacterial toxins and protects cells from intoxication
Orbit mini Publication in The FASEB Journal (2018) Authors: Schnell L., Felix I., Müller B., Sadi M., von Bank F., Papatheodorou P., Popoff M.R., Aktories K., Waltenberger E., Benz R., Weichbrodt C., Fauler M., Frick M., Barth H.

The antibiotic bacitracin (Bac) inhibits cell wall synthesis of gram-positive bacteria. Here, we discovered a totally different activity of Bac: the neutralization of bacterial exotoxins. Bac prevented intoxication of mammalian cells with the binary enterotoxins Clostridiumbotulinum C2, C. perfringens ι, C. difficile transferase (CDT), and Bacillus anthracis lethal toxin. The transport (B) subunits of these toxins deliver their respective enzyme (A) subunits into cells. Following endocytosis, the B subunits form pores in membranes of endosomes, which mediate translocation of the A subunits into the cytosol. Bac inhibited formation of such B pores in lipid bilayers in vitro and in living cells, thereby preventing translocation of the A subunit into the cytosol. Bac preserved the epithelial integrity of toxin-treated CaCo-2 monolayers, a model for the human gut epithelium. In conclusion, Bac should be discussed as a therapeutic option against infections with medically relevant toxin-producing bacteria, including C. difficile and B. anthracis, because it inhibits bacterial growth and neutralizes the secreted toxins.

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2020 – Activation of the archaeal ion channel MthK is exquisitely regulated by temperature
Orbit mini Publication in eLife (2020) Authors: Jiang Y., Idikuda V., Chowdhury S., Chanda B.

Physiological response to thermal stimuli in mammals is mediated by a structurally diverse class of ion channels, many of which exhibit polymodal behavior. To probe the diversity of biophysical mechanisms of temperature-sensitivity, we characterized the temperature-dependent activation of MthK, a two transmembrane calcium-activated potassium channel from thermophilic archaebacteria. Our functional complementation studies show that these channels are more efficient at rescuing K+ transport at 37°C than at 24°C. Electrophysiological activity of the purified MthK is extremely sensitive (Q10 >100) to heating particularly at low-calcium concentrations whereas channels lacking the calcium-sensing RCK domain are practically insensitive. By analyzing single-channel activities at limiting calcium concentrations, we find that temperature alters the coupling between the cytoplasmic RCK domains and the pore domain. These findings reveal a hitherto unexplored mechanism of temperature-dependent regulation of ion channel gating and shed light on ancient origins of temperature-sensitivity.

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2019 – Arg-8 of yeast subunit e contributes to the stability of F-ATP synthase dimersand to the generation of the full-conductance megachannel
Orbit mini Publication in Journal of Biological Chemistry (2019) Authors: Guo L., Carraro M., Carrer A., Minervini G., Urbani A., Masgras I., Tosatto S.C.E., Szabò I., Bernardi P., Lippe G.

The mitochondrial F-ATP synthase is a complex molecular motor arranged in V-shaped dimers that is responsible for most cellular ATP synthesis in aerobic conditions. In the yeast F-ATP synthase, subunits e and g of the FO sector constitute a lateral domain, which is required for dimer stability and cristae formation. Here, by using site-directed mutagenesis we identified Arg-8 of subunit e as a critical residue in mediating interactions between subunits e and g, most likely through an interaction with Glu-83 of subunit g. Consistent with this hypothesis (i) substitution of Arg-8 in subunit e (eArg-8) with Ala or Glu or of Glu-83 in subunit g (gGlu-83) with Ala or Lys destabilized the digitonin-extracted F-ATP synthase, resulting in decreased dimer formation, as revealed by blue-native electrophoresis; and (ii) simultaneous substitution of eArg-8 with Glu and of gGlu-83 with Lys rescued digitonin-stable F-ATP synthase dimers. When tested in lipid bilayers for generation of Ca2+-dependent channels, wild-type dimers displayed the high-conductance channel activity expected for the mitochondrial megachannel/permeability transition pore, whereas dimers obtained at low digitonin concentrations from the Arg-8 variants displayed currents of strikingly small conductance. Remarkably, double replacement of eArg-8 with Glu and of gGlu-83 with Lys restored high-conductance channels indistinguishable from those seen in wild-type enzymes. These findings suggest that the interaction of subunit e with subunit g is important for generation of the full-conductance megachannel from F-ATP synthase.

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2019 – Purification of Functional Human TRP Channels Recombinantly Produced in Yeast
Orbit mini Publication in Cells (2019) Authors: Zhang L., Wang K., Klaerke D.A., Calloe K., Lowrey L., Pedersen P.A., Gourdon P., Gotfryd K.

Background: Human transient receptor potential (TRP) channels constitute a large family of ion-conducting membrane proteins that allow the sensation of environmental cues. As the dysfunction of TRP channels contributes to the pathogenesis of many widespread diseases, including cardiac disorders, these proteins also represent important pharmacological targets. TRP channels are typically produced using expensive and laborious mammalian or insect cell-based systems. Methods: We demonstrate an alternative platform exploiting the yeast Saccharomyces cerevisiae capable of delivering high yields of functional human TRP channels. We produce 11 full-length human TRP members originating from four different subfamilies, purify a selected subset of these to a high homogeneity and confirm retained functionality using TRPM8 as a model target. Results: Our findings demonstrate the potential of the described production system for future functional, structural and pharmacological studies of human TRP channels.

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2017 – Molecular determinants of permeation in a fluoride-specific ion channel
Orbit mini in eLife (2017) Authors: Last .B., Sun S., Pham M.C., Miller C.

Fluoride ion channels of the Fluc family combat toxicity arising from accumulation of environmental F-. Although crystal structures are known, the densely packed pore region has precluded delineation of the ion pathway. Here we chart out the Fluc pore and characterize its chemical requirements for transport. A ladder of H-bond donating residues creates a ‘polar track’ demarking the ion-conduction pathway. Surprisingly, while track polarity is well conserved, polarity is nonetheless functionally dispensable at several positions. A threonine at one end of the pore engages in vital interactions through its β-branched methyl group. Two critical central phenylalanines that directly coordinate F- through a quadrupolar-ion interaction cannot be functionally substituted by aromatic, non-polar, or polar sidechains. The only functional replacement is methionine, which coordinates F- through its partially positive γ-methylene in mimicry of phenylalanine’s quadrupolar interaction. These results demonstrate the unusual chemical requirements for selectively transporting the strongly H-bonding F- anion.

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2018 – Dynamics and number of trans-SNARE complexes determine nascent fusion pore properties
Orbit mini Publication in Nature (2018) Authors: Bao H., Das D., Courtney N.A., Jiang Y., Briguglio J.S., Lou X., Roston D., Cui Q., Chanda B., Chapman E.R.

The fusion pore is the first crucial intermediate formed during exocytosis, yet little is known about the mechanisms that determine the size and kinetic properties of these transient structures1. Here, we reduced the number of available SNAREs (proteins that mediate vesicle fusion) in neurons and observed changes in transmitter release that are suggestive of alterations in fusion pores. To investigate these changes, we employed reconstituted fusion assays using nanodiscs to trap pores in their initial open state. Optical measurements revealed that increasing the number of SNARE complexes enhanced the rate of release from single pores and enabled the escape of larger cargoes. To determine whether this effect was due to changes in nascent pore size or to changes in stability, we developed an approach that uses nanodiscs and planar lipid bilayer electrophysiology to afford microsecond resolution at the single event level. Both pore size and stability were affected by SNARE copy number. Increasing the number of vesicle (v)-SNAREs per nanodisc from three to five caused a twofold increase in pore size and decreased the rate of pore closure by more than three orders of magnitude. Moreover, pairing of v-SNAREs and target (t)-SNAREs to form trans-SNARE complexes was highly dynamic: flickering nascent pores closed upon addition of a v-SNARE fragment, revealing that the fully assembled, stable SNARE complex does not form at this stage of exocytosis. Finally, a deletion at the base of the SNARE complex, which mimics the action of botulinum neurotoxin A, markedly reduced fusion pore stability. In summary, trans-SNARE complexes are dynamic, and the number of SNAREs recruited to drive fusion determines fundamental properties of individual pores.

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2016 – Mechanistic signs of double-barreled structure in a fluoride ion channel
Orbit mini Publication in eLIFE (2016) Authors: Last N.B., Kolmakova-Partensky L., Shane T., Miller C.

The Fluc family of F− ion channels protects prokaryotes and lower eukaryotes from the toxicity of environmental F−. In bacteria, these channels are built as dual-topology dimers whereby the two subunits assemble in antiparallel transmembrane orientation. Recent crystal structures suggested that Fluc channels contain two separate ion-conduction pathways, each with two F− binding sites, but no functional correlates of this unusual architecture have been reported. Experiments here fill this gap by examining the consequences of mutating two conserved F−-coordinating phenylalanine residues. Substitution of each phenylalanine specifically extinguishes its associated F− binding site in crystal structures and concomitantly inhibits F− permeation. Functional analysis of concatemeric channels, which permit mutagenic manipulation of individual pores, show that each pore can be separately inactivated without blocking F− conduction through its symmetry-related twin. The results strongly support dual-pathway architecture of Fluc channels.

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2021 – Design, assembly, and characterization of membrane-spanning DNA nanopores
Orbit 16 and Orbit mini Publication in Nature Protocols (2021) Authors: Lanphere C., Offenbartl-Stiegert D., Dorey A., Pugh G., Georgiou E., Xing Y., Burns J.R., Howorka S.

DNA nanopores are bio-inspired nanostructures that control molecular transport across lipid bilayer membranes. Researchers can readily engineer the structure and function of DNA nanopores to synergistically combine the strengths of DNA nanotechnology and nanopores. The pores can be harnessed in a wide range of areas, including biosensing, single-molecule chemistry, and single-molecule biophysics, as well as in cell biology and synthetic biology. Here, we provide a protocol for the rational design of nanobarrel-like DNA pores and larger DNA origami nanopores for targeted applications. We discuss strategies for the pores’ chemical modification with lipid anchors to enable them to be inserted into membranes such as small unilamellar vesicles (SUVs) and planar lipid bilayers. The procedure covers the self-assembly of DNA nanopores via thermal annealing, their characterization using gel electrophoresis, purification, and direct visualization with transmission electron microscopy and atomic force microscopy. We also describe a gel assay to determine pore–membrane binding and discuss how to use single-channel current recordings and dye flux assays to confirm transport through the pores. We expect this protocol to take approximately 1 week to complete for DNA nanobarrel pores and 2–3 weeks for DNA origami pores.

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2019 – Synthetic protein-conductive membrane nanopores built with DNA
Orbit 16 and Orbit mini Publication in Nature Communications (2019)    Authors: Diederichs T, Pugh G., Dorey A., Xing, Y., Burns J.R., Nguyen Q.H., Tornow M., Tampé R., & Howorka S

Nanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator CaVity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.

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2020 – Electrophysiology on Channel-Forming Proteins in Artificial Lipid Bilayers
Orbit 16 and Orbit mini Chapter in Patch Clamp Electrophysiology (2020) Authors: Zaitseva E., Obergrussberger A., Weichbrodt C., Boukhet M., Bernhard F., Hein C., Baaken G., Fertig N., Behrends J.C.

Chapter 4: Electrophysiology on Channel-Forming Proteins in Artificial Lipid Bilayers: Next-Generation Instrumentation for Multiple Recordings in Parallel Abstract: Artificial lipid bilayers have been used for several decades to study channel-forming pores and ion channels in membranes. Until recently, the classical two-chamber setups have been primarily used for studying the biophysical properties of pore forming proteins. Within the last 10 years, instruments for automated lipid bilayer measurements have been developed and are now commercially available. This chapter focuses on protein purification and reconstitution of channel-forming proteins into lipid bilayers using a classic setup and on the commercially available systems, the Orbit mini and Orbit 16.

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2022 – A reversibly gated protein-transporting membrane channel made of DNA
Orbit Mini Publication in Nature Communications (2022) Authors: Dey S., Dorey A., Abraham L., Xing Y., Zhang I., Howorka S., Yan H.

Controlled transport of biomolecules across lipid bilayer membranes is of profound significance in biological processes. In cells, cargo exchange is mediated by dedicated channels that respond to triggers, undergo a nanomechanical change to reversibly open, and thus regulate cargo flux. Replicating these processes with simple yet programmable chemical means is of fundamental scientific interest. Artificial systems that go beyond nature’s remit in transport control and cargo are also of considerable interest for biotechnological applications but challenging to build. Here, we describe a synthetic channel that allows precisely timed, stimulus-controlled transport of folded and functional proteins across bilayer membranes. The channel is made via DNA nanotechnology design principles and features a 416 nm2 opening cross-section and a nanomechanical lid which can be controllably closed and re-opened via a lock-and-key mechanism. We envision that the functional DNA device may be used in highly sensitive biosensing, drug delivery of proteins, and the creation of artificial cell networks.

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2022 – Highly shape- and size-tunable membrane nanopores made with DNA
Orbit 16, Orbit mini and Vesicle Prep Pro Publication in Nature Nanotechnology (2022) Authors: Xing Y., Dorey A., Jayasinghe L., Howorka S.

Membrane nanopores are key for molecular transport in biology, portable DNA sequencing, label-free single-molecule analysis and nanomedicine. Transport traditionally relies on barrel-like channels of a few nanometres width, but there is considerable scientific and technological interest for much wider structures of tunable shape. Yet, these nanopores do not exist in nature and are challenging to build using existing de novo routes for proteins. Here, we show that rational design with DNA can drastically expand the structural and functional range of membrane nanopores. Our design strategy bundles DNA duplexes into pore subunits that modularly arrange to form tunable pore shapes and lumen widths of up to tens of nanometres. Functional units for recognition or signalling can be optionally attached. By dialling in essential parameters, we demonstrate the utility and potential of the custom-engineered nanopores by electrical direct single-molecule sensing of 10-nm-sized proteins using widely used research and hand-held analysis devices. The designer nanopores illustrate how DNA nanotechnology can deliver functional biomolecular structures to be used in synthetic biology, single-molecule enzymology and biophysical analysis, as well as portable diagnostics and environmental screening.

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