Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools...Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states.The utilization of protein/gene interaction and genetic variation databases,coupled with pathway analysis can facilitate the identification of potential drug targets.By bridging the gap between molecular-level information and disease understanding,this review contributes insights into the impactful utilization of computational methods,paving the way for targeted interventions and therapeutic advancements in biomedical research.展开更多
Bone morphogenetic proteins(BMPs)are a family of potent,multifunctional growth factors belonging to transforming growth factor-(TGF-).They are highly conservative in structures.Over 20 members of BMPs with varying fun...Bone morphogenetic proteins(BMPs)are a family of potent,multifunctional growth factors belonging to transforming growth factor-(TGF-).They are highly conservative in structures.Over 20 members of BMPs with varying functions such as embryogenesis,skeletal formation,hematopoiesis and neurogenesis have been identified in human body.BMPs are unique growth factors that can induce the formation of bone tissue individually.BMPs can induce the differentiation of bone marrow mesenchymal stem cells into osteoblastic lineage and promote the proliferation of osteoblasts and chondrocytes.BMPs stimulate the target cells by specific membrane-bound receptors and signal transduced through mothers against decapentaplegic(Smads)and mitogen activated protein kinase(MAPK)pathways.It has been demonstrated that BMP-2,BMP-4,BMP-6,BMP-7,and BMP-9 play an important role in bone formation.This article focuses on the molecular characterization of BMPs family members,mechanism of osteogenesis promotion,related signal pathways of osteogenic function,relationships between structure and osteogenetic activity,and the interactions among family members at bone formation.展开更多
心肌细胞损伤与多种心血管疾病的发生发展有关,而氧化应激和细胞凋亡是造成心肌损伤的重要原因。硫氧还蛋白相互作用蛋白(thioredoxin-interacting protein,TXNIP)可调控细胞氧化还原状态,并诱导氧化应激的产生,最终可诱导炎症或细胞凋...心肌细胞损伤与多种心血管疾病的发生发展有关,而氧化应激和细胞凋亡是造成心肌损伤的重要原因。硫氧还蛋白相互作用蛋白(thioredoxin-interacting protein,TXNIP)可调控细胞氧化还原状态,并诱导氧化应激的产生,最终可诱导炎症或细胞凋亡。miR-16-5p能抑制脂多糖(lipopolysaccharide,LPS)诱导的炎症反应和A549细胞损伤。但TXNIP是否受miR-16-5p的调控还鲜有报道。本实验旨在研究miR-16-5p与TXNIP的关系,以及miR-16-5p是否通过结合TXNIP影响心肌细胞氧化应激和凋亡。通过TargetScan数据库预测到TXNIP与miR-16-5p存在结合位点。双荧光素酶报告结果验证miR-16-5p靶向调控TXNIP。转染miR-16-5p过表达载体和TXNIP抑制表达载体后,用流式细胞术检测细胞凋亡率。结果显示,细胞凋亡率(10.44±1.13 vs 29.65±2.87,P<0.01)、(13.54±1.33 vs 29.14±2.76,P<0.01)均降低。采用丙二醛(MDA)、超氧化物歧化酶(SOD)、谷胱甘肽过氧化物酶(GSH-Px)试剂盒分别检测丙二醛含量和SOD、GSH-Px活力。结果显示,miR-16-5p组丙二醛含量降低(13.58±1.55 vs 42.18±4.69,P<0.01),SOD活力(79.68±7.65 vs 34.87±3.49,P<0.01)、GSH-Px活力(687.99±35.42 vs 376.48±29.87,P<0.01)升高;si-TXNIP组丙二醛含量(18.69±1.84 vs 45.21±4.33,P<0.01)降低,SOD活力(71.65±7.32 vs 31.69±4.05,P<0.01)、GSH-Px活力(654.12±34.57 vs 367.43±33.54,P<0.01)升高。以上结果表明,过表达miR-16-5p或可抑制TXNIP表达,均可抑制脂多糖诱导的心肌细胞凋亡和氧化应激反应。综上所述,miR-16-5p可通过抑制TXNIP表达抑制脂多糖诱导的心肌细胞损伤。展开更多
Influenza virus contains three integral membrane proteins:haemagglutinin,neuraminidase,and matrix protein(M1 and M2).Among them,M2 protein functions as an ion channel,important for virus uncoating in endosomes of viru...Influenza virus contains three integral membrane proteins:haemagglutinin,neuraminidase,and matrix protein(M1 and M2).Among them,M2 protein functions as an ion channel,important for virus uncoating in endosomes of virus-infected cells and essential for virus replication.In an effort to explore potential new functions of M2 in the virus life cycle,we used yeast two-hybrid system to search for M2-associated cellular proteins.One of the positive clones was identified as human Hsp40/Hdj1,a DnaJ/Hsp40 family protein.Here,we report that both BM2(M2 of influenza B virus)and A/M2(M2 of influenza A virus)interacted with Hsp40 in vitro and in vivo.The region of M2-Hsp40 interaction has been mapped to the CTD1 domain of Hsp40.Hsp40 has been reported to be a regulator of PKR signaling pathway by interacting with p58^(IPK) that is a cellular inhibitor of PKR.PKR is a crucial component of the host defense response against virus infection.We therefore attempted to understand the relationship among M2,Hsp40 and p58^(IPK) by further experimentation.The results demonstrated that both A/M2 and BM2 are able to bind to p58^(IPK)in vitro and in vivo and enhance PKR autophosphorylation probably via forming a stable complex with Hsp40 and P58^(IPK),and consequently induce cell death.These results suggest that influenza virus M2 protein is involved in p58^(IPK)mediated PKR regulation during influenza virus infection,therefore affecting infected-cell life cycle and virus replication.展开更多
基金This work was supported by EU funding within the NextGenerationEU-MUR PNRR Extended Partnership Initiative on Emerging Infectious Diseases(Project No.PE00000007,INF-ACT)。
文摘Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states.The utilization of protein/gene interaction and genetic variation databases,coupled with pathway analysis can facilitate the identification of potential drug targets.By bridging the gap between molecular-level information and disease understanding,this review contributes insights into the impactful utilization of computational methods,paving the way for targeted interventions and therapeutic advancements in biomedical research.
基金This work was supported by National Natural Science Foundation Funding(3110131631371805)Program for New Century Excellent Talents in University of Ministry of Education of China(NCET-11-0796)and Heilongjiang Province Postdoctoral Science Foundation.
文摘Bone morphogenetic proteins(BMPs)are a family of potent,multifunctional growth factors belonging to transforming growth factor-(TGF-).They are highly conservative in structures.Over 20 members of BMPs with varying functions such as embryogenesis,skeletal formation,hematopoiesis and neurogenesis have been identified in human body.BMPs are unique growth factors that can induce the formation of bone tissue individually.BMPs can induce the differentiation of bone marrow mesenchymal stem cells into osteoblastic lineage and promote the proliferation of osteoblasts and chondrocytes.BMPs stimulate the target cells by specific membrane-bound receptors and signal transduced through mothers against decapentaplegic(Smads)and mitogen activated protein kinase(MAPK)pathways.It has been demonstrated that BMP-2,BMP-4,BMP-6,BMP-7,and BMP-9 play an important role in bone formation.This article focuses on the molecular characterization of BMPs family members,mechanism of osteogenesis promotion,related signal pathways of osteogenic function,relationships between structure and osteogenetic activity,and the interactions among family members at bone formation.
文摘心肌细胞损伤与多种心血管疾病的发生发展有关,而氧化应激和细胞凋亡是造成心肌损伤的重要原因。硫氧还蛋白相互作用蛋白(thioredoxin-interacting protein,TXNIP)可调控细胞氧化还原状态,并诱导氧化应激的产生,最终可诱导炎症或细胞凋亡。miR-16-5p能抑制脂多糖(lipopolysaccharide,LPS)诱导的炎症反应和A549细胞损伤。但TXNIP是否受miR-16-5p的调控还鲜有报道。本实验旨在研究miR-16-5p与TXNIP的关系,以及miR-16-5p是否通过结合TXNIP影响心肌细胞氧化应激和凋亡。通过TargetScan数据库预测到TXNIP与miR-16-5p存在结合位点。双荧光素酶报告结果验证miR-16-5p靶向调控TXNIP。转染miR-16-5p过表达载体和TXNIP抑制表达载体后,用流式细胞术检测细胞凋亡率。结果显示,细胞凋亡率(10.44±1.13 vs 29.65±2.87,P<0.01)、(13.54±1.33 vs 29.14±2.76,P<0.01)均降低。采用丙二醛(MDA)、超氧化物歧化酶(SOD)、谷胱甘肽过氧化物酶(GSH-Px)试剂盒分别检测丙二醛含量和SOD、GSH-Px活力。结果显示,miR-16-5p组丙二醛含量降低(13.58±1.55 vs 42.18±4.69,P<0.01),SOD活力(79.68±7.65 vs 34.87±3.49,P<0.01)、GSH-Px活力(687.99±35.42 vs 376.48±29.87,P<0.01)升高;si-TXNIP组丙二醛含量(18.69±1.84 vs 45.21±4.33,P<0.01)降低,SOD活力(71.65±7.32 vs 31.69±4.05,P<0.01)、GSH-Px活力(654.12±34.57 vs 367.43±33.54,P<0.01)升高。以上结果表明,过表达miR-16-5p或可抑制TXNIP表达,均可抑制脂多糖诱导的心肌细胞凋亡和氧化应激反应。综上所述,miR-16-5p可通过抑制TXNIP表达抑制脂多糖诱导的心肌细胞损伤。
基金supported by National Natural Sciences Foundation of China(NSFC)(Grant Nos.30670091 and 30599434)National Basic Research Program(Project 973)of China Ministry of Science and Technology(Grant No.2011CB504703)+1 种基金National Key Technologies R&D Program(Grant No.2006BAD06A01)GFG is a leading principal investigator of the NSFC Innovative Research Group(Grant No.81021003).
文摘Influenza virus contains three integral membrane proteins:haemagglutinin,neuraminidase,and matrix protein(M1 and M2).Among them,M2 protein functions as an ion channel,important for virus uncoating in endosomes of virus-infected cells and essential for virus replication.In an effort to explore potential new functions of M2 in the virus life cycle,we used yeast two-hybrid system to search for M2-associated cellular proteins.One of the positive clones was identified as human Hsp40/Hdj1,a DnaJ/Hsp40 family protein.Here,we report that both BM2(M2 of influenza B virus)and A/M2(M2 of influenza A virus)interacted with Hsp40 in vitro and in vivo.The region of M2-Hsp40 interaction has been mapped to the CTD1 domain of Hsp40.Hsp40 has been reported to be a regulator of PKR signaling pathway by interacting with p58^(IPK) that is a cellular inhibitor of PKR.PKR is a crucial component of the host defense response against virus infection.We therefore attempted to understand the relationship among M2,Hsp40 and p58^(IPK) by further experimentation.The results demonstrated that both A/M2 and BM2 are able to bind to p58^(IPK)in vitro and in vivo and enhance PKR autophosphorylation probably via forming a stable complex with Hsp40 and P58^(IPK),and consequently induce cell death.These results suggest that influenza virus M2 protein is involved in p58^(IPK)mediated PKR regulation during influenza virus infection,therefore affecting infected-cell life cycle and virus replication.
