Thermodynamic profile of mutual subunit control in a heteromeric receptor

Cyclic nucleotide-gated (CNG) ion channels of olfactory neurons are tetrameric membrane receptors that are composed of two A2 subunits, one A4 subunit, and one B1b subunit. Each subunit carries a cyclic nucleotide-binding domain in the carboxyl terminus, and the channels are activated by the binding of cyclic nucleotides. The mechanism of cooperative channel activation is still elusive. Using a complete set of engineered concatenated olfactory CNG channels, with all combinations of disabled binding sites and fit analyses with systems of allosteric models, the thermodynamics of microscopic cooperativity for ligand binding was subunit- and state-specifically quantified. We show, for the closed channel, that preoccupation of each of the single subunits increases the affinity of each other subunit with a Gibbs free energy (ΔΔG) of ∼−3.5 to ∼−5.5 kJ ⋅ mol−1, depending on the subunit type, with the only exception that a preoccupied opposite A2 subunit has no effect on the other A2 subunit. Preoccupation of two neighbor subunits of a given subunit causes the maximum affinity increase with ΔΔG of ∼−9.6 to ∼−9.9 kJ ⋅ mol−1. Surprisingly, triple preoccupation leads to fewer negative ΔΔG values for a given subunit as compared to double preoccupation. Channel opening increases the affinity of all subunits. The equilibrium constants of closed–open isomerizations systematically increase with progressive liganding. This work demonstrates, on the example of the heterotetrameric olfactory CNG channel, a strategy to derive detailed insights into the specific mutual control of the individual subunits in a multisubunit membrane receptor.

Experimental Study on the Effect of Triangular Plate Barrier Height on Flow Velocity Distribution in Open Channels

Open and closed channel flow flows are distinct, the flow in the channels will constantly change. The flow will also be altered if the water level or flow velocity changes. It was found that employing the Pitot Tube Portable yielded findings identical to those calculated by other methods. A water transfer system is made up of natural or artificial structures via which water is moved from one site to another. The carrier building may be open or closed, depending on whether you want to utilize it as a shipping or receiving location. An open channel with a relatively narrow opening at the top is known as an open conduit. The speed data collection technique is carried out vertically, with a review point as illustrated above. The velocity of the flow was measured using a Pitot Tube Portable Automatic tool. The results are entered into the Froude number (fr) after each review point to determine the type of velocity flow at each Review point. The normal flow velocity distribution pattern emerges at the measurement sites of 450 cm, 500 cm, and 550 cm.

ANALISIS PERPANJANGAN RUNWAY BANDAR UDARA INTERNASIONAL ADI SOEMARMO SOLO JAWA TENGAH

Solo City is one of the cities that has the largest airport in Central Java, namely Adi Soemarmo International Airport. Adi Soemarmo Airport has a runway length of 2600 m x 45 m. To make the city of Solo a hub in Java, where major cities outside Java, especially East and West Indonesia can land directly in Solo, Adi Soemarmo Airport requires development. Adi Soemarmo Solo Airport development is planned to add flight routes and international passengers (Source: http://www.dephub.go.id).Based on the results of calculations that refer to the International Civil Aviation Organization (ICAO) standard with Boeing 777-300ER and 747-100 planes, a runway length of 3,700 m is needed. For runway capacity, the annual demand of 31,676 operations per year is smaller than the annual service volume of 210,000 operations per year so that the runway capacity has not been exceeded.To determine runway pavement thickness using planes with the largest single wheel load, namely B747-100 so that B-777-300ER is not used. For pavement thickness using Equivalent Aircraft Method from FAA with CBR Method Flexible Pavement B-747-100 graph calculation. Results:The total pavement thickness is 31 in ? 89 cm, Surface thickness (P-403 HMA) of 5 in ? 13 cm, Base course thickness (P-304 Cement Treat Base) is 6 in ? 15 cm, The thickness of the subbase course (P-154 sub-course) is 24 in ? 61 cm. For the calculation of drainage, the result is a closed channel (pipe) with an inlet dimension of 0.25 m x 0.25 m with a distance between 50 m inlet. AbstrakKota Solo merupakan salah satu kota yang memiliki bandara terbesar di Jawa Tengah yaitu Bandara Internasional Adi Soemarmo. Bandara Adi Soemarmo memiliki panjang landasan pacu 2600 m x 45 m. Untuk menjadikan Kota Solo sebagai hub di Jawa yang kota-kota besar di luar Jawa khususnya Indonesia Timur dan Barat dapat mendarat langsung di Solo, Bandara Adi Soemarmo membutuhkan pembangunan. Pembangunan Bandara Adi Soemarmo Solo direncanakan untuk menambah rute penerbangan dan penumpang internasional (Sumber: http://www.dephub.go.id).Berdasarkan hasil perhitungan yang mengacu pada standar International Civil Aviation Organization (ICAO) dengan pesawat Boeing 777-300ER dan 747-100, dibutuhkan panjang landasan sepanjang 3.700 m. Untuk kapasitas runway, kebutuhan tahunan sebesar 31.676 operasi per tahun lebih kecil dari volume layanan tahunan sebesar 210.000 operasi per tahun sehingga kapasitas runway belum terlampaui.Untuk menentukan ketebalan perkerasan runway menggunakan pesawat dengan beban roda tunggal terbesar yaitu B747 -100 sehingga B-777-300ER tidak digunakan. Untuk ketebalan perkerasan menggunakan Metode Pesawat Udara Ekuivalen dari FAA dengan metode CBR Metode Perkerasan Fleksibel B-747-100 perhitungan grafik. Hasil:Ketebalan total perkerasan jalan adalah 31 inci ? 89 cm, Ketebalan permukaan (P-403 HMA) 5 in ? 13 cm,Ketebalan lapisan dasar (P-304 Cement Treat Base) adalah 6 inci ? 15 cm, Ketebalan dari subbase course (P-154 sub-course) adalah 24 inci ? 61 cm. Untuk perhitungan drainase didapatkan saluran tertutup (pipa) dengan dimensi inlet 0,25 m x 0,25 m dengan jarak inlet antara 50 m.

In silico Exploration of Interactions Between Potential COVID-19 Antiviral Treatments and the Pore of the hERG Potassium Channel—A Drug Antitarget

Background: In the absence of SARS-CoV-2 specific antiviral treatments, various repurposed pharmaceutical approaches are under investigation for the treatment of COVID-19. Antiviral drugs considered for this condition include atazanavir, remdesivir, lopinavir-ritonavir, and favipiravir. Whilst the combination of lopinavir and ritonavir has been previously linked to prolongation of the QTc interval on the ECG and risk of torsades de pointes arrhythmia, less is known in this regard about atazanavir, remdesivir, and favipiravir. Unwanted abnormalities of drug-induced QTc prolongation by diverse drugs are commonly mediated by a single cardiac anti-target, the hERG potassium channel. This computational modeling study was undertaken in order to explore the ability of these five drugs to interact with known determinants of drug binding to the hERG channel pore.Methods: Atazanavir, remdesivir, ritonavir, lopinavir and favipiravir were docked to in silico models of the pore domain of hERG, derived from cryo-EM structures of hERG and the closely related EAG channel.Results: Atazanavir was readily accommodated in the open hERG channel pore in proximity to the S6 Y652 and F656 residues, consistent with published experimental data implicating these aromatic residues in atazanavir binding to the channel. Lopinavir, ritonavir, and remdesivir were also accommodated in the open channel, making contacts in a model-dependent fashion with S6 aromatic residues and with residues at the base of the selectivity filter/pore helix. The ability of remdesivir (at 30 μM) to inhibit the channel was confirmed using patch-clamp recording. None of these four drugs could be accommodated in the closed channel structure. Favipiravir, a much smaller molecule, was able to fit within the closed channel and could adopt multiple binding poses in the open channel, but with few simultaneous interactions with key binding residues. Only favipiravir and remdesivir showed the potential to interact with lateral pockets below the selectivity filter of the channel.Conclusions: All the antiviral drugs studied here can, in principle, interact with components of the hERG potassium channel canonical binding site, but are likely to differ in their ability to access lateral binding pockets. Favipiravir's small size and relatively paucity of simultaneous interactions may confer reduced hERG liability compared to the other drugs. Experimental structure-function studies are now warranted to validate these observations.

Integrated Magnetohydrodynamic Pump with Magnetic Composite Substrate and Laser-Induced Graphene Electrodes

An integrated polymer-based magnetohydrodynamic (MHD) pump that can actuate saline fluids in closed-channel devices is presented. MHD pumps are attractive for lab-on-chip applications, due to their ability to provide high propulsive force without any moving parts. Unlike other MHD devices, a high level of integration is demonstrated by incorporating both laser-induced graphene (LIG) electrodes as well as a NdFeB magnetic-flux source in the NdFeB-polydimethylsiloxane permanent magnetic composite substrate. The effects of transferring the LIG film from polyimide to the magnetic composite substrate were studied. Operation of the integrated magneto hydrodynamic pump without disruptive bubbles was achieved. In the studied case, the pump produces a flow rate of 28.1 µL/min. while consuming ~1 mW power.

Architecture and structural dynamics of the heteromeric GluK2/K5 kainate receptor

Kainate receptors (KARs) are L-glutamate-gated ion channels that regulate synaptic transmission and modulate neuronal circuits. KARs have strict assembly rules and primarily function as heteromeric receptors in the brain. A longstanding question is how KAR heteromer subunits organize and coordinate together to fulfill their signature physiological roles. Here we report structures of the GluK2/GluK5 heteromer in apo, antagonist-bound, and desensitized states. The receptor assembles with two copies of each subunit, ligand binding domains arranged as two heterodimers, and GluK5 subunits proximal to the channel. Strikingly, during desensitization GluK2 but not GluK5 subunits undergo major structural rearrangements to facilitate channel closure. We show how the large conformational differences between antagonist-bound and desensitized states are mediated by the linkers connecting the pore helices to the ligand-binding domains. This work presents the first KAR heteromer structure, reveals how its subunits are organized, and resolves how the heteromer can accommodate functionally-distinct closed channel structures.

Structural basis of ClpXP recognition and unfolding of ssrA-tagged substrates

When ribosomes fail to complete normal translation, all cells have mechanisms to ensure degradation of the resulting partial proteins to safeguard proteome integrity. In Escherichia coli and other eubacteria, the tmRNA system rescues stalled ribosomes and adds an ssrA tag or degron to the C-terminus of the incomplete protein, which directs degradation by the AAA+ ClpXP protease. Here, we present cryo-EM structures of ClpXP bound to the ssrA degron. C-terminal residues of the ssrA degron initially bind in the top of an otherwise closed ClpX axial channel and subsequently move deeper into an open channel. For short-degron protein substrates, we show that unfolding can occur directly from the initial closed-channel complex. For longer degron substrates, our studies illuminate how ClpXP transitions from specific recognition into a nonspecific unfolding and translocation machine. Many AAA+ proteases and protein-remodeling motors are likely to employ similar multistep recognition and engagement strategies.

Pathways for nicotinic receptor desensitization

Nicotinic acetylcholine receptors (AChRs) are ligand-gated ion channels that generate transient currents by binding agonists and switching rapidly between closed- and open-channel conformations. Upon sustained exposure to ACh, the cell response diminishes slowly because of desensitization, a process that shuts the channel even with agonists still bound. In liganded receptors, the main desensitization pathway is from the open-channel conformation, but after agonists dissociate the main recovery pathway is to the closed-channel conformation. In this Viewpoint, I discuss two mechanisms that can explain the selection of different pathways, a question that has puzzled the community for 60 yr. The first is based on a discrete-state model (the “prism”), in which closed, open, and desensitized conformational states interconnect directly. This model predicts that 5% of unliganded AChRs are desensitized. Different pathways are taken with versus without agonists because ligands have different energy properties (φ values) at the transition states of the desensitization and recovery reactions. The second is a potential energy surface model (the “monkey saddle”), in which the states connect indirectly at a shared transition state region. Different pathways are taken because agonists shift the position of the gating transition state relative to the point where gating and desensitization conformational trajectories intersect. Understanding desensitization pathways appears to be a problem of kinetics rather than of thermodynamics. Other aspects of the two mechanisms are considered, as are experiments that may someday distinguish them.