Free Protein Research Articles

HIV-1 Nef is carried on the surface of extracellular vesicles.

Extracellular vesicles (EVs) serve as pivotal mediators of intercellular communication in both health and disease, delivering biologically active molecules from vesicle-producing cells to recipient cells. In the context of HIV infection, EVs have been shown to carry the viral protein Nef, a key pathogenic factor associated with HIV-related co-morbidities. Despite this recognition, the specific localisation of Nef within the vesicles has remained elusive. This study addresses this critical knowledge gap by investigating Nef-containing EVs. Less than 1% of the total released Nef was associated with EVs; most Nef existed as free protein released by damaged cells. Nevertheless, activity of EV-associated Nef in downregulating the major cholesterol transporter ABCA1, a critical aspect linked to the pathogenic effects of Nef, was comparable to that of free Nef present in the supernatant. Through a series of biochemical and microscopic assays, we demonstrate that the majority of EV-associated Nef molecules are localised on the external surface of the vesicles. This distinctive distribution prompts the consideration of Nef-containing EVs as potential targets for immunotherapeutic interventions aimed at preventing or treating HIV-associated co-morbidities. In conclusion, our results shed light on the localisation and functional activity of Nef within EVs, providing valuable insights for the development of targeted immunotherapies to mitigate the impact of HIV-associated co-morbidities.

Recent advances in protein precipitation-based methods for drug-target screening

Drug targets are biological macromolecules that bind drug molecules in vivo. Therefore, the system-wide identification of drug targets plays a vital role in fully understanding the mechanism of drug action, efficacy, and side effects. The unbiased screening of drug targets may accelerate the process of drug discovery and candidate screening. Mass spectrometry is a key tool for large-scale protein identification and accurate quantification owing to its high acquisition speed, resolution, and sensitivity. Mass spectrometry-based proteomics has been widely used for drug-target screening. It can systematically identify the protein-target landscape of a drug and elucidate drug-protein interactions. Commonly used drug-target characterization methods, such as labeling-based affinity enrichment, require the chemical derivatization of drug molecules, which is not only time-consuming but may also affect the affinity of the drug towards its targets. Furthermore, the spatial effects of the derivatization groups may block interactions between the drug and its targets. Considering the disadvantages of affinity-enrichment methods, strategies that do not require chemical derivatization have received widespread attention. Proteins may undergo denaturation, unfolding, and precipitation under different conditions such as high temperatures, extreme pH, denaturants, and mechanical stress. Binding to small-molecule drugs may alter the folding balance of target proteins. The conformational stability of target proteins can be stabilized by binding with drugs, and protein-drug complexes are more resistant than free proteins to the precipitation induced by different conditions. Based on this mechanism, various large-scale drug-target identification methods using protein precipitation have been developed by combining proteomics and mass spectrometry analysis, including thermal proteome profiling and solvent-, mechanical stress-, and pH-induced protein precipitation. These methods have been successfully applied to the characterization of small-molecule drug targets. In this review, we describe the protein precipitation-based methods used for the high-throughput discovery of drug targets and elucidation of the interactions between drugs and proteins in the past decade. We also summarize the characteristics of each method and discuss their application potential in drug-efficacy evaluation and drug discovery.

Every minute counts: A comparison of thawing times and haemostatic quality of plasma thawed at 37°C and 45°C using four different methods.

Having faster plasma thawing devices could be beneficial for transfusion services, as it may improve the rapid availability of thawed plasma for bleeding patients, and it might remove the need to have extended pre-thawed plasma: thus, reducing unnecessary plasma wastage. The aims of this study were to assess (a) the thawing times and (b) in vitro haemostatic quality of thawed plasma using Barkey Plasmatherm V (PTV) at 37 and 45°C versus Barkey Plasmatherm Classic (PTC) at 37 and 45°C, Sarstedt Sahara-III Maxitherm (SS-III) at 37°C and Helmer Scientific Thermogenesis Thermoline (TT) at 37°C. Haemostatic quality was assessed using LG-Octaplas at three different time points: baseline (5 min), 24 and 120 h after thawing. The thawing time (SD) of 2 and 4 units was significantly different between different thawers. PTV at 45°C was the fastest method for both 2 and 4 units (7.06 min [0.68], 9.6 min [0.87], respectively). SS-III at 37°C being the slowest method (24.69 min [2.09] and 27.18 min [4.4], respectively) (p = < 0.05). Baseline measurements for all assays showed no significant difference in the prothrombin time, fibrinogen, FII, FV, protein C activity or free protein S antigen between all methods tested. However, at baseline PTV (both 37°C and 45°C) had significantly higher levels of FVII, FVIII and FXI and shortened activated partial thromboplastin time. PTV was the quickest method at thawing plasma at both 37 and at 45°C. The haemostatic quality of plasma thawed at 45 versus 37°C was not impaired. Thawing frozen plasma at 45°C should be considered.

Regulation of YAP translocation by myeloid Pten deficiency alleviates acute lung injury via inhibition of oxidative stress and inflammation

BackgroundPhosphatase and tensin homolog deleted on chromosome 10 (PTEN) is intricately involved in modulating the inflammatory response in acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). Nevertheless, the myeloid PTEN governing Hippo-YAP pathway mediated oxidative stress and inflammation in lipopolysaccharide (LPS)-induced ALI remains to be elucidate. MethodsThe floxed Pten (PtenFL/FL) and myeloid-specific Pten knockout (PtenM−KO) mice were intratracheal instill LPS (5 mg/kg) to establish ALI, then Yap siRNA mix with the mannose-conjugated polymers was used to knockdown endogenous macrophage YAP in some PtenM−KO mice before LPS challenged. The bone marrow-derived macrophages (BMMs) from PtenFL/FL and PtenM−KO mice were obtained, and BMMs were transfected with CRISPR/Cas9-mediated glycogen synthase kinase 3 Beta (GSK3β) knockout (KO) or Yes-associated protein (YAP) KO vector subjected to LPS (100 ng/ml) challenged or then cocultured with MLE12 cells. ResultsHere, our findings demonstrate that myeloid-specific PTEN deficiency exerts a protective against LPS-induced oxidative stress and inflammation dysregulated in ALI model. Moreover, ablation of the PTEN-YAP axis in macrophages results in reduced nuclear factor-E2-related factor-2 (NRF2) expression, a decrease in antioxidant gene expression, augmented levels of free radicals, lipid and protein peroxidation, heightened generation of pro-inflammatory cytokines, ultimately leading to increased apoptosis in MLE12 cells. Mechanistically, it is noteworthy that the deletion of myeloid PTEN promotes YAP translocation and regulates NRF2 expression, alleviating LPS-induced ALI via the inhibition of GSK3β and MST1 binding. ConclusionsOur study underscores the crucial role of the myeloid PTEN-YAP-NRF2 axis in governing oxidative stress and inflammation dysregulated in ALI, indicating its potential as a therapeutic target for ALI.

Ramadan intermittent fasting is associated with improved anticoagulant activity among healthy people: a case–control study

Data on the pathophysiological mechanisms of hemostatic alterations in the thrombotic events that occur during Ramadan intermittent fasting (RIF), particularly in the natural coagulation inhibitors, are very limited. Thus, our objective was to evaluate the effect of RIF on the natural anticoagulants level, antithrombin, protein C, and total and free protein S (PS) in healthy participants. Participants were divided into two groups. Group I consisted of 29 healthy fasting participants whose blood samples were taken after 20 days of fasting. Group II included 40 healthy non-fasting participants whose blood samples were taken 2–4 weeks before the month of Ramadan. Coagulation screening tests including prothrombin time (PT), activated partial thromboplastin time (APTT) and plasma fibrinogen level, natural anticoagulants; antithrombin, protein C, free and total PS and C4 binding protein (C4BP) levels were evaluated in the two groups. High levels of total and free PS without change in antithrombin, protein C, and C4BP levels were noted in the fasting group as compared with non-fasting ones (p < 0.05). PT and APTT showed no difference between the two groups. However, the fibrinogen level was higher in the fasting group. In conclusion, RIF was found to be associated with improved anticoagulant activity in healthy participants, which may provide temporal physiological protection against the development of thrombosis in healthy fasting people.

Free radical-induced soybean protein isolate -curcumin conjugates: Characterization, antioxidant and in vitro digestion characteristics

Natural soybean protein isolate（SPI) is vulnerable to environmental factors that compromise its functionality. One effective method to improve this functionality is through free radical induction. In this study, SPI and curcumin (Cur) were utilized to prepare SPI-Cur conjugates using the free radical induction method. The formation mechanism, structure, and functional properties of these conjugates were subsequently. The results indicated that at pH 9, the SPI-Cur conjugate formed hydroxyquinone dimers, which exhibited higher inhibition of digestive enzymes and increased stability through free radical-induced reactions. Furthermore, the antioxidant properties of SPI-Cur conjugates increased significantly, with increases of 9.17-, 2.3-, and 7.70-fold in DPPH, ABTS, and reducing power, respectively (p < 0.05). Circular dichroism analysis revealed increases in the secondary structure of proteins in SPI-Cur conjugates α-helix from 0.40% to 1.47%, β-sheet from 28.70% to 98.38% (pH 3 to pH 9), β-turns from 70.83% to 0.15%, and Random coils from 0.00% to 81.21%. These results suggest a novel approach for creating SPI-Cur conjugates through free radical-induced reactions, which could aid in the development of a continuous delivery system for polyphenols based on SPI and improve the high-value utilization of SPI.

β-Cyclocitral from Lavandula angustifolia Mill. Exerts Anti-Aging Effects on Yeasts and Mammalian Cells via Telomere Protection, Antioxidative Stress, and Autophagy Activation.

We used a replicative lifespan (RLS) experiment of K6001 yeast to screen for anti-aging compounds within lavender extract (Lavandula angustifolia Mill.), leading to the discovery of β-cyclocitral (CYC) as a potential anti-aging compound. Concurrently, the chronological lifespan (CLS) of YOM36 yeast and mammalian cells confirmed the anti-aging effect of CYC. This molecule extended the yeast lifespan and inhibited etoposide (ETO)-induced cell senescence. To understand the mechanism of CYC, we analyzed its effects on telomeres, oxidative stress, and autophagy. CYC administration resulted in notable increases in the telomerase content, telomere length, and the expression of the telomeric shelterin protein components telomeric-repeat binding factor 2 (TRF2) and repressor activator protein 1 (RAP1). More interestingly, CYC reversed H2O2-induced telomere damage and exhibited strong antioxidant capacity. Moreover, CYC improved the survival rate of BY4741 yeast under oxidative stress induced by 6.2 mM H2O2, increasing the antioxidant enzyme activity while reducing the reactive oxygen species (ROS), reactive nitrogen species (RNS), and malondialdehyde (MDA) levels. Additionally, CYC enhanced autophagic flux and free green fluorescent protein (GFP) expression in the YOM38-GFP-ATG8 yeast strain. However, CYC did not extend the RLS of K6001 yeast mutants, such as Δsod1, Δsod2, Δcat, Δgpx, Δatg2, and Δatg32, which lack antioxidant enzymes or autophagy-related genes. These findings reveal that CYC acts as an anti-aging agent by modifying telomeres, oxidative stress, and autophagy. It is a promising compound with potential anti-aging effects and warrants further study.

Enhancing the quality of highland barley noodles by Lactobacillus plantarum pre-fermentation: Insights into its underlying mechanism

To improve highland barley noodles (HBNs) quality, the highland barley flour (HBF) was pre-fermented by Lactobacillus plantarum in this study. The changes in the quality of HBNs, the hydration properties and microstructure of the dietary fiber (DF), and the conformation and cross-linking of the protein in HBNs were measured. With the extension of pre-fermentation time (0–4 h), the overall acceptance of HBNs increased from 7.83 to 8.27, along with a 5.9% reduction in hardness and a 4.5% increase in springiness of HBNs. Meanwhile, confocal laser scanning microscopy (CLSM) revealed that the physical structure of the DF gradually disintegrated, which caused a significant (p < 0.05) decrease in its water retention capacity. In addition, spectral analysis showed a continual increase (from 19.62% to 30.15%) in β-turn content of the protein. The content of the free sulfhydryl group and sodium dodecyl sulfate extractable protein (SDSEP) decreased by 18.1% and 4.12%, respectively. However, with the further extension of pre-fermentation time (6–8 h), the degradation in HBNs sensory quality occurred, accompanied by a significant (p < 0.05) decrease in pH (5.95–5.01). These findings suggested that a moderate duration (4 h) of HBF pre-fermentation could effectively improve the quality of HBNs.

Influences of non-rubber components on the molecular network and viscoelasticity of natural rubber gum

The molecular network of natural rubber (NR) gum is determined by the interparticle diffusion when NR latex coagulates. However, the roles played by the non-rubber components (NRC) species on the heterogeneous network structure and on the viscoelasticity of NR gum have not been throughly investigated. Here, the molecular relaxation was studied by linear rheology. In addition, the inter- and intra-cycle nonlinearities under large amplitude oscillatory shear (LAOS) were studied for gums with extracted and added NRC. It was found that the high molecular weight free protein restricts the interdiffusion and improves the entanglement density, while the added lipid induces homogeneous distribution of NRC. The physical associations coming from free proteins increase the segment friction and retard the terminal relaxation. Onset of the strain softening was found to be induced by entangled network density. Both the elastic and viscous LAOS nonlinearities can be regulated by adjusting the NRC species. This work sheds light on the contributions of major NRC species on the network structure and nonlinear viscoelasticity of NR gum.

Quasielastic neutron scattering study on low-hydrated myoglobin inside silica nanopores

In this study, nanosecond-scale dynamics of low-hydrated myoglobin (Mb) encapsulated in mesoporous silica (MPS) with 7.8 nm pores was investigated by using high resolution (energy resolution: 1 μeV) neutron backscattering spectroscopy. The apparent hydration level of the encapsulated myoglobin was 0.06, which was deduced by assuming a uniform distribution of water within myoglobin encapsulated mesoporous silica. The mean square displacement of myoglobin derived from an elastic fixed-window scan was essentially proportional to temperature in the range 120–300 K, indicating the absence of dynamical transition induced by the onset of translational diffusion in the hydration D2O. Since the width of quasielastic neutron scattering (QENS) peaks of the encapsulated Mb was Q-independent at 220, 240, and 265 K, the observed nanosecond-scale dynamics was attributed to internal motions of the encapsulated Mb, such as slow motions of amino acid groups or side chains. The fraction of immobile H-atoms in Mb was estimated to be above 0.8, which was larger than that for a free protein with a similar molecular weight to Mb. The large immobile fraction indicates that the nanosecond-scale motions of amino acid residues and side chains in the vicinity of the pore wall are restricted by the interfacial interactions with the rigid pore wall.

The Influence of Zinc Oxide Nanoparticles and Salt Stress on the Morphological and Some Biochemical Characteristics of Solanum lycopersicum L. Plants.

Salinity reduces crop yields and quality, causing global economic losses. Zinc oxide nanoparticles (ZnO-NPs) improve plant physiological and metabolic processes and abiotic stress resistance. This study examined the effects of foliar ZnO-NPs at 75 and 150 mg/L on tomato Kecskeméti 549 plants to alleviate salt stress caused by 150 mM NaCl. The precipitation procedure produced ZnO-NPs that were characterized using UV-VIS, TEM, STEM, DLS, EDAX, Zeta potential, and FTIR. The study assessed TPCs, TFCs, total hydrolyzable sugars, total free amino acids, protein, proline, H2O2, and MDA along with plant height, stem width, leaf area, and SPAD values. The polyphenolic burden was also measured by HPLC. With salt stress, plant growth and chlorophyll content decreased significantly. The growth and development of tomato plants changed by applying the ZnO-NPs. Dosages of ZnO-NPs had a significant effect across treatments. ZnO-NPs also increased chlorophyll, reduced stress markers, and released phenolic chemicals and proteins in the leaves of tomatoes. ZnO-NPs reduce salt stress by promoting the uptake of minerals. ZnO-NPs had beneficial effects on tomato plants when subjected to salt stress, making them an alternate technique to boost resilience in saline soils or low-quality irrigation water. This study examined how foliar application of chemically synthesized ZnO-NPs to the leaves affected biochemistry, morphology, and phenolic compound synthesis with and without NaCl.

Effect of Pod Storage and Drying Temperature on Fermentation Dynamics and Final Bean Quality of Cacao Nacional in Ecuador.

The impact of pod storage (PS) and two drying temperatures of fermented cocoa beans was investigated in Ecuador. Therefore, four variations were simultaneously carried out three times at two locations, independently: 0, 3, and 5 days of PS, dried at 60 °C and 0 days of PS, dried at 80 °C. Pod weight during storage, pulp content, pH, temperature, microbial counts, total free amino acids, protein profiles, sugars, organic acids, cut-test, fermentation index, and sensory profiles were analyzed. Minor differences in fermentation dynamics and bean quality were found between variations with and without PS. A rather accelerated fermentation with pod-stored beans was observed (e.g., faster color change, slightly lower pH in cotyledon after 48 h), along with a significantly higher maximal temperature during 24-42 h (43.1 ± 3.2 °C compared to 39.2 ± 2.0 °C without PS). More well-fermented beans were reached with PS (52.3 ± 22.6%) than without (62.7 ± 9.2%). Differences during fermentation were observed between the locations (e.g., pH, acids, sugars), but sensory evaluation indicated that the impact of location was mitigated with PS. Drying at 80 °C showed no adverse effects, as evidenced by the results of the cut-test and fermentation index. However, sensory evaluations revealed significant differences between 80 °C and 60 °C, with the former exhibiting more bitter and astringent cocoa liquor.

Fucoidan alleviates the inhibition of protein digestion by chitosan and its oligosaccharides

Chitosan (CTS) and chitosan oligosaccharides (COS) have been widely applied in food industry due to their bioactivities and functions. However, CTS and COS with positive charges could interact with proteins, such as whey protein isolate (WPI), influencing their digestion. Interaction among CTS/COS, FUC, and WPI/enzymes was studied by spectroscopy, chromatography, and chemical methods in order to reveal the role of FUC in relieving the inhibition of protein digestibility by CTS/COS and demonstrate the action mechanisms. As shown by the results, the addition of FUC increased degree of hydrolysis (DH) and free protein in the mixture of CTS and WPI to 3.1-fold and 1.8-fold, respectively, while raise DH value and free protein in the mixture of COS and WPI to 6.7-fold and 1.2-fold, respectively. The interaction between amino, carboxyl, sulfate, and hydroxyl groups from carbohydrates and protein could be observed, and notably, FUC could interact with CTS/COS preferentially to prevent CTS/COS from combining with WPI. In addition, the addition of FUC could also relieve the combination of CTS to trypsin, increasing the fluorescence intensity and concentration of trypsin by 83.3 % and 4.8 %, respectively. Thus, the present study demonstrated that FUC could alleviate the inhibitory effect of CTS/COS on protein digestion.

Thawed drip and its membrane-separated components: Role in retarding myofibrillar protein gel deterioration during freezing-thawing cycles

Myofibrillar proteins are crucial for gel formation in processed meat products such as sausages and meat patties. Freeze-thaw cycles can alter protein properties, impacting gel stability and product quality. This study aims to investigate the potential of thawed drip and its membrane-separated components as potential antifreeze agents to retard denaturation, oxidation and gel deterioration of myofibrillar proteins during freezing-thawing cycles of pork patties. The thawed drip and its membrane-separated components of > 10 kDa and < 10 kDa, along with deionized water, were added to minced pork at 10 % mass fraction and subjected to increasing freeze–thaw cycles. Results showed that the addition of thawed drip and its membrane separation components inhibited denaturation and structural changes of myofibrillar proteins, evidenced by reduced surface hydrophobicity and carbonyl content, increased free sulfhydryl groups, protein solubility and α-helix, as compared to the deionized water group. Correspondingly, improved gel properties including water-holding capacity, textural parameters and denser network structure were observed with the addition of thawed drip and its membrane separation components. Denaturation and oxidation of myofibrillar proteins were positively correlated with gel deterioration during freezing-thawing cycles. We here propose a role of thawed drip and its membrane separation components as cryoprotectants against myofibrillar protein gel deterioration during freeze-thawing cycles.

Physicochemical characterization of the fraction components of the theabrownin isolates from Pu'er tea

This study focuses on the isolation of theabrownins (TBs) from Pu'er tea. This isolation process involves low temperature water extraction, membrane separation, and multi-stage extraction with organic solvents. Subsequently, purification was performed using column chromatography with macroporous adsorbent resin D-101 and ethanol aqueous solution with a concentration of 0–64.81 g/100g. Five purified fractions were obtained, namely TBs-D1, TBs-D2, TBs-D3, TBs-D4, and TBs-D5, collectively referred to as TBs-D(1–5). These fractions were found to contain TBs and polysaccharides but lacked catechins, caffeine, theaflavin, and free protein. The average molecular weights of these fraction components exceeded 104 Da. These results indicated that TBs-D(1–5) were not free, but combined with tea polysaccharide conjugates (TPC), that is, TBs-TPC complexes. Furthermore, ultraviolet–visible spectrophotometry and Flourier transformation infrared spectroscopy confirmed the nature of TBs-D(1–5) as TBs-TPC complexes. Fluorescence spectra revealed that polysaccharides exert a quenching effect on the intrinsic fluorescence of TBs. Atomic force microscopy indicated that the sample forms a spherical cluster due to the aggregation of theabrownin molecules. Additionally, measurements of interfacial tension and water contact angle demonstrated that TBs-D(1–5) exhibit some amphiphilic properties. This research provides a theoretical foundation for the industrial production and utilization of TBs.

Viral Kinetics Model of SARS-CoV-2 Infection Informs Drug Discovery, Clinical Dose, and Regimen Selection.

Quantitative systems pharmacology (QSP) has been an important tool to project safety and efficacy of novel or repurposed therapies for the SARS-CoV-2 virus. Here, we present a QSP modeling framework to predict response to antiviral therapeutics with three mechanisms of action (MoA): cell entry inhibitors, anti-replicatives, and neutralizing biologics. We parameterized three distinct model structures describing virus-host interaction by fitting to published viral kinetics data of untreated COVID-19 patients. The models were used to test theoretical behaviors and map therapeutic design criteria of the different MoAs, identifying the most rapid and robust antiviral activity from neutralizing biologic and anti-replicative MoAs. We found good agreement between model predictions and clinical viral load reduction observed with anti-replicative nirmatrelvir/ritonavir (Paxlovid®) and neutralizing biologics bamlanivimab and casirivimab/imdevimab (REGEN-COV®), building confidence in the modeling framework to inform a dose selection. Finally, the model was applied to predict antiviral response with ensovibep, a novel DARPin therapeutic designed as a neutralizing biologic. We developed a new in silico measure of antiviral activity, area under the curve (AUC) of free spike protein concentration, as a metric with larger dynamic range than viral load reduction. By benchmarking to bamlanivimab predictions, we justified dose levels of 75, 225, and 600 mg ensovibep to be administered intravenously in a Phase 2 clinical investigation. Upon trial completion, we found model predictions to be in good agreement with the observed patient data. These results demonstrate the utility of this modeling framework to guide the development of novel antiviral therapeutics.

Pregnancy influences expression of interferon-stimulated genes, progesterone receptor and progesterone-induced blocking factor in ovine thyroid.

Embryonic interferon-tau (IFNT) and progesterone affect expression of interferonstimulated genes (ISGs), progesterone receptor (PGR) and progesterone-induced blocking factor (PIBF) in the ovine thyroid. Thyroids of ewes were sampled at day 16 of nonpregnancy, days 13, 16, and 25 of pregnancy, and real-time quantitative polymerase chain reaction assay, western blot and immunohistochemistry were used to detect expression of ISGs, PGR, and PIBF. Free ISG15 protein was undetected, but ISG15 conjugated proteins upregulated at day 16 of pregnancy, and expression levels of ISG15 conjugated proteins, PGR isoform (70 kDa), PIBF, interferon-gamma-inducible protein 10 and myxovirusresistance protein 1 peaked, but expression level of signal transducer and activator of transcription 1 was the lowest at day 16 of pregnancy. In addition, the expression levels of PGR isoform (70 kDa) and signal transducer and activator of transcription 1 (STAT1) decreased, but levels of PGR isoform (43 kDa), 2',5'-oligoadenylate synthetase, IP-10 and MX1 increased at day 25 of pregnancy comparing with day 16 of the estrous cycle. Early pregnancy affects expression of ISGs, PGR, and PIBF in maternal thyroid through IFNT and progesterone, which may regulate thyroid autoimmunity and thyroid hormone secretion in ewes.

Free ribosomal proteins as culprits for nucleolar stress

Nucleolar stress has been consistently linked to age-related diseases. In this issue, Sirozh etal.1 find that the common molecular signature of nucleolar stress is the accumulation of free ribosomal proteins, which leads to premature aging in mice; however, it can be reversed by mTOR inhibition.

The apo-acyl coenzyme A binding protein of Leishmania major forms a unique ‘AXXA’ motif mediated dimer

Acyl-Coenzyme A binding domain containing proteins (ACBDs) are ubiquitous in nearly all eukaryotes. They can exist as a free protein, or a domain of a large, multidomain, multifunctional protein. Besides modularity, ACBDs also display multiplicity. The same organism may have multiple ACBDs, differing in sequence and organization. By virtue of this diversity, ACBDs perform functions ranging from transport, synthesis, trafficking, signal transduction, transcription, and gene regulation. In plants and some microorganisms, these ACBDs are designated ACBPs (acyl-CoA binding proteins). The simplest ACBD/ACBP is a small, ∼10 kDa, soluble protein, comprising the acyl-CoA binding (ACB) domain. Most of these small ACBDs exist as monomers, while a few show a tendency to oligomerize. In sync with those studies, we report the crystal structure of two ACBDs from Leishmania major, named ACBP103, and ACBP96 based on the number of residues present. Interestingly, ACBP103 crystallized as a monomer and a dimer under different crystallization conditions. Careful examination of the dimer disclosed an exposed ‘AXXA’ motif in the helix I of the two ACBP103 monomers, aligned in a head-to-tail arrangement in the dimer. Glutaraldehyde cross-linking studies confirm that apo-ACBP103 can self-associate in solution. Isothermal titration calorimetry studies further show that ACBP103 can bind ligands ranging from C8 – to C20-CoA, and the data could be best fit to a ‘two sets of sites’/sequential binding site model. Taken together, our studies show that Leishmania major ACBP103 can self-associate in the apo-form through a unique dimerization motif, an interaction that may play an important role in its function.

Characterization and anti-aging activities of polysaccharide from Rana dybowskii Guenther.

Introduction: Rana dybowskii Guenther (RDG), as a traditional Chinese medicine, has been shown to have antioxidant effects. However, studies on the anti-aging effect of RDG are still limited. Methods: In this study, we prepared polysaccharides from the skin of RDG (RDGP) by hot water extraction, alcohol precipitation, ion-exchange chromatography and gel chromatography. The proteins were removed using the Sevage method in combination with an enzymatic method. The structural features were analyzed using high-performance gel permeation chromatography, β-elimination reaction and Fourier transform infrared spectra. The anti-aging effect of RDGP was investigated by using D-Gal to establish an aging model in mice, and pathological changes in the hippocampus were observed under a microscope. Results: We obtained the crude polysaccharide DGP from the skin of RDG, with a yield of 61.8%. The free protein was then removed by the Sevage method to obtain DGPI and deproteinated by enzymatic hydrolysis combined with the Sevage method to further remove the bound protein to obtain the high-purity polysaccharide DGPII. Then, DGPIa (1.03 × 105Da) and DGPIIa (8.42 × 104Da) were obtained by gel chromatography, monosaccharide composition analysis showed that they were composed of Man, GlcA, GalNAc, Glc, Gal, Fuc with molar ratios of 1: 4.22 : 1.55: 0.18 : 8.05: 0.83 and 0.74 : 1.78: 1: 0.28: 5.37 : 0.36, respectively. The results of the β-elimination reaction indicated the presence of O-glycopeptide bonds in DGPIa. The Morris water maze test indicated that mice treated with DGPIIa exhibited a significantly shorter escape latency and increased time spent in the target quadrant as well as an increase in the number of times they traversed the platform. Pathologic damage to the hippocampus was alleviated in brain tissue stained with hematoxylin-eosin. In addition, DGPIIa enhanced the activities of SOD, CAT, and GSH-Px and inhibited the level of MDA in the serum and brain tissues of aging mice. Discussion: These results suggest that RDGP has potential as a natural antioxidant and provide useful scientific information for anti-aging research.