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Chen Xu Bing Wang Lin Yang Lucas Zhongming Hu Lanxing Yi Yaxuan Wang Shenglan Chen Andrew Emili Cuihong Wan 《基因组蛋白质组与生物信息学报(英文版)》2022,20(4):715-727
Synechocystis sp. PCC 6803(hereafter: Synechocystis) is a model organism for studying photosynthesis, energy metabolism, and environmental stress. Although known as the first fully sequenced phototrophic organism, Synechocystis still has almost half of its proteome without functional annotations. In this study, by using co-fractionation coupled with liquid chromatographytandem mass spectrometry(LC-MS/MS), we define 291 multi-protein complexes, encompassing24,092 protein±protein interactions(PPIs... 相似文献
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<正>Artificial intelligence(AI) is a powerful approach for solving complex problems in the processing, analysis, and interpretation of omics data, as well as the integration of multi-omics and clinical data. In recent years, AI has enabled remarkable breakthroughs across diverse biomedical fields, such as genomic variant interpretation, protein structure prediction, disease diagnosis, and drug discovery. 相似文献
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Wubing Zhang Shourya S.Roy Burman Jiaye Chen Katherine A.Donovan Yang Cao Chelsea Shu Boning Zhang Zexian Zeng Shengqing Gu Yi Zhang Dian Li Eric S.Fischer Collin Tokheim X.Shirley Liu 《基因组蛋白质组与生物信息学报(英文版)》2022,(5):882-898
Targeted protein degradation(TPD) has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell’s endogenous protein degradation machinery. However, the susceptibility of proteins for targeting by TPD approaches, termed‘‘degradability”, is largely unknown. Here, we developed a machine learning model, model-free analysis of protein degradability(MAPD), to predict degradability from features intrinsic to protein targets. MAPD shows accurate perf... 相似文献
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Biofabrication with chitosan 总被引:14,自引:0,他引:14
Yi H Wu LQ Bentley WE Ghodssi R Rubloff GW Culver JN Payne GF 《Biomacromolecules》2005,6(6):2881-2894
The traditional motivation for integrating biological components into microfabricated devices has been to create biosensors that meld the molecular recognition capabilities of biology with the signal processing capabilities of electronic devices. However, a different motivation is emerging; biological components are being explored to radically change how fabrication is achieved at the micro- and nanoscales. Here we review biofabrication, the use of biological materials for fabrication, and focus on three specific biofabrication approaches: directed assembly, where localized external stimuli are employed to guide assembly; enzymatic assembly, where selective biocatalysts are enlisted to build macromolecular structure; and self-assembly, where information internal to the biological material guides its own assembly. Also reviewed are recent results with the aminopolysaccharide chitosan, a material that offers a combination of properties uniquely suited for biofabrication. In particular, chitosan can be directed to assemble in response to locally applied electrical signals, and the chitosan backbone provides sites that can be employed for the assembly of proteins, nucleic acids, and virus particles. 相似文献
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A novel δ-endotoxin gene was cloned from a Bacillus thuringiensis strain with activity against Locusta migratoria manilensis by PCR-based genome walking. The sequence of the cry gene was 3,432 bp long, and it encoded a Cry protein of 1,144 amino acid residues with a molecular mass of 129,196.5 kDa, which exhibited 62% homology with Cry7Ba1 in the amino acid sequence. The δ-endotoxin with five conserved sequence blocks in the amino-terminal region was designated Cry7Ca1 (GenBank accession no. ). Protein structure analysis suggested that the activated toxin of Cry7Ca1 has three domains: 227 residues forming 7 α-helices (domain I); 213 residues forming three antiparallel β-sheets (domain II); and 134 residues forming a β-sandwich (domain III). The three domains, respectively, exhibited 47, 44, and 34% sequence identity with corresponding domains of known Cry toxins. SDS-PAGE and Western blot analysis showed that Cry7Ca1, encoded by the full-length open reading frame of the cry gene, the activated toxin 1, which included three domains but without the N-terminal 54 amino acid residues and the C terminus, and the activated toxin 2, which included three domains and N-terminal 54 amino acid residues but without the C terminus, could be expressed in Escherichia coli. Bioassay results indicated that the expressed proteins of Cry7Ca1 and the activated toxins (toxins 1 and 2) showed significant activity against 2nd instar locusts, and after 7 days of infection, the estimated 50% lethal concentrations (LC50s) were 8.98 μg/ml for the expressed Cry7Ca1, 0.87 μg/ml for the activated toxin 1, and 4.43 μg/ml for the activated toxin 2. The δ-endotoxin also induced histopathological changes in midgut epithelial cells of adult L. migratoria manilensis. EF486523相似文献
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腐马素是由串珠镰刀菌产生的真菌毒素,其中腐马素B1可引发马脑白质软化症等疾病。本文用高效液相色谱法从串珠镰刀菌玉米培养物中分离出了腐马素B1并通过紫外光谱和快原子轰击质谱进行了鉴定。 相似文献
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Acute promyelocytic leukemia (APL) cells are characterized by PML/RARalpha fusion protein, high responsiveness to arsenic trioxide (ATO)-induced cytotoxicity and an abundant generation of reactive oxygen species (ROS). In this study we investigated the association among these three features in APL-derived NB4 cells. We found that NADPH oxidase-derived ROS generation was more abundant in NB4 cells compared with monocytic leukemia U937 cells. By using PR9, a sub-line of U937 stably transduced with the inducible PML/RARalpha expression vectors, we attributed disparities on ROS generation and ATO sensitivity to the occurrence of PML/RARalpha fusion protein, since PML/RARalpha-expressing cells appeared higher NADPH oxidase activity, higher ROS level and higher sensitivity to ATO. On the other hand, the basal intensity of cAMP signaling pathway was compared between NB4 and U937 as well as between PR9 cells with or without PML/RARalpha, demonstrating that PML/RARalpha-expressing cells had an impaired cAMP signaling pathway which relieved its inhibitory effect on NADPH oxidase derived ROS generation. In summary, the present study demonstrated the correlation of PML/RARalpha with cAMP signaling pathway, NADPH oxidase and ROS generation in APL cells. PML/RARalpha that bestows NB4 cells various pathological features, paradoxically also endows these cells with the basis for susceptibility to ATO-induced cytotoxcity. 相似文献
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The biological effects of rare-earth ions on the organism have been studied using Pr3+ as a probe ion and Escherichia coli cell as a target. Atomic force microscopy (AFM) observation of the surface of E. coli cells shows that the presence of Pr3+ substantially changes the structure of the outer membrane. By induced coupled plasma-mass spectrometry (ICP-MS), more Cu2+ was found in the cells grown in the presence of Pr3+, indicating changes of cell permeability. Using energy dispersive X-ray spectroscopy (EDX), Ca2+ is found on the outer surface of the original cell. It is proposed that Pr3+ can replace Ca2+ from the binding sites because of their close ionic radii and similar ligand speciality. 相似文献