Short Loop Research Articles

SARS-CoV-2 S protein harbors furin cleavage site located in a short loop between antiparallel β-strand

Furin cleavage site (FCS) of the SARS-CoV-2 S protein, which connects the S1/S2 junction, is essential for facilitating fusion with the host cells. Wild-type (Wt) SARS-CoV-2 S protein, PDB ID: 6yvb, lacks a sequence of amino acid residues, including the FCS that links the S1/S2 junction. For the first time, we demonstrated that a stretch of 14 amino acid residues (677QTNSPRRARSVASQ689) forms an antiparallel β-sheet comprising of PRRAR sequence in the FCS within a short loop. Upon comparing the loop content of the S1/S2 junction with that of Wt SARS-CoV-2 containing PRRAR in the FCS, we observed a decrease in antiparallel β-sheet content and an increase in loop content in the B.1.1.7 variant with HRRAR in the FCS. This short loop within antiparallel β-sheet can serve as a docking site for various proteases, including TMPRSS2 and α1AT. We performed a 300-ns simulation of the SARS-CoV-2 receptor binding domain (RBD) using several antibacterial and antiviral ligands commonly used to treat various infections. Our findings indicate that the receptor binding domain (RBD) comprising the receptor binding motif (RBM) utilizes β6 and a significant portion of the loop to bind with ligands, suggesting its potential for treating SARS-CoV-2 infections.

Unraveling the Membrane Topology of TMEM151A: A Step Towards Understanding its Cellular Role

Transmembrane protein 151A (TMEM151A) has been identified as a causative gene for paroxysmal kinesigenic dyskinesia, though its molecular function remains almost completely unknown. Understanding the membrane topology of transmembrane proteins is crucial for elucidating their functions and possible interacting partners. In this study, we utilized molecular dynamics simulations, immunocytochemistry, and electron microscopy to define the topology of TMEM151A. Our results validate a starting AlphaFold model of TMEM151A and reveal that it comprises a transmembrane domain with two membrane-spanning alpha helices connected by a short extracellular loop and an intramembrane helix-hinge-helix structure. Notably, most of the protein is oriented towards the intracellular side of the membranes with a large cytosolic domain featuring a combination of alpha-helix and beta-sheet structures, as well as the protein N- and C-termini. These insights into TMEM151A’s topology and orientation of its domains with respect of the cell membranes provide essential information for future functional studies and represent a first fundamental step for understanding its role in the pathogenesis of paroxysmal kinesigenic dyskinesia.

Diagnostics and surgical management children with superior mesenteric artery syndrome

BACKGROUND: Superior mesenteric artery syndrome causes chronic duodenal obstruction. Studies on this disease are limited; therefore, several difficulties in the diagnosis and treatment of such patients remain. AIM: This study aimed to present the experience of treating children with superior mesenteric artery syndrome. MATERIALS AND METHODS: The treatment results of 45 patients with superior mesenteric artery syndrome was retrospectively studied. The children complained of abdominal pain, nausea, occasional vomiting, belching, bloating, and constipation. The diagnosis was confirmed during a comprehensive examination, including ultrasound, esophagogastroduodenoscopy, X-ray contrast examination, computed tomography, and relaxation duodenography. Conservative therapy was performed in 38 (84,4%) children, and 21 (55,3%) children showed satisfactory results. In case of ineffectiveness of conservative measures (17 cases) or in a decompensated state (7 cases), indications for surgical treatment were provided. Furthermore, 24 (53,3%) children underwent surgery. Duodenal drainage surgeries were performed in 20 (83,3%) patients with subcompensation of duodenostasis. Of these patients, 10 (41,7%) underwent lower duodenojejunostomy with a switched-off Roux-en-Y loop (Gregory–Smirnov’s operation) and the other 10 (41,7%) underwent anterior mesenteric duodenojejunostomy (Robinson’s operation). Laparotomic access was used in 14 cases (70,0%) and laparoscopic in 6 (30,0%) cases. Owing to decompensation of duodenostasis, the duodenum was excluded from passage by economical resection of the gastric outlet with gastrojejunostomy on a short loop with additional formation of a lower duodenojejunostomy according to Roux in 4 (16,7%) cases. Laparotomic access was used in all cases. RESULTS: No intraoperative complications were noted. In the early postoperative period, two children developed anastomositis after Robinson’s operation and two patients after Gregory–Smirnov’s operation, which was treated with conservative measures. In long-term followup (up to 15 years), a satisfactory result was achieved in 87.5% of cases. CONCLUSIONS: Superior mesenteric artery syndrome is a relatively rare cause of chronic duodenal obstruction in children. When selecting patients for surgical treatment, other diseases should be excluded. Surgical correction includes various options for duodenal drainage operations that can be successfully performed using laparoscopic access. In case of decompensation of duodenostasis, it may be crucial to exclude the duodenum from the passage.

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

Functionality of chimeric TssA proteins in the type VI secretion system reveals sheath docking specificity within their N-terminal domains

The genome of Pseudomonas aeruginosa encodes three type VI secretion systems, each comprising a dozen distinct proteins, which deliver toxins upon T6SS sheath contraction. The least conserved T6SS component, TssA, has variations in size which influence domain organisation and structure. Here we show that the TssA Nt1 domain interacts directly with the sheath in a specific manner, while the C-terminus is essential for oligomerisation. We built chimeric TssA proteins by swapping C-termini and showed that these can be functional even when made of domains from different TssA sub-groups. Functional specificity requires the Nt1 domain, while the origin of the C-terminal domain is more permissive for T6SS function. We identify two regions in short TssA proteins, loop and hairpin, that contribute to sheath binding. We propose a docking mechanism of TssA proteins with the sheath, and a model for how sheath assembly is coordinated by TssA proteins from this position.

Abstract PO3-24-09: May ESR1 mutant breast cancer cells influence fibroblast phenotype?

Abstract For almost 50 years, it has been postulated that carcinogenesis relies on the intrinsic genetic abnormalities of tumor cells, but in the last decades, it has been reported that their functional interactions with the tumor microenvironment (TME) might affect therapy response and contribute to the disease progression. Based on these observations, the aim of the present study was to investigate the functional interactions between one of the essential components of TME, the fibroblasts, and breast cancer (BC) cells, expressing mutations in the hormone-binding domain (HBD) of the gene encoding for the estrogen receptor alpha (ESR1). Thus, we employed estrogen receptor-positive MCF-7 BC cells CRISPR engineered to express the Y537S-HBD mutation. Y537S is the most commonly detected mutation harbored in HBD-ESR1 and is a major contributor to endocrine therapy resistance and poor clinical outcome in BC. We collected conditioned media (CM) from BC cells and fibroblasts isolated from primary human tissues (normal fibroblasts, NFs, and cancer-associated fibroblasts, CAFs) in order to assess in vitro co-culture systems that can mimic the complex in vivo TME. It was interesting to observe that CAFs displayed a significant increase in their proliferation and migration when exposed to CM of mutant BC cells with respect to the parental ones. These latter findings fit with the immunofluorescence analysis showing a more evident formation of actin stress fibers. However, proteomic analysis demonstrated, in the same circumstances, more significant changes in NFs than in CAFs. Among the up-regulated proteins revealed by NFs upon Y537S-CM exposure, most of them overlap the up-regulated proteins featuring the intrinsic phenotype of CAFs, mainly involved in the cellular ultrastructural organization (i.e. cytoskeleton, focal adhesion, vesicle, and organelle) as evidenced by Metacore functional analysis. On the other side, we demonstrated that mutant clones showed more aggressive behavior in terms of proliferation, growth, migration, and invasion, compared to the parental counterpart upon exposure to the CM-derived from NFs and CAFs. This led us to further investigate the intrinsic properties of the mutated clones through their genomic and proteomic profiles that evidenced, by using Metacore software, an enrichment of insulin-like growth factor 1 receptor (IGF1R) pathway. The relevance of the latter datum was confirmed by the higher content of the IGF-1 ligand found in the secretome of mutant cells. Thus, the short autocrine loop maintaining IGF1/IGF1R signaling activation in mutant clones might reasonably play an important role in mediating the autocrine and paracrine effects between mutant cells and fibroblasts. For instance, the pharmacological blockade of IGF1R signaling interfered with the reciprocal interactions between fibroblasts and BC cells that sustained tumor growth and progression as evidenced in both “in vitro” and “in vivo” experiments. In conclusion, our study addressed the IGF1R pathway as a potential druggable target helpful to disconnect mutant breast cancer cell-fibroblast crosstalk that potentiates breast tumor growth and progression. Citation Format: Luca Gelsomino, Amanda Caruso, Rocco Malivindi, Adel Elisabetta Leonetti, Emine Tasan, Salvatore Panza, Giuseppina Daniela Naimo, Ines Barone, Cinzia Giordano, Daniela Bonofiglio, Loredana Mauro, Guowei Gu, Suzanne Fuqua, Stefania Catalano, Sebastiano Andò. May ESR1 mutant breast cancer cells influence fibroblast phenotype? [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-24-09.

A Family of Si and SiC Devices-Based Short Commutation Loop Hybrid-NPC Rectifiers

A Family of Si and SiC Devices-Based Short Commutation Loop Hybrid-NPC Rectifiers

Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions.

Quadruplex-duplex (QD) junctions, which represent unique structural motifs of both biological and technological significance, have been shown to constitute high-affinity binding sites for various ligands. A QD hybrid construct based on a human telomeric sequence, which harbors a duplex stem-loop in place of a short lateral loop, is structurally characterized by NMR. It folds into two major species with a (3+1) hybrid and a chair-type (2+2) antiparallel quadruplex domain coexisting in a K+ buffer solution. The antiparallel species is stabilized by an unusual capping structure involving a thymine and protonated adenine base AH+ of the lateral loop facing the hairpin duplex to form a T·AH+·G·C quartet with the interfacial G·C base pair at neutral pH. Addition and binding of Phen-DC3 to the QD hybrid mixture by its partial intercalation at corresponding QD junctions leads to a topological transition with exclusive formation of the (3+1) hybrid fold. In agreement with the available experimental data, such an unprecedented discrimination of QD junctions by a ligand can be rationalized following an induced fit mechanism.

Solvable models for 2+1D quantum critical points: Loop soups of 1+1D conformal field theories

We construct a class of solvable models for 2+1D quantum critical points by attaching 1+1D conformal field theories (CFTs) to fluctuating domain walls forming a “loop soup”. Specifically, our local Hamiltonian attaches gapless spin chains to the domain walls of a triangular lattice Ising antiferromagnet. The macroscopic degeneracy between antiferromagnetic configurations is split by the Casimir energy of each decorating CFT, which is usually negative and thus favors a short loop phase with a finite gap. However, we found a set of 1D CFT Hamiltonians for which the Casimir energy is effectively positive, making it favorable for domain walls to coalesce into a single “snake” which is macroscopically long and thus hosts a CFT with a vanishing gap. The snake configurations are geometrical objects also known as fully-packed self-avoiding walks or Hamiltonian walks which are described by an \mathrm{O}O(n=0) loop ensemble with a non-unitary 2+0D CFT description. Combining this description with the 1+1D decoration CFT, we obtain a 2+1D theory with unusual critical exponents and entanglement properties. Regarding the latter, we show that the log contributions from the decoration CFTs conspire with the spatial distribution of loops crossing the entanglement cut to generate a “non-local area law”. Our predictions are verified by Monte Carlo simulations.

Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions.

The main function of dUTPases is to regulate the cellular levels of dUTP and dTTP, thereby playing a crucial role in DNA repair mechanisms. Despite the fact that mutant organisms with obliterated dUTPase enzymatic activity remain viable, it is not possible to completely knock out the dut gene due to the lethal consequences of such a mutation for the organism. As a result, it is considered that this class of enzymes performs an additional function that is essential for the organism's survival. In this study, we provide evidence that the dUTPase of bacteriophage T5 fulfills a supplemental function, in addition to its canonical role. We determined the crystal structure of bacteriophage T5 dUTPase with a resolution of 2.0 Å, and we discovered a distinct short loop consisting of six amino acid residues, representing a unique structural feature specific to the T5-like phages dUTPases. The removal of this element did not affect the overall structure of the homotrimer, but it had significant effects on the development of the phage. Furthermore, it was shown that the enzymatic function and the novel function of the bacteriophage T5 dUTPase are unrelated and independent from each other.

(Invited) Designing Sustainable Battery Technologies

Sustainability in battery technologies needs to be considered from the outset, however sustainability means many things, and needs to be considered holistically from materials, manufacturing, life-time and recyclability. Three different aspects of sustainable considerations within lithium-ion and sodium-ion technology development are discussed; materials developments, cell lifetime and optimisations, and design for recycling.The cell is comprised of a nickel based layered oxide material cathode with hard carbon anode. To maximise energy density and life-time degradation of the bulk and surface of the O3-type oxides require stabilisation.1 We discuss the optimisation of a facile method for manufacturing a stabilised O3- type layered oxide via simultaneous doping and surface coating. A higher average voltage is obtained, which stabilised the high voltage phase transition to higher voltages, and results in longer-cycle life.2 To understand the sodium-ion cell in more detail, we have performed a detailed electrochemical analysis of a hard-carbon and layered oxide cathode and extracted parameters for multi-physics models. The kinetics and thermodynamics have been studied at different temperatures, and the limitations of the cell elucidated.Finally design for remanufacture is also discussed, utilising water-based binder systems we show differences in delamination and material recovery. Utilising different recycling schemes through shredding and physical processing through to disassembly processes improvements in recovery rates are required. Particularly for low value materials, where the techno-economics of the processes do not currently work. Direct recycling of materials reclaimed from the batteries, wherever possible allows value within the material design to be maintained, rather than relying directly upon elemental value. Aspects of direct loop recycling and short loop recycling are discussed with respect to current lithium-ion technologies, and the ability to directly translate this to sodium-ion.3 In conclusion three aspects for sustainability considerations are discussed with respect to the materials life-cycle; active material optimisation, longevity and life-time when in use and electrode developments for recycling.41 T. Song and E. Kendrick, J. Phys. Mater., 2021, 4, 32004.2 T. Song, L. Chen, D. Gastol, B. Dong, J. F. Marco, F. Berry, P. Slater, D. Reed and E. Kendrick, Chem. Mater., 2022, 34, 4153–4165.3 G. D. J. Harper, E. Kendrick, et al. J. Phys. Energy, 2023, 5, 021501.4 Picture created by DALL-E 2 algorithm with Nightcafe Figure 1

Reduction of fines in recycled paper white water via cellulase enzymes

Due to the high wastepaper recyclability and water-loop system closure, packaging paper mills struggle with increased fines, causing runnability issues. Cellulase enzymes are a preferred treatment choice for the improvement of the pulp refining in stock preparation area but are not widely used or easy to introduce in the production process. Different cellulase enzymes were tested, and those with the highest activity were introduced to the white-water (WW) samples with the aim to reduce fines content as potentially new enzyme applications on the paper machine. The first portion of the study involved the development of an experiment model to find and confirm the optimal enzyme process parameters (40 °C, pH 5.7, reaction time 3 h, and 0.18% v/v enzyme addition) for laboratory made white-water. The second portion of the study included turbidity, colloidal charge, flow cytometry (FCM), and chemical oxygen demand (COD) analysis on industrial and laboratory made white-water samples at optimized process parameters. Obtained results corresponded to reduced fines content in white-water samples, which justified commercial usage of cellulase enzymes on recycled paper machine short loop and potentially increased machine runnability without negative influence on wastewater treatment plant.

Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens.

Enzymes with expanded substrate specificity are good starting points for the design of biocatalysts for target reactions. However, the structural basis of the expanded substrate specificity is still elusive, especially in the superfamily of pyridoxal-5'-phosphate-dependent transaminases, which are characterized by a conserved organization of both the active site and functional dimer. Here, we analyze the structure-function relationships in a non-canonical D-amino acid transaminase from Blastococcus saxobsidens, which is active towards D-amino acids and primary (R)-amines. A detailed study of the enzyme includes a kinetic analysis of its substrate scope and a structural analysis of the holoenzyme and its complex with phenylhydrazine-a reversible inhibitor and analogue of (R)-1-phenylethylamine-a benchmark substrate of (R)-selective amine transaminases. We suggest that the features of the active site of transaminase from B. saxobsidens, such as the flexibility of the R34 and R96 residues, the lack of bulky residues in the β-turn at the entrance to the active site, and the short O-pocket loop, facilitate the binding of substrates with and without α-carboxylate groups. The proposed structural determinants of the expanded substrate specificity can be used for the design of transaminases for the stereoselective amination of keto compounds.

Advanced Process Monitoring Through Fault Detection and Classification for the Process Development of Tantalum Nitride Thin-Film Resistors

This paper discusses the optimization of an advanced process monitoring scheme with interdicting fault detection and classification (FDC) capabilities that improved the control over the process development of Tantalum Nitride thin film resistors (TaN TFR). Its implementation in a high-volume manufacturing environment resulted in a reduction of misprocessed wafers, shorter equipment downtime, higher throughput, enhanced process visibility, and yield improvement. Along with optimizing FDC capabilities, implementing a short loop sampling plan reduced the turnaround time for early electrical characterization by a factor of four; this allowed for timely inline adjustments within the fabrication process to tighten the statistical process control (SPC) over the distribution of the process control monitor (PCM) TaN resistor value and improve thin film uniformity.

Corticosteroid-induced chromatin loop dynamics at the FKBP5 gene.

FKBP5 is a 115-kb-long glucocorticoid-inducible gene implicated in psychiatric disorders. To investigate the complexities of chromatin interaction frequencies at the FKBP5 topologically associated domain (TAD), we deployed 15 one-to-all chromatin capture viewpoints near gene promoters, enhancers, introns, and CTCF-loop anchors. This revealed a "one-TAD-one-gene" structure encompassing the FKBP5 promoter and its enhancers. The FKBP5 promoter and its two glucocorticoid-stimulated enhancers roam the entire TAD while displaying subtle cell type-specific interactomes. The FKBP5 TAD consists of two nested CTCF loops that are coordinated by one CTCF site in the eighth intron of FKBP5 and another beyond its polyadenylation site, 61kb further. Loop extension correlates with transcription increases through the intronic CTCF site. This is efficiently compensated for, since the short loop is restored even under high transcription regimes. The boundaries of the FKBP5 TAD consist of divergent CTCF site patterns, harbor multiple smaller genes, and are resilient to glucocorticoid stimulation. Interestingly, both FKBP5 TAD boundaries harbor H3K27me3-marked heterochromatin blocks that may reinforce them. We propose that cis-acting genetic and epigenetic polymorphisms underlying FKBP5 expression variation are likely to reside within a 240-kb region that consists of the FKBP5 TAD, its left sub-TAD, and both its boundaries.

GraS signaling in Staphylococcus aureus is regulated by a single D35 residue in the extracellular loop.

Bacterial two-component systems are crucial features of bacterial pathogens such as methicillin-resistant Staphylococcus aureus to overcome environmental and antimicrobial stresses by activating regulons to interfere with the bactericidal mechanisms. GraRS is a unique subset of two-component systems belonging to the intramembrane-sensing histidine kinase family (IM-HK) and is responsible for resistance to cationic host defense peptides. However, the precise manner by which the short 9-residue extracellular loop of the membrane sensor GraS detects the antimicrobial peptides and transduces the signal is not comprehensively understood. Here, we show that a single point mutation (D35A) in the extracellular loop of GraS blocked activation of GraRS, but this effect was also abrogated with graS mutations in the N-terminal transmembrane segments without any accompanying effect on GraS protein expression. Additionally, mutations in H120 and T172 in the dimerization/histidine phosphotransfer (DHp) domain of GraS increased activation without any accompanying enhancement in dimerization, likely due to disruption of the H120-T172 interaction that restricts rotational movements of the DHp helices since swapping H120 and T172 did not alter GraS activation. Notably, the enhancing effects of H120 and T172 mutations were abolished with a D35 mutation, highlighting the pivotal role of D35 in the 9-residue extracellular loop of GraS in GraR phosphorylation. In summary, our study delivers the significance of the D35 in the extracellular loop of GraS and ensuing changes in the N-terminal transmembrane helices as a model to illustrate signaling in the IM-HK subset of two-component regulatory systems. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen capable of infecting skin, blood, internal organs, and artificial medical devices. Generally, personal hygiene and a robust immune system can limit the spread of this pathogen; however, MRSA possesses an assortment of phenotypic tools to survive the hostile host environment including host defense peptides. More specifically, S. aureus utilizes two-component systems to sense noxious environmental cues to respond to harmful environmental elements. Our study focused on a two-component system called GraRS that S. aureus deploys against host defense peptides. We showed that one single residue in the extracellular loop of GraS and the adjacent membrane segment controlled the activation of GraRS, indicating the importance of a well-tuned-charged residue in the extracellular loop of GraS for sensing activity.

Modeling of Transverse Oscillations Driven by p-modes in Short Coronal Loops

Recent observations have revealed two types of decayless transverse oscillations in short coronal loops: one with short periods scaling with loop lengths, and the other with longer periods that exhibit a peak at around 5 minutes in the period distribution. To understand such a difference in period, we work in the framework of ideal MHD and model a short coronal loop embedded in an atmosphere with density stratification from the chromosphere to the corona. An inclined p-mode-like driver with a period of 5 minutes is launched at one loop footpoint. It is discovered that two types of decayless transverse oscillations can be excited in the loop. We interpret the 5 minutes periodicity as being directly driven by the footpoint driver, while the others, with periods of several tens of seconds, are regarded as kink eigenmodes of different harmonics. Therefore, our simulation shows that both types of decayless oscillations found in observations can be excited by p-modes in one short coronal loop. This study extends our understanding of ubiquitous decayless transverse oscillations in the corona. Furthermore, it suggests that p-modes could be an important energy source for coronal heating by driving decayless transverse oscillations.

Multiple-Branch Optical Frequency Transfer Without the Frequency Allocation Constraints

We report on the realization of a multiple-branch optical frequency transfer method, which can be adopted to deliver an optical reference to multiple independent remote sites. In comparison with the previous techniques, the proposed technique mitigates the frequency allocation constraints of the driving frequencies for the acousto-optic modulators (AOMs) at the remote sites by adding a short loop fiber link at the local site. The end-to-end optical path phase noise detection and compensation for each remote site is simultaneously performed at the remote site, which significantly simplifies the configuration at the local site, and can improve the signal-to-noise ratio (SNR) and reduce the cycle slip rate. We also conduct theoretical analysis for the effect of frequency aliasing from the perspective of different refractive index in triple-pass optical frequency transfer, analyze the effect of the SNR and cycle slips on the fractional frequency instability, and present a comprehensive equation for calculating noise contributions from end-to-end optical frequency transfer over the multiple-branch fiber network, demonstrating that the implementation of the fiber noise cancellation (FNC) for the each branch consisting of two fiber topologies with the single FNC setup is practical. This technique paves the way to integrate the optical frequency networks into the existing fiber communication networks with the higher compatibility and reliability.

Structural insights into a bacterial β-glucosidase capable of degrading sesaminol triglucoside to produce sesaminol: toward the understanding of the aglycone recognition mechanism by the C-terminal lid domain.

The sesaminol triglucoside (STG)-hydrolyzing β-glucosidase from Paenibacillus sp. (PSTG1), which belongs to glycoside hydrolase family 3 (GH3), is a promising catalyst for the industrial production of sesaminol. We determined the X-ray crystal structure of PSTG1 with bound glycerol molecule in the putative active site. PSTG1 monomer contained typical three domains of GH3 with the active site in domain 1 (TIM barrel). In addition, PSTG1 contained an additional domain (domain 4) at the C-terminus that interacts with the active site of the other protomer as a lid in the dimer unit. Interestingly, the interface of domain 4 and the active site forms a hydrophobic cavity probably for recognizing the hydrophobic aglycone moiety of substrate. The short flexible loop region of TIM barrel was found to be approaching the interface of domain 4 and the active site. We found that n-heptyl-β-D-thioglucopyranoside detergent acts as an inhibitor for PSTG1. Thus, we propose that the recognition of hydrophobic aglycone moiety is important for PSTG1-catalyzed reactions. Domain 4 might be a potential target for elucidating the aglycone recognition mechanism of PSTG1 as well as for engineering PSTG1 to create a further excellent enzyme to degrade STG more efficiently to produce sesaminol.

Effect of plasma process on n-GaN surface probed with electrochemical short loop

Plasma etching treatments are important steps in GaN-based devices fabrication, but can create defects on GaN surfaces. These surface defects can strongly alter device performances. The main objective of this work is to characterize the impact of different plasma etching recipes using an innovative electrochemical short loop based on Mott-Schottky (MS) method. The effect of defects has been studied in terms of Fermi Level pinning. Barrier height has been identified as a relevant criteria to describe surface damage induced by plasma treatment. Probing Conventional LETI plasma etching process with the Mott-Schottky method demonstrates a good reproducibility of the electrochemical data and confirms the reliability of the developed method. Various electrochemical tests conducted on 3 plasmas recipes demonstrated that: 1) the RIE etching is damaging, 2) the optimized RIE (Steady A) is less damaging than the other RIE (Steady B) and 3) the RIE associated with ALE process shows the least damaging plasma recipe, as expected.