Gate Loop Research Articles

A Mechanistic Approach on Perception Mode of ABA Receptors (PYLs) to Novel Opabactin Analogues.

This study explored the structural mechanisms governing the binding of opabactin (OP) analogues 2-6 to abscisic acid (ABA) receptors by employing a combination of micro-scale thermophoresis (MST), phosphatase activity inhibition assays, and molecular dynamics simulations. The compounds 3-6 selectively activated PYR1, PYL2, and PYL6, while exhibiting minimal activity against PYL10, thus identifying them as selective ABA receptor agonists. Additionally, these analogues exerted a significant inhibitory effect on the phosphatase HAB1 upon binding to the receptors. The molecular dynamics simulations further elucidated the detailed binding interactions between various OP analogues and the ABA receptor PYR1, highlighting their role in inducing conformational changes within the receptor. Specifically, the study focused on the facilitation of the closure of the Gate and CL1 loops and the fine-tuning of the Latch loop to enhance the plasticity of the binding pocket, thereby influencing receptor-ligand interactions. The investigation emphasized the critical role of conserved water molecules in stabilizing the ligand-PYLs-PP2Cs complexes. Furthermore, free energy decomposition calculations demonstrated that the ligand's affinity was significantly affected by its ability to establish polar contacts between the polar groups within the ligand tail and the residues at the base of the binding pocket. This research lays a robust foundation for the development of novel ABA functional analogues with improved activity.

Structural insights into translocation and tailored synthesis of hyaluronan.

Hyaluronan (HA) is an essential component of the vertebrate extracellular matrix. It is a heteropolysaccharide of N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA) reaching several megadaltons in healthy tissues. HA is synthesized and translocated in a coupled reaction by HA synthase (HAS). Here, structural snapshots of HAS provide insights into HA biosynthesis, from substrate recognition to HA elongation and translocation. We monitor the extension of a GlcNAc primer with GlcA, reveal the coordination of the uridine diphosphate product by a conserved gating loop and capture the opening of a translocation channel to coordinate a translocating HA polymer. Furthermore, we identify channel-lining residues that modulate HA product lengths. Integrating structural and biochemical analyses suggests an avenue for polysaccharide engineering based on finely tuned enzymatic activity and HA coordination.

Molecular mechanism of β-arrestin-2 pre-activation by phosphatidylinositol 4,5-bisphosphate

Phosphorylated residues of G protein-coupled receptors bind to the N-domain of arrestin, resulting in the release of its C-terminus. This induces further allosteric conformational changes, such as polar core disruption, alteration of interdomain loops, and domain rotation, which transform arrestins into the receptor-activated state. It is widely accepted that arrestin activation occurs by conformational changes propagated from the N- to the C-domain. However, recent studies have revealed that binding of phosphatidylinositol 4,5-bisphosphate (PIP2) to the C-domain transforms arrestins into a pre-active state. Here, we aimed to elucidate the mechanisms underlying PIP2-induced arrestin pre-activation. We compare the conformational changes of β-arrestin-2 upon binding of PIP2 or phosphorylated C-tail peptide of vasopressin receptor type 2 using hydrogen/deuterium exchange mass spectrometry (HDX-MS). Introducing point mutations on the potential routes of the allosteric conformational changes and analyzing these mutant constructs with HDX-MS reveals that PIP2-binding at the C-domain affects the back loop, which destabilizes the gate loop and βXX to transform β-arrestin-2 into the pre-active state.

High-Speed and High-Temperature Switching Operations of a SiC Power MOSFET Using a SiC CMOS Gate Driver Installed inside a Power Module

In this study, the simultaneous realization of high-speed and high-temperature switching operations is demonstrated using a custom-made high-speed and high-temperature power module installed with a silicon carbide (SiC) CMOS gate driver, which can reduce gate loop inductance and operate at high temperatures. Approximate switching speeds of 70 and 60 V/ns are achieved during the turn-on and turn-off operations, respectively, at 300°C, 600 V DC bus voltage, and 20 A load current using the developed module. The switching speed remained above 50 V/ns in the temperature range from room temperature to 300°C. Numerical calculations based on the static properties of the SiC power MOSFET and CMOS gate driver can predict the actual switching properties over a wide temperature range when the developed module incorporating the fabricated SiC CMOS gate driver is used.

Mechanistic insights into lanthipeptide modification by a distinct subclass of LanKC enzyme that forms dimers

Naturally occurring lanthipeptides, peptides post-translationally modified by various enzymes, hold significant promise as antibiotics. Despite extensive biochemical and structural studies, the events preceding peptide modification remain poorly understood. Here, we identify a distinct subclass of lanthionine synthetase KC (LanKC) enzymes with distinct structural and functional characteristics. We show that PneKC, a member of this subclass, forms a dimer and possesses GTPase activity. Through three cryo-EM structures of PneKC, we illustrate different stages of peptide PneA binding, from initial recognition to full binding. Our structures show the kinase domain complexed with the PneA core peptide and GTPγS, a phosphate-bound lyase domain, and an unconventional cyclase domain. The leader peptide of PneA interact with a gate loop, transitioning from an extended to a helical conformation. We identify a dimerization hot spot and propose a “negative cooperativity” mechanism toggling the enzyme between tense and relaxed conformation. Additionally, we identify an important salt bridge in the cyclase domain, differing from those in in conventional cyclase domains. These residues are highly conserved in the LanKC subclass and are part of two signature motifs. These results unveil potential differences in lanthipeptide modification enzymes assembly and deepen our understanding of allostery in these multifunctional enzymes.

Coupling sensor to enzyme in the voltage sensing phosphatase

Voltage-sensing phosphatases (VSPs) dephosphorylate phosphoinositide (PIP) signaling lipids in response to membrane depolarization. VSPs possess an S4-containing voltage sensor domain (VSD), resembling that of voltage-gated cation channels, and a lipid phosphatase domain (PD). The mechanism by which voltage turns on enzyme activity is unclear. Structural analysis and modeling suggest several sites of VSD-PD interaction that could couple voltage sensing to catalysis. Voltage clamp fluorometry reveals voltage-driven rearrangements in three sites implicated earlier in enzyme activation—the VSD-PD linker, gating loop and R loop—as well as the N-terminal domain, which has not yet been explored. N-terminus mutations perturb both rearrangements in the other segments and enzyme activity. Our results provide a model for a dynamic assembly by which S4 controls the catalytic site.

Quantization Conductance of InSb Quantum-Well Two-Dimensional Electron Gas Using Novel Spilt Gate Structures

Electron transport behaviour in InSb semiconductor significantly changes when the conduction is restricted to two-dimensions. Semiconductor materials are an effective tools to characterize the electron transport in this aspect because the energy separation between transverse modes in a low-dimensional semiconductor device are always inversely proportional to the effective mass, in the same way as for sub-bands in a parabolic potential. Therefore, in this article, a range of novel device geometries were designed, fabricated and characterized to investigate ballistic transport of electrons in low-dimensional InSb structures using surface gated devices to restrict the degrees of freedom (dimensionality) of the active conducting channel. In this framework, designs of gates (i.e., line, loop and solid discussed later) have been used over a range of gate dimensions. Consistent measurement of quantised conductance would be promising for both low power electronics and low temperature transport physics where split gates are typically used for charge sensing. This article presents an experimental results of quantization conductance obtained for the range geometries of novel gates, and some model consideration of the implications of the material choice. Furthermore, the etching techniques (wet and dry) exhibited a significant decrease of ohmic contact resistance from around 35kΩ to only roughly 250Ω at room temperature. Interestingly a possible 0.7 anomaly conduction was observed with a loop gate structure. This work showed perfectly that the two-dimensional electron gases can be formed in narrow gap InSb QWs which makes this configuration device promising candidate for topological quantum computing and next generation integrated circuit applications. Keywords: Quantization conductance, InSb QW, 2DEG, spilt gate structure, ballistic transport.

Roles of the gate loop in β-arrestin-1 conformational dynamics and phosphorylated receptor interaction

Arrestins interact with phosphorylated G protein-coupled receptors (GPCRs) and regulate the homologous desensitization and internalization of GPCRs. The gate loop in arrestins is a critical region for both stabilization of the basal state and interaction with phosphorylated receptors. We investigated the roles of specific residues in the gate loop (K292, K294, and H295) using β-arrestin-1 and phosphorylated C-tail peptide of vasopressin receptor type 2 (V2Rpp) as a model system. We measured the binding affinity of V2Rpp and analyzed conformational dynamics of β-arrestin-1. Our results suggest that K294 plays a critical role in the interaction with V2Rpp without influencing the overall conformation of the V2Rpp-bound state. The residues K292 and H295 contribute to the stability of the polar core in the basal state and form a specific conformation of the finger loop in the V2Rpp-bound state.

Design of Half-Bridge Switching Power Module Based on Parallel-Connected SiC MOSFETs for LLC Resonant Converter with Symmetrical Structure and Low Parasitic Inductance

SiC MOSFETs are used in many power conversion applications because of their superior characteristics, such as fast switching speed, low on-resistance, and high operating temperature. In certain high-power systems, SiC MOSFETs are connected in parallel to enhance their current capacity and power efficiency. However, compared with Si-based devices, the current imbalance caused by the parasitic inductance difference becomes more severe when driving SiC MOSFETs in parallel, owing to the fast switching speed. Furthermore, the power loop inductance imbalance that occurs when constructing a half-bridge with parallel SiC MOSFETs has rarely been addressed in previous studies. In this study, a half-bridge switching power module based on parallel-connected SiC MOSFETs is proposed to solve the current imbalance through a symmetric structure of the gate and power loops. The effects of the magnitude and imbalance of the gate and power loop inductances in the half-bridge structure based on parallel-connected devices are also explained. A detailed printed circuit board layout of the proposed switching power module is provided, and the inductance symmetry is verified through simulations. A double-pulse test is conducted to verify the current-balancing capability of the proposed switching power module. In addition, an LLC resonant converter is designed using the proposed switching power module, and the power loss between parallel SiC MOSFETs is compared. The experimental results indicate the total power loss error between the parallel-connected SiC MOSFETs of the proposed power module is only 1.94%.

Pivotal role of S5 segment and S5–S6 luminal loop in the channel gating of type 1 ryanodine receptor (RyR1)

Pivotal role of S5 segment and S5–S6 luminal loop in the channel gating of type 1 ryanodine receptor (RyR1)

Construction of Big Data Information Security Protection System in Industrial Internet Environment

Abstract With the continuous development and integration of information technology and industrialization-related technologies, industrial Internet control system security attacks occur frequently, and it is more and more important to build an information security protection system. This study focuses on the research improvement from two aspects of access control and intrusion prevention and designs an industrial Internet security access control strategy based on the homomorphic encryption algorithm of the Hyper Elliptic Curve Cryptosystem (HCC) and the key splitting algorithm based on threshold. Meanwhile, the convolutional neural network, two-way gating loop unit, and multi-head attention mechanism are integrated to construct the CMAG intrusion detection model. The encryption algorithm and CMAG model are applied and analyzed. The encryption and decryption times of this paper’s algorithm are both relatively smooth, with an average time consumption of about 1.93ms and 0.46ms, respectively, and significantly better than other algorithms with the increase in the number of bits. The throughput of this paper’s encryption algorithm is 13.68 KB/s, which is approximately 2 times, 19 times, and 29 times higher than the throughput of GM, ElGamal, and Paillier algorithms, respectively. The other algorithms cannot match its throughput rate during decryption. The CMAG model has an accuracy of 99.14%, which is better than that of the other models, and its average checking accuracy, average recall, and average F1-Score are 0.9889, 0.9783, and 0.9834, respectively, which are 1.25%-5.16%, 4.31%-7.19%, and 3.32%, respectively, compared with that of the other three algorithms. 7.19% and 3.32%-6.76%, respectively. This paper is of great practical significance for the construction and optimization of a big data information security protection system in an industrial Internet environment.

Universality of critical active site glutamate as an acid-base catalyst in serine hydroxymethyltransferase function.

Serine hydroxymethyltransferase (SHMT) is a key enzyme in the one-carbon metabolic pathway, utilizing the vitamin B6 derivative pyridoxal 5'-phosphate (PLP) and vitamin B9 derivative tetrahydrofolate (THF) coenzymes to produce essential biomolecules. Many types of cancer utilize SHMT in metabolic reprogramming, exposing the enzyme as a compelling target for antimetabolite chemotherapies. In pursuit of elucidating the catalytic mechanism of SHMT to aid in the design of SHMT-specific inhibitors, we have used room-temperature neutron crystallography to directly determine the protonation states in a model enzyme Thermus thermophilus SHMT (TthSHMT), which exhibits a conserved active site compared to human mitochondrial SHMT2 (hSHMT2). Here we report the analysis of TthSHMT, with PLP in the internal aldimine form and bound THF-analog, folinic acid (FA), by neutron crystallography to reveal H atom positions in the active site, including PLP and FA. We observed protonated catalytic Glu53 revealing its ability to change protonation state upon FA binding. Furthermore, we obtained X-ray structures of TthSHMT-Gly/FA, TthSHMT-l-Ser/FA, and hSHMT2-Gly/FA ternary complexes with the PLP-Gly or PLP-l-Ser external aldimines to analyze the active site configuration upon PLP reaction with an amino acid substrate and FA binding. Accurate mapping of the active site protonation states together with the structural information gained from the ternary complexes allow us to suggest an essential role of the gating loop conformational changes in the SHMT function and to propose Glu53 as the universal acid-base catalyst in both THF-independent and THF-dependent activities of SHMT.

Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae.

Halo blight is a plant disease that leads to a significant decrease in the yield of common bean crops and kiwi fruits. The infection is caused by Pseudomonas syringae pathovars that produce phaseolotoxin, an antimetabolite which targets arginine metabolism, particularly by inhibition of ornithine transcarbamylase (OTC). OTC is responsible for production of citrulline from ornithine and carbamoyl phosphate. Here we present the first crystal structures of the plant OTC from Arabidopsis thaliana (AtOTC). Structural analysis of AtOTC complexed with ornithine and carbamoyl phosphate reveals that OTC undergoes a significant structural transition when ornithine enters the active site, from the opened to the closed state. In this study we discuss the mode of OTC inhibition by phaseolotoxin, which seems to be able to act only on the fully opened active site. Once the toxin is proteolytically cleaved, it mimics the reaction transition state analogue to fit inside the fully closed active site of OTC. Additionally, we indicate the differences around the gate loop region which rationally explain the resistance of some bacterial OTCs to phaseolotoxin.

Gate Voltage Oscillation Model and Suppression Method for Enhancement‐Mode GaN Devices in Half‐Bridge Circuits

This article analyzes the issue of gate voltage oscillations in AlGaN/GaN high electron mobility transistors based on the half‐bridge circuit. With the influence of the parasitic parameters, the variation of high drain‐source voltage (Vds) can affect the gate‐source voltage (Vgs), thus resulting in serious gate voltage oscillations, which may cause over‐voltage, false turn‐on/off, and even gate breakdown. A large‐signal model is proposed to study this oscillations phenomenon. The oscillation model of Vgs is proposed as a step response of Vds. Based on the model, the influence of Vds and circuit parameters on Vgs are investigated, and guidelines to suppress the oscillation are given. Reducing the gate and power loop inductance in PCB wiring and increasing the gate resistance of inactive switch can significantly suppress the oscillation. Finally, the model is verified by both simulation results and experimental results.

Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8

Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate- and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loopwith the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation.

A Review of High-Speed GaN Power Modules: State of the Art, Challenges, and Solutions

Wide bandgap (WBG) devices are a desirable choice for high-density energy conversion systems. In high-speed hard-switching applications, voltage overshoot across device terminals, oscillations at gate loop and Electro-magnetic Interference (EMI) becomes harder to mitigate and overall system reliability is reduced. To address the key challenges and harness the benefits offered by these latest generations of devices, improved and advanced packaging structures are required, as packaging technology often has a critical impact on module performance and reliability. This paper summarizes the design procedure for power modules, essential parts, and available materials for the fabrication of a power module package. Moreover, it provides a review of commercially available gallium nitride based high electron mobility transistors (GaN HEMTs) and state-of-the-art module packaging technologies adopted for them with a focus on module layout, module integration trends, and identifying their impacts on the GaN HEMT’s performance. Through this review, the paper also discusses major challenges faced by designers with GaN HEMTs in power electronics applications and their potential solutions, which is critical for the mainstream adoptions of GaN HEMTs and defining the future technology roadmap.

Ferrite Beads Design to Improve Turn-Off Characteristics of Cascode GaN HEMTs: An Optimum Design Method

In this paper, an optimum ferrite beads design method is proposed to suppress the self-sustained turn-off oscillation of cascode gallium nitride high-electron-mobility transistors (GaN HEMTs). At first, the impacts of gate loop beads and power loop beads on the turn-off oscillation of cascode GaN HEMTs are analyzed. The analysis reveals the weak damping effect of gate loop beads on the turn-off oscillation. Next, an analytical method is proposed to design the power loop beads that can achieve maximum effective damping on the turn-off oscillation. The power loop beads introduce extra stray inductance in the power loop, which can induce high voltage overshoot. To tackle the problem, an optimum design method is proposed so that the power loop beads can suppress the oscillation while mitigating the voltage overshoot. The accuracy of the proposed model is validated by the experimental data in the end.

Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis

Transcriptional pauses mediate regulation of RNA biogenesis. DNA-encoded pause signals trigger pausing by stabilizing RNA polymerase (RNAP) swiveling and inhibiting DNA translocation. The N-terminal domain (NGN) of the only universal transcription factor, NusG/Spt5, modulates pausing through contacts to RNAP and DNA. Pro-pausing NusGs enhance pauses, whereas anti-pausing NusGs suppress pauses. Little is known about pausing and NusG in the human pathogen Mycobacterium tuberculosis (Mtb). We report that MtbNusG is pro-pausing. MtbNusG captures paused, swiveled RNAP by contacts to the RNAP protrusion and nontemplate-DNA wedged between the NGN and RNAP gate loop. In contrast, anti-pausing Escherichia coli (Eco) NGN contacts the MtbRNAP gate loop, inhibiting swiveling and pausing. Using CRISPR-mediated genetics, we show that pro-pausing NGN is required for mycobacterial fitness. Our results define an essential function of mycobacterial NusG and the structural basis of pro- versus anti-pausing NusG activity, with broad implications for the function of all NusG orthologs.

Ketosynthase mutants enable short-chain fatty acid biosynthesis in E. coli

Cells build fatty acids in tightly regulated assembly lines, or fatty acid synthases (FASs), in which β-ketoacyl-acyl carrier protein (ACP) synthases (KSs) catalyze sequential carbon-carbon bond forming reactions that generate acyl-ACPs of varying lengths—precursors for a diverse set of lipids and oleochemicals. To date, most efforts to control fatty acid synthesis in engineered microbes have focused on modifying termination enzymes such as acyl-ACP thioesterases, which release free fatty acids from acyl-ACPs. Changes to the substrate specificity of KSs provide an alternative—and, perhaps, more generalizable—approach that focuses on controlling the acyl-ACPs available for downstream products. This study combines mutants of FabF and FabB, the two elongating KSs of the E. coli FAS, with in vitro and in vivo analyses to explore the use of KS mutants to control fatty acid synthesis. In vitro, single amino acid substitutions in the gating loop and acyl binding pocket of FabF shifted the product profiles of reconstituted FASs toward short chains and showed that KS mutants, alone, can cause large shifts in average length (i.e., 6.5–13.5). FabB, which is essential for unsaturated fatty acid synthesis, blunted this effect in vivo, but exogenously added cis-vaccenic acid (C18:1) enabled sufficient transcriptional repression of FabB to restore it. Strikingly, a single mutant of FabB afforded titers of octanoic acid as high as those generated by an engineered thioesterase. Findings indicate that fatty acid synthesis must be decoupled from microbial growth to resolve the influence of KS mutants on fatty acid profiles but show that these mutants offer a versatile approach for tuning FAS outputs.

Quasi Markov state models elucidates the role of bacterial RNA polymerase loading gate and trigger loop dynamics in antibiotics inhibition.

The rise of antibiotic resistance urges the development of new antibiotics. Bacterial RNA Polymerase (RNAP) transcribes DNA to RNA and is an effective target for antibiotics. RNAP has a crab-claw-like shape with two pincers, clamp and β-lobe domains, forming a loading gate. During the initiation of transcription,the opening of the loading gate is necessary to load the template DNA. Myx is an antibiotic that binds to the switch 2 region, under the clamp, to prevent clamp closing/opening and inhibit transcription initiation. To study the inhibition mechanism of Myx in atomic resolution, we built quasi-Markov State Models (qMSM) based on extensive molecular dynamics (MD) simulations. qMSM can obtain the slow timescale dynamics of complex conformational change using shorter MD simulations compared to traditional MSM. qMSM identifies four states of clamp opening: closed, two partially closed, and open states. We have shown that the opening of the Myx binding site only occurs in a partially closed state, which allows binding of Myx. This suggests that Myx selectively binds to a partially closed state and follows the conformational selection mechanism. Notably, we find that β-lobe opening is sufficient for loading of DNA during transcription initiation. This highlights the critical role of β-lobe to initiate transcription and β-lobe's potential as a target for future antibiotics development. We also utilize qMSMto study the folding of the trigger loop (TL) of RNAP. During RNA elongation, TL closes/folds to stabilize the NTP substrate in the active site for catalysis. CBR is antibiotics that inhibit the folding of TL. Studying the molecular mechanism of TL folding will be useful to understand the inhibition mechanism of antibiotics, CBR, and future drug design targeting TL.