121 research outputs found

    Prediction of Order Parameters based on Protein NMR Structure Ensemble and Machine Learning

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    The fast motions of proteins at the picosecond to nanosecond timescale, known as fast dynamics, are closely related to protein conformational entropy and rearrangement, which in turn affect catalysis, ligand binding and protein allosteric effects. The most used NMR approach to study fast protein dynamics is the model free method, which uses order parameter S2 to describe the amplitude of the internal motion of local group. However, to obtain order parameter through NMR experiments is quite complex and lengthy. In this paper, we present a machine learning approach for predicting order parameters based on protein NMR structure ensemble. A random forest model is used to learn the relationship between order parameters and structural features. Our method achieves high accuracy in predicting order parameters for a test dataset of 10 proteins, with a Pearson correlation coefficient of 0.817 and a root-mean-square error of 0.131

    Long-Term Dietary Supplementation with Betaine Improves Growth Performance, Meat Quality and Intramuscular Fat Deposition in Growing-Finishing Pigs

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    This study was designed to investigate the effects of dietary betaine supplementation on growth performance, meat quality and muscle lipid metabolism of growing-finishing pigs. Thirty-six crossbred pigs weighing 24.68 ± 0.97 kg were randomly allotted into two treatments consisting of a basal diet supplemented with 0 or 1200 mg/kg betaine. Each treatment included six replications of three pigs per pen. Following 119 days of feeding trial, dietary betaine supplementation significantly enhanced average daily gain (ADG) (p < 0.05) and tended to improve average daily feed intake (ADFI) (p = 0.08) and decreased the feed intake to gain ratio (F/G) (p = 0.09) in pigs during 100~125 kg. Furthermore, a tendency to increase ADG (p = 0.09) and finial body weight (p = 0.09) of pigs over the whole period was observed in the betaine diet group. Betaine supplementation significantly increased a*45 min and marbling and decreased b*24 h and cooking loss in longissimus lumborum (p < 0.05), tended to increase intramuscular fat (IMF) content (p = 0.08), however had no significant influence on carcass characteristics (p > 0.05). Betaine supplementation influenced the lipid metabolism of pigs, evidenced by a lower serum concentration of low-density lipoprotein cholesterol (p < 0.05), an up-regulation of mRNA abundance of fatty acid synthase and acetyl-CoA carboxylase (p < 0.05), and a down-regulation of mRNA abundance of lipolysis-related genes, including the silent information regulators of transcription 1 (p = 0.08), peroxisome proliferator-activated receptorα (p < 0.05), peroxisome proliferator-activated receptor gamma coactivator-1α (p = 0.07) and carnitine palmitoyl transferase 1 (p < 0.05) in longissimus lumborum. Moreover, betaine markedly improved the expression of microRNA-181a (miR-181a) (p < 0.05) and tended to enhance miR-370 (p = 0.08). Overall, betaine supplementation at 1200 mg/kg could increase the growth performance of growing-finishing pigs. Furthermore, betaine had a trend to improve meat quality and IMF content via increasing lipogenesis and down-regulating the abundance of genes associated with lipolysis, respectively, which was associated with the regulation of miR-181a and miR-370 expression by betaine

    Epigallocatechin-3-Gallate Alleviates Liver Oxidative Damage Caused by Iron Overload in Mice through Inhibiting Ferroptosis

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    Ferroptosis, a form of regulated cell death, has been widely explored as a novel target for the treatment of diseases. The failure of the antioxidant system can induce ferroptosis. Epigallocatechin-3-Gallate (EGCG) is a natural antioxidant in tea; however, whether EGCG can regulate ferroptosis in the treatment of liver oxidative damage, as well as the exact molecular mechanism, is unknown. Here, we discovered that iron overload disturbed iron homeostasis in mice, leading to oxidative stress and damage in the liver by activating ferroptosis. However, EGCG supplementation alleviated the liver oxidative damage caused by iron overload by inhibiting ferroptosis. EGCG addition increased NRF2 and GPX4 expression and elevated antioxidant capacity in iron overload mice. EGCG administration attenuates iron metabolism disorders by upregulating FTH/L expression. Through these two mechanisms, EGCG can effectively inhibit iron overload-induced ferroptosis. Taken together, these findings suggest that EGCG is a potential ferroptosis suppressor, and may be a promising therapeutic agent for iron overload-induced liver disease

    Easily Established and Multifunctional Synthetic Nanobody Libraries as Research Tools

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    Nanobodies, or VHHs, refer to the antigen-binding domain of heavy-chain antibodies (HCAbs) from camelids. They have been widely used as research tools for protein purification and structure determination due to their small size, high specificity, and high stability, overcoming limitations with conventional antibody fragments. However, animal immunization and subsequent retrieval of antigen-specific nanobodies are expensive and complicated. Construction of synthetic nanobody libraries using DNA oligonucleotides is a cost-effective alternative for immunization libraries and shows great potential in identifying antigen-specific or even conformation-specific nanobodies. This review summarizes and analyses synthetic nanobody libraries in the current literature, including library design and biopanning methods, and further discusses applications of antigen-specific nanobodies obtained from synthetic libraries to research

    Protein conformational exchanges modulated by the environment of outer membrane vesicles

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    Protein function, in many cases, is highly related to its frustration status and hence intimately coupled to the dynamics and conformational equilibria of the protein. The environment surrounding proteins is critical for their dynamics and can dra-matically affect the conformational equilibria and subsequently activities of proteins. However, it is yet unclear how protein conformational equilibria are modulated by their crowded native environments. Here we revealed the immunity protein Im7 was less frustrated and shifted toward its ground state in OMVs than in the aqueous solution. Further experiments showed both macromolecular crowding and quinary interactions with the periplasmic components stabilized the ground state of Im7. Our studies highlight the key role of the OMVs environment played on protein conformational equilibria and subsequently conformation-related protein functions. Furthermore, the long-lasting NMR measurement time of proteins within OMVs underlies it could serve as a promising system to investigate protein structures and dynamics in situ via nuclear magnetic spectroscopy

    1,25-Dihydroxyvitamin D3 Negatively Regulates the Inflammatory Response to Porcine Epidemic Diarrhea Virus Infection by Inhibiting NF-κB and JAK/STAT Signaling Pathway in IPEC-J2 Porcine Epithelial Cells

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    Porcine epidemic diarrhea virus (PEDV) infection causes watery diarrhea and vomiting in piglets. The pathogenesis of PEDV infection is related to intestinal inflammation. It is known that 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) has potent anti-inflammatory activity, but it is unknown whether 1,25(OH)2D3 can inhibit the PEDV-induced inflammatory response and the underlying mechanism. We used transcriptome analysis, gene and protein expression, RNA interference and overexpression, and other techniques to study the anti-inflammatory effects of 1,25(OH)2D3 on PEDV infection in IPEC-J2 cells. The results showed that interleukin 19 (IL-19) and C-C motif chemokine ligand 20 (CCL20) gene expression were enhanced with the increase in PEDV infection time in IPEC-J2 cells. Interestingly, 1,25(OH)2D3 supplementation obviously inhibited IL-19 and CCL20 expression induced by PEDV. Meanwhile, we also found that 1,25(OH)2D3 reduced p-NF-κB, p-STAT1, and p-STAT3 protein levels induced by PEDV at 24 h post-infection. IκBα and SOCS3, NF-κB, and STAT inhibitor respectively, were increased by 1,25(OH)2D3 supplementation upon PEDV infection. In addition, 1,25(OH)2D3 supplementation inhibited ISG15 and MxA expression induced by PEDV. Although 1,25(OH)2D3 suppressed the JAK/STAT signal pathway and antiviral gene expression, it had no significant effects on PEDV replication and IFN-α-induced antiviral effects. In addition, when the vitamin D receptor (VDR) was silenced by siRNA, the anti-inflammatory effect of 1,25(OH)2D3 was inhibited. Meanwhile, the overexpression of VDR significantly downregulated IL-19 and CCL20 expression induced by PEDV infection. Together, our results provide powerful evidence that 1,25(OH)2D3 could alleviate PEDV-induced inflammation by regulating the NF-κB and JAK/STAT signaling pathways through VDR. These results suggest that vitamin D could contribute to inhibiting intestinal inflammation and alleviating intestinal damage in PEDV-infected piglets, which offers new approaches for the development of nutritional strategies to prevent PEDV infection in piglets

    Protective effects of sodium butyrate on rotavirus inducing endoplasmic reticulum stress-mediated apoptosis via PERK-eIF2α signaling pathway in IPEC-J2 cells

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    Abstract Background Rotavirus (RV) is a major pathogen that causes severe gastroenteritis in infants and young animals. Endoplasmic reticulum (ER) stress and subsequent apoptosis play pivotal role in virus infection. However, the protective mechanisms of intestinal damage caused by RV are poorly defined, especially the molecular pathways related to enterocytes apoptosis. Thus, the aim of this study was to investigate the protective effect and mechanism of sodium butyrate (SB) on RV-induced apoptosis of IPEC-J2 cells. Results The RV infection led to significant cell apoptosis, increased the expression levels of ER stress (ERS) markers, phosphorylated protein kinase-like ER kinase (PERK), eukaryotic initiation factor 2 alpha (eIF2α), caspase9, and caspase3. Blocking PERK pathway using specific inhibitor GSK subsequently reversed RV-induced cell apoptosis. The SB treatment significantly inhibited RV-induced ERS by decreasing the expression of glucose regulated protein 78 (GRP78), PERK, and eIF2α. In addition, SB treatment restrained the ERS-mediated apoptotic pathway, as indicated by downregulation of C/EBP homologous protein (CHOP) mRNA level, as well as decreased cleaved caspase9 and caspase3 protein levels. Furthermore, siRNA-induced GPR109a knockdown significantly suppressed the protective effect of SB on RV-induced cell apoptosis. Conclusions These results indicate that SB exerts protective effects against RV-induced cell apoptosis through inhibiting ERS mediated apoptosis by regulating PERK-eIF2α signaling pathway via GPR109a, which provide new ideas for the prevention and control of RV

    Roseltide rT7 is a disulfide-rich, anionic, and cell-penetrating peptide that inhibits proteasomal degradation

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    Disulfide-rich plant peptides with molecular masses of 2-6 kDa represent an expanding class of peptidyl-type natural products with diverse functions. They are structurally compact, hyperstable, and underexplored as cell-penetrating agents that inhibit intracellular functions. Here, we report the discovery of an anionic, 34-residue peptide, the disulfide-rich roseltide rT7 from Hibiscus sabdariffa (of the Malvaceae family) that penetrates cells and inhibits their proteasomal activities. Combined proteomics and NMR spectroscopy revealed that roseltide rT7 is a cystine-knotted, six-cysteine hevein-like cysteine-rich peptide. A pair-wise comparison indicated that roseltide rT7 is >100-fold more stable against protease degradation than its S-alkylated analog. Confocal microscopy studies and cell-based assays disclosed that after roseltide rT7 penetrates cells, it causes accumulation of ubiquitinated proteins, inhibits human 20S proteasomes, reduces tumor necrosis factor-induced IκBα degradation, and decreases expression levels of intercellular adhesion molecule-1. Structure-activity studies revealed that roseltide rT7 uses a canonical substrate-binding mechanism for proteasomal inhibition enabled by an IIML motif embedded in its proline-rich and exceptionally long intercysteine loop 4. Taken together, our results provide mechanistic insights into a novel disulfide-rich, anionic, and cell-penetrating peptide, representing a potential lead for further development as a proteasomal inhibitor in anti-cancer or anti-inflammatory therapies.Ministry of Education (MOE)Nanyang Technological UniversityPublished versionThis work was supported in part by Nanyang Technological University Internal Funding–Synzymes and Natural Products (SYNC) and AcRF Tier 3 funding Grant MOE2016-T3-1-00
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