Academic literature on the topic 'IBP1 fold'

Using a snake toxin as a proteic antigen (Ag), two murine toxin–specific monoclonal antibodies (mAbs), splenocytes, and two murine Ag–specific T cell hybridomas, we showed that soluble protein A (SpA) from Staphylococcus aureus and protein G from Streptococcus subspecies, two Ig binding proteins (IBPs), not only abolish the capacity of the mAbs to decrease Ag presentation but also increase Ag presentation 20–100-fold. Five lines of evidence suggest that this phenomenon results from binding of an IBP–Ab–Ag complex to B cells possessing IBP receptors. First, we showed that SpA is likely to boost presentation of a free mAb, suggesting that the IBP-boosted presentation of an Ag in an immune complex results from the binding of IBP to the mAb. Second, FACS® analyses showed that an Ag–Ab complex is preferentially targeted by SpA to a subpopulation of splenocytes mainly composed of B cells. Third, SpA-dependent boosted presentation of an Ag–Ab complex is further enhanced when splenocytes are enriched in cells containing SpA receptors. Fourth, the boosting effect largely diminishes when splenocytes are depleted of cells containing SpA receptors. Fifth, the boosting effect occurs only when IBP simultaneously contains a Fab and an Fc binding site. Altogether, our data suggest that soluble IBPs can bridge immune complexes to APCs containing IBP receptors, raising the possibility that during an infection process by bacteria secreting these IBPs, Ag-specific T cells may activate IBP receptor–containing B cells by a mechanism of intermolecular help, thus leading to a nonspecific immune response.

Development is orchestrated by regulatory elements that turn genes ON or OFF in precise spatial and temporal patterns. Many safety mechanisms prevent inappropriate action of a regulatory element on the wrong gene promoter. In flies and mammals, dedicated DNA elements (insulators) recruit protein factors (insulator binding proteins, or IBPs) to shield promoters from regulatory elements. In mammals, a single IBP called CCCTC-binding factor (CTCF) is known, whereas genetic and biochemical analyses in Drosophila have identified a larger repertoire of IBPs. How insulators function at the molecular level is not fully understood, but it is currently thought that they fold chromosomes into conformations that affect regulatory element-promoter communication. Here, we review the discovery of insulators and describe their properties. We discuss recent genetic studies in flies and mice to address the question: Is gene insulation important for animal development? Comparing and contrasting observations in these two species reveal that they have different requirements for insulation, but that insulation is a conserved and critical gene regulation strategy.

Background. The aim was to investigate the influence of propionic acid (PA) on the endoplasmic reticulum (ER), unfolded protein response (UPR) state, and astrocyte/microglia markers in rat ventromedial hypothalamus (VMH) after type 2 diabetes mellitus (T2DM). Methods. Male Wistar rats were divided: (1) control, (2) T2DM, and groups that received the following (14 days, orally): (3) metformin (60 mg/kg), (4) PA (60 mg/kg), and (5) PA+metformin. Western blotting, RT-PCR, transmission electron microscopy, and immunohistochemical staining were performed. Results. We found T2DM-associated enlargement of ER cisterns, while drug administration slightly improved VMH ultrastructural signs of damage. GRP78 level was 2.1-fold lower in T2DM vs. control. Metformin restored GRP78 to control, while PA increased it by 2.56-fold and metformin+PA—by 3.28-fold vs. T2DM. PERK was elevated by 3.61-fold in T2DM, after metformin—by 4.98-fold, PA—5.64-fold, and metformin+PA—3.01-fold vs. control. A 2.45-fold increase in ATF6 was observed in T2DM. Metformin decreased ATF6 content vs. T2DM. Interestingly, PA exerted a more pronounced lowering effect on ATF6, while combined treatment restored ATF6 to control. IRE1 increased in T2DM (2.4-fold), metformin (1.99-fold), and PA (1.45-fold) groups vs. control, while metformin+PA fully normalized its content. The Iba1 level was upregulated in T2DM (5.44-fold) and metformin groups (6.88-fold). Despite PA treatment leading to a further 8.9-fold Iba1 elevation, PA+metformin caused the Iba1 decline vs. metformin and PA treatment. GFAP level did not change in T2DM but rose in metformin and PA groups vs. control. PA+metformin administration diminished GFAP vs. PA. T2DM-induced changes were associated with dramatically decreased ZO-1 levels, while PA treatment increased it almost to control values. Conclusions. T2DM-induced UPR imbalance, activation of microglia, and impairments in cell integrity may trigger VMH dysfunction. Drug administration slightly improved ultrastructural changes in VMH, normalized UPR, and caused an astrocyte activation. PA and metformin exerted beneficial effects for counteracting diabetes-induced ER stress in VMH.

ABSTRACT A novel antimicrobial enzyme system, the Curvularia haloperoxidase system, was examined with the aim of elucidating its mechanism of antibacterial action. Escherichia coli strain MG1655 was stressed with sublethal concentrations of the enzyme system, causing a temporary arrest of growth. The expression of genes altered upon exposure to the Curvularia haloperoxidase system was analyzed by using DNA microarrays. Only a limited number of genes were involved in the response to the Curvularia haloperoxidase system. Among the induced genes were the ibpA and ibpB genes encoding small heat shock proteins, a gene cluster of six genes (b0301-b0306) of unknown function, and finally, cpxP, a member of the Cpx pathway. Knockout mutants were constructed with deletions in b0301-b0306, cpxP, and cpxARP, respectively. Only the mutant lacking cpxARP was significantly more sensitive to the enzyme system than was the wild type. Our results demonstrate that DNA microarray technology cannot be used as the only technique to investigate the mechanisms of action of new antimicrobial compounds. However, by combining DNA microarray analysis with the subsequent creation of knockout mutants, we were able to pinpoint one of the specific responses of E. coli—namely, the Cpx pathway, which is important for managing the stress response from the Curvularia haloperoxidase system.

Abstract A new chiral reversed-phase (RP)-HPLC method with UV detection was developed. Enantioselective resolution of ibuprofen (IBP) was achieved using (3R,4S)-4-(3,5-dinitrobenzamido)-3-(3-(trioxysilyl)-propyl)-1,2,3,4-tetrahydro-phenanthrene [(R,R)-Whelk-O2] chiral stationary phase (4.6 mm id × 250 mm, 10 μm) with a mobile phase composed of ethanol–water (30 + 70, v/v) containing 100 mM ammonium acetate at a flow rate of 1.3 mL/min using diode array detector at λ 220 nm. Calibration curves were linear over the concentration range of 20–180 μg/mL for both IBP enantiomers. Mean % recoveries ±SD of 99.74 ± 1.73 and 99.60 ± 0.93 were obtained for dexibuprofen (dex-IBP) and levoibuprofen (levo-IBP), respectively. Intra- and interday precision calculated as RSD, % were not more than 1.66% for dex-IBP and 1.93% for levo-IBP. The detection limits were 2.09 and 2.06 μg/mL for dex-IBP and levo-IBP, respectively. The method was successfully applied for the determination of dex-IBP in tablet dosage form.

Abstract Background Changes in dopamine beta-hydroxylase (DBH) and anomalies in dopaminergic machinery have been shown in inflammatory bowel disease (IBD) patients and related animal models. Thus, we aimed to evaluate the dopaminergic pathways in IBD patients as well as in a mouse model of dextran sodium sulphate (DSS)-induced ileitis. Methods Colon biopsies (CB) obtained from healthy volunteers (N=3) and matched-IBD patients (N=3), were used to evaluate DBH immunoreactivity by confocal microscopy. Male C57/Bl6 (8±2 weeks old; N=16 mice) received 1.5% DSS in drinking water for 5 days, then switched to regular drinking water for 3 days. Inflammatory cytokines (IL-1β, TNFα, IL-6) were measured to assess ileitis severity. Changes in ileal muscle tension were isometrically recorded following 30 μM dopamine or 30 μM SKF38393 (a dopamine receptor 1 (D1R) agonist) or 30 μM bromocriptine (a D2R agonist). Immunofluorescence distribution of Iba1 (a macrophage specific marker), D1R, DBH and dopamine transporter (DAT) were determined in longitudinal muscle-myenteric plexus whole-mount preparations (LMMPs) by confocal microscopy. D1R and D2R mRNA transcripts were evaluated by qRT-PCR. Results CB from IBD patients and LMMPs from DSS mice showed a significant increase of DBH immunoreactivity compared to healthy patients and sham mice (+25% [p<0.01], +20% [p<0.01], respectively). DSS treatment caused a significant increase of DAT and D1R immunoreactivity as well as D1R mRNA levels (+27% [p<0.05], +24% [p<0.05], +6-fold [p<0.05], respectively), accompanied by a significant reduction of dopamine-mediated relaxation (-27% [p<0.01]). SKF38393 determined a marked inhibitory response in ileal preparations from DSS mice compared to sham mice (+73% [p<0.01]), suggesting that dopamine responses are mainly mediated through D1R. A 2-fold increase of resident Iba1+ macrophages was observed in the myenteric plexus of DSS mice associated with a 2.9- and 1.5-fold enhancement of IL-6 and IL-1β mRNA levels, respectively. Conclusion Human colitis and mouse ileitis affect dopamine machinery in the enteric nervous system. Experimentally induced ileitis impairs dopaminergic neurotransmission altering D1R-mediated responses. These findings provide novel information on the involvement of dopaminergic pathways in IBD.

Bisphosphonates (BPs) may play an important role in minimizing osteolysis. In this work two new bisphosphonates pertaining to second and third generations respectively, have been synthesized and incorporated onto a chemically enriched hydroxyapatite. BP synthesis has been performed by adding H3PO3, PCl3 and methanesulfonic acid over 4-aminophenyl acetic acid (APBP) and 1-H-indole-3-acetic acid (IBP) respectively at 65°C in a N2 atmosphere. These compounds bear a primary amine group bonded to an aromatic ring, and a secondary amine group within a heterocyclic ring respectively. A chemically enriched hydroxyapatite with a chemical content corresponding to a 50% fluorided hydroxyapatite has been synthesized. Ceramic bodies manufactured by uniaxial pressure followed by cold isostatic press have a 97% density and submicron grain size. The BP was adsorbed onto the surface by immersion in a stirred solution at 37°C for 48 hours. A 10-fold decrease of the surface energy was observed for bodies modified with the APBP whereas only a 25 % decrease is obtained for bodies loaded with the bisphosphonate loaded with the IBP.

Abstract Introduction: The isoprenoid biosynthetic pathway (IBP) is responsible for the production of key sterol and nonsterol species, including farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP) which serve as substrates for protein isoprenylation reactions. Several agents known to target the IBP have been observed to have cytotoxic effects in multiple myeloma cells. Thalidomide (Thal) has emerged as an effective agent for treating multiple myeloma. While Thal has been noted to have a variety of direct and indirect effects on myeloma cells, the precise mechanism of action remains unknown. Aim: We examined interactions between inhibitors of the IBP and Thal in multiple myeloma cells. The mechanisms underlying the observed differential sensitivity to these agents were explored. Methods: Studies were performed in three human multiple myeloma cell lines (RPMI-8226, U266, H929). Cytotoxicity was assessed via MTT assays, while apoptosis induction was determined by Annexin V staining and evaluation of PARP cleavage. Western blot analysis was used to evaluate inhibition of protein isoprenylation. Intracellular FPP and GGPP levels were measured via enzymatic coupling to fluorescently-tagged peptides, HPLC fractionation and fluorescence detection. Pharmacologic manipulation of the IBP was achieved with the following agents: lovastatin (Lov) as an HMG-CoA reductase inhibitor, zoledronic acid (ZA) as a FPP synthase inhibitor, digeranyl bisphosphonate (DGBP) as a GGPP synthase inhibitor, FTI-277 as a farnesyl transferase inhibitor (FTI), and GGTI-286 as a geranylgeranyl transferase I inhibitor (GGTI). Results: Addition of Thal to Lov (at both 24 & 48h), zoledronic acid (at 48h), or DGBP (at 24 & 48h) in RPMI-8266 cells results in marked enhancement in cytotoxicity. Isobologram analysis could not be performed as Thal by itself does induce cytotoxicity in MTT assays. Although Lov induces cytotoxicity in a concentration- and time-dependent manner in the U266 and H929 cells, the addition of Thal did not result in increased cytotoxicity. Neither ZA nor DGBP induced cytotoxicity in the U266 cell line, while the H929 cell line showed effects only at 48 hours. Addition of Thal to FTI or GGTI did not result in enhanced cytotoxicity in tested cell lines. Annexin V experiments confirmed enhanced induction of apoptosis in RPMI-8226 cells incubated with the combination of Thal/Lov or Thal/DGBP. Add-back experiments revealed that the enhanced cytotoxicity/induction of apoptosis observed with the addition of Thal could be prevented with the addition of mevalonate or GGPP in Lov-treated cells or GGPP in DGBP-treated cells. PARP cleavage was demonstrated in RPMI-8226 and H929 cells treated with Lov or DGBP (with or without Thal) and in U266 cells treated with Lov. As expected, Lov resulted in the accumulation of unmodified forms of proteins normally farnesylated (Ras) and geranylgeranylated (Rap1a and Rab6) in these cells. Interestingly however, while DGBP led to accumulation of unmodified Rap1a and Rab6 in RPMI-8226 and H929 cells, no effect was seen in the U266 line. Examination of intracellular levels of FPP and GGPP revealed that the U266 line has markedly larger pools of FPP (8.5-fold) and GGPP (2.7-fold) compared to RPMI-8226 and that treatment with DGBP only partially depletes U266 cells of GGPP. Conclusions: These studies demonstrate an interaction between thalidomide and IBP inhibitors in multiple myeloma cells. These effects appear dependent on depletion of GGPP. Since treatment with a geranylgeranyl transferase-I inhibitor does not produce similar results, this suggests that substrates of geranylgeranyl transferase-II, such as the Rab proteins, may play critical roles in myeloma pathophysiology. The finding that intracellular levels of FPP and GGPP vary markedly amongst cell lines explains differential sensitivity of these cells to pharmacologic manipulation of the IBP and may also influence sensitivity to chemotherapeutic agents. Further studies will determine the extent to which isoprenoid pool sizes vary in primary samples and may ultimately allow for the identification of multiple myeloma patients who would benefit from the addition of an IBP inhibitor to their treatment plan. Figure Figure

Preterm births are the leading cause of neonatal death in the United States. Previously, a spontaneous preterm birth (sPTB) predictor based on the ratio of two proteins, IBP4/SHBG, was validated as a predictor of sPTB in the Proteomic Assessment of Preterm Risk (PAPR) study. In particular, a proteomic biomarker threshold of −1.37, corresponding to a ~two-fold increase or ~15% risk of sPTB, significantly stratified earlier deliveries. Guidelines for molecular tests advise replication in a second independent study. Here we tested whether the significant association between proteomic biomarker scores above the threshold and sPTB, and associated adverse outcomes, was replicated in a second independent study, the Multicenter Assessment of a Spontaneous Preterm Birth Risk Predictor (TREETOP). The threshold significantly stratified subjects in PAPR and TREETOP for sPTB (p = 0.041, p = 0.041, respectively). Application of the threshold in a Kaplan–Meier analysis demonstrated significant stratification in each study, respectively, for gestational age at birth (p < 001, p = 0.0016) and rate of hospital discharge for both neonate (p < 0.001, p = 0.005) and mother (p < 0.001, p < 0.001). Above the threshold, severe neonatal morbidity/mortality and mortality alone were 2.2 (p = 0.0083,) and 7.4-fold higher (p = 0.018), respectively, in both studies combined. Thus, higher predictor scores were associated with multiple adverse pregnancy outcomes.

Una proteina in grado di legare i cristalli di ghiaccio è definita proteina legante il ghiaccio o IBP acronimo dall’inglese ice-binding protein. Le IBP grazie alla loro capacità di abbassare il punto di congelamento dell’acqua, aumentando il gap di isteresi termica (TH). Questo intervallo è definito come la differenza tra il punto di fusione e di congelamento dell’acqua. La seconda attività delle IBP è l’inibizione della ricristallizzazione del ghiaccio (ice recrystallization inhibition, IRI). Infatti, queste proteine stabilizzano i piccoli cristalli di ghiaccio impedendo la formazione di cristalli di ghiaccio di grosse dimensioni che sono dannosi per le cellule. Le IBP sono state identificate in numerosi organismi tra cui pesci, insetti, batteri, alghe e lieviti. Queste proteine rappresentano un esempio di evoluzione convergente, infatti tutte le IBP condividono lo stesso meccanismo di legame con il ghiaccio nonostante una sorprendente diversità strutturale e funzionale. Questo lavoro di tesi è focalizzato sulla caratterizzazione funzionale e strutturale di EfcIBP, una IBP batterica identificata da analisi di metagenomica effettuate sul ciliato Antartico Euplotes focardii e sul consorzio batterico ad esso associato. La struttura 3D di EfcIBP è stata risolta mediante cristallografia ai raggi X e consiste in un β-solenoide con un α-elica parallela all’asse principale della proteina. L’analisi strutturale ha permesso di identificare tre diverse facce del solenoide denominate A, B e C. Simulazioni di docking suggeriscono che EfcIBP è in grado di legare i cristalli di ghiaccio tramite le facce B e C del solenoide. Questa ipotesi è stata verificata attraverso la progettazione razionale di 6 varianti che sono state prodotte e saggiate per la loro attività. In generale, questi risultati indicano che EfcIBP è in grado di legare i cristalli di ghiaccio attraverso le facce B e C del solenoide. Questa peculiarità strutturale si riflette in un’insolita combinazione di attività di IRI e TH. Infatti, EfcIBP presenta una notevole attività di IRI in un intervallo di concentrazione nanomolare e una attività di isteresi termica di 0.53°C alla concentrazione di 50 μM che la rende una IBP moderata. All’interno del gap di TH, i cristalli di ghiaccio presentano una forma esagonale, mentre a temperature al di sotto della temperatura di congelamento presentano una forma a “Saturno". La proteina chimerica formata dalla “green fluorescent protein” e da EfcIBP è stata utilizzata per determinare a quali piani del cristallo di ghiaccio la proteina è in grado di legarsi e con quale cinetica. I dati sperimentali suggeriscono che le peculiarità funzionali di EfcIBP sono dovute alla sua capacità di legare velocemente i piani basali e piramidali del cristallo di ghiaccio. Questi dati, insieme alla presenza di una sequenza segnale per la secrezione, suggeriscono che EfcIBP è secreta e svolge la funzione di mantenere liquido l’ambiente circostante aumentando lo spazio vitale. In conclusione, EfcIBP è un nuovo tipo di IBP con proprietà insolite di legame al ghiaccio e di attività di IRI. Questo studio ha contribuito ad identificare una nuova classe di IBP moderate che potrebbero essere sfruttate come crioprotettori in diversi settori come la criobiologia e quello alimentare.
Ice-binding proteins (IBPs) are characterized by the ability to control the growth of ice crystals. IBPs are active in increasing thermal hysteresis (TH) gap as they decrease the freezing point of water. On the other hand, IBPs can inhibit ice recrystallization (IRI) and stabilize small ice crystals at the expense of the harmful, large ones. IBPs have been identified in several organisms including higher Eukaryotes and microorganisms such as bacteria, yeasts and algae. Although IBPs share the ability to bind ice crystals, proteins from different sources present different 3D structures, from α-helix to β-solenoid proteins. This thesis is focused on the structural and functional characterization of EfcIBP, a bacterial IBP identified by metagenomic analysis of the Antarctic ciliate Euplotes focardii and the associated consortium of non-cultivable bacteria. The 3D structure of EfcIBP, solved by X-ray crystallography, consists in a β-solenoid with an α-helix aligned along the axis of the β-helix. It is possible to distinguish three different faces: A, B and C. Docking simulations suggest that B and C faces are involved in ice binding. This hypothesis was tested by the rational design of six variants that were produced and assayed for their activity. Overall, these experiments indicate that both solenoid faces contribute to the activity of EfcIBP. EfcIBP displays remarkable IRI activity at nanomolar concentration and a TH activity of 0.53°C at the concentration of 50 μM. The atypical combination between these two activities could stem from the ability of this protein to bind ice crystals through two faces of the solenoid. In the presence of EfcIBP, ice crystals show a hexagonal trapezohedron shape within the TH gap, and a unique “Saturn-shape” below the freezing point. A chimeric protein consisting of the fusion between EfcIBP and the green fluorescent protein was used to deeper investigate on this aspects by analyses of fluorescence ice plane affinity and binding kinetics. Overall, experimental data suggest that the EfcIBP unique pattern of ice growth and burst are due to its high rate of binding at the basal and the pyramidal near-basal planes of ice crystals. These data, together with the signal sequence for the secretion, suggest that EfcIBP is secreted in local environment where it becomes active in increasing the habitable space. In conclusion, EfcIBP is a new type of IBP with unusual properties of ice shaping and IRI activity. This study opens new scenarios in the field of IBPs by contributing to identify a new class of moderate IBPs potentially exploitable as cryoprotectants in several fields, such as cryobiology and food science.