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
The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many pro...The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many protein com-plexes are available in the protein data bank,their assembly/disassembly orders of subunits are largely unknown.In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex,computational methods can be used to predict the assembly/disassembly order.Since sampling is a nontrivial issue in simulating the assembly/disassembly process,coarse-grained simulations are more efficient than atomic simulations are.In this work,we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations.The protocols were illustrated via two protein complexes,and the predicted assembly/disassembly orders were consistent with the available experimental data.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
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
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
We studied the difference in thermostability of photosystem Ⅱ （PSII） and leaf lipid composition between a T-DNA insertion mutant rice （Oryza sativa L.） VG28 and its wild type Zhonghuau. Native green gel and SDS-P...We studied the difference in thermostability of photosystem Ⅱ （PSII） and leaf lipid composition between a T-DNA insertion mutant rice （Oryza sativa L.） VG28 and its wild type Zhonghuau. Native green gel and SDS-PAGE electrophoreses revealed that the mutant VG28 lacked all light-harvesting chlorophyll a/b protein complexes. Both the mutant and wild type were sensitive to high temperatures, and the maximal efficiency of PSII photochemistry （FJ Fm） and oxygen-evolving activity of PSII in leaves significantly decreased with increasing temperature. However, the PSII activity of the mutant was markedly more sensitive to high temperatures than that of the wild type. Lipid composition analysis showed that the mutant had less phosphatidylglycerol and sulfoquinovosyl diacylglycerol compared with the wild type. Fatty acid analysis revealed that the mutant had an obvious decrease in the content of 16：1t and a marked increase in the content of 18：3 compared with the wild type. The effects of lipid composition and unsaturation of membrane lipids on the thermostability of PSII are discussed.展开更多
Rapidly identifying protein complexes is significant to elucidate the mechanisms of macromolecular interactions and to further investigate the overlapping clinical manifestations of diseases.To date,existing computati...Rapidly identifying protein complexes is significant to elucidate the mechanisms of macromolecular interactions and to further investigate the overlapping clinical manifestations of diseases.To date,existing computational methods majorly focus on developing unsupervised graph clustering algorithms,sometimes in combination with prior biological insights,to detect protein complexes from protein-protein interaction(PPI)networks.However,the outputs of these methods are potentially structural or functional modules within PPI networks.These modules do not necessarily correspond to the actual protein complexes that are formed via spatiotemporal aggregation of subunits.In this study,we propose a computational framework that combines supervised learning and dense subgraphs discovery to predict protein complexes.The proposed framework consists of two steps.The first step reconstructs genome-scale protein co-complex networks via training a supervised learning model of l2-regularized logistic regression on experimentally derived co-complexed protein pairs;and the second step infers hierarchical and balanced clusters as complexes from the co-complex networks via effective but computationally intensive k-clique graph clustering method or efficient maximum modularity clustering(MMC)algorithm.Empirical studies of cross validation and independent test show that both steps achieve encouraging performance.The proposed framework is fundamentally novel and excels over existing methods in that the complexes inferred from protein co-complex networks are more biologically relevant than those inferred from PPI networks,providing a new avenue for identifying novel protein complexes.展开更多
Cotton provides the most abundant natural fiber for the textile industry.The mature cotton fiber largely consists of secondary cell walls with the highest proportion of cellulose and a small amount of hemicellulose an...Cotton provides the most abundant natural fiber for the textile industry.The mature cotton fiber largely consists of secondary cell walls with the highest proportion of cellulose and a small amount of hemicellulose and lignin.To dissect the roles of hemicellulosic polysaccharides during fiber development,four IRREGULAR XYLEM 15(IRX15)genes,GhIRX15-1/-2/-3/-4,were functionally characterized in cotton.These genes encode DUF579 domain-containing proteins,which are homologs of AtIRX15 involved in xylan biosynthesis.The four GhIRX15 genes were predominantly expressed during fiber secondary wall thickening,and the encoded proteins were localized to the Golgi apparatus.Each GhIRX15 gene could restore the xylan deficient phenotype in the Arabidopsis irx15irx15l double mutant.Silencing of GhIRX15s in cotton resulted in shorter mature fibers with a thinner cell wall and reduced cellulose content as compared to the wild type.Intriguingly,GhIRX15-2 and GhIRX15-4 formed homodimers and heterodimers.In addition,the GhIRX15s showed physical interaction with glycosyltransferases GhGT43C,GhGT47A and GhGT47B,which are responsible for synthesis of the xylan backbone and reducing end sequence.Moreover,the GhIRX15s can form heterocomplexes with enzymes involved in xylan modification and side chain synthesis,such as GhGUX1/2,GhGXM1/2 and GhTBL1.These findings suggest that GhIRX15s participate in fiber xylan biosynthesis and modulate fiber development via forming large multiprotein complexes.展开更多
Proteins usually bind together to form complexes, which play an important role in cellular activities. Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein...Proteins usually bind together to form complexes, which play an important role in cellular activities. Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein-protein interaction networks. We present a novel framework （CPL） that detects protein complexes by propagating labels through interactions in a network, in which labels denote complex identifiers. With proper propagation in CPL, proteins in the same complex will be assigned with the same labels. CPL does not make any strong assumptions about the topological structures of the complexes, as in previous methods. Tile CPL algorithm is tested on several publicly available yeast protein-protein interaction networks and compared with several state-of-the-art methods. The results suggest that CPL performs better than the existing methods. An analysis of the functional homogeneity based on a gene ontology analysis shows that the detected complexes of CPL are highly biologically relevant.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
Evidence shows that biological systems are composed of separable functional modules. Identifying protein complexes is essential for understanding the principles of cellular functions. Many methods have been proposed t...Evidence shows that biological systems are composed of separable functional modules. Identifying protein complexes is essential for understanding the principles of cellular functions. Many methods have been proposed to mine protein complexes from protein-protein interaction networks. However, the performances of these algorithms are not good enough since the protein-protein interactions detected from experiments are not complete and have noise. This paper presents an analysis of the topological properties of protein complexes to show that although proteins from the same complex are more highly connected than proteins from different complexes, many protein complexes are not very dense （density ≥0.8）. A method is then given to mine protein complexes that are relatively dense （density ≥0.4）. In the first step, a topology property is used to identify proteins that are probably in a same complex. Then, a possible boundary is calculated based on a minimum vertex cut for the protein complex. The final complex is formed by the proteins within the boundary. The method is validated on a yeast protein-protein interaction network. The results show that this method has better performance in terms of sensitivity and specificity compared with other methods. The functional consistency is also good.展开更多
Proteins interact with each other to form protein complexes, and cell functionality depends on both protein interactions and these complexes. Based on the assumption that protein complexes are highly connected and cor...Proteins interact with each other to form protein complexes, and cell functionality depends on both protein interactions and these complexes. Based on the assumption that protein complexes are highly connected and correspond to the dense regions in Protein-protein Interaction Networks（PINs）, many methods have been proposed to identify the dense regions in PINs. Because protein complexes may be formed by proteins with similar properties,such as topological and functional properties, in this paper, we propose a protein complex identification framework（KCluster）. In KCluster, a PIN is divided into K subnetworks using a K-means algorithm, and each subnetwork comprises proteins of similar degrees. We adopt a strategy based on the expected number of common neighbors to detect the protein complexes in each subnetwork. Moreover, we identify the protein complexes spanning two subnetworks by combining closely linked protein complexes from different subnetworks. Finally, we refine the predicted protein complexes using protein subcellular localization information. We apply KCluster and nine existing methods to identify protein complexes from a highly reliable yeast PIN. The results show that KCluster achieves higher Sn and Sp values and f-measures than other nine methods. Furthermore, the number of perfect matches predicted by KCluster is significantly higher than that of other nine methods.展开更多
To develop an economical and feasible approach to probe protein complexes, differential centrifugation and three-dimensional polyacrylamide gel electrophoresis （PAGE） were performed to separate protein complexes fro...To develop an economical and feasible approach to probe protein complexes, differential centrifugation and three-dimensional polyacrylamide gel electrophoresis （PAGE） were performed to separate protein complexes from the cell lysate of human pancreatic cancer cell line, SW1990, followed by mass spectrometric identification. Four macromolecular protein complexes were separated and identified unambiguously.展开更多
A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells.For a complete understanding of human cellular functions,it is crucial to have a compre...A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells.For a complete understanding of human cellular functions,it is crucial to have a comprehensive atlas of human protein complexes.Unfortunately,we still lack such a comprehensive atlas of experimentally validated protein complexes,which prevents us from gaining a complete understanding of the compositions and functions of human protein complexes,as well as the underlying biological mechanisms.To fill this gap,we built Human Protein Complexes Atlas(HPC-Atlas),as far as we know,the most accurate and comprehensive atlas of human protein complexes available to date.We integrated two latest protein interaction networks,and developed a novel computational method to identify nearly 9000 protein complexes,including many previously uncharacterized complexes.Compared with the existing methods,our method achieved outstanding performance on both testing and independent datasets.Furthermore,with HPC-Atlas we identified 751 severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)-affected human protein complexes,and 456 multifunctional proteins that contain many potential moonlighting proteins.These results suggest that HPC-Atlas can serve as not only a computing framework to effectively identify biologically meaningful protein complexes by integrating multiple protein data sources,but also a valuable resource for exploring new biological findings.The HPCAtlas webserver is freely available at http://www.yulpan.top/HPC-Atlas.展开更多
Objective The aim of this study was to enhance the treatment effect of tumor purified autogenous heat shock protein 70-peptide complexes(HSP70-PCs)on HER-3-overexpressing breast cancer.Methods In this study,we first s...Objective The aim of this study was to enhance the treatment effect of tumor purified autogenous heat shock protein 70-peptide complexes(HSP70-PCs)on HER-3-overexpressing breast cancer.Methods In this study,we first studied the expression of HER-3 in breast cancer tissues and its relationship with patient characteristics.We then purified HSP70-PCs from primary breast cancer cells with different HER-2 and HER-3 expression profiles and determined the cytotoxicity of autogenous dendritic cells(DCs)and CD8+T cells induced by these complexes.Third,recombinant human HSP70-HER-3 protein complexes were used to inhibit the autogenous HSP70-PCs purified from HER-3-overexpressing breast cancer cells,and the resulting immunological response was examined.Results The results show that HSP70-PCs can be combined with recombinant HSP70-HER-3 protein complexes to induce stronger immunological responses than autogenous HSP70-PCs alone and that these treatments induce autogenous CD8+T cell killing of HER-3-positive breast cancer cells.Conclusion These findings provide a new direction for HSP70-DC-based immunotherapy for patients with HER-3-overexpressing breast cancer.展开更多
The protein connector enhancer of kinase suppressor of Ras 2(CNKSR2),present in both the postsynaptic density and cytoplasm of neurons,is a scaffolding protein with several protein-binding domains.Variants of the CNKS...The protein connector enhancer of kinase suppressor of Ras 2(CNKSR2),present in both the postsynaptic density and cytoplasm of neurons,is a scaffolding protein with several protein-binding domains.Variants of the CNKSR2 gene have been implicated in neurodevelopmental disorders,particularly intellectual disability,although the precise mechanism involved has not yet been fully understood.Research has demonstrated that CNKSR2 plays a role in facilitating the localization of postsynaptic density protein complexes to the membrane,thereby influencing synaptic signaling and the morphogenesis of dendritic spines.However,the function of CNKSR2 in the cytoplasm remains to be elucidated.In this study,we used immunoprecipitation and high-resolution liquid chromatography-mass spectrometry to identify the interactors of CNKSR2.Through a combination of bioinformatic analysis and cytological experiments,we found that the CNKSR2 interactors were significantly enriched in the proteome of the centrosome.We also showed that CNKSR2 interacted with the microtubule protein DYNC1H1 and with the centrosome marker CEP290.Subsequent colocalization analysis confirmed the centrosomal localization of CNKSR2.When we downregulated CNKSR2 expression in mouse neuroblastoma cells(Neuro 2A),we observed significant changes in the expression of numerous centrosomal genes.This manipulation also affected centrosome-related functions,including cell size and shape,cell proliferation,and motility.Furthermore,we found that CNKSR2 interactors were highly enriched in de novo variants associated with intellectual disability and autism spectrum disorder.Our findings establish a connection between CNKSR2 and the centrosome,and offer new insights into the underlying mechanisms of neurodevelopmental disorders.展开更多
Cryo-electron microscopy makes use of transmission electron microscopy to image vitrified biological samples and reconstruct their three-dimensional structures from two-dimensional projections via computational approa...Cryo-electron microscopy makes use of transmission electron microscopy to image vitrified biological samples and reconstruct their three-dimensional structures from two-dimensional projections via computational approaches. After over40 years of development, this technique is now reaching its zenith and reforming the research paradigm of modern structural biology. It has been gradually taking over X-ray crystallography as the mainstream method. In this review, we briefly introduce the history of cryo-EM, recent technical development and its potential power to reveal dynamic structures. The technical barriers and possible approaches to tackle the upcoming challenges are discussed.展开更多
Objectives:Although Yes-associated protein 1(YAP1)is an important oncogene in hepatocellular carcinoma(HCC)progression,its nuclear localization prevents it from being considered a potential therapeutic target.Recently...Objectives:Although Yes-associated protein 1(YAP1)is an important oncogene in hepatocellular carcinoma(HCC)progression,its nuclear localization prevents it from being considered a potential therapeutic target.Recently,studies have reported that coatomer protein complex subunit beta 2(COPB2)also plays a critical role in HCC development;however its mechanism of action is unclear.This study aimed to investigate the role of COPB2 and YAP1 in the progression of HCC and to elucidate the underlying mechanisms.Methods:COPB2 and YAP1 expression in HCC tissues were first analyzed by database searches and immunohistochemistry.Nomogram and artificial neural network models were established based on COPB2 and YAP1 expression.Cell proliferation was detected by cell counting kit-8 and clone formation assay,while cell migration and invasion were assessed using Transwell assays.Finally,the potential mechanisms underlying COPB2 regulation of YAP1 nuclear translocation were explored by immunofluorescence assay and Western blot.Results:COPB2 combined with YAP1 expression was associated with overall postoperative survival in HCC patients and was an independent prognostic factor.High expression of both COPB2 and YAP1 in patients may reduce the efficacy of postoperative transarterial chemoembolization therapy.In vitro experiments revealed that COPB2 affected the sensitivity of HCC cells to Cisplatin(DDP)by regulating YAP1 nuclear translocation.Conclusions:Our findings suggest that COPB2/YAP1 affects the drug sensitivity of HCC cells to DDP and that targeting COPB2/YAP1 may be a promising strategy for the precision treatment of HCC.展开更多
Prostate cancer is a major public health concern world-wide, being one of the most prevalent cancers in men. Great improvements have been made both in terms of early diagnosis and therapeutics. However, there is still...Prostate cancer is a major public health concern world-wide, being one of the most prevalent cancers in men. Great improvements have been made both in terms of early diagnosis and therapeutics. However, there is still an urgent need for reliable biomarkers that could overcome the lack of cancer-specifcity of prostate-specifc antigen, as well as alternative therapeutic targets for advanced metastatic cases. Reversible phosphorylation of proteins is a post-translational modifcation critical to the regulation of numerous cellular processes. Phosphoprotein phosphatase 1 （PPP1） is a major serine/threonine phos-phatase, whose specifcity is determined by its interacting proteins. These interactors can be PPP1 substrates, regulators, or even both. Deregulation of this protein-protein interaction network alters cell dynamics and underlies the development of several cancer hallmarks. Therefore, the identification of PPP1 interactome in specific cellular context is of crucial importance. The knowledge on PPP1 complexes in prostate cancer remains scarce, with only 4 holoenzymes characterized in human prostate cancer models. However, an increasing number of PPP1 interactors have been identifed as expressed in human prostate tissue, including the tumor suppressors TP53 and RB1. Efforts should be made in order to identify the role of such proteins in prostate carcinogenesis, since only 26 have yet well-recognized roles. Here, we revise literature and human protein databases to provide an in-depth knowledge on the biological significance of PPP1 complexes in human prostate carcinogenesis and their potential use as therapeutic targets for the development of new therapies for prostate cancer.展开更多
Salmonella and E.coli possess different surface protein structures that can induce protective immune responses.Identification of these proteins capacitates development of diverse applications in prevention and diagnos...Salmonella and E.coli possess different surface protein structures that can induce protective immune responses.Identification of these proteins capacitates development of diverse applications in prevention and diagnosis that contribute to effectively control disease-causing enterobacteria pathogens such as Salmonella and E.coli.A simple procedure for obtaining protein complexes of Salmonella serotypes and E.coli is performed in this study.A sonication process with heat treatment of whole bacteria induced the release of protein complexes.Concentration of the protein extract was quantified using protein quantification Kits-Rapid,and protein complex profile was obtained by SDS-PAGE(Sodium dodecyl sulfate polyacrylamide gel electrophoresis)and silver staining.The concentrations of protein ranged from 29.45 to 45.35μg/mL in the Salmonella protein extracts,and from 25.35 to 36.72μg/mL in the E.coli protein extracts.Six major groups of proteins from E.coli(YfiO,NipB,OmpF,YfgL,Talc,YaeT)and four major groups of proteins from Salmonella(Flagellin,OmpA,Porin,SEF21)were preliminarily determined by a simple procedure of extraction based on the molecular weight.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This work was supported by the National Key Research and Development Program of China(2021YFA1301504)the Chinese Academy of Sciences Strategic Priority Research Program(XDB37040202)the National Natural Science Foundation of China(91953101).
文摘The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many protein com-plexes are available in the protein data bank,their assembly/disassembly orders of subunits are largely unknown.In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex,computational methods can be used to predict the assembly/disassembly order.Since sampling is a nontrivial issue in simulating the assembly/disassembly process,coarse-grained simulations are more efficient than atomic simulations are.In this work,we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations.The protocols were illustrated via two protein complexes,and the predicted assembly/disassembly orders were consistent with the available experimental data.
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.
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.
文摘We studied the difference in thermostability of photosystem Ⅱ （PSII） and leaf lipid composition between a T-DNA insertion mutant rice （Oryza sativa L.） VG28 and its wild type Zhonghuau. Native green gel and SDS-PAGE electrophoreses revealed that the mutant VG28 lacked all light-harvesting chlorophyll a/b protein complexes. Both the mutant and wild type were sensitive to high temperatures, and the maximal efficiency of PSII photochemistry （FJ Fm） and oxygen-evolving activity of PSII in leaves significantly decreased with increasing temperature. However, the PSII activity of the mutant was markedly more sensitive to high temperatures than that of the wild type. Lipid composition analysis showed that the mutant had less phosphatidylglycerol and sulfoquinovosyl diacylglycerol compared with the wild type. Fatty acid analysis revealed that the mutant had an obvious decrease in the content of 16：1t and a marked increase in the content of 18：3 compared with the wild type. The effects of lipid composition and unsaturation of membrane lipids on the thermostability of PSII are discussed.
文摘Rapidly identifying protein complexes is significant to elucidate the mechanisms of macromolecular interactions and to further investigate the overlapping clinical manifestations of diseases.To date,existing computational methods majorly focus on developing unsupervised graph clustering algorithms,sometimes in combination with prior biological insights,to detect protein complexes from protein-protein interaction(PPI)networks.However,the outputs of these methods are potentially structural or functional modules within PPI networks.These modules do not necessarily correspond to the actual protein complexes that are formed via spatiotemporal aggregation of subunits.In this study,we propose a computational framework that combines supervised learning and dense subgraphs discovery to predict protein complexes.The proposed framework consists of two steps.The first step reconstructs genome-scale protein co-complex networks via training a supervised learning model of l2-regularized logistic regression on experimentally derived co-complexed protein pairs;and the second step infers hierarchical and balanced clusters as complexes from the co-complex networks via effective but computationally intensive k-clique graph clustering method or efficient maximum modularity clustering(MMC)algorithm.Empirical studies of cross validation and independent test show that both steps achieve encouraging performance.The proposed framework is fundamentally novel and excels over existing methods in that the complexes inferred from protein co-complex networks are more biologically relevant than those inferred from PPI networks,providing a new avenue for identifying novel protein complexes.
基金supported by the National Natural Science Foundation of China(31970516 and 32372104)the Foundation of Hubei Hongshan Laboratory(2021hszd014).
文摘Cotton provides the most abundant natural fiber for the textile industry.The mature cotton fiber largely consists of secondary cell walls with the highest proportion of cellulose and a small amount of hemicellulose and lignin.To dissect the roles of hemicellulosic polysaccharides during fiber development,four IRREGULAR XYLEM 15(IRX15)genes,GhIRX15-1/-2/-3/-4,were functionally characterized in cotton.These genes encode DUF579 domain-containing proteins,which are homologs of AtIRX15 involved in xylan biosynthesis.The four GhIRX15 genes were predominantly expressed during fiber secondary wall thickening,and the encoded proteins were localized to the Golgi apparatus.Each GhIRX15 gene could restore the xylan deficient phenotype in the Arabidopsis irx15irx15l double mutant.Silencing of GhIRX15s in cotton resulted in shorter mature fibers with a thinner cell wall and reduced cellulose content as compared to the wild type.Intriguingly,GhIRX15-2 and GhIRX15-4 formed homodimers and heterodimers.In addition,the GhIRX15s showed physical interaction with glycosyltransferases GhGT43C,GhGT47A and GhGT47B,which are responsible for synthesis of the xylan backbone and reducing end sequence.Moreover,the GhIRX15s can form heterocomplexes with enzymes involved in xylan modification and side chain synthesis,such as GhGUX1/2,GhGXM1/2 and GhTBL1.These findings suggest that GhIRX15s participate in fiber xylan biosynthesis and modulate fiber development via forming large multiprotein complexes.
基金supported by the National Natural Science Foundation of China under Grant Nos.61271346,61172098,and91335112the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No.20112302110040the Fundamental Research Funds for the Central Universities of China under Grant No.HIT.KISTP.201418
文摘Proteins usually bind together to form complexes, which play an important role in cellular activities. Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein-protein interaction networks. We present a novel framework （CPL） that detects protein complexes by propagating labels through interactions in a network, in which labels denote complex identifiers. With proper propagation in CPL, proteins in the same complex will be assigned with the same labels. CPL does not make any strong assumptions about the topological structures of the complexes, as in previous methods. Tile CPL algorithm is tested on several publicly available yeast protein-protein interaction networks and compared with several state-of-the-art methods. The results suggest that CPL performs better than the existing methods. An analysis of the functional homogeneity based on a gene ontology analysis shows that the detected complexes of CPL are highly biologically relevant.
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
基金Supported in part by the National Natural Science Foundation of China (Nos.61232001 and 61073036)
文摘Evidence shows that biological systems are composed of separable functional modules. Identifying protein complexes is essential for understanding the principles of cellular functions. Many methods have been proposed to mine protein complexes from protein-protein interaction networks. However, the performances of these algorithms are not good enough since the protein-protein interactions detected from experiments are not complete and have noise. This paper presents an analysis of the topological properties of protein complexes to show that although proteins from the same complex are more highly connected than proteins from different complexes, many protein complexes are not very dense （density ≥0.8）. A method is then given to mine protein complexes that are relatively dense （density ≥0.4）. In the first step, a topology property is used to identify proteins that are probably in a same complex. Then, a possible boundary is calculated based on a minimum vertex cut for the protein complex. The final complex is formed by the proteins within the boundary. The method is validated on a yeast protein-protein interaction network. The results show that this method has better performance in terms of sensitivity and specificity compared with other methods. The functional consistency is also good.
基金supported by the National Natural Science Foundation of China (Nos. 61232001, 61379108, and 61472133)
文摘Proteins interact with each other to form protein complexes, and cell functionality depends on both protein interactions and these complexes. Based on the assumption that protein complexes are highly connected and correspond to the dense regions in Protein-protein Interaction Networks（PINs）, many methods have been proposed to identify the dense regions in PINs. Because protein complexes may be formed by proteins with similar properties,such as topological and functional properties, in this paper, we propose a protein complex identification framework（KCluster）. In KCluster, a PIN is divided into K subnetworks using a K-means algorithm, and each subnetwork comprises proteins of similar degrees. We adopt a strategy based on the expected number of common neighbors to detect the protein complexes in each subnetwork. Moreover, we identify the protein complexes spanning two subnetworks by combining closely linked protein complexes from different subnetworks. Finally, we refine the predicted protein complexes using protein subcellular localization information. We apply KCluster and nine existing methods to identify protein complexes from a highly reliable yeast PIN. The results show that KCluster achieves higher Sn and Sp values and f-measures than other nine methods. Furthermore, the number of perfect matches predicted by KCluster is significantly higher than that of other nine methods.
基金Project supported by the National High-Tech R＆D Program of China （863 Program, No. 2006AA02Z154） and the National Natural Science Foundation of China （No. 21075 137）.
文摘To develop an economical and feasible approach to probe protein complexes, differential centrifugation and three-dimensional polyacrylamide gel electrophoresis （PAGE） were performed to separate protein complexes from the cell lysate of human pancreatic cancer cell line, SW1990, followed by mass spectrometric identification. Four macromolecular protein complexes were separated and identified unambiguously.
基金supported by the National Natural Science Foundation of China(Grant Nos.61972100 and 62172300).
文摘A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells.For a complete understanding of human cellular functions,it is crucial to have a comprehensive atlas of human protein complexes.Unfortunately,we still lack such a comprehensive atlas of experimentally validated protein complexes,which prevents us from gaining a complete understanding of the compositions and functions of human protein complexes,as well as the underlying biological mechanisms.To fill this gap,we built Human Protein Complexes Atlas(HPC-Atlas),as far as we know,the most accurate and comprehensive atlas of human protein complexes available to date.We integrated two latest protein interaction networks,and developed a novel computational method to identify nearly 9000 protein complexes,including many previously uncharacterized complexes.Compared with the existing methods,our method achieved outstanding performance on both testing and independent datasets.Furthermore,with HPC-Atlas we identified 751 severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)-affected human protein complexes,and 456 multifunctional proteins that contain many potential moonlighting proteins.These results suggest that HPC-Atlas can serve as not only a computing framework to effectively identify biologically meaningful protein complexes by integrating multiple protein data sources,but also a valuable resource for exploring new biological findings.The HPCAtlas webserver is freely available at http://www.yulpan.top/HPC-Atlas.
基金Supported by a grant from the National Natural Science Foundation of China(No.81260392).
文摘Objective The aim of this study was to enhance the treatment effect of tumor purified autogenous heat shock protein 70-peptide complexes(HSP70-PCs)on HER-3-overexpressing breast cancer.Methods In this study,we first studied the expression of HER-3 in breast cancer tissues and its relationship with patient characteristics.We then purified HSP70-PCs from primary breast cancer cells with different HER-2 and HER-3 expression profiles and determined the cytotoxicity of autogenous dendritic cells(DCs)and CD8+T cells induced by these complexes.Third,recombinant human HSP70-HER-3 protein complexes were used to inhibit the autogenous HSP70-PCs purified from HER-3-overexpressing breast cancer cells,and the resulting immunological response was examined.Results The results show that HSP70-PCs can be combined with recombinant HSP70-HER-3 protein complexes to induce stronger immunological responses than autogenous HSP70-PCs alone and that these treatments induce autogenous CD8+T cell killing of HER-3-positive breast cancer cells.Conclusion These findings provide a new direction for HSP70-DC-based immunotherapy for patients with HER-3-overexpressing breast cancer.
基金supported by the National Nature Science Foundation of China,No.32101020(to JL)the Natural Science Foundation of Shandong Province,Nos.ZR2020MC071(to JL),ZR2023MH327(to HZ)+1 种基金the Integrated Project of Major Research Plan of National Natural Science Foundation of China,No.92249303(to PL)the Natural Science Foundation of Qingdao,No.23-2-1-193-zyyd-jch(to HZ)。
文摘The protein connector enhancer of kinase suppressor of Ras 2(CNKSR2),present in both the postsynaptic density and cytoplasm of neurons,is a scaffolding protein with several protein-binding domains.Variants of the CNKSR2 gene have been implicated in neurodevelopmental disorders,particularly intellectual disability,although the precise mechanism involved has not yet been fully understood.Research has demonstrated that CNKSR2 plays a role in facilitating the localization of postsynaptic density protein complexes to the membrane,thereby influencing synaptic signaling and the morphogenesis of dendritic spines.However,the function of CNKSR2 in the cytoplasm remains to be elucidated.In this study,we used immunoprecipitation and high-resolution liquid chromatography-mass spectrometry to identify the interactors of CNKSR2.Through a combination of bioinformatic analysis and cytological experiments,we found that the CNKSR2 interactors were significantly enriched in the proteome of the centrosome.We also showed that CNKSR2 interacted with the microtubule protein DYNC1H1 and with the centrosome marker CEP290.Subsequent colocalization analysis confirmed the centrosomal localization of CNKSR2.When we downregulated CNKSR2 expression in mouse neuroblastoma cells(Neuro 2A),we observed significant changes in the expression of numerous centrosomal genes.This manipulation also affected centrosome-related functions,including cell size and shape,cell proliferation,and motility.Furthermore,we found that CNKSR2 interactors were highly enriched in de novo variants associated with intellectual disability and autism spectrum disorder.Our findings establish a connection between CNKSR2 and the centrosome,and offer new insights into the underlying mechanisms of neurodevelopmental disorders.
文摘Cryo-electron microscopy makes use of transmission electron microscopy to image vitrified biological samples and reconstruct their three-dimensional structures from two-dimensional projections via computational approaches. After over40 years of development, this technique is now reaching its zenith and reforming the research paradigm of modern structural biology. It has been gradually taking over X-ray crystallography as the mainstream method. In this review, we briefly introduce the history of cryo-EM, recent technical development and its potential power to reveal dynamic structures. The technical barriers and possible approaches to tackle the upcoming challenges are discussed.
文摘Objectives:Although Yes-associated protein 1(YAP1)is an important oncogene in hepatocellular carcinoma(HCC)progression,its nuclear localization prevents it from being considered a potential therapeutic target.Recently,studies have reported that coatomer protein complex subunit beta 2(COPB2)also plays a critical role in HCC development;however its mechanism of action is unclear.This study aimed to investigate the role of COPB2 and YAP1 in the progression of HCC and to elucidate the underlying mechanisms.Methods:COPB2 and YAP1 expression in HCC tissues were first analyzed by database searches and immunohistochemistry.Nomogram and artificial neural network models were established based on COPB2 and YAP1 expression.Cell proliferation was detected by cell counting kit-8 and clone formation assay,while cell migration and invasion were assessed using Transwell assays.Finally,the potential mechanisms underlying COPB2 regulation of YAP1 nuclear translocation were explored by immunofluorescence assay and Western blot.Results:COPB2 combined with YAP1 expression was associated with overall postoperative survival in HCC patients and was an independent prognostic factor.High expression of both COPB2 and YAP1 in patients may reduce the efficacy of postoperative transarterial chemoembolization therapy.In vitro experiments revealed that COPB2 affected the sensitivity of HCC cells to Cisplatin(DDP)by regulating YAP1 nuclear translocation.Conclusions:Our findings suggest that COPB2/YAP1 affects the drug sensitivity of HCC cells to DDP and that targeting COPB2/YAP1 may be a promising strategy for the precision treatment of HCC.
基金Supported by Fundao para a Ciência e Tecnologia(FCT)(PTDC/QUI-BIQ/118492/2010)Fundo Europeu de Desenvolvimento Regional(FEDER)(FCOMP-01-0124-FEDER-020895),Portugal
文摘Prostate cancer is a major public health concern world-wide, being one of the most prevalent cancers in men. Great improvements have been made both in terms of early diagnosis and therapeutics. However, there is still an urgent need for reliable biomarkers that could overcome the lack of cancer-specifcity of prostate-specifc antigen, as well as alternative therapeutic targets for advanced metastatic cases. Reversible phosphorylation of proteins is a post-translational modifcation critical to the regulation of numerous cellular processes. Phosphoprotein phosphatase 1 （PPP1） is a major serine/threonine phos-phatase, whose specifcity is determined by its interacting proteins. These interactors can be PPP1 substrates, regulators, or even both. Deregulation of this protein-protein interaction network alters cell dynamics and underlies the development of several cancer hallmarks. Therefore, the identification of PPP1 interactome in specific cellular context is of crucial importance. The knowledge on PPP1 complexes in prostate cancer remains scarce, with only 4 holoenzymes characterized in human prostate cancer models. However, an increasing number of PPP1 interactors have been identifed as expressed in human prostate tissue, including the tumor suppressors TP53 and RB1. Efforts should be made in order to identify the role of such proteins in prostate carcinogenesis, since only 26 have yet well-recognized roles. Here, we revise literature and human protein databases to provide an in-depth knowledge on the biological significance of PPP1 complexes in human prostate carcinogenesis and their potential use as therapeutic targets for the development of new therapies for prostate cancer.
文摘Salmonella and E.coli possess different surface protein structures that can induce protective immune responses.Identification of these proteins capacitates development of diverse applications in prevention and diagnosis that contribute to effectively control disease-causing enterobacteria pathogens such as Salmonella and E.coli.A simple procedure for obtaining protein complexes of Salmonella serotypes and E.coli is performed in this study.A sonication process with heat treatment of whole bacteria induced the release of protein complexes.Concentration of the protein extract was quantified using protein quantification Kits-Rapid,and protein complex profile was obtained by SDS-PAGE(Sodium dodecyl sulfate polyacrylamide gel electrophoresis)and silver staining.The concentrations of protein ranged from 29.45 to 45.35μg/mL in the Salmonella protein extracts,and from 25.35 to 36.72μg/mL in the E.coli protein extracts.Six major groups of proteins from E.coli(YfiO,NipB,OmpF,YfgL,Talc,YaeT)and four major groups of proteins from Salmonella(Flagellin,OmpA,Porin,SEF21)were preliminarily determined by a simple procedure of extraction based on the molecular weight.
