Plants have evolved complex immune networks to adapt to survival needs,and their immune mechanisms have unique regulatory patterns to cope with different environments.In rice,the maintenance of immune balance involves...Plants have evolved complex immune networks to adapt to survival needs,and their immune mechanisms have unique regulatory patterns to cope with different environments.In rice,the maintenance of immune balance involves the synergistic action of many factors.Yue Wu et al.'s latest research results on the immunomodulatory mechanism of rice(ROD1 and the interaction between various proteins in rice)are introduced in this paper.展开更多
Mosquito-borne flaviviruses,such as Zika virus(ZIKV)and dengue virus(DENV),cause diverse severe clinical manifestations including fever,rash,hepatitis,arthralgia,and congenital anomalies.Here,we identified a host fact...Mosquito-borne flaviviruses,such as Zika virus(ZIKV)and dengue virus(DENV),cause diverse severe clinical manifestations including fever,rash,hepatitis,arthralgia,and congenital anomalies.Here,we identified a host factor,the adaptor protein complex 1 gamma 1 subunit(AP1G1),which plays an important role in both ZIKV and dengue virus 2(DENV2)infections.We explored the role of AP1G1 in ZIKV and DENV2 infections using CRISPR/Cas9 gene editing technology and RNA interference(RNAi)techniques.Knockout or silencing of AP1G1 decreases the replication of ZIKV and DENV2 in multiple human cell lines.Intriguingly,depletion of AP1G1 results in a significant reduction in ZIKV at an early stage,but decreases DENV2 replication levels during the late stage,suggesting that AP1G1 plays distinct roles in the infection by ZIKV and DENV2.Furthermore,we determined that AP1G1 mediates ZIKV-endosomal membrane fusion through inhibitor experiments and fluorescence labeling assays.Mechanistically,we found that AP1G1 exerts its pro-viral effect through binding to the ZIKV envelope glycoprotein(E protein).This interaction promotes the fusion of viral and endosomal membranes,during which the ZIKV genomic RNAs are released from the endosome into the cytoplasm,a process that facilitates viral replication.However,for DENV2 infection,AP1G1 primarily affects its viral RNA replication stage,rather than the fusion of virus-endosomal membrane.Taken together,our work demonstrates that AP1G1 plays a pro-viral role in both ZIKV and DENV2 infections via distinct mechanisms,highlighting its potential as a therapeutic target for antiviral strategies.展开更多
The changes of chlorophyll_protein complexes and photosynthetic activities of chloroplast isolated from lotus ( Nelumbo nucifera Gaertn.) seeds germinating under illumination were studied. SDS PAGE analysis of c...The changes of chlorophyll_protein complexes and photosynthetic activities of chloroplast isolated from lotus ( Nelumbo nucifera Gaertn.) seeds germinating under illumination were studied. SDS PAGE analysis of chlorophyll_protein complexes showed that there was only the light harvesting chlorophyll a/b protein complex from PSⅡ (LHCⅡ) precursor in chloroplast from lotus seeds germinated for 2 to 6 days, while LHC Ⅱ 1, and the chlorophyll_protein complex of PSⅠ (CPⅠ) appeared on the 8th day of germination and PSⅡ reaction center complex appeared later. Studies on the polypeptides composition of the chloroplast revealed the following results: 1) Small amount of the 27 kD polypeptide was synthesized in invisible light; 2) The 30 kD polypeptide existed previously in the plumules of the dry seeds; 3) The amount of the 30 kD polypeptide was more than any other polypeptides before germination and decreased gradually throughout germination, while the 27 kD polypeptide changed in the opposite way; 4) In the process of germination, measurement of the electron transport rate and the fluorescence induction kinetics at room temperature showed that PSⅡ activities and efficiency of primary light energy transformation were only experimentally measurable after 7 days of germination and gradually increased afterwards. At the same time, the chl a/b ratio rose from the lower value to normal; 5) The changes of chloroplast membrane components and its functions are concomitant in concert with that of the ultrastructure of chloroplast membranes during germination, as shown in our earlier work . The results have proved again that a different developmental pathway of chloroplast is likely to exist in the lotus plumules, which might provide an important clue for N. nucifera in having an unique position in the phylogeny of the angiosperm.展开更多
Polycomb group （PCG） complexes are epigenetic regulatory complexes that conduct transcriptional repression of target genes via modifying the chromatin. The two best characterized forms of PCG complexes, polycomb rep...Polycomb group （PCG） complexes are epigenetic regulatory complexes that conduct transcriptional repression of target genes via modifying the chromatin. The two best characterized forms of PCG complexes, polycomb repressive complexes 1 and 2 （PRC1 and PRC2）, are required for maintaining the sternness of embryonic stem cells and many types of adult stem cells. The spectra of target genes for PRCs are dynamically changing with cell differentiation, which is essential for proper decisions on cell fate during developmental processes, Chromobox （CBX） family proteins are canonical components in PRC1, responsible for targeting PRC1 to the chromatin. Recent studies highlight the function specifications among CBX family members in undifferentiated and differentiated stem cells, which reveal the interplay between compositional diversity and functional specificity of PRCI. In this review, we summarize the current knowledge about targeting and functional mechanisms of PRCs, emphasizing the recent breakthroughs related to CBX proteins under a number of physiological and pathological conditions.展开更多
Soy protein isolate(SPI)is a commercial protein with balanced amino acids,while the poor solubility impedes its use in traditional foods.To overcome the problem,the complex coacervation of SPI/Flammulina velutipes pol...Soy protein isolate(SPI)is a commercial protein with balanced amino acids,while the poor solubility impedes its use in traditional foods.To overcome the problem,the complex coacervation of SPI/Flammulina velutipes polysaccharide(FVP)were investigated.Initial results revealed that the suitable amounts of FVP contributed to reducing the turbidity of SPI solution.Under electrostatic interaction,the formation of SPI/FVP coacervates were spontaneous and went through a nucleation and growth process.Low salt concentration(C_(NaCl)=10,50 mmol/L)led to an increase in the critical pH values(pHc,pHφ1)while the critical pH values decreased when C_(NaCl)≥100 mmol/L.The concentration of NaCl ions increased the content ofα-helix.With the increase of FVP,the critical pH values decreased and the content ofβ-sheet increased through electrostatic interaction.At SPI/FVP ratio of 10:1 and 15:1,the complex coacervation of SPI/FVP were saturated,and the coacervates had the same storage modulus value.SPI/FVP coacervates exhibited solid-like properties and presented the strongest storage modulus at C_(NaCl)=50 mmol/L.The optimal pH,SPI/FVP ratio and NaCl concentration of complex coacervation were collected,and the coacervates demonstrated a valuable application potential to protect and deliver bioactives and food ingredients.展开更多
Complex coacervation of whey protein（WP） with acacia gum（AG） was carried out in water with the presence of dodecyl acetate （DA）,a component of insect sex pheromones,in order to obtain microcapsules with DA as th...Complex coacervation of whey protein（WP） with acacia gum（AG） was carried out in water with the presence of dodecyl acetate （DA）,a component of insect sex pheromones,in order to obtain microcapsules with DA as the core material and WP-AG coacervate as the wall materials.Through variations in wall/core ratios,concentrations of the wall materials in capsule preparations,DA encapsulation was optimized,which showed a high DA encapsulation was achieved when coacervation was conducted at pH 3.5 with wall/core mass ratio at 3 combined with concentration of wall materials at 1.0 wt%.Morphology and the structure of DA loaded microcapsules were examined by scanning electron microscope,which showed the microcapsules were of core/shell structure with DA encapsulated in the inner of the microcapsules.DA release was examined and the behavior of the release was discussed.展开更多
OBJECTIVE: To study the efficacy and explore the mechanism of the anti-tumor immunity elicited by heat shock protein 70-peptide complexes (HSP70-PC) derived from tumor cells. METHODS: Cells culture, flow cytometric an...OBJECTIVE: To study the efficacy and explore the mechanism of the anti-tumor immunity elicited by heat shock protein 70-peptide complexes (HSP70-PC) derived from tumor cells. METHODS: Cells culture, flow cytometric analysis, affinity chromatography for protein purification, SDS-PAGE, Western-blotting and animal experiment were used. RESULTS: HSP70-PC immunization rendered protective effect to both naive tumorl-bearing mice. All of the naive mice obtained complete resistance to Hcaf cell attack; 40% of the tumor-bearing mice survived for over 90 days, whereas the mice of control group died within 2 weeks (P展开更多
The cytosolic chaperonin T-complex protein 1-ring complex(TRiC)or chaperonin containing T-complex protein 1(CCT)is essential in de novo folding of approximately 10%of the eukaryotic,newly translated polypeptides as we...The cytosolic chaperonin T-complex protein 1-ring complex(TRiC)or chaperonin containing T-complex protein 1(CCT)is essential in de novo folding of approximately 10%of the eukaryotic,newly translated polypeptides as well as misfolded proteins.There is a close link between the TRiC/CCT cytosolic chaperonin and neurodegenerative diseases(Lopez et al.,2015).A lot of research suggests that CCT plays neuroprotective roles in neurodegenerative diseases including Huntington’s disease(Lopez et al.,2015).Either overexpression of a single or all eight subunits(CCT1-8)or treatment of the substrate-binding apical domain of yeast CCT1(ApiCCT1)prevented mutant Huntingtin aggregation and improved cellular and neuronal functions(Zhao et al.,2016).Importantly,our recent study has demonstrated that both CCT and ApiCCT could reduce mutant Huntingtin level and enhance both anterograde and retrograde axonal transport of brain-derived neurotrophic factor.These results led to restoration of the trophic status of striatal neurons from a bacterial artificial chromosome transgenic mouse model of Huntington’s disease(Zhao et al.,2016).Axonal transport is regulated by many factors including microtubule-associated protein tau,which promotes tubulin polymerization and stabilizes microtubules.Impaired interaction between tau and microtubules plays a vital role in the pathogenesis of multiple neurodegenerative diseases(Wang and Mandelkow,2016).Interestingly,tau phosphorylation is also observed in brains of several Huntington’s disease mouse models and Huntington’s disease patients(Gratuze et al.,2016).In a recent study,we explored if CCT subunit has any effect on axonal transport in a tau-dependent pathway(Chen et al.,2018b).We focused on the retrograde axonal transport of brain-derived neurotrophic factor,as neurotrophic factor-mediated signaling in the form of signaling endosome is essential in both the developing and the mature nervous system and dysregulation of trafficking of neurotrophic factors is tightly linked to disorders of the nervous system(Chen et al.,2018a).We found that the expression of a single CCT subunit(CCT5)significantly promoted retrograde axonal transport of brain-derived neurotrophic factor in primary cortical neurons.Mechanically,CCT regulated the level of cyclin-dependent kinase 5(CDK5)/p35/p25 and,subsequently contributed to CCT-induced tau phosphorylation,which induced detachment of tau from microtubules(Chen et al.,2018b)(Figure 1).展开更多
This paper proposes a novel four-dimensional approach to the structural study of protein complexes. In the approach, the surface of a protein molecule is to be described using the intersection of a pair of four-dimens...This paper proposes a novel four-dimensional approach to the structural study of protein complexes. In the approach, the surface of a protein molecule is to be described using the intersection of a pair of four-dimensional triangular cones (with multiple top vertexes). As a mathematical toy model of protein complexes, we consider complexes of closed trajectories of n-simplices (n=2,3,4...), where the design problem of protein complexes corresponds to an extended version of the Hamiltonian cycle problem. The problem is to find “a set of” closed trajectories of n-simplices which fills the n-dimensional region defined by a given pair of n+1 -dimensional triangular cones. Here we give a solution to the extended Hamiltonian cycle problem in the case of n=2 using the discrete differential geometry of triangles (i.e., 2-simplices).展开更多
The prediction of intrinsically disordered proteins is a hot research area in bio-information.Due to the high cost of experimental methods to evaluate disordered regions of protein sequences,it is becoming increasingl...The prediction of intrinsically disordered proteins is a hot research area in bio-information.Due to the high cost of experimental methods to evaluate disordered regions of protein sequences,it is becoming increasingly important to predict those regions through computational methods.In this paper,we developed a novel scheme by employing sequence complexity to calculate six features for each residue of a protein sequence,which includes the Shannon entropy,the topological entropy,the sample entropy and three amino acid preferences including Remark 465,Deleage/Roux,and Bfactor(2STD).Particularly,we introduced the sample entropy for calculating time series complexity by mapping the amino acid sequence to a time series of 0-9.To our knowledge,the sample entropy has not been previously used for predicting IDPs and hence is being used for the first time in our study.In addition,the scheme used a properly sized sliding window in every protein sequence which greatly improved the prediction performance.Finally,we used seven machine learning algorithms and tested with 10-fold cross-validation to get the results on the dataset R80 collected by Yang et al.and of the dataset DIS1556 from the Database of Protein Disorder(DisProt)(https://www.disprot.org)containing experimentally determined intrinsically disordered proteins(IDPs).The results showed that k-Nearest Neighbor was more appropriate and an overall prediction accuracy of 92%.Furthermore,our method just used six features and hence required lower computational complexity.展开更多
Protein–protein interactions (PPI) are important for many biological processes. Theoretical understanding of the structurally determining factors of interaction sites will help to understand the underlying mechanism ...Protein–protein interactions (PPI) are important for many biological processes. Theoretical understanding of the structurally determining factors of interaction sites will help to understand the underlying mechanism of protein–protein interactions. At the same time, understanding the complex structure of proteins helps to explore their function. And accurately predicting protein complexes from PPI networks helps us understand the relationship between proteins. In the past few decades, scholars have proposed many methods for predicting protein interactions and protein complex structures. In this review, we first briefly introduce the methods and servers for predicting protein interaction sites and interface residue pairs, and then introduce the protein complex structure prediction methods including template-based prediction and template-free prediction. Subsequently, this paper introduces the methods of predicting protein complexes from the PPI network and the method of predicting missing links in the PPI network. Finally, it briefly summarizes the application of machine/deep learning models in protein structure prediction and action site prediction.展开更多
In analyses of protein families that may serve as drug targets,membrane-associated G-protein-coupled receptors(GPCRs)dominate,followed by ion channels,transporters,and—to a lesser extent—membrane-bound enzymes.Howev...In analyses of protein families that may serve as drug targets,membrane-associated G-protein-coupled receptors(GPCRs)dominate,followed by ion channels,transporters,and—to a lesser extent—membrane-bound enzymes.However,various challenges put such membrane proteins among key groups of underutilized opportunities for the application of therapeutic antibodies.Antibodies hold the promise of exquisite specificity,as they are able to target even specific conformations of a particular membrane protein,as well as adaptability through engineering into various antibody formats.However,the ease of raising and isolating specific,effective antibodies targeting membrane proteins depends on many factors.In particular,the generation of specific antibodies is easier when targeting larger,simpler,extracellular domains with greater uniqueness of amino acid sequence.The rareness of such ideal conditions is illustrated by the limited number of approved biologics for targeting GPCRs and other complex membrane proteins.Challenges in developing antibodies to complex membrane proteins such as GPCRs,ion channels,transporters,and membrane-bound enzymes can be addressed by the design of the antigen,antibody-generation strategies,lead optimization technologies,and antibody modalities.A better understanding of the membrane proteins being targeted would facilitate mechanism-based drug discovery.This review describes the advantages and challenges of targeting complex membrane proteins with antibodies and discusses the preparation of membrane protein antigens and antibody generation,illustrated by select examples of success.展开更多
Nine pigment-protein complexes were separated and characterized from intact Chroomonasplacoidea chloroplasts by IEF. The bands Ⅰ-Ⅵ with their isoelectric points （pI） values from 4 to 6 were phycocyanin components;...Nine pigment-protein complexes were separated and characterized from intact Chroomonasplacoidea chloroplasts by IEF. The bands Ⅰ-Ⅵ with their isoelectric points （pI） values from 4 to 6 were phycocyanin components; bands Ⅷ and Ⅸ （pI = 2.8-3.6） were chlorophyll-protein complexes. According to absorption and fluorescence spectra, band VII was designated as a novel phycocyanin-Chla/c2-protein complex （pI ≈ 3.4-3.7）. These results indicated that phycocyanin is structurally and functionally coupled with chlorophyll-protein complex in C. placoidea, and probably interacted with electrostatic force in combination.展开更多
Objective:To explore the in vivo anticancer,anti-angiogenesis and immunomodulatory efficacies of the bioactive polysaccharide isolated from cold aqueous extract of Jania rubens(JCEM) and Pterocladia capillacea(PCEM) a...Objective:To explore the in vivo anticancer,anti-angiogenesis and immunomodulatory efficacies of the bioactive polysaccharide isolated from cold aqueous extract of Jania rubens(JCEM) and Pterocladia capillacea(PCEM) as well as hot aqueous extract of Enteromorpha intestinalis(EHEM) against hepatocellular carcinoma rat model(HCC) and to study their chemical composition.Methods:The sugars and amino acids composition of the bioactive polysaccharides of JCEM,PCEM and EHEM were determined using gas liquid chromatography and amino acid analyzer,respectively.These polysaccharide extracts(20 mg/kg b.wt.for 5 weeks) were assessed on hepatocarcinogenesis in rats and α-fetoprotein(AFP),carcinoembryonic antigen(CEA),glypican-3(GPC-3),hepatocyte growth factor(HGF) and vascular endothelial growth factor(VEGF) and Ig G levels were evaluated.Results:The GLC analysis of JCEM,PCEM and EHEM polysaccharide revealed the presence of 10,9 and10 sugars,in addition the amino acid analyser enable identification of 16,15 and 15 amino acids,respectively.These polysaccharide extracts of JCEM,PCEM and EHEM produced significant decrease in serum AFP,CEA,GPC-3,HGF and VEGF compared with untreated HCC group.JCEM,PCEM and EHEM had an immunostimulatory responses by increasing the IgG levels as compared by naive value(1.23,1.53 and 1.17 folds),respectively.The bioactive polysaccharides in HCC induced rats improved the humoral immune response.The photomicrographs of liver tissue sections of the groups of HCC treated with polysaccharide extracts of Jania rubens and Enteromorpha intestinalis showed intact histological structure.Moreover,fractions HE1,HE4,HE7 obtained from polysaccharide of EHEM showed moderate cytotoxic activity against Hep G2 in vitro with IC_(50) 73.1,42.6,76.2 μg/mL.However,fractions of PCEM and JCEM show no or weak cytotoxicity against Hep G2 in vitro where the cytotoxic activity of their crude polysaccharide extract proved synergetic effect.Conclusions:The pronounced antitumor activity of sulphated polysaccharide-protein complexes of JCEM and EHEM is due to direct cytotoxic activity,anti-hepatocarcinogensis,and anti-angiogenesis.In addition,JCEM,PCEM and EHEM had an immunostimulatory response and improved the humoral immune response in HCC induced rats.展开更多
High-throughput techniques,such as the yeast-two-hybrid system,produce mass protein-protein interaction data. The new technique makes it possible to predict protein complexes by com-putation. A novel method,named DSDA...High-throughput techniques,such as the yeast-two-hybrid system,produce mass protein-protein interaction data. The new technique makes it possible to predict protein complexes by com-putation. A novel method,named DSDA,has been put forward to predict protein complexes via dense subgraph because the proteins among a protein complex have a much tighter relation among them than with others. This method chooses a node with its neighbors to form the initial subgraph,and chooses a node which has the tightest relation with the subgraph according to greedy strategy,then the chosen node is added into the initial subgraph until the subgraph density is below the threshold value. The ob-tained subgraph is then removed from the network and the process continues until no subgraph can be detected. Compared with other algorithms,DSDA can predict not only non-overlap protein com-plexes but also overlap protein complexes. The experiment results show that DSDA predict as many protein complexes as possible. And in Y78K network the accuracy of DSDA is as twice times as that of RNSC and MCL.展开更多
The application of phenylfluorone (PF)-Mo(VI) complex as a spectroscopic probe is studied. In the presence of OP microemulsion at pH 3.04, PF-Mo(Ⅵ) complex combines protein rapidly to form a stable compound and the a...The application of phenylfluorone (PF)-Mo(VI) complex as a spectroscopic probe is studied. In the presence of OP microemulsion at pH 3.04, PF-Mo(Ⅵ) complex combines protein rapidly to form a stable compound and the absorbance at 527 nm is in proportion to the concentration of protein in the range 0-16 μg mL-1 for bovine serum albumin (BSA). OP microemuslion media is introduced into protein determination, it has increased markedly the sensitivity of the system. The molar absorption coefficient was 5.98×l06 L mol-1 cm-1 for BSA. The assay, with sensitivity, simplicity and tolerance to many foreign substances, is applied to the determination of protein in samples with satisfactory results. Moreover, the binding number of BSA with the complex, which is determined by molar ratio and slope ratio methods, is in good agreement.展开更多
Discharge of whey proteins is still a current practice by small cheese producers. The development of low-cost alternatives for recovery of these proteins is fundamental for small producers who cannot apply expensive t...Discharge of whey proteins is still a current practice by small cheese producers. The development of low-cost alternatives for recovery of these proteins is fundamental for small producers who cannot apply expensive techniques. The present study investigated the complex coacervation technique as a cheap technology to recover proteins from sweet whey using carboxymethylcellulose, and the coacervate used as an ingredient in the formulation of probiotic fermented milk. The nutritional properties of whey-carboxymethylcellulose coacervates (WP-CMC) were evaluated in trials with animals (rats) using casein as a reference. All these parameters—the coefficient of feed efficiency (CEA), protein digestibility-corrected amino acid score (PDCAAS), and net protein ratio (NPR), as well as weight gain—were determined to evaluate protein quality. A sensory acceptance test was applied to evaluate the sensory characteristics of the product. The complex coacervation technique recovered 86% of the protein from sweet whey. No significant (p > 0.05) differences were observed in the biological tests for both groups (WP-CMC and Casein groups) when NPR (4.98 to 5.04), digestibility (92.35 to 90.64), and CEA (0.40 to 0.42) were evaluated. Probiotic fermented milk beverage containing WP-CMC (0.78%) and guar gum (0.68%) presented good acceptability as determined by sensory evaluation. WP-CMC can be considered an ingredient with high nutritional and biological value that could be applied in probiotic fermented milk as an alternative to small producers to allocate the residual whey from cheese manufacture.展开更多
Reconstituting membrane proteins in liposomes and determining their structure is a common method for determining membrane protein structures using single-particle cryo-electron microscopy(cryo-EM).However,the strong s...Reconstituting membrane proteins in liposomes and determining their structure is a common method for determining membrane protein structures using single-particle cryo-electron microscopy(cryo-EM).However,the strong signal of liposomes under cryo-EM imaging conditions often interferes with the structural determination of the embedded membrane proteins.Here,we propose a liposome signal subtraction method based on single-particle two-dimensional(2D)classification average images,aimed at enhancing the reconstruction resolution of membrane proteins.We analyzed the signal distribution characteristics of liposomes and proteins within the 2D classification average images of protein–liposome complexes in the frequency domain.Based on this analysis,we designed a method to subtract the liposome signals from the original particle images.After the subtraction,the accuracy of single-particle three-dimensional(3D)alignment was improved,enhancing the resolution of the final 3D reconstruction.We demonstrated this method using a PIEZO1-proteoliposome dataset by improving the resolution of the PIEZO1 protein.展开更多
基金support of the National Natural Science Foundation of China(32472594)the Independent Deployment Project of Institute of Zoology,Chinese Academy of Sciences(2023IOZ010).
文摘Plants have evolved complex immune networks to adapt to survival needs,and their immune mechanisms have unique regulatory patterns to cope with different environments.In rice,the maintenance of immune balance involves the synergistic action of many factors.Yue Wu et al.'s latest research results on the immunomodulatory mechanism of rice(ROD1 and the interaction between various proteins in rice)are introduced in this paper.
基金supported by the National Natural Science Foundation of China(No.82471389,No.32470986,No.82271385)Natural Science Foundation of Guangdong Province(No.2024A1515010471).
文摘Mosquito-borne flaviviruses,such as Zika virus(ZIKV)and dengue virus(DENV),cause diverse severe clinical manifestations including fever,rash,hepatitis,arthralgia,and congenital anomalies.Here,we identified a host factor,the adaptor protein complex 1 gamma 1 subunit(AP1G1),which plays an important role in both ZIKV and dengue virus 2(DENV2)infections.We explored the role of AP1G1 in ZIKV and DENV2 infections using CRISPR/Cas9 gene editing technology and RNA interference(RNAi)techniques.Knockout or silencing of AP1G1 decreases the replication of ZIKV and DENV2 in multiple human cell lines.Intriguingly,depletion of AP1G1 results in a significant reduction in ZIKV at an early stage,but decreases DENV2 replication levels during the late stage,suggesting that AP1G1 plays distinct roles in the infection by ZIKV and DENV2.Furthermore,we determined that AP1G1 mediates ZIKV-endosomal membrane fusion through inhibitor experiments and fluorescence labeling assays.Mechanistically,we found that AP1G1 exerts its pro-viral effect through binding to the ZIKV envelope glycoprotein(E protein).This interaction promotes the fusion of viral and endosomal membranes,during which the ZIKV genomic RNAs are released from the endosome into the cytoplasm,a process that facilitates viral replication.However,for DENV2 infection,AP1G1 primarily affects its viral RNA replication stage,rather than the fusion of virus-endosomal membrane.Taken together,our work demonstrates that AP1G1 plays a pro-viral role in both ZIKV and DENV2 infections via distinct mechanisms,highlighting its potential as a therapeutic target for antiviral strategies.
文摘The changes of chlorophyll_protein complexes and photosynthetic activities of chloroplast isolated from lotus ( Nelumbo nucifera Gaertn.) seeds germinating under illumination were studied. SDS PAGE analysis of chlorophyll_protein complexes showed that there was only the light harvesting chlorophyll a/b protein complex from PSⅡ (LHCⅡ) precursor in chloroplast from lotus seeds germinated for 2 to 6 days, while LHC Ⅱ 1, and the chlorophyll_protein complex of PSⅠ (CPⅠ) appeared on the 8th day of germination and PSⅡ reaction center complex appeared later. Studies on the polypeptides composition of the chloroplast revealed the following results: 1) Small amount of the 27 kD polypeptide was synthesized in invisible light; 2) The 30 kD polypeptide existed previously in the plumules of the dry seeds; 3) The amount of the 30 kD polypeptide was more than any other polypeptides before germination and decreased gradually throughout germination, while the 27 kD polypeptide changed in the opposite way; 4) In the process of germination, measurement of the electron transport rate and the fluorescence induction kinetics at room temperature showed that PSⅡ activities and efficiency of primary light energy transformation were only experimentally measurable after 7 days of germination and gradually increased afterwards. At the same time, the chl a/b ratio rose from the lower value to normal; 5) The changes of chloroplast membrane components and its functions are concomitant in concert with that of the ultrastructure of chloroplast membranes during germination, as shown in our earlier work . The results have proved again that a different developmental pathway of chloroplast is likely to exist in the lotus plumules, which might provide an important clue for N. nucifera in having an unique position in the phylogeny of the angiosperm.
基金Project supported by the Fundamental Research Funds for the Central Universities from Lanzhou University (No.lzujbky-2014-87),China
文摘Polycomb group （PCG） complexes are epigenetic regulatory complexes that conduct transcriptional repression of target genes via modifying the chromatin. The two best characterized forms of PCG complexes, polycomb repressive complexes 1 and 2 （PRC1 and PRC2）, are required for maintaining the sternness of embryonic stem cells and many types of adult stem cells. The spectra of target genes for PRCs are dynamically changing with cell differentiation, which is essential for proper decisions on cell fate during developmental processes, Chromobox （CBX） family proteins are canonical components in PRC1, responsible for targeting PRC1 to the chromatin. Recent studies highlight the function specifications among CBX family members in undifferentiated and differentiated stem cells, which reveal the interplay between compositional diversity and functional specificity of PRCI. In this review, we summarize the current knowledge about targeting and functional mechanisms of PRCs, emphasizing the recent breakthroughs related to CBX proteins under a number of physiological and pathological conditions.
基金supported by the National Key R&D Program of China (2017YFD0400205)Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYCX19_1402)
文摘Soy protein isolate(SPI)is a commercial protein with balanced amino acids,while the poor solubility impedes its use in traditional foods.To overcome the problem,the complex coacervation of SPI/Flammulina velutipes polysaccharide(FVP)were investigated.Initial results revealed that the suitable amounts of FVP contributed to reducing the turbidity of SPI solution.Under electrostatic interaction,the formation of SPI/FVP coacervates were spontaneous and went through a nucleation and growth process.Low salt concentration(C_(NaCl)=10,50 mmol/L)led to an increase in the critical pH values(pHc,pHφ1)while the critical pH values decreased when C_(NaCl)≥100 mmol/L.The concentration of NaCl ions increased the content ofα-helix.With the increase of FVP,the critical pH values decreased and the content ofβ-sheet increased through electrostatic interaction.At SPI/FVP ratio of 10:1 and 15:1,the complex coacervation of SPI/FVP were saturated,and the coacervates had the same storage modulus value.SPI/FVP coacervates exhibited solid-like properties and presented the strongest storage modulus at C_(NaCl)=50 mmol/L.The optimal pH,SPI/FVP ratio and NaCl concentration of complex coacervation were collected,and the coacervates demonstrated a valuable application potential to protect and deliver bioactives and food ingredients.
文摘Complex coacervation of whey protein（WP） with acacia gum（AG） was carried out in water with the presence of dodecyl acetate （DA）,a component of insect sex pheromones,in order to obtain microcapsules with DA as the core material and WP-AG coacervate as the wall materials.Through variations in wall/core ratios,concentrations of the wall materials in capsule preparations,DA encapsulation was optimized,which showed a high DA encapsulation was achieved when coacervation was conducted at pH 3.5 with wall/core mass ratio at 3 combined with concentration of wall materials at 1.0 wt%.Morphology and the structure of DA loaded microcapsules were examined by scanning electron microscope,which showed the microcapsules were of core/shell structure with DA encapsulated in the inner of the microcapsules.DA release was examined and the behavior of the release was discussed.
文摘OBJECTIVE: To study the efficacy and explore the mechanism of the anti-tumor immunity elicited by heat shock protein 70-peptide complexes (HSP70-PC) derived from tumor cells. METHODS: Cells culture, flow cytometric analysis, affinity chromatography for protein purification, SDS-PAGE, Western-blotting and animal experiment were used. RESULTS: HSP70-PC immunization rendered protective effect to both naive tumorl-bearing mice. All of the naive mice obtained complete resistance to Hcaf cell attack; 40% of the tumor-bearing mice survived for over 90 days, whereas the mice of control group died within 2 weeks (P
文摘The cytosolic chaperonin T-complex protein 1-ring complex(TRiC)or chaperonin containing T-complex protein 1(CCT)is essential in de novo folding of approximately 10%of the eukaryotic,newly translated polypeptides as well as misfolded proteins.There is a close link between the TRiC/CCT cytosolic chaperonin and neurodegenerative diseases(Lopez et al.,2015).A lot of research suggests that CCT plays neuroprotective roles in neurodegenerative diseases including Huntington’s disease(Lopez et al.,2015).Either overexpression of a single or all eight subunits(CCT1-8)or treatment of the substrate-binding apical domain of yeast CCT1(ApiCCT1)prevented mutant Huntingtin aggregation and improved cellular and neuronal functions(Zhao et al.,2016).Importantly,our recent study has demonstrated that both CCT and ApiCCT could reduce mutant Huntingtin level and enhance both anterograde and retrograde axonal transport of brain-derived neurotrophic factor.These results led to restoration of the trophic status of striatal neurons from a bacterial artificial chromosome transgenic mouse model of Huntington’s disease(Zhao et al.,2016).Axonal transport is regulated by many factors including microtubule-associated protein tau,which promotes tubulin polymerization and stabilizes microtubules.Impaired interaction between tau and microtubules plays a vital role in the pathogenesis of multiple neurodegenerative diseases(Wang and Mandelkow,2016).Interestingly,tau phosphorylation is also observed in brains of several Huntington’s disease mouse models and Huntington’s disease patients(Gratuze et al.,2016).In a recent study,we explored if CCT subunit has any effect on axonal transport in a tau-dependent pathway(Chen et al.,2018b).We focused on the retrograde axonal transport of brain-derived neurotrophic factor,as neurotrophic factor-mediated signaling in the form of signaling endosome is essential in both the developing and the mature nervous system and dysregulation of trafficking of neurotrophic factors is tightly linked to disorders of the nervous system(Chen et al.,2018a).We found that the expression of a single CCT subunit(CCT5)significantly promoted retrograde axonal transport of brain-derived neurotrophic factor in primary cortical neurons.Mechanically,CCT regulated the level of cyclin-dependent kinase 5(CDK5)/p35/p25 and,subsequently contributed to CCT-induced tau phosphorylation,which induced detachment of tau from microtubules(Chen et al.,2018b)(Figure 1).
文摘This paper proposes a novel four-dimensional approach to the structural study of protein complexes. In the approach, the surface of a protein molecule is to be described using the intersection of a pair of four-dimensional triangular cones (with multiple top vertexes). As a mathematical toy model of protein complexes, we consider complexes of closed trajectories of n-simplices (n=2,3,4...), where the design problem of protein complexes corresponds to an extended version of the Hamiltonian cycle problem. The problem is to find “a set of” closed trajectories of n-simplices which fills the n-dimensional region defined by a given pair of n+1 -dimensional triangular cones. Here we give a solution to the extended Hamiltonian cycle problem in the case of n=2 using the discrete differential geometry of triangles (i.e., 2-simplices).
文摘The prediction of intrinsically disordered proteins is a hot research area in bio-information.Due to the high cost of experimental methods to evaluate disordered regions of protein sequences,it is becoming increasingly important to predict those regions through computational methods.In this paper,we developed a novel scheme by employing sequence complexity to calculate six features for each residue of a protein sequence,which includes the Shannon entropy,the topological entropy,the sample entropy and three amino acid preferences including Remark 465,Deleage/Roux,and Bfactor(2STD).Particularly,we introduced the sample entropy for calculating time series complexity by mapping the amino acid sequence to a time series of 0-9.To our knowledge,the sample entropy has not been previously used for predicting IDPs and hence is being used for the first time in our study.In addition,the scheme used a properly sized sliding window in every protein sequence which greatly improved the prediction performance.Finally,we used seven machine learning algorithms and tested with 10-fold cross-validation to get the results on the dataset R80 collected by Yang et al.and of the dataset DIS1556 from the Database of Protein Disorder(DisProt)(https://www.disprot.org)containing experimentally determined intrinsically disordered proteins(IDPs).The results showed that k-Nearest Neighbor was more appropriate and an overall prediction accuracy of 92%.Furthermore,our method just used six features and hence required lower computational complexity.
基金Project supported by the National Natural Science Foundation of China (Grant No. 31670725)。
文摘Protein–protein interactions (PPI) are important for many biological processes. Theoretical understanding of the structurally determining factors of interaction sites will help to understand the underlying mechanism of protein–protein interactions. At the same time, understanding the complex structure of proteins helps to explore their function. And accurately predicting protein complexes from PPI networks helps us understand the relationship between proteins. In the past few decades, scholars have proposed many methods for predicting protein interactions and protein complex structures. In this review, we first briefly introduce the methods and servers for predicting protein interaction sites and interface residue pairs, and then introduce the protein complex structure prediction methods including template-based prediction and template-free prediction. Subsequently, this paper introduces the methods of predicting protein complexes from the PPI network and the method of predicting missing links in the PPI network. Finally, it briefly summarizes the application of machine/deep learning models in protein structure prediction and action site prediction.
基金This work was partly supported by the Cancer Prevention and Research Institute of Texas,USA(PR150551 and RP190561)the Welch Foundation(AU-0042-20030616)+1 种基金The work was also supported by the National Natural Science Foundation of China(31700778 and 31320103918)Jiangsu Province’s Key Laboratory of Medicine(XK201135).
文摘In analyses of protein families that may serve as drug targets,membrane-associated G-protein-coupled receptors(GPCRs)dominate,followed by ion channels,transporters,and—to a lesser extent—membrane-bound enzymes.However,various challenges put such membrane proteins among key groups of underutilized opportunities for the application of therapeutic antibodies.Antibodies hold the promise of exquisite specificity,as they are able to target even specific conformations of a particular membrane protein,as well as adaptability through engineering into various antibody formats.However,the ease of raising and isolating specific,effective antibodies targeting membrane proteins depends on many factors.In particular,the generation of specific antibodies is easier when targeting larger,simpler,extracellular domains with greater uniqueness of amino acid sequence.The rareness of such ideal conditions is illustrated by the limited number of approved biologics for targeting GPCRs and other complex membrane proteins.Challenges in developing antibodies to complex membrane proteins such as GPCRs,ion channels,transporters,and membrane-bound enzymes can be addressed by the design of the antigen,antibody-generation strategies,lead optimization technologies,and antibody modalities.A better understanding of the membrane proteins being targeted would facilitate mechanism-based drug discovery.This review describes the advantages and challenges of targeting complex membrane proteins with antibodies and discusses the preparation of membrane protein antigens and antibody generation,illustrated by select examples of success.
文摘Nine pigment-protein complexes were separated and characterized from intact Chroomonasplacoidea chloroplasts by IEF. The bands Ⅰ-Ⅵ with their isoelectric points （pI） values from 4 to 6 were phycocyanin components; bands Ⅷ and Ⅸ （pI = 2.8-3.6） were chlorophyll-protein complexes. According to absorption and fluorescence spectra, band VII was designated as a novel phycocyanin-Chla/c2-protein complex （pI ≈ 3.4-3.7）. These results indicated that phycocyanin is structurally and functionally coupled with chlorophyll-protein complex in C. placoidea, and probably interacted with electrostatic force in combination.
基金the National Research Centre for the financial support with Grant No.9080104
文摘Objective:To explore the in vivo anticancer,anti-angiogenesis and immunomodulatory efficacies of the bioactive polysaccharide isolated from cold aqueous extract of Jania rubens(JCEM) and Pterocladia capillacea(PCEM) as well as hot aqueous extract of Enteromorpha intestinalis(EHEM) against hepatocellular carcinoma rat model(HCC) and to study their chemical composition.Methods:The sugars and amino acids composition of the bioactive polysaccharides of JCEM,PCEM and EHEM were determined using gas liquid chromatography and amino acid analyzer,respectively.These polysaccharide extracts(20 mg/kg b.wt.for 5 weeks) were assessed on hepatocarcinogenesis in rats and α-fetoprotein(AFP),carcinoembryonic antigen(CEA),glypican-3(GPC-3),hepatocyte growth factor(HGF) and vascular endothelial growth factor(VEGF) and Ig G levels were evaluated.Results:The GLC analysis of JCEM,PCEM and EHEM polysaccharide revealed the presence of 10,9 and10 sugars,in addition the amino acid analyser enable identification of 16,15 and 15 amino acids,respectively.These polysaccharide extracts of JCEM,PCEM and EHEM produced significant decrease in serum AFP,CEA,GPC-3,HGF and VEGF compared with untreated HCC group.JCEM,PCEM and EHEM had an immunostimulatory responses by increasing the IgG levels as compared by naive value(1.23,1.53 and 1.17 folds),respectively.The bioactive polysaccharides in HCC induced rats improved the humoral immune response.The photomicrographs of liver tissue sections of the groups of HCC treated with polysaccharide extracts of Jania rubens and Enteromorpha intestinalis showed intact histological structure.Moreover,fractions HE1,HE4,HE7 obtained from polysaccharide of EHEM showed moderate cytotoxic activity against Hep G2 in vitro with IC_(50) 73.1,42.6,76.2 μg/mL.However,fractions of PCEM and JCEM show no or weak cytotoxicity against Hep G2 in vitro where the cytotoxic activity of their crude polysaccharide extract proved synergetic effect.Conclusions:The pronounced antitumor activity of sulphated polysaccharide-protein complexes of JCEM and EHEM is due to direct cytotoxic activity,anti-hepatocarcinogensis,and anti-angiogenesis.In addition,JCEM,PCEM and EHEM had an immunostimulatory response and improved the humoral immune response in HCC induced rats.
基金Supported by the National Natural Science Foundation of China (60803025)
文摘High-throughput techniques,such as the yeast-two-hybrid system,produce mass protein-protein interaction data. The new technique makes it possible to predict protein complexes by com-putation. A novel method,named DSDA,has been put forward to predict protein complexes via dense subgraph because the proteins among a protein complex have a much tighter relation among them than with others. This method chooses a node with its neighbors to form the initial subgraph,and chooses a node which has the tightest relation with the subgraph according to greedy strategy,then the chosen node is added into the initial subgraph until the subgraph density is below the threshold value. The ob-tained subgraph is then removed from the network and the process continues until no subgraph can be detected. Compared with other algorithms,DSDA can predict not only non-overlap protein com-plexes but also overlap protein complexes. The experiment results show that DSDA predict as many protein complexes as possible. And in Y78K network the accuracy of DSDA is as twice times as that of RNSC and MCL.
文摘The application of phenylfluorone (PF)-Mo(VI) complex as a spectroscopic probe is studied. In the presence of OP microemulsion at pH 3.04, PF-Mo(Ⅵ) complex combines protein rapidly to form a stable compound and the absorbance at 527 nm is in proportion to the concentration of protein in the range 0-16 μg mL-1 for bovine serum albumin (BSA). OP microemuslion media is introduced into protein determination, it has increased markedly the sensitivity of the system. The molar absorption coefficient was 5.98×l06 L mol-1 cm-1 for BSA. The assay, with sensitivity, simplicity and tolerance to many foreign substances, is applied to the determination of protein in samples with satisfactory results. Moreover, the binding number of BSA with the complex, which is determined by molar ratio and slope ratio methods, is in good agreement.
基金Financial supports from the Natural Science Foundation of Shandong Province(Y2000B09)Shandong Provincial Science and Technology Program(03C05)are gratefully acknowledged
文摘Discharge of whey proteins is still a current practice by small cheese producers. The development of low-cost alternatives for recovery of these proteins is fundamental for small producers who cannot apply expensive techniques. The present study investigated the complex coacervation technique as a cheap technology to recover proteins from sweet whey using carboxymethylcellulose, and the coacervate used as an ingredient in the formulation of probiotic fermented milk. The nutritional properties of whey-carboxymethylcellulose coacervates (WP-CMC) were evaluated in trials with animals (rats) using casein as a reference. All these parameters—the coefficient of feed efficiency (CEA), protein digestibility-corrected amino acid score (PDCAAS), and net protein ratio (NPR), as well as weight gain—were determined to evaluate protein quality. A sensory acceptance test was applied to evaluate the sensory characteristics of the product. The complex coacervation technique recovered 86% of the protein from sweet whey. No significant (p > 0.05) differences were observed in the biological tests for both groups (WP-CMC and Casein groups) when NPR (4.98 to 5.04), digestibility (92.35 to 90.64), and CEA (0.40 to 0.42) were evaluated. Probiotic fermented milk beverage containing WP-CMC (0.78%) and guar gum (0.68%) presented good acceptability as determined by sensory evaluation. WP-CMC can be considered an ingredient with high nutritional and biological value that could be applied in probiotic fermented milk as an alternative to small producers to allocate the residual whey from cheese manufacture.
基金Project supported by the National Natural Science Foundation of China (Grant Nos.32241023 and 92254306)the Fund from the Tsinghua–Peking Joint Center for Life SciencesBeijing Frontier Research Center for Biological Structure。
文摘Reconstituting membrane proteins in liposomes and determining their structure is a common method for determining membrane protein structures using single-particle cryo-electron microscopy(cryo-EM).However,the strong signal of liposomes under cryo-EM imaging conditions often interferes with the structural determination of the embedded membrane proteins.Here,we propose a liposome signal subtraction method based on single-particle two-dimensional(2D)classification average images,aimed at enhancing the reconstruction resolution of membrane proteins.We analyzed the signal distribution characteristics of liposomes and proteins within the 2D classification average images of protein–liposome complexes in the frequency domain.Based on this analysis,we designed a method to subtract the liposome signals from the original particle images.After the subtraction,the accuracy of single-particle three-dimensional(3D)alignment was improved,enhancing the resolution of the final 3D reconstruction.We demonstrated this method using a PIEZO1-proteoliposome dataset by improving the resolution of the PIEZO1 protein.
