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Systems understanding of plant–pathogen interactions through genome-wide proteinprotein interaction

Hong LI,Ziding ZHANG

《农业科学与工程前沿(英文)》 2016年 第3卷 第2期   页码 102-112 doi: 10.15302/J-FASE-2016100

摘要: Plants are frequently affected by pathogen infections. To effectively defend against such infections, two major modes of innate immunity have evolved in plants; pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity. Although the molecular components as well as the corresponding pathways involved in these two processes have been identified, many aspects of the molecular mechanisms of the plant immune system remain elusive. Recently, the rapid development of omics techniques (e.g., genomics, proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogen interactions from a systems perspective and studies on protein–protein interactions (PPIs) between plants and pathogens have been carried out and characterized at the network level. In this review, we introduce experimental and computational identification methods of PPIs, popular PPI network analysis approaches, and existing bioinformatics resources/tools related to PPIs. Then, we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions, including pathogen-centric PPI networks, plant-centric PPI networks and interspecies PPI networks between plants and pathogens. We anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen interactions and will offer some new opportunities for crop protection and improvement.

关键词: plant–pathogen interactions     systems biology     omics     plant immunity     protein–protein interaction     network    

Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

《化学科学与工程前沿(英文)》 2019年 第13卷 第1期   页码 133-139 doi: 10.1007/s11705-018-1737-4

摘要: In , the global transcriptional regulatory factor CodY can interact with the promoter DNA to regulate the growth, metabolism, environmental adaptation and other biological activities of the strains. In order to study the mechanism of interaction between CodY and its target DNA, molecular docking and molecular dynamics simulations were used to explore the binding process at molecular level. Through the calculations of the free energy of binding, hydrogen bonding and energy decomposition, nine key residues of CodY were identified, corresponding to SER184, SER186, SER208, THR217, ARG218, SER219, ASN223, LYS242 and GLY243, among which SER186, ARG218 and LYS242 play a vital role in DNA binding. Our research results provide important theoretical guidance for using wet-lab methods to study and optimize the metabolic network regulated by CodY.

关键词: CodY     DNA     molecular docking     molecular dynamics    

Atomistic characterization of binding modes and affinity of peptide inhibitors to amyloid-

Fufeng LIU,Wenjie DU,Yan SUN,Jie ZHENG,Xiaoyan DONG

《化学科学与工程前沿(英文)》 2014年 第8卷 第4期   页码 433-444 doi: 10.1007/s11705-014-1454-6

摘要: The aggregation of amyloid -protein (A ) is tightly linked to the pathogenesis of Alzheimer’s disease. Previous studies have found that three peptide inhibitors (i.e., KLVFF, VVIA, and LPFFD) can inhibit A aggregation and alleviate A -induced neurotoxicity. However, atomic details of binding modes and binding affinities between these peptide inhibitors and A have not been revealed. Here, using molecular dynamics simulations and molecular mechanics Poisson Boltzmann surface area (MM/PBSA) analysis, we examined the effect of three peptide inhibitors (KLVFF, VVIA, and LPFFD) on their sequence-specific interactions with A and the molecular basis of their inhibition. All inhibitors exhibit varied binding affinity to A , in which KLVFF has the highest binding affinity, whereas LPFFD has the least. MM/PBSA analysis further revealed that different peptide inhibitors have different modes of interaction with A , consequently hotspot binding residues, and underlying driving forces. Specific residue-based interactions between inhibitors and A were determined and compared for illustrating different binding and inhibition mechanisms. This work provides structure-based binding information for further modification and optimization of these three peptide inhibitors to enhance their binding and inhibitory abilities against A aggregation.

关键词: Alzheimer’s disease     amyloid β-protein     peptide inhibitors     protein-protein interaction     molecular dynamics simulation    

Overlap maximum matching ratio (OMMR): a new measure to evaluate overlaps of essential modules

Xiao-xia ZHANG,Qiang-hua XIAO,Bin LI,Sai HU,Hui-jun XIONG,Bi-hai ZHAO

《信息与电子工程前沿(英文)》 2015年 第16卷 第4期   页码 293-300 doi: 10.1631/FITEE.1400282

摘要: Protein complexes are the basic units of macro-molecular organizations and help us to understand the cell’s mechanism. The development of the yeast two-hybrid, tandem affinity purification, and mass spectrometry high-throughput proteomic techniques supplies a large amount of protein-protein interaction data, which make it possible to predict overlapping complexes through computational methods. Research shows that overlapping complexes can contribute to identifying essential proteins, which are necessary for the organism to survive and reproduce, and for life’s activities. Scholars pay more attention to the evaluation of protein complexes. However, few of them focus on predicted overlaps. In this paper, an evaluation criterion called overlap maximum matching ratio (OMMR) is proposed to analyze the similarity between the identified overlaps and the benchmark overlap modules. Comparison of essential proteins and gene ontology (GO) analysis are also used to assess the quality of overlaps. We perform a comprehensive comparison of serveral overlapping complexes prediction approaches, using three yeast protein-protein interaction (PPI) networks. We focus on the analysis of overlaps identified by these algorithms. Experimental results indicate the important of overlaps and reveal the relationship between overlaps and identification of essential proteins.

关键词: Protein-protein interaction network     Essential protein modules     Overlap     Overlap maximum matching ratio    

The role of protein kinase C epsilon in neural signal transduction and neurogenic diseases

null

《医学前沿(英文)》 2011年 第5卷 第1期   页码 70-76 doi: 10.1007/s11684-011-0119-9

摘要:

Protein kinase C epsilon (PKC ?) is one of major isoforms in novel PKC family. Although it has been extensively characterized in the past decade, the role of PKC ? in neuron is still not well understood. Advances in molecular biology have now removed significant barriers to the direct investigation of PKC ? functions in vivo, and PKC ? has been increasingly implicated in the neural biological functions and associated neurogenic diseases. Recent studies have provided important insights into the influence of PKC ? on cortical processing at both the single cell level and network level. These studies provide compelling evidence that PKC ? could regulate distinct aspects of neural signal transduction and suggest that the coordinated actions of a number of molecular signals contribute to the specification and differentiation of PKC ? signal pathway in the developing brain.

关键词: protein kinase C ?     signal transduction     neurogenic disease    

Wheat gluten protein and its impacts on wheat processing quality

Wujun MA, Zitong YU, Maoyun SHE, Yun ZHAO, Shahidul ISLAM

《农业科学与工程前沿(英文)》 2019年 第6卷 第3期   页码 279-287 doi: 10.15302/J-FASE-2019267

摘要:

Before the advent of the wheat genomic era, a wide range of studies were conducted to understand the chemistry and functions of the wheat storage proteins, which are the major determinants of wheat flour the suitability of wheat flour for various end products, such as bread, noodles and cakes. Wheat grain protein is divided into gluten and non-gluten fractions and the wheat processing quality mainly depends on the gluten fractions. Gluten provides the unique extensibility and elasticity of dough that are essential for various wheat end products. Disulfide bonds are formed between cysteine residues, which is the chemical bases for the physical properties of dough. Based on the SDS-extractability, grain protein is divided into SDS-unextractable polymeric protein (UPP) and SDS-extractable polymeric protein. The percentage of UPP is positively related to the formation of disulfide bonds in the dough matrix. In the wheat genomic era, new glutenins with long repetitive central domains that contain a high number of consensus hexapeptide and nonapeptide motifs as well as high content of cysteine and glutamine residues should be targeted.

关键词: wheat gluten     consensus motifs     disulfide bonds     SDS-unextractable polymeric protein     glutenins     gliadins     processing quality     storage protein    

Construction of sustainable, colored and multifunctional protein silk fabric using biomass riboflavin

《化学科学与工程前沿(英文)》 2023年 第17卷 第8期   页码 1131-1139 doi: 10.1007/s11705-023-2321-0

摘要: Riboflavin sodium phosphate has been confirmed as a promising biomass product derived from natural plants. In this paper, a novel method of dyeing and multifunctional modification of silk fabric by impregnation with riboflavin sodium phosphate was proposed, such that protein silk fabric can be endowed with bright yellow color and multi-functionality. The results of this paper confirmed that the pH and concentration of riboflavin sodium phosphate solution are critical factors for dyeing and multifunctional modification. Attractively, the photochromic performance was one of the most distinctive features of the modified silk fabric, and the dyed silk fabric turned into fluorescent green from original yellow under 365 nm ultraviolet lamp. Furthermore, the modified silk fabric exhibited good antibacterial properties with a high inhibition rate of 92% for Escherichia coli. Besides, the flame retardancy of silk fabric was significantly improved after modification. The damaged length of modified silk fabric with 40% owf riboflavin sodium phosphate was lower than 10.4 cm and passed the B1 classification. As revealed by the result of this paper, riboflavin sodium phosphate is sufficiently effective in serving as an eco-friendly multifunctional agent for strengthening the add-value of silk textiles.

关键词: biomass     riboflavin sodium phosphate     silk protein     multifunctional modification     flame retardant    

Antithrombin deficiency and decreased protein C activity in a young man with venous thromboembolism:

null

《医学前沿(英文)》 2018年 第12卷 第3期   页码 319-323 doi: 10.1007/s11684-017-0553-4

摘要:

Antithrombin and protein C are two crucial members in the anticoagulant system and play important roles in hemostasis. Mutations in and lead to deficiency or dysfunction of the two proteins, which could result in venous thromboembolism (VTE). Here, we report a Chinese 22-year-old young man who developed recurrent and serious VTE in cerebral veins, visceral veins, and deep veins of the lower extremity. Laboratory tests and direct sequencing of and were conducted for the patient and his family members. Coagulation tests revealed that the patient presented type I antithrombin deficiency combined with decreased protein C activity resulting from a small insertion mutation c.848_849insGATGT in and a short deletion variant c.572_574delAGA in . This combination of the two mutations was absent in 400 healthy subjects each from southern and northern China. Then, we summarized all the mutations of the and gene reported in the Chinese Han population. This study demonstrates that the combination of antithrombin deficiency and decreased protein C activity can result in severe VTE and that the coexistence of different genetic factors may increase the risk of VTE.

关键词: antithrombin deficiency     protein C activity     mutation     variant     venous thromboembolism     anticoagulants    

Interspecies transmission and evolution of the emerging coronaviruses: perspectives from bat physiology and protein

Baicheng HUANG, Kegong TIAN

《农业科学与工程前沿(英文)》 2020年 第7卷 第2期   页码 218-226 doi: 10.15302/J-FASE-2020324

摘要:

Emergent coronaviruses (CoVs) such as SARS-CoV and MERS-CoV have posed great threats to public health worldwide over the past two decades. Currently, the emergence of SARS-CoV-2 as a pandemic causes greater public health concern. CoV diversity is due to the large size and replication mechanisms of the genomes together with having bats as their optimum natural hosts. The ecological behavior and unique immune characteristics of bats are optimal for the homologous recombination of CoVs. The relationship of spatial structural characteristics of the spike protein, a protein that is critical for recognition by host receptors, in different CoVs may provide evidence in explaining the coevolution of CoVs and their hosts. This information may help to enhance our understanding of CoV evolution and thus provide part of the basis of preparations for any future outbreaks.

关键词: bat     coronavirus     evolution     host receptor     spike protein     transmission    

Elevated C-reactive protein levels predict worsening prognosis in Chinese patients with first-onset stroke

Jiangtao YAN, Rutai HUI, Daowen WANG

《医学前沿(英文)》 2009年 第3卷 第1期   页码 30-35 doi: 10.1007/s11684-009-0005-x

摘要: The role of high sensitivity C-reactive protein (hsCRP) in predicting prognosis after stroke in the Asian population has not been investigated. We hypothesized that elevated levels of hsCRP were associated with worsening prognosis after stroke in Chinese patients. Two hundred and ninety consecutive patients with first-onset stroke and 290 age- and gender-matched control subjects without any cerebrovascular disease were enrolled for study. Plasma hsCRP level was detected and subsequent vascular events and death were recorded in both groups over a 5-year period. Compared to control group, patients presenting with stroke had higher plasma hsCRP level (3.3 ± 3.8 1.3 ± 2.2 mg/L, < 0.01). Furthermore, in the group of patients with stroke, the mean plasma hsCRP level was higher in patients who developed subsequent vascular diseases or died as compared with the patients without further complications (4.4 ± 4.3 2.7 ± 3.3 mg/L, < 0.01). Compared to the lowest tertile of hsCRP level, the relative risk for vascular events or death in stroke patients was 2.91 in the highest tertile of hsCRP (95% CI, 1.54–5.50, = 0.001). This increase in relative risk for vascular events or death in stroke patients continued after adjustment for age, sex and other cardiovascular risk factors such as hypertension and diabetes ( : 2.771, 95% CI: 1.367–5.617, = 0.005). These findings indicate that increased hsCRP level is associated with worsening prognosis after stroke in Chinese patients and suggests that inflammation is correlated with stroke outcome.

关键词: C-reactive protein     inflammation     stroke    

Recombinant protein diannexin prevents preeclampsia-like symptoms in a pregnant mouse model via reducing

《医学前沿(英文)》 2022年 第16卷 第6期   页码 919-931 doi: 10.1007/s11684-021-0918-6

摘要: Preeclampsia (PE) is characterized by placenta-mediated pregnancy complication. The only effective treatment for PE is the delivery of the placenta. However, this treatment may cause preterm birth and neonatal death. Therefore, preventing PE is needed. The mechanism of PE involves abnormal placentation, which leads to the release of anti-angiogenic and inflammatory mediators into maternal circulation. These mediators contribute to systemic vascular dysfunction, inflammatory responses, and excessive thrombin generation. Microparticles (MPs) are reportedly involved in PE by promoting the thromboinflammatory response. This study describes a strategy to prevent PE by reducing MP release using the recombinant protein, diannexin. Results showed that the patients with PE had elevated MP number and procoagulant activity and increased NLRP3 inflammasome activation. Additionally, diannexin remarkably reduced the release of MPs from activated cells by binding to phosphatidylserine exposed on the surface of activated cells. Moreover, in vivo results showed that diannexin could prevent PE-like symptoms by decreasing MPs and NLRP3 inflammasome activation in pregnant mice. Furthermore, diannexin effectively inhibited trophoblast cell activation and NLRP3 inflammasome activation in vitro. These findings suggested that diannexin inhibited MP release and might be an effective therapeutic strategy for preventing PE.

关键词: preeclampsia     recombinant protein diannexin     microparticle     NLRP3 inflammasome     phosphatidylserin    

Investigation of hydrolysis conditions and properties on protein hydrolysates from flatfish skin

Hua ZHANG, Hongji ZHU, Shipeng WANG, Weihua WANG

《化学科学与工程前沿(英文)》 2013年 第7卷 第3期   页码 303-311 doi: 10.1007/s11705-013-1341-6

摘要: Response surface method (RSM), based on Box-Behnken design, was used to optimize the enzymatic hydrolysis conditions of flatfish skin protein hydrolysates (FSPH). Among the tested proteases, the combination of nutrase and trypsin was selected. The optimal hydrolysis conditions were as follows: pH 7.3, temperature 51.8°C, and the enzyme/substrate (E/S) ratio 2.5; under these conditions, the maximum peptide yield (PY) was 69.41±0.43%. The physiochemical analysis showed that the amino acids (His, Asp and Glu) of FSPH accounted for 18.15%, and FSPH was a mixture of polypeptides mostly distributed among 900–2000 Da. FSPH could exhibit a 93% chelating effect on ferrous ion at a concentration of 400 μg/mL, and also a notable reducing power. This study showed bioprocess for the production of FSPH for the first time, which had a good potential for valuable ingredients in the food, cosmetic and medicine industries.

关键词: flatfish skin     protein hydrolysates     metal chelating activity     reducing power    

Correlativity study between expression of DNA double-strand break repair protein and radiosensitivity

Liang ZHUANG, Shiying YU, Xiaoyuan HUANG, Yang CAO, Huihua XIONG

《医学前沿(英文)》 2009年 第3卷 第1期   页码 26-29 doi: 10.1007/s11684-009-0008-7

摘要: DNA double-strand break (DSB) is generally regarded as the most lethal of all DNA lesions after radiation. Ku80, DNA-PK catalytic subunit (DNA-PKcs) and ataxia telangiectasia mutated (ATM) proteins are major DSB repair proteins. In this study, survival fraction at 2Gy (SF2) values of eight human tumor cell lines (including four human cervical carcinoma cell lines HeLa, SiHa, C33A, Caski, three human breast carcinoma cell lines MCF-7, MDA-MB-231, MDA-MB-453, and one human lung carcinoma cell line A549) were acquired by clone formation assay, and western blot was applied to detect the expressions of Ku80, DNA-PKcs and ATM protein. The correlativity of protein expression with SF2 value was analyzed by Pearson linear correlation analysis. We found that the expression of same protein in different cell lines and the expression of three proteins in the same cell line had a significant difference. The SF2 values were also different in eight tumor cell lines and there was a positive correlativity between the expression of DNA-PKcs and SF2 ( =0.723, = 0.043), but Ku80 and ATM expression had no correlation with SF2 ( >0.05). These findings suggest that the expression level of DNA-PKcs protein can be an indicator for predicting the radiosensitivity of tumor cells.

关键词: Ku80     DNA-PK(cs)-binding protein     human     ataxia telangiectasia mutated protein     tumor cell lines     radiosensitivity    

Protein phosphatase 2A, a key player in Alzheimer’s disease

Rong LIU, Qing TIAN

《医学前沿(英文)》 2009年 第3卷 第1期   页码 8-12 doi: 10.1007/s11684-009-0017-6

摘要: Protein phosphatase 2A (PP2A) is the predominant serine/threonine phosphatase in eukaryotic cells. In the brains of patients with Alzheimer’s disease (AD), decreased PP2A activities were observed, which is suggested to be involved in neurofibrillary tangle (NFT) formation, disturbed amyloid precursor protein (APP) secretion and neurodegeneration in AD brain. Based on our research and other previous findings, decreased PP2Ac level, decreased PP2A holoenzyme composition, increased level of PP2A inhibitors, increased PP2Ac Leu309 demethylation and Tyr307 phosphorylation underlie PP2A inactivation in AD. β-amyloid (Aβ) over-production, estrogen deficiency and impaired homocysteine metabolism are the possible up-stream factors that inactivate PP2A in AD neurons. Further studies are required to disclose the role of PP2A in Alzheimer’s disease.

关键词: protein phosphatase 2A     Alzheimer’s disease     holoenzyme composition     protein phosphatase 2A inhibitors     Leu309 demethylation     Tyr307 phosphorylation    

Molecular mechanisms of leukemia-associated protein degradation

Ying-Li WU, Guo-Qiang CHEN, Hu-Chen ZHOU,

《医学前沿(英文)》 2010年 第4卷 第4期   页码 363-370 doi: 10.1007/s11684-010-0210-7

摘要: Chemical biology, using small molecules as probes to study the cellular signaling network, has developed rapidly in recent years. The interaction between chemistry and biology not only provides new insight into the understanding of cellular activities, but also generates new lead compounds for the treatment of diseases. Transcription factors and kinases such as retinoic acid receptor-alpha (RARα), acute myeloid leukemia 1 (AML1), CAAT/enhancer-binding protein α (C/EBPα), c-myc, and c-abl play important roles in the differentiation of hematopoietic stem/progenitor cells. Abnormalities in these proteins may cause the dysregulation of hematopoiesis and even the occurrence of leukemia. Ubiquitin-mediated protein degradation represents a critical mechanism in regulating the cellular levels and functions of these proteins. Thus, targeting protein degradation has been emerging as an important strategy to conquer malignant diseases. In this review, we will summarize the recent advances in the understanding of the roles of protein degradation in leukemia, with an emphasis on the mechanisms revealed by small molecules.

关键词: protein degradation     leukemia     chemical biology     transcription factors     oncoprotein    

标题 作者 时间 类型 操作

Systems understanding of plant–pathogen interactions through genome-wide proteinprotein interaction

Hong LI,Ziding ZHANG

期刊论文

Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

期刊论文

Atomistic characterization of binding modes and affinity of peptide inhibitors to amyloid-

Fufeng LIU,Wenjie DU,Yan SUN,Jie ZHENG,Xiaoyan DONG

期刊论文

Overlap maximum matching ratio (OMMR): a new measure to evaluate overlaps of essential modules

Xiao-xia ZHANG,Qiang-hua XIAO,Bin LI,Sai HU,Hui-jun XIONG,Bi-hai ZHAO

期刊论文

The role of protein kinase C epsilon in neural signal transduction and neurogenic diseases

null

期刊论文

Wheat gluten protein and its impacts on wheat processing quality

Wujun MA, Zitong YU, Maoyun SHE, Yun ZHAO, Shahidul ISLAM

期刊论文

Construction of sustainable, colored and multifunctional protein silk fabric using biomass riboflavin

期刊论文

Antithrombin deficiency and decreased protein C activity in a young man with venous thromboembolism:

null

期刊论文

Interspecies transmission and evolution of the emerging coronaviruses: perspectives from bat physiology and protein

Baicheng HUANG, Kegong TIAN

期刊论文

Elevated C-reactive protein levels predict worsening prognosis in Chinese patients with first-onset stroke

Jiangtao YAN, Rutai HUI, Daowen WANG

期刊论文

Recombinant protein diannexin prevents preeclampsia-like symptoms in a pregnant mouse model via reducing

期刊论文

Investigation of hydrolysis conditions and properties on protein hydrolysates from flatfish skin

Hua ZHANG, Hongji ZHU, Shipeng WANG, Weihua WANG

期刊论文

Correlativity study between expression of DNA double-strand break repair protein and radiosensitivity

Liang ZHUANG, Shiying YU, Xiaoyuan HUANG, Yang CAO, Huihua XIONG

期刊论文

Protein phosphatase 2A, a key player in Alzheimer’s disease

Rong LIU, Qing TIAN

期刊论文

Molecular mechanisms of leukemia-associated protein degradation

Ying-Li WU, Guo-Qiang CHEN, Hu-Chen ZHOU,

期刊论文