Fourth Loop Research Articles

On β-function of N = 2 supersymmetric integrable sigma-models

We study the regularization scheme dependence of Kähler (N = 2) supersymmetric sigma models. At the one-loop order the metric β function is the same as in the non-supersymmetric case and it coincides with the Ricci tensor. The first correction in the MS scheme is known to appear in the fourth loop [1, 2]. We show that for certain integrable Kähler backgrounds, such as the complete T-dual of η-deformed CPn\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ \\mathbbm{CP}(n) $$\\end{document} sigma models, there is a scheme in which the fourth loop contribution vanishes.

MYADM binds human parechovirus 1 and is essential for viral entry

Human parechoviruses (PeV-A) are increasingly being recognized as a cause of infection in neonates and young infants, leading to a spectrum of clinical manifestations ranging from mild gastrointestinal and respiratory illnesses to severe sepsis and meningitis. However, the host factors required for parechovirus entry and infection remain poorly characterized. Here, using genome-wide CRISPR/Cas9 loss-of-function screens, we identify myeloid-associated differentiation marker (MYADM) as a host factor essential for the entry of several human parechovirus genotypes including PeV-A1, PeV-A2 and PeV-A3. Genetic knockout of MYADM confers resistance to PeV-A infection in cell lines and in human gastrointestinal epithelial organoids. Using immunoprecipitation, we show that MYADM binds to PeV-A1 particles via its fourth extracellular loop, and we identify critical amino acid residues within the loop that mediate binding and infection. The demonstrated interaction between MYADM and PeV-A1, and its importance specifically for viral entry, suggest that MYADM is a virus receptor. Knockout of MYADM does not reduce PeV-A1 attachment to cells pointing to a role at the post-attachment stage. Our study suggests that MYADM is a multi-genotype receptor for human parechoviruses with potential as an antiviral target to combat disease associated with emerging parechoviruses.

CRISPR/Cas9 bioluminescence-based assay for monitoring CFTR trafficking to the plasma membrane.

CFTR is a membrane protein that functions as an ion channel. Mutations that disrupt its biosynthesis, trafficking or function cause cystic fibrosis (CF). Here, we present a novel in vitro model system prepared using CRISPR/Cas9 genome editing with endogenously expressed WT-CFTR tagged with a HiBiT peptide. To enable the detection of CFTR in the plasma membrane of live cells, we inserted the HiBiT tag in the fourth extracellular loop of WT-CFTR. The 11-amino acid HiBiT tag binds with high affinity to a large inactive subunit (LgBiT), generating a reporter luciferase with bright luminescence. Nine homozygous clones with the HiBiT knock-in were identified from the 182 screened clones; two were genetically and functionally validated. In summary, this work describes the preparation and validation of a novel reporter cell line with the potential to be used as an ultimate building block for developing unique cellular CF models by CRISPR-mediated insertion of CF-causing mutations.

EPS3.10 Novel CFTR modulator combinations directly address the ΔF508-CFTR NBD1 stability defect and enable full CFTR correction

Objectives: CFTR mutations cause Cystic Fibrosis (CF). CFTR modulating drugs have improved CF outcomes, however, current drugs do not restore normal CFTR function to most patients. ΔF508, the most prevalent CF mutation, causes a loss of F508 within CFTR’s first Nucleotide Binding Domain (NBD1). This destabilizes NBD1 and impairs CFTR folding and function. ΔF508 also impairs CFTR domain-domain assembly, weakening the interface of NBD1 with CFTR’s fourth intracellular loop (ICL4) and transmembrane domain 1 (TMD1). Combining CFTR suppressor mutations that stabilize NBD1 with others that improve CFTR assembly can correct ΔF508 to wild-type (WT) levels. Without NBD1 stabilization, correction is significantly reduced. Drugs that stabilize NBD1 thus have the potential to improve treatment, but no current drugs fully address this defect. To restore WT function to ΔF508-CFTR, Sionna aims to discover and develop small molecule NBD1 stabilizers and CFTR assembly correctors for use in combination.

G1 Cell Cycle Arrest Is Induced by the Fourth Extracellular Loop of Meningococcal PorA in Epithelial and Endothelial Cells

Neisseria meningitidis is the most frequent cause of bacterial meningitis and is one of the few bacterial pathogens that can breach the blood-brain barrier (BBB). The 37/67 kDa laminin receptor (LamR) was previously identified as a receptor mediating meningococcal binding to rodent and human brain microvascular endothelial cells, which form part of the BBB. The meningococcal surface proteins PorA and PilQ were identified as ligands for this receptor. Subsequently, the fourth extracellular loop of PorA (PorA-Loop4) was identified as the LamR-binding moiety. Here, we show that PorA-Loop4 targets the 37 kDa laminin receptor precursor (37LRP) on the cell surface by demonstrating that deletion of this loop abrogates the recruitment of 37LRP under meningococcal colonies. Using a circularized peptide corresponding to PorA-Loop4, as well as defined meningococcal mutants, we demonstrate that host cell interaction with PorA-Loop4 results in perturbation of p-CDK4 and Cyclin D1. These changes in cell cycle control proteins are coincident with cellular responses including inhibition of cell migration and a G1 cell cycle arrest. Modulation of the cell cycle of host cells is likely to contribute to the pathogenesis of meningococcal disease.

Structure–Function Analysis of a Quinone-Dependent Dehydrogenase Capable of Deoxynivalenol Detoxification

The pyrroloquinoline quinone (PQQ)-dependent dehydrogenase DepA detoxifies deoxynivalenol (DON) by converting the C3-OH into a keto group. Herein, two crystal structures of DepA and its complex with PQQ were determined, together with biochemical evidence confirming the interactions of DepA with PQQ and DON and revealing a unique tyrosine residue important for substrate selection. Furthermore, four loops over the active site essential for DepA activity were identified, of which three loops were stabilized by PQQ, and the fourth loop invisible in both structures was considered important for binding DON, together constituting a lid for the active site. Preliminary engineering of the loop showed its potential for enzyme improvement. This study provides structural insights into how a PQQ-dependent dehydrogenase is equipped with the function of DON conversion and for the first time shows the necessity of a lid structure for PQQ-dependent dehydrogenase activity, laying foundation for structure-based design to enhance catalysis efficiency.

A purine and a backbone discontinuous site alter the structure and thermal stability of DNA minidumbbells containing two pentaloops.

Minidumbbell (MDB) is a noncanonical DNA structure found to form in several pyrimidine-rich short tandem repeats associated with neurodegenerative diseases. The most recently reported MDB contains two pentaloops formed by ATTCT repeats. Here, we studied the effects of a purine residue and a backbone discontinuous site on the structure and thermal stability of MDBs containing two pentaloops. It was found that a purine as the fourth loop residue improved the thermal stability of MDBs containing two regular pentaloops, while a backbone discontinuous site between the third and fourth, or between the fourth and fifth loop residues enhanced the thermal stability of MDBs containing a regular and a quasi pentaloops. The results of this study provide new insights into the sequence criteria and structural basis of MDBs.

NMR solution structures of d(GGCCTG)n repeats associated with spinocerebellar ataxia type 36

Expansion of d(GGCCTG)n hexanucleotide repeats in the NOP56 gene is the genetic cause of spinocerebellar ataxia type 36 (SCA36) which is an inheritable neurodegenerative disease. Non-B DNA is known to be the structural intermediate causing repeat expansions. Yet, the structure and mechanism of genetic instability of d(GGCCTG)n repeats remain elusive. In this work, we investigated the solution structures of sequences containing two to eight GGCCTG repeats using nuclear magnetic resonance (NMR) spectroscopy. They were found to form diverse secondary structures, including hairpin, duplex and G-quadruplex (G4). Intriguingly, the hairpin structure was present in all the investigated sequences. The NMR solution structure of the hairpin formed by d(GGCCTG)2 was determined, disclosing an unprecedented CCTGGG hexanucleotide loop in which the first and sixth loop residues formed a Watson-Crick loop-closing base pair, the second and third loop residues stacked in the major groove, whereas the fourth and fifth loop residues formed a G·G mismatch. Apart from the hairpin, antiparallel G4 and palindromic duplex structures were found to form in d(GGCCTG)2 and d(GGCCTG)3–8, respectively. Results of this work provide new insights into the genetic instability of d(GGCCTG)n repeats and structure-based drug design for SCA36.

Small Molecule Receptor Binding Inhibitors with In Vivo Efficacy against Botulinum Neurotoxin Serotypes A and E.

Botulinum neurotoxins (BoNTs) are the most poisonous substances in nature. Currently, the only therapy for botulism is antitoxin. This therapy suffers from several limitations and hence new therapeutic strategies are desired. One of the limitations in discovering BoNT inhibitors is the absence of an in vitro assay that correlates with toxin neutralization in vivo. In this work, a high-throughput screening assay for receptor-binding inhibitors against BoNT/A was developed. The assay is composed of two chimeric proteins: a receptor-simulating protein, consisting of the fourth luminal loop of synaptic vesicle protein 2C fused to glutathione-S-transferase, and a toxin-simulating protein, consisting of the receptor-binding domain of BoNT/A fused to beta-galactosidase. The assay was applied to screen the LOPAC1280 compound library. Seven selected compounds were evaluated in mice exposed to a lethal dose of BoNT/A. The compound aurintricarboxylic acid (ATA) conferred 92% protection, whereas significant delayed time to death (p < 0.005) was observed for three additional compounds. Remarkably, ATA was also fully protective in mice challenged with a lethal dose of BoNT/E, which also uses the SV2 receptor. This study demonstrates that receptor-binding inhibitors have the potential to serve as next generation therapeutics for botulism, and therefore the assay developed may facilitate discovery of new anti-BoNT countermeasures.

Effects of Original Compounds GSB-106, GML-3, and GZK-111 in an Experimental Lipopolysaccharide-Induced Anhedonia Model

Antidepressant activities of the original compounds GSB-106 [bis(N-monosuccinyl-L-seryl-L-lysine) hexamethylenediamide], a mimetic of the fourth loop of brain-derived neurotrophic factor (BDNF); GML-3(N-butyl-N-methyl-1-phenylpyrrolo[1,2-a]pyrazine-3-carboxamide), a ligand of 18 kDa translocator protein (TSPO); and GZK-111 (N-phenylacetylglycyl-L-proline ethyl ester), a substitute dipeptide that is biotransformed into the neuropeptide cyclo-L-prolylglycine that affects AMPA receptors; were previously revealed at V. V. Zakusov Institute of Pharmacology in experimental models of the depressive state caused by unescapable stress conditions. The present article studied the antidepressant effects of GSB-106, GML-3, and GZK-111 in an inflammatory model of the depressive state induced by lipopolysaccharide (LPS) in male C57Bl/6 mice with an assessment of anhedonia based on the consumption of sucrose solution. LPS in a single dose of 0.5 mg/kg intraperitoneally (i.p.) caused a marked decrease of 39% (p ≤ 0.01) in the consumption of 1% sucrose solution as compared to the control group. GSB-106 administered perorally at a dose of 0.5 mg/kg 24 h after LPS increased by 20% (p ≤ 0.05) sucrose consumption reduced by LPS in mice. GML-3 administered once perorally at doses of 0.5 and 1.0 mg/kg increased sucrose consumption by 29 and 21% (p ≤ 0.01), respectively. GZK-111 administered once i.p. at a dose of 1.0 mg/kg increased sucrose consumption by 17% (p ≤ 0.05). The obtained data confirmed the antidepressant properties of GSB-106, GML-3, and GZK-111.

A case study of thermal analysis of a solar assisted absorption air-conditioning system using R-410A for domestic applications

Sustainable future and green environment goals quest for the development of technologies to utilize renewable energy resources to power the people. This study focuses on the designing, modelling, and simulation of an absorption solar air-conditioning system. Key performance parameters are identified, optimized for maximum efficiency and simulated in transient energy simulation software TRNSYS ®. The designed model comprises five thermal loops: a solar loop consisting of an evacuated glass tube solar collector having R-410A as heat transfer fluid in it and a heat exchanger heat tank, second loop has an absorption chiller, and an auxiliary furnace with hot water stream, third is the cooling tower loop, the fourth loop is of chilled water from the chiller and the final thermal loop is for air delivery of cooling to each room. The system is simulated using Lahore, Pakistan's climate conditions and offered a good tendency for the proposed system to meet air-conditioning demand at the domestic level. The average collector outlet temperature value of 78 °C has been recorded throughout the week. Collector provides useful energy gain at an average rate of 71,065 kJ/h. Average storage tank temperature at the outlet of heat exchanger is 92°C. Average room temperature values of three rooms are 27°C, 30°C and 19°C respectively.

New insights into structure and function of bis-phosphinic acid derivatives and implications for CFTR modulation

C407 is a compound that corrects the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein carrying the p.Phe508del (F508del) mutation. We investigated the corrector effect of c407 and its derivatives on F508del-CFTR protein. Molecular docking and dynamics simulations combined with site-directed mutagenesis suggested that c407 stabilizes the F508del-Nucleotide Binding Domain 1 (NBD1) during the co-translational folding process by occupying the position of the p.Phe1068 side chain located at the fourth intracellular loop (ICL4). After CFTR domains assembly, c407 occupies the position of the missing p.Phe508 side chain. C407 alone or in combination with the F508del-CFTR corrector VX-809, increased CFTR activity in cell lines but not in primary respiratory cells carrying the F508del mutation. A structure-based approach resulted in the synthesis of an extended c407 analog G1, designed to improve the interaction with ICL4. G1 significantly increased CFTR activity and response to VX-809 in primary nasal cells of F508del homozygous patients. Our data demonstrate that in-silico optimized c407 derivative G1 acts by a mechanism different from the reference VX-809 corrector and provide insights into its possible molecular mode of action. These results pave the way for novel strategies aiming to optimize the flawed ICL4–NBD1 interface.

Design and Synthesis of Dipeptide Nerve Growth Factor Loop 1 Mimetics and In Vitro Studies of their Neuroprotective and Differentiation-Inducing Activities

Previous studies at the V. V. Zakusov Science Research Institute of Pharmacology created a dimeric dipeptide mimetic of the most exposed fourth loop of nerve growth factor (NGF), bis-(N-monosuccinyl-L-glutamyl-Llysine) hexamethylenediamide (GK-2), which activates specific TrkA receptors and has neuroprotective activity in vitro (at 105 to 109 M) and in vivo (0.1 – 10 mg/kg, i.p., or p.o.). The present report describes the construction and synthesis of a mimetic of the first loop of NGF based on the β-turn (-Lys32-Gly33-Lys34-Glu35-), bis-(N-aminocaproyl-glycyl-L-lysine) hexamethylenediamide (GK-6). The structure of GK-6 preserves the central dipeptide fragment of the β-turn -Gly33-Lys34-, the Lys32 residue being substituted by its bioisostere – a 6-aminocaproic acid residue - and the dimeric structure of NGF being reproduced by dimerization at the C-terminal using a bivalent hexamethylenediamine spacer. Structure-activity relationships of GK-6 were studied by sequential substitution of the side groups of the peptide by hydrogen to produce bis-(N-acetyl-glycyl-Llysine) hexamethylenediamide (GTS-611) and bis-(N-aminocaproyl-glycyl-glycine) hexamethylenediamine (GTS-613). Mimetic GL-6 and its analogs GTS-613, which contains the N-aminocaproyl radical, had neuroprotective effects at concentrations of 106 and 105M in conditions of oxidative stress in HT-22 neuron cultures. Dipeptide GTS-611, in which the aminocaproyl fragment was replaced by an acetyl residue, had no neuroprotective activity in these conditions, pointing to the importance of Lys32 in NGF for this property. In contrast to the loop 4 mimetic GK-2, the loop 1 mimetics GK-6 and GTS-611 showed differentiation-inducing activity on PC12 cells.

Entre golpes brandos e rígidos: uma análise crítica do livro Guerras hibridas, de Andrew Koybko

The aim of this essay is to present a critical analysis of Andrew Korybko's approach on “hybrid warfare”. Initially we will introduce the concept as established by Korybko in his book entitled Hybrid wars: the indirect adaptive approach to regime change. Other concepts he used will be analyzed and articulated, such as indirect approach (Liddel Hart), fourth generation warfare (William Lind), five rings (John Warden), OODA loop (John Boyd and Robert Greene) and chaos theory (Steve Mann), among others. The article will present Korybko’s view, whereby hybrid warfare is composed by two distinct tactics, colour revolution/soft coup and unconventional warfare/hard coup, being a geopolitical strategy currently used by the government of the United States of America to destabilize governments not aligned with American interests. Finally, we will present a critical analysis of Korybko's approach to the theme and concepts.

Screening study of nerve growth factor's and brain-derived neurotrophic factor's mimetics effects at the experimental depression model

At the Zakusov Institute of Pharmacology designed and synthesized dimeric dipeptide mimetics of the 1st (GK-6) and 4th (GK-2) nerve growth factor loops, 1st (GSB-214), 2nd (GTS-201) and 4th (GSB -106, GSB-106Ac) brain-derived neurotrophic factor loops. Antidepressant activity of GSB-106 has already been established by oral and intraperitoneal administration in 0.1-5.0 mg/kg doses. Newly synthesized mimetics were studied in comparison with GSB-106 for antidepressant-like activity in the forced swim test on male Balb/c mice with a single intraperitoneal administration. It was found that only mimetic of the fourth brain-derived neurotrophic factor loop GSB-106Ac, varied from GSB-106 by replace monosuccinyl fragment to acetyl, has antidepressant activity in doses of 1.0 mg / kg and 5.0 mg / kg.

PH dependence of the Slc4a11-mediated H+ conductance is influenced by intracellular lysine residues and modified by disease-linked mutations.

SLC4A11 is the only member of the SLC4 family that transports protons rather than bicarbonate. SLC4A11 is expressed in corneal endothelial cells, and its mutation causes corneal endothelial dystrophy, although the mechanism of pathogenesis is unknown. We previously demonstrated that the magnitude of the H+ conductance (Gm) mediated by SLC4A11 is increased by rises in intracellular as well as extracellular pH (pHi and pHe). To better understand this feature and whether it is altered in disease, we studied the pH dependence of wild-type and mutant mouse Slc4a11 expressed in Xenopus oocytes. Using voltage-clamp circuitry in conjunction with a H+-selective microelectrode and a microinjector loaded with NaHCO3, we caused incremental rises in oocyte pHi and measured the effect on Gm. We find that the rise of Gm has a steeper pHi dependence at pHe =8.50 than at pHe =7.50. Data gathered at pHe =8.50 can be fit to the Hill equation enabling the calculation of a pK value that reports pHi dependence. We find that mutation of lysine residues that are close to the first transmembrane span (TM1) causes an alkaline shift in pK. Furthermore, two corneal-dystrophy-causing mutations close to the extracellular end of TM1, E399K and T401K (E368K and T370K in mouse), cause an acidic shift in pK, while a third mutation in the fourth intracellular loop, R804H (R774H in mouse), causes an alkaline shift in pK. This is the first description of determinants of SLC4A11 pH dependence and the first indication that a shift in pH dependence could modify disease expressivity in some cases of corneal dystrophy.

DEVELOPMENT AND VALIDATION OF THE TECHNIQUE DEFINITION OF THE INDICATOR «RESIDUAL ORGANIC SOLVENTS» IN SUBSTANCE GSB-106

The technique of identification and quantitative determination definition of residual organic solvents in the original substance synthesized in FSBSI «Research Institute of Pharmacology named after V.V. Zakusov» on the basis of structure of the fourth loop of BDNF (GSB-106) is developed using method of gas-liquid chromatography (GLC) with static vapor-phase extraction. The developed conditions of analysis allowed to effectively divide chromatographic peaks of all organic solvents used in the course of synthesis and purification of substance at the last stages: methanol, pyridine, ethanol, acetic acid. The validation of the technique proved its specificity, linearity, correctness.

Transmembrane Nox4 topology revealed by topological determination by Ubiquitin Fusion Assay, a novel method to uncover membrane protein topology

The NADPH oxidase Nox4 is a multi-pass membrane protein responsible for the generation of reactive oxygen species that are implicated in cellular signaling but may also cause pathological situations when dysregulated. Although topological organization of integral membrane protein dictates its function, only limited experimental data describing Nox4's topology are available.To provide deeper insight on Nox4 structural organization, we developed a novel method to determinate membrane protein topology in their cellular environment, named Topological Determination by Ubiquitin Fusion Assay (ToDUFA). It is based on the proteolytic capacity of the deubiquitinase enzymes to process ubiquitin fusion proteins. This straightforward method, validated on two well-known protein's topologies (IL1RI and Nox2), allowed us to discriminate rapidly the topological orientation of protein's domains facing either the nucleocytosolic or the exterior/luminal compartments. Using this method, we were able for the first time to determine experimentally the topology of Nox4 which consists of 6 transmembrane domains with its N- and C-terminus moieties facing the cytosol. While the first, third and fifth loops of Nox4 protein are extracellular; the second and fourth loops are located in the cytosolic side. This approach can be easily extended to characterize the topology of all others members of the NADPH oxidase family or any multi-pass membrane proteins.Considering the importance of protein topology knowledge in cell biology research and pharmacological development, we believe that this novel method will represent a widely useful technique to easily uncover complex membrane protein's topology.

ТЕПЛОГИДРАВЛИЧЕСКАЯ МОДЕЛЬ РЕАКТОРНОЙ УСТАНОВКИ С ЖИДКОМЕТАЛЛИЧЕСКИМ ТЕПЛОНОСИТЕЛЕМ

This paper presents the results of calculations on the heat-hydraulic model of a reactor with lead coolant, which is based on the design scheme for the ATHLET code, obtained on the basis of public information on the BREST-OD-300. In the model used in this work, firstly, the descending sections of each loop are interconnected by transverse hydraulic connections and, secondly, the in-reactor space from the lower pressure collector of the reactor to the upper distributing collector of the reactor is also divided into a system of parallel cross-linked channels. The model includes a reactor, four circuits with main circulation pumps, two sectional steam generators on each loop. The secondary loop for each steam generator has a feed pump. The article describes the method of obtaining the initial stationary state for the developed scheme and presents the results of the calculation of the transitional regime associated with the disconnection of one of the MCP with saving the reactor power. It is shown that in the emergency loop a reverse coolant current occurs when the MCP is disconnected. This leads to the fact that less coolant flow passes through the core.The cold coolant from the fourth loop is not fed to the entrance to the core, but is mixed in the upper distributing collector after the core.

Synthesis and In Vitro Neuroprotective Activity of Analogs with Various Spacer Lengths of a Dimeric Dipeptide Mimetic (GK-2) of Nerve Growth Factor

Dimeric dipeptide mimetic GK-2 or hexamethylenediamide bis-(N-monosuccinyl-L-glutamyl-L-lysine), which activated TrkA receptors and exhibited neuroprotective activity in vitro (10–5 – 10–9 M) and in vivo (0.05 – 5 mg/kg i.p.), was designed by us earlier based on the beta-turn of the nerve growth factor (NGF) fourth loop. The effect of dimerizing spacer length on the manifestation of neuroprotective activity was studied by synthesizing GK-2 (11 σ-bonds) analogs tetramethylenediamide bis-(N-monosuccinyl-L-glutamyl-Llysine) (GK-2c); pentamethylenediamide bis-(N-monosuccinyl-L-glutamyl-L-lysine) (GK-2b); and trimethylenediamide bis-(N-monosuccinyl-L-glutamyl-L-lysyl-6-aminohexanoic acid) (GK-2a) containing 9, 10, and 22 σ-bonds, respectively, between the lysine Cα-atoms of the dipeptide fragments. Neuroprotective activity was investigated in vitro using HT-22 mouse hippocampal neuronal cell culture under H2O2-induced oxidative stress and showed that the neuroprotective activity as measured by the minimum effective concentration was 104 times less if the distance between the dipeptide fragments increased from 11 to 22 σ-bonds. The neuroprotective activity decreased insignificantly if this distance was decreased from 11 to 10 σ bonds (GK-2b) and disappeared with 9 σ -bonds (GK-2c). Therefore, the hexamethylene spacer was optimal although the distance between the corresponding amino-acid moieties of natural NGF from an x-ray structure analysis was considerably greater at 33 σ-bonds. This contradiction could have arisen because two ionically bound mimetic molecules interacted with TrkA receptors. Another possible explanation was that TrkA molecules could approach closer in the presence of bis-dipeptide GK-2 than NGF.