目的:以纯化的壶瓶碎米荠含硒蛋白(selenium-containing protein from Cardamine hupingshanensis,S P C H)为研究对象,对其结构特性和缓解运动性疲劳作用进行评价。方法:采用聚丙烯酰胺凝胶电泳(polyacrylamide gelelectrophoresis,PA...目的:以纯化的壶瓶碎米荠含硒蛋白(selenium-containing protein from Cardamine hupingshanensis,S P C H)为研究对象,对其结构特性和缓解运动性疲劳作用进行评价。方法:采用聚丙烯酰胺凝胶电泳(polyacrylamide gelelectrophoresis,PAGE)和十二烷基硫酸钠-PAGE(sodium dodecyl sulfate-PAGE,SDS-PAGE)、氨基酸组成分析、基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization time of flight mass spectrometry,MALDI-TOF-MS)分析,对SPCH的纯度、亚基组成、氨基酸组成及含量进行评价并初步预测SPCH的匹配蛋白。采用小鼠负重游泳实验,通过检测游泳时间、血乳酸(blood lactic acid,BLA)、肝糖原和血尿素氮(blood urea nitrogen,BUN)水平,评价SPCH对小鼠运动性疲劳的影响。结果:SPCH可能由3个分子质量分别为37、39、40 k D的亚基组成,与之相匹配的蛋白可能是DING protein、Predicted protein和Chalcone synthase。SPCH能显著延长小鼠负重游泳时间(P<0.01),同时增强清除乳酸的能力(P<0.01),增加肝糖原含量(P<0.01),还具有降低BUN水平的能力(P<0.05)。结论:SPCH对小鼠具有较好的缓解运动性疲劳作用,可考虑将其开发成为缓解运动性疲劳的营养补充剂。展开更多
This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an import...This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an important role in their functions. In our mathematical toy models, proteins are represented as a loop of triangles (2D model) or tetrahedra (3D model), where their interactions are defined as fusion of loops. The purpose of this paper is to describe the conditions for loop fusion using the language of cohomology. In particular, this paper uses cohomology to describe the conditions for “allosteric regulation”, which has been attracted attention in safer drug discovery. I hope that this paper will provide a new perspective on the mechanism of allosteric regulation. Advantages of the model include its topological nature. That is, we can deform the shape of loops by deforming the shape of triangles (or tetrahedra) as long as their folded structures are preserved. Another advantage is the simplicity of the “allosteric regulation” mechanism of the model. Furthermore, the effect of the “post-translational modification” can be understood as a resolution of singularities of a flow of triangles (or tetrahedra). No prior knowledge of either protein science, exterior calculus, or cohomology theory is required. The author hopes that this paper will facilitate the interaction between mathematics and protein science.展开更多
Protein tertiary structure is indispensible in revealing the biological functions of proteins. De novo perdition of protein tertiary structure is dependent on protein fold recognition. This study proposes a novel meth...Protein tertiary structure is indispensible in revealing the biological functions of proteins. De novo perdition of protein tertiary structure is dependent on protein fold recognition. This study proposes a novel method for prediction of protein fold types which takes primary sequence as input. The proposed method, PFP-RFSM, employs a random forest classifier and a comprehensive feature representation, including both sequence and predicted structure descriptors. Particularly, we propose a method for generation of features based on sequence motifs and those features are firstly employed in protein fold prediction. PFP-RFSM and ten representative protein fold predictors are validated in a benchmark dataset consisting of 27 fold types. Experiments demonstrate that PFP-RFSM outperforms all existing protein fold predictors and improves the success rates by 2%-14%. The results suggest sequence motifs are effective in classification and analysis of protein sequences.展开更多
Large and well ordered two dimensional (2D) crystals of the light harvesting chlorophyll a/b protein complexes (LHC II) from cucumber and spinach chloroplasts were produced by the so called batch method. The two dimen...Large and well ordered two dimensional (2D) crystals of the light harvesting chlorophyll a/b protein complexes (LHC II) from cucumber and spinach chloroplasts were produced by the so called batch method. The two dimensional structures of these crystals were examined at about 1.5 nm resolution by electron microscopy and image processing. The projection maps showed that there were similar, but not identical, structure features between two different LHC II complexes. A comparison between 2D crystal formations of the two different LHC II complexes was done and some factors affecting 2D crystallization of the membrane proteins were analyzed. The relations of the structures of the LHC II complexes to their polypeptide components and Chl a/b ratio were also discussed.展开更多
文摘目的:以纯化的壶瓶碎米荠含硒蛋白(selenium-containing protein from Cardamine hupingshanensis,S P C H)为研究对象,对其结构特性和缓解运动性疲劳作用进行评价。方法:采用聚丙烯酰胺凝胶电泳(polyacrylamide gelelectrophoresis,PAGE)和十二烷基硫酸钠-PAGE(sodium dodecyl sulfate-PAGE,SDS-PAGE)、氨基酸组成分析、基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization time of flight mass spectrometry,MALDI-TOF-MS)分析,对SPCH的纯度、亚基组成、氨基酸组成及含量进行评价并初步预测SPCH的匹配蛋白。采用小鼠负重游泳实验,通过检测游泳时间、血乳酸(blood lactic acid,BLA)、肝糖原和血尿素氮(blood urea nitrogen,BUN)水平,评价SPCH对小鼠运动性疲劳的影响。结果:SPCH可能由3个分子质量分别为37、39、40 k D的亚基组成,与之相匹配的蛋白可能是DING protein、Predicted protein和Chalcone synthase。SPCH能显著延长小鼠负重游泳时间(P<0.01),同时增强清除乳酸的能力(P<0.01),增加肝糖原含量(P<0.01),还具有降低BUN水平的能力(P<0.05)。结论:SPCH对小鼠具有较好的缓解运动性疲劳作用,可考虑将其开发成为缓解运动性疲劳的营养补充剂。
文摘This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an important role in their functions. In our mathematical toy models, proteins are represented as a loop of triangles (2D model) or tetrahedra (3D model), where their interactions are defined as fusion of loops. The purpose of this paper is to describe the conditions for loop fusion using the language of cohomology. In particular, this paper uses cohomology to describe the conditions for “allosteric regulation”, which has been attracted attention in safer drug discovery. I hope that this paper will provide a new perspective on the mechanism of allosteric regulation. Advantages of the model include its topological nature. That is, we can deform the shape of loops by deforming the shape of triangles (or tetrahedra) as long as their folded structures are preserved. Another advantage is the simplicity of the “allosteric regulation” mechanism of the model. Furthermore, the effect of the “post-translational modification” can be understood as a resolution of singularities of a flow of triangles (or tetrahedra). No prior knowledge of either protein science, exterior calculus, or cohomology theory is required. The author hopes that this paper will facilitate the interaction between mathematics and protein science.
文摘Protein tertiary structure is indispensible in revealing the biological functions of proteins. De novo perdition of protein tertiary structure is dependent on protein fold recognition. This study proposes a novel method for prediction of protein fold types which takes primary sequence as input. The proposed method, PFP-RFSM, employs a random forest classifier and a comprehensive feature representation, including both sequence and predicted structure descriptors. Particularly, we propose a method for generation of features based on sequence motifs and those features are firstly employed in protein fold prediction. PFP-RFSM and ten representative protein fold predictors are validated in a benchmark dataset consisting of 27 fold types. Experiments demonstrate that PFP-RFSM outperforms all existing protein fold predictors and improves the success rates by 2%-14%. The results suggest sequence motifs are effective in classification and analysis of protein sequences.
文摘Large and well ordered two dimensional (2D) crystals of the light harvesting chlorophyll a/b protein complexes (LHC II) from cucumber and spinach chloroplasts were produced by the so called batch method. The two dimensional structures of these crystals were examined at about 1.5 nm resolution by electron microscopy and image processing. The projection maps showed that there were similar, but not identical, structure features between two different LHC II complexes. A comparison between 2D crystal formations of the two different LHC II complexes was done and some factors affecting 2D crystallization of the membrane proteins were analyzed. The relations of the structures of the LHC II complexes to their polypeptide components and Chl a/b ratio were also discussed.
