A protein complex recognition method based on spatial-temporal graph convolution neural network / 南方医科大学学报

OBJECTIVE@#To propose a new method for mining complexes in dynamic protein network using spatiotemporal convolution neural network.@*METHODS@#The edge strength, node strength and edge existence probability are defined for modeling of the dynamic protein network. Based on the time series information and structure information on the graph, two convolution operators were designed using Hilbert-Huang transform, attention mechanism and residual connection technology to represent and learn the characteristics of the proteins in the network, and the dynamic protein network characteristic map was constructed. Finally, spectral clustering was used to identify the protein complexes.@*RESULTS@#The simulation results on several public biological datasets showed that the F value of the proposed algorithm exceeded 90% on DIP dataset and MIPS dataset. Compared with 4 other recognition algorithms (DPCMNE, GE-CFI, VGAE and NOCD), the proposed algorithm improved the recognition efficiency by 34.5%, 28.7%, 25.4% and 17.6%, respectively.@*CONCLUSION@#The application of deep learning technology can improve the efficiency in analysis of dynamic protein networks.

A four-protein metabolon assembled by a small peptide protein creates the pentacyclic carbonate ring of aldgamycins

Organic carbonates (OCs) are a class of compounds featured by a carbonyl flanked by two alkoxy/aryloxy groups. They exist in either linear or cyclic forms, of which the majority encountered in nature adopt a pentacyclic structure. However, the enzymatic basis for pentacyclic carbonate ring formation remains elusive. Here, we reported that a four-protein metabolon (AlmUII-UV) assembled by a small peptide protein (AlmUV) appends a reactive

The role of the mTORC1 signaling pathway during osteogenic differentiation of mouse bone marrow mesenchymal cells under tension stress / 口腔疾病防治

Objective@# To investigate the expression of the mTORC1 signaling pathway during the osteogenic differentiation of mouse bone marrow mesenchymal cells (BMMSCs) under cyclic uniaxial tension and explore its possible role.@*Methods @# The BMMSCs of mice were affected by uniaxial dynamic tensile force. Western blot was used to detect the expression changes of major molecules (mTOR, Raptor, S6K) in the endogenous mTORC1 signaling pathway at 0, 1, 2, 4, and 8 hours after stretching. Chemical colorimetry, ELISA and PCR were used to detect alkaline phosphatase (ALP), osteocalcin (OCN) and Runx2 mRNA, respectively. Then, inhibition, activation and control groups were established by administration of the drugs PP242, MHY1485 and PBS, respectively. Two hours after the stress, the expression of S6K was detected by western blot, and the expression of the osteogenic signal was continuously detected by the above methods.@*Results @#Western blot analysis showed that the main molecules of the mTORC1 signaling pathway were all expressed within 8 hours after traction, and the highest expression was 2 hours after the stress. Compared with those in the control group, the ALP activity and OCN expression decreased and the Runx2 mRNA levels increased after the mTORC1 signal pathway was inhibited (P ＜ 0.001); ALP activity and OCN expression increased after the mTORC1 signal pathway was activated, while the Runx2 mRNA levels decreased (P ＜ 0.001). @*Conclusion @#The mTORC1 signaling pathway participates in the osteogenic differentiation of mouse BMMSCs under tension. The osteogenesis of BMMSCs under cyclic uniaxial tension would be enhanced if the mTORC1 signaling pathway was activated.

Targeting an oncogenic kinase/phosphatase signaling network for cancer therapy

Protein kinases and phosphatases signal by phosphorylation and dephosphorylation to precisely control the activities of their individual and common substrates for a coordinated cellular outcome. In many situations, a kinase/phosphatase complex signals dynamically in time and space through their reciprocal regulations and their cooperative actions on a substrate. This complex may be essential for malignant transformation and progression and can therefore be considered as a target for therapeutic intervention. p38 is a unique MAPK family member that contains a PDZ motif at its C-terminus and interacts with a PDZ domain-containing protein tyrosine phosphatase PTPH1. This PDZ-coupled binding is required for both PTPH1 dephosphorylation and inactivation of p38 and for p38 phosphorylation and activation of PTPH1. Moreover, the p38/PTPH1 complex can further regulate their substrates phosphorylation and dephosphorylation, which impacts Ras transformation, malignant growth and progression, and therapeutic response. This review will use the p38/PTPH1 signaling network as an example to discuss the potential of targeting the kinase/phosphatase signaling complex for development of novel targeted cancer therapy.

MIPCE: An MI-based protein complex extraction technique.

Protein–protein interaction (PPI) networks are believed to be important sources of information related to biological processes and complex metabolic functions of the cell. Identifying protein complexes is of great importance for understanding cellular organization and functions of organisms. In this work, a method is proposed, referred to as MIPCE, to find protein complexes in a PPI network based on mutual information.MIPCE has been biologically validated by GO-based score and satisfactory results have been obtained. We have also compared our method with some wellknown methods and obtained better results in terms of various parameters such as precession, recall and F-measure.

The effect of combination of docosahexaenoic acid and 5-fluorouracil on the proliferation of human gastric cancer cell line AGS and the expression of mitochondrial respiratory membrane protein complexes / 西安交通大学学报(医学版)

Objective To investigate the inhibitory effects of docosahexaenoic acid (DHA)and 5-fluorouracil (5-FU)in combination on human gastric cancer cell line AGS in vitro .Methods Human gastric cancer line AGS was treated with different concentrations of DHA and 5-FU alone or in combination.The inhibition of cell proliferation was evaluated by MTT assay.Dose of median (IC50 )of drugs (alone or in combination)and the combination index (CI)were calculated using the median-effect equation and the combination index equation of Chou-Talalay.Flow cytometry was used to detect the cell cycle distribution.The expression of mitochondrial respiratory membrane protein complex in AGS cells was analyzed with Western blot.Results DHA and 5-FU alone or in combination could markedly suppress the proliferation of AGS in significantly time-dependent and dose-dependent manners (P <0.05).IC50 values with DHA or 5-FU administered for 24 h and 48 h were 5 1.60 μg/mL (DHA:24 h),34.82 μg/mL (DHA:48 h),45.90 μg/mL (5-FU:24 h),and 1 6.86 μg/mL (5-FU:48 h), respectively.DHA remarkably strengthened the inhibitory effect of 5-FU and decreased IC50 of 5-FU by 3.56 -2.1 5 folds.The combination of DHA and 5-FU showed synergism.Flow cytometry showed that AGS cells treated with DHA and 5-FU were arrested in G0/G1 phase and the proportion of AGS cells in G0/G1 phase increased compared with that in the control group,DHA group and 5-FU group,while the proportion of the cells in S phase decreased significantly (P < 0.05 ).Western blot showed after treatment with DHA and 5-FU for 48 h,the expression of mitochondrial respiratory membrane protein complex was significantly decreased compared with control group,DHA group and 5-FU group (P <0.05).Conclusion DHA could act synergistically with 5-FU in inhibiting the growth of gastric carcinoma cells,and meanwhile decrease the dose of 5-FU.The mechanism may be associated with cell cycle arrest in G0/G1 phase and interference in the energy metabolism of AGS cells due to inhibition of the expression of mitochondrial oxidative respiratory chain complexes by the two compounds.

Development of a new coating substrate for human embryonic stem cell culture / 中国实验动物学报

Objective To reduce the animal component contamination for human embryonic stem cells ( hESCs ) and to simplify hESCs culture process , we develop a new coating substrate which can support the hESCs growth without dif -ferentiation, and is easy to store and use. Methods Mouse embryonic fibroblasts(MEF)were fixed on the surface of plate by methanol.hESCs were cultured on this new substrate and were passaged every 5 to 6 days.After 10 passages, we checked the cell morphology , alkaline phosphatase expression , embryonic specific markers and the differentiation ability in vitro.Results After 10 passages , the hESCs grew well on this new substrate and maintained the typical hESCs morpholo -gy.Alkaline phosphatase staining was positive .Immunofluorescence staining showed that the expressions of Oct 4, SSEA4, Tra-1-60 were positive .The cells formed embryoid body in vitro .Conclusions This methanol-fixed MEF substrate can support the growth of undifferentiated hESCs .The coating material can be produced in large scale and stored for a long time.It provides a new and relatively easy way to amplify hESCs .

Identification of the N-terminal Glycine-arginine Rich (GAR) Domain in Giardia lamblia Fibrillarin and Evidence of its Essentiality for snoRNA Binding.

Aims: Study the role of glycine-arginine rich (GAR) domain of fibrillarin in Giardia lamblia. Study Design: Identifying a specific glycine arginine rich (GAR) sequence of Giardia fibrillarin which plays an important role in ribonucleoprotein particles complex formation with snoRNA during post transcriptional modifications of rRNA. The present study uses Electrophoretic Mobiliy Shift Assay (EMSA) to detect protein-RNA interactions. 32P labeled snoRNA incubated with purified fibrillarin or GAR domain truncated fibrillarin protein were separated by a non denaturing polyacrylamide gel where the band patterns suggested the interaction of the RNAs with both proteins. Place and Duration of Study: Department of Parasitology, National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research, Kolkata, between January 2011 and July 2012. Methodology: Homology analysis of G. lamblia fibrillarin was performed with fibrillarins from Homo sapiens, Mus musculus and Arabidopsis thaliana to determine the conserved domain by ClustalW analysis. Cloning, expression and purification of fibrillarin and GAR domain truncated fibrillarin were done to study the role of GAR domain in snoRNA-fibrillarin binding by EMSA and Gradient EMSA. Immunoblot assay of purified GAR domain truncated fibrillarin was performed by using polyclonal antibody of purified recombinant giardia fibrillarin protein. Results: Gel retardation assay showed that snoRNA does not bind with GAR domain truncated fibrillarin to form any RNP complex. Similarly in gradient EMSA the GAR domain truncated fibrillarin does not bind with any of the in vitro transcribed snoRNA even at much higher concentration than they do for full length purified recombinant fibrillarin. Conclusion: The amino terminal conserved glycine arginine rich (GAR) domain is present in Giardia lamblia fibrillarin and is essential for binding with snoRNA of this protein.

Establishment of SAV stablely expressed cell pool and purification of SAV interacting protein complex / 中国药学杂志

OBJECTIVE: To Establish HEK293 cell model in which SAV is stably expressing and purification of SAV interacting protein complex. METHODS: RT-PCR was used to amplify SAV gene segment in HEK293 cells and then the PCR product was cloned into pBabe-SBP-FLAG vector with BamH I and EcoR I restriction enzyme cutting sites. Co-transfection of pBabe-SBP-FLAG-SAV and the packing plasmids into HEK293T cells to produce retroviruses which will be used for infection of HEK293 cells. Stable cell pool was selected by puromycine for 2 weeks and SAV expression was detected by Western-blot. SAV interacting protein complex was purified by streptavidin beads from the stable cell pool and virulized by silver staining. RESULTS: pBabe-SBP-FLAG-SAV expression vector was successfully constructed. FLAG-SBP tagged SAV in HEK293 stable cell pool was detected by straight Western-blot and IP-Western-blot. SAV interacting protein complex was captured by streptavidin beads and some specific bands purified from SAV stable cell pool was visualized compare to control in silver stainning. CONCLUSION: pBabe-SBP-FLAG-SAV eukaryotic expression plasmid and the stable cell pool is successfully constructed and the interacting protein complex is purified by streptavidin beads, which provide a foundation for further investigation of SAV.

Niemann-Pick type C1 protein influences the delivery of cholesterol to the SREBP: SCAP complex

The proposed role of Niemann-Pick type C1 protein (NPC1) in the delivery of low-density lipoprotein (LDL) cholesterol to the sterol regulatory element binding protein (SREBP):SREBP cleavage activation protein (SCAP) complex in the endoplasmic reticulum has been largely based on indirect studies and remains contentious. The major aim of the present study was to assess whether NPC1 is involved in the delivery of LDL cholesterol to the SREBP:SCAP complex. A cell line stably expressing green fluorescence protein-SCAP was cultured in the presence of U18666A, which can induce a Niemann-Pick type C disease phenotype, in order to locate the SREBP:SCAP complex by fluorescence microscopy. Our major finding was that defective NPC1 caused a delay in the ability of LDL cholesterol to suppress SREBP processing. This was shown in a time-course experiment by the effect of LDL on green fluorescence protein-SCAP movement when cells were treated with pharmacological agents to induce a Niemann-Pick type C disease phenotype. We demonstrated directly by fluorescence microscopy that defective NPC1 causes a delay in LDL cholesterol delivery to the endoplasmic reticulum where SCAP senses cholesterol.

Mechanism of epileptic seizures in the neuron-specific adaptor protein complex type 3B knockout mice / 中华神经科杂志

Objective To explore the mechanism of spontaneous seizures in adaptor protein complex type 3B knockout mice(AP3M2KO mice).Methods AP3M2KO mice were generated.Seizures and electroencephalogram(EEG)were monitored using video camera and telemetry system.Glutamate and GABA releases were determined using in vivo microdialysis method.Results AP3M2KO mice began to suffer from spontaneous seizures 8 weeks after the birth,but did not show any other behavior abnormality.The onset of ictal discharge over the temporal region was synchronized with seizures.There were no significant differences in basal glutamate and GABA releases in hippocampus between AP3M2KO((0.35±0.08)pmol/20μl and(2.94±1.69)fmol/20μl,respectively)and wild-type mice.However,the 50 mmol/L K+-evoked GABA release was impaired in AP3M2KO mice((63.5±11.8)fmol/20μl vs(209.2±63.7)fmol/20 μl,t=4.405,P＜0.05),whereas no significant difference was found in K+-evoked glutamate release.Conclusions AP3M2KO mice suffer from epileptic seizures similar to the clinical features of human epilepsy.The impairment of inhibitory GABAergic transmission iS involved in the mechanism of spontaneous seizures in AP3M2KO mice.

Tandem affinity purification technique: an extraordinary valuable tool for purifying protein complexes / 基础医学与临床

It's a multi-protein complex and not single protein that accomplish most of cellular activity.Therefore,to identify and analyze the composition of protein complex is necessary for studying the function of proteins.Tandem affinity purification technique(TAP) enables the effective purification of complex under physiological conditions without knowledge of the complex composition and function.Now,it has been adapted to analyze the composition of the protein complexes in yeast.Combined with mass spectrometry,TAP can identify the interacting proteins of target protein and offer great help for opening protein interacting network and function out.

Effect of S100A8/A9 Protein Complex on F-actin Network in Human Cervical Carcinoma Cell Line,CasKi Cells / 中国微创外科杂志

Objective To investigate the effect of S100A8/A9 protein complex on the surface morphology and the F-actin network in human cervical carcinoma cell line,CasKi cells.Methods After being cultured with 20 ?g/ml S100A8/A9 protein complex,the cell skeleton of the CasKi cells were observed under a confocal scanning fluorescence microscope by staining the F-actin network.Atomic force microscopy(AFM) was employed to reveal the change of ultrastructure of the cell surface in vivo.ResultsAfter being cultured with the S100A8/A9 protein complex for 24 hours,the F-actin network disorder was revealed.Most of the F-actins distributed peripherally.The OD value of the F-actin decreased significantly from 92.42?5.16 to 57.67?3.70 after been treated with the S100A8/A9(t=5.268,P=0.000).The AFM showed a withdrawing morphology with reduced pseudopodia and destruction of stress fibers. Conclusion S100A8/A9 protein complex can change the ultrastructure of the surface of CasKi cells and its stress fibers by re-distributing of the F-actin in the cells.

Immunologic reactivity of a lipopolysaccharide-protein complex of type A Pasteurella multocida in mice

The immunologic reactivity of a lipopolysaccharide (LPS)-protein complex isolated from a potassium thiocyanate extract of a Pasteurella multocida (capsular type A and somatic type 3) strain was evaluated in mice. The LPS-protein complex provided 100% protection in mice against a challenge with the homologous strain. However, when the complex was fractionated into LPS and protein moieties by phenol-water treatment, both components lacked immunogenicity. The complex and extracted components were mitogenic for mouse B lymphocytes with the protein moiety the most active. Although immune serum against the LPS-protein complex protected mice against challenge thereby indicating a role for humoral immunity, the LPS-protein complex of P. multocida was also found to induce cell-mediated immunity. This cell-mediated immunity was demonstrated in mice immunized with the complex by: (1). mitogenic responses of T lymphocytes, (2). induction of delayed type hypersensitivity reaction in the hind footpads, and (3). enhanced resistance to challenge infection with Salmonella enteritidis.

Characterization of cytoplasmic Form of Human CTLA - 4 Molecule / 대한면역학회지

CTLA-4 (=CD152), a T cell activation antigen, has been known to be homologous to CD28 in its molecular and genomic structure. Both of these two molecules are sharing their counterreceptors, B7 (CDSO) and B7-2 (CD86) and are known to play a crucial role in T cell activation. In previous our study it was reported that there are 2 forms of CTLA-4 antigen in activated human T cells, 30 kD membrane-bound form and 34 kD cytosolic-sequestered form and the former was less than 5 % of total of this antigen induced. Aims of this study are to confirm previous finding by using flow cytometry and to characterize the cytoplasmic form of human CTLA-4 by using ultrafiltration and immunoprecipitation techniques. In PHA stimulated peripheral blood lymphocyte surface expression of CTLA-4 was less than 2.1% of any of CD4+, CD8+ and CD56+ subsets. And the 34 kD form of CTLA-4 was detected in CDS+ subset only. This discrepancy confirms that 34 kD antigen is the cytoplasmic form of human CTLA-4. In ultrafiltration and subsequent Western blot analysis study this 34 kD antigen was detected in >100 kD fraction only. And in non-reducing condition this antigen formed high molecular weght complex (MW > 350 kD). In immunoprecipitation study using anti-peptide A antibody it was found that this high molecular weight complex consists of the 34 kD cytoplasmic form of CTLA-4 and previously unknown 54 kD antigen and 46 kD antigen at 1:1:8-10 ratio. And none of these 3 molecules were identified in membrane fraction of activated human T cell. The result of this study implies that CTLA-4 molecule induced upon T cell activation mainly sequestered in cytoplasrn and another signal is necessary to target this antigen on the activated T cell surface.

Type 1 fimbriation is negatively regulated by cyclic AMP and its receptor protein via conjugative plasmid F in Escherichia coli K-12.

Expression of fimbriation was studied in Escherichia coli K-12 CA8000 HfrH, and its cya, crp and MS2 resistant mutants. The cells of cya+ crp+ parent strain were observed to be flagellated bacilli, lacking fimbriae, unable to agglutinate erythrocytes and deficient in ability to produce surface pellicle during growth in stationary culture. The cells of cya and crp mutants were observed to be cocci or coccobacilli devoid of flagella, having haemagglutinating activity, fimbriated and capable of producing surface pellicle in stationary cultures. The fimbriation and haemagglutinating activities were lower in cya mutants grown with cAMP supplementation. The cya and crp mutants produced relatively small, smooth and compact colonies consisting mostly of fimbriated cells, like those of earlier described Fim σ mutants. The cya+ crp+ MS2 resistant mutant produced large sized colonies like those of parent but was deficient in conjugal donor ability. It resembled cya and crp mutants in haemagglutinating and fimbriation properties. The cya and crp mutants have been earlier shown to be deficient in several Tra functions including conjugal donor ability. It is concluded that Escherichia coli K-12 cells express fimbriation when Tra functions of F-plasmid carried in them are not expressed either due to deficiency of active cAMPreceptor protein complex or mutation in F-plasmid or when F-plasmid is absent.

Novel tertiary structures and stereospecificities of periplasmic binding proteins involved in active transport and chemotaxis.

Binding proteins, which are located in the periplasmic space of Gram-negative bacteria, are essential components of osmotic shock-sensitive active transport systems and Chemotaxis. Described briefly herein are the high resolution molecular structures of four binding proteins specific for (i) L-arabinose, (ii) sulphate, (iii) D-galactose, and (iv) leucine, isoleucine or valine which we have recently determined. The first three proteins contained bound substrates. Several novel substrate binding properties of the arabinose- and sulphatebinding proteins as revealed by structure refinement at 1·7 Å resolution are also presented. These results have profound significance in understanding both protein structures and substrate-protein interactions.