This paper describes a case study of 3D protein structure prediction of six sequences from protein data bank （PDB） by genetic algorithm and tabu search （GATS）, where off-lattice AB model is considered as a simplif...This paper describes a case study of 3D protein structure prediction of six sequences from protein data bank （PDB） by genetic algorithm and tabu search （GATS）, where off-lattice AB model is considered as a simplified model of protein structure. The lowest-energy values required for forming the native conformation of proteins are searched by GATS, and then the coarse structures （i.e., simplified structure） of the proteins are obtained according to the multiple angle parameters corresponding to the lowest energies. All the coarse structures form single hydrophobic cores surrounded by hydrophilic residues, which stay on the right side of the actual characteristic of protein structure. It demonstrates that this approach can predict the 3D protein structure effectively.展开更多
Fusarium head blight (FHB) is a destructive disease of wheat and other cereals. FHB occurs in Europe, North America and around the world causing significant losses in production and endangers human and animal health. ...Fusarium head blight (FHB) is a destructive disease of wheat and other cereals. FHB occurs in Europe, North America and around the world causing significant losses in production and endangers human and animal health. In this article, we provide the strategic steps for the specific target selection for the phytopathogen system wheat-Fusarium graminearum. The economic impact of FHB leads to the need for innovation. Currently used fungicides have been shown to be effective over the years, but recently cereal infecting Fusaria have developed resistance. Our work presents a new perspective on target selection to allow the development of new fungicides. We developed an innovative approach combining both genomic analysis and molecular modeling to increase the discovery for new chemical compounds with both safety and low environmental impact. Our protein targets selection revealed 13 candidates with high specificity, essentiality and potentially assayable with a favorable accessibility to drug activity. Among them, three proteins: trichodiene synthase, endoglucanase-5 and ERG6 were selected for deeper structural analyses to identify new putative fungicides. Overall, the bioinformatics filtering for novel protein targets applied for agricultural purposes is a response to the demand for chemical crop protection. The availability of the genome, secretome and PHI-base allowed the enrichment of the search that combined experimental data in planta. The homology modeling and molecular dynamics simulations allowed the acquisition of three robust and stable conformers. From this step, approximately ten thousand compounds have been virtually screened against three candidates. Forty-five top-ranked compounds were selected from docking results as presenting better interactions and energy at the binding pockets and no toxicity. These compounds may act as inhibitors and lead to the development of new fungicides.展开更多
3-dimension HPNX offiattice model is developed from the 2-dimension HP offiattice model. In the HP model, 20 types of amino acid monomers are divided into two classes, H （non-polar monomer） and P （polar monomer）. ...3-dimension HPNX offiattice model is developed from the 2-dimension HP offiattice model. In the HP model, 20 types of amino acid monomers are divided into two classes, H （non-polar monomer） and P （polar monomer）. In the HPNX model, polar monomers are split into positively charged （P）, negatively charged （N） and neutral （X） monomers. A new evolutionary algorithm is applied to study long chains of the HPNX offiattice protein model. This method successfully predict the structures of several proteins in the 3-dimension space that are similar to the structures gotten by X-Ray Crystallography and NMR and published in the PDB（Protein Data Bank）.展开更多
The full-length sequence of the odorant binding protein 5 gene,HarmOBP5,was obtained from an antennae cDNA library of cotton bollworm,Helicoverpa armigera （Hübner）.The cDNA contains a 444 bp open reading frame,...The full-length sequence of the odorant binding protein 5 gene,HarmOBP5,was obtained from an antennae cDNA library of cotton bollworm,Helicoverpa armigera （Hübner）.The cDNA contains a 444 bp open reading frame,encoding a protein with 147 amino acids,namely HarmOBP5.HarmOBP5 was expressed in Escherichia coli and the recombinant protein was purified by affinity chromatography.SDS-PAGE and Western blot analysis demonstrated that the purified protein can be used for further investigation of its binding characteristics.Competitive binding assays with 113 odorant chemicals indicated that HarmOBP5 has strong affinity to some special plant volatiles,including （E）-β-farnesene,ethyl butyrate,ethyl heptanoate,and acetic acid 2-methylbutyl ester.Based on three-dimensional （3D） model of AaegOBP1 from Aedes aegypti,a 3D model of HarmOBP5 was predicted.The model revealed that some key binding residues in HarmOBP5 may play important roles in odorant perception of H.armigera.This study provides clues for better understanding physiological functions of OBPs in H.armigera and other insects.展开更多
目的基于高精度3D打印技术研究三文鱼植物基替代物。方法以豌豆分离蛋白(pea protein isolate,PPI)、魔芋胶(konjac gum,KGM)和天然胡萝卜粉为原辅料,进行精准3D复合打印生产模拟三文鱼色泽、质构的植物基替代物。考察不同物料比例对油...目的基于高精度3D打印技术研究三文鱼植物基替代物。方法以豌豆分离蛋白(pea protein isolate,PPI)、魔芋胶(konjac gum,KGM)和天然胡萝卜粉为原辅料,进行精准3D复合打印生产模拟三文鱼色泽、质构的植物基替代物。考察不同物料比例对油墨可打印性的影响;选取有代表性的油墨配方,对其流变特性、水分分布情况、微观结构进行表征。结果PPI和KGM浓度的升高都增强了体系与水结合的能力,且PPI浓度过高时(20%,m:m)影响了KGM与水结合形成稳定凝胶的能力。PPI15KGM5配方可形成致密的网格结构,增强了体系的稳定性,拥有良好的剪切恢复特性,有利于3D打印;而PPI20KGM3配方具有更好的机械性能和结构强度,但是由于PPI浓度过高影响KGM形成稳定凝胶结构,其剪切恢复特性较差。流变学参数η、τ_(y)、G'、屈服应变及剪切恢复特性对油墨3D打印过程影响显著。结论通过调整3D打印精细化程度(350µm和500µm)和模型填充度,生产了具有差异化质构的高蛋白含量(15%,m:m)产品。其中,部分产品的粘性和弹性与真实三文鱼类似,这为开发3D打印生产植物基替代物提供了新的视角。展开更多
Cold-inducible RNA-binding protein(CIRP) is a kind of RNA binding proteins that plays important roles in many physiological processes. The CIRP has been widely studied in mammals and amphibians since it was first clon...Cold-inducible RNA-binding protein(CIRP) is a kind of RNA binding proteins that plays important roles in many physiological processes. The CIRP has been widely studied in mammals and amphibians since it was first cloned from mammals. On the contrary, there are little reports in teleosts. In this study, the Po CIRP gene of the Japanese flounder was cloned and sequenced. The genomic sequence consists of seven exons and six introns. The putative Po CIRP protein of flounder was 198 amino acid residues long containing the RNA recognition motif(RRM). Phylogenetic analysis showed that the flounder Po CIRP is highly conserved with other teleost CIRPs. The 5' flanking sequence was cloned by genome walking and many transcription factor binding sites were identified. There is a Cp Gs region located in promoter and exon I region and the methylation state is low. Quantitative real-time PCR analysis uncovered that Po CIRP gene was widely expressed in adult tissues with the highest expression level in the ovary. The m RNA of the Po CIRP was maternally deposited and the expression level of the gene was regulated up during the gastrula and neurula stages. In order to gain the information how the protein interacts with m RNA, we performed the modeling of the 3D structure of the flounder Po CIRP. The results showed a cleft existing the surface of the molecular. Taken together, the results indicate that the CIRP is a multifunctional molecular in teleosts and the findings about the structure provide valuable information for understanding the basis of this protein's function.展开更多
基金Supported by the National Natural Science Foundation of China (60975031)the Scientific Research Foundation for the Returned Overseas Chinese Scholars of Ministry of Education of China, the Open Foundation of State Key Laboratory of Bioelectronics of Southeast University, China, and the Natural Science Foundation of Hubei Province, China (2008CDB344 and 2009CDA034)
文摘This paper describes a case study of 3D protein structure prediction of six sequences from protein data bank （PDB） by genetic algorithm and tabu search （GATS）, where off-lattice AB model is considered as a simplified model of protein structure. The lowest-energy values required for forming the native conformation of proteins are searched by GATS, and then the coarse structures （i.e., simplified structure） of the proteins are obtained according to the multiple angle parameters corresponding to the lowest energies. All the coarse structures form single hydrophobic cores surrounded by hydrophilic residues, which stay on the right side of the actual characteristic of protein structure. It demonstrates that this approach can predict the 3D protein structure effectively.
文摘Fusarium head blight (FHB) is a destructive disease of wheat and other cereals. FHB occurs in Europe, North America and around the world causing significant losses in production and endangers human and animal health. In this article, we provide the strategic steps for the specific target selection for the phytopathogen system wheat-Fusarium graminearum. The economic impact of FHB leads to the need for innovation. Currently used fungicides have been shown to be effective over the years, but recently cereal infecting Fusaria have developed resistance. Our work presents a new perspective on target selection to allow the development of new fungicides. We developed an innovative approach combining both genomic analysis and molecular modeling to increase the discovery for new chemical compounds with both safety and low environmental impact. Our protein targets selection revealed 13 candidates with high specificity, essentiality and potentially assayable with a favorable accessibility to drug activity. Among them, three proteins: trichodiene synthase, endoglucanase-5 and ERG6 were selected for deeper structural analyses to identify new putative fungicides. Overall, the bioinformatics filtering for novel protein targets applied for agricultural purposes is a response to the demand for chemical crop protection. The availability of the genome, secretome and PHI-base allowed the enrichment of the search that combined experimental data in planta. The homology modeling and molecular dynamics simulations allowed the acquisition of three robust and stable conformers. From this step, approximately ten thousand compounds have been virtually screened against three candidates. Forty-five top-ranked compounds were selected from docking results as presenting better interactions and energy at the binding pockets and no toxicity. These compounds may act as inhibitors and lead to the development of new fungicides.
基金Supported by the National Natural Science Foundation of China (1027109)
文摘3-dimension HPNX offiattice model is developed from the 2-dimension HP offiattice model. In the HP model, 20 types of amino acid monomers are divided into two classes, H （non-polar monomer） and P （polar monomer）. In the HPNX model, polar monomers are split into positively charged （P）, negatively charged （N） and neutral （X） monomers. A new evolutionary algorithm is applied to study long chains of the HPNX offiattice protein model. This method successfully predict the structures of several proteins in the 3-dimension space that are similar to the structures gotten by X-Ray Crystallography and NMR and published in the PDB（Protein Data Bank）.
基金supported by the National Basic Research Program of China(2012CB114104)the National Natural Science Foundation of China(30871640,31071694)+1 种基金the National High-Tech R&D Program of China(2008AA02Z307)the International Cooperation and Exchange Foundation of NSFC-RS of China(31111130203).
文摘The full-length sequence of the odorant binding protein 5 gene,HarmOBP5,was obtained from an antennae cDNA library of cotton bollworm,Helicoverpa armigera （Hübner）.The cDNA contains a 444 bp open reading frame,encoding a protein with 147 amino acids,namely HarmOBP5.HarmOBP5 was expressed in Escherichia coli and the recombinant protein was purified by affinity chromatography.SDS-PAGE and Western blot analysis demonstrated that the purified protein can be used for further investigation of its binding characteristics.Competitive binding assays with 113 odorant chemicals indicated that HarmOBP5 has strong affinity to some special plant volatiles,including （E）-β-farnesene,ethyl butyrate,ethyl heptanoate,and acetic acid 2-methylbutyl ester.Based on three-dimensional （3D） model of AaegOBP1 from Aedes aegypti,a 3D model of HarmOBP5 was predicted.The model revealed that some key binding residues in HarmOBP5 may play important roles in odorant perception of H.armigera.This study provides clues for better understanding physiological functions of OBPs in H.armigera and other insects.
文摘目的基于高精度3D打印技术研究三文鱼植物基替代物。方法以豌豆分离蛋白(pea protein isolate,PPI)、魔芋胶(konjac gum,KGM)和天然胡萝卜粉为原辅料,进行精准3D复合打印生产模拟三文鱼色泽、质构的植物基替代物。考察不同物料比例对油墨可打印性的影响;选取有代表性的油墨配方,对其流变特性、水分分布情况、微观结构进行表征。结果PPI和KGM浓度的升高都增强了体系与水结合的能力,且PPI浓度过高时(20%,m:m)影响了KGM与水结合形成稳定凝胶的能力。PPI15KGM5配方可形成致密的网格结构,增强了体系的稳定性,拥有良好的剪切恢复特性,有利于3D打印;而PPI20KGM3配方具有更好的机械性能和结构强度,但是由于PPI浓度过高影响KGM形成稳定凝胶结构,其剪切恢复特性较差。流变学参数η、τ_(y)、G'、屈服应变及剪切恢复特性对油墨3D打印过程影响显著。结论通过调整3D打印精细化程度(350µm和500µm)和模型填充度,生产了具有差异化质构的高蛋白含量(15%,m:m)产品。其中,部分产品的粘性和弹性与真实三文鱼类似,这为开发3D打印生产植物基替代物提供了新的视角。
基金supported by the National High Technology R&D Program of China (2012AA10A402)the National Natural Science Foundation of China (31172385)
文摘Cold-inducible RNA-binding protein(CIRP) is a kind of RNA binding proteins that plays important roles in many physiological processes. The CIRP has been widely studied in mammals and amphibians since it was first cloned from mammals. On the contrary, there are little reports in teleosts. In this study, the Po CIRP gene of the Japanese flounder was cloned and sequenced. The genomic sequence consists of seven exons and six introns. The putative Po CIRP protein of flounder was 198 amino acid residues long containing the RNA recognition motif(RRM). Phylogenetic analysis showed that the flounder Po CIRP is highly conserved with other teleost CIRPs. The 5' flanking sequence was cloned by genome walking and many transcription factor binding sites were identified. There is a Cp Gs region located in promoter and exon I region and the methylation state is low. Quantitative real-time PCR analysis uncovered that Po CIRP gene was widely expressed in adult tissues with the highest expression level in the ovary. The m RNA of the Po CIRP was maternally deposited and the expression level of the gene was regulated up during the gastrula and neurula stages. In order to gain the information how the protein interacts with m RNA, we performed the modeling of the 3D structure of the flounder Po CIRP. The results showed a cleft existing the surface of the molecular. Taken together, the results indicate that the CIRP is a multifunctional molecular in teleosts and the findings about the structure provide valuable information for understanding the basis of this protein's function.
