Domain database is essential for domain property research. Eliminatingredundant information in database query is very important for database quality. Here we report themanual construction of a non-redundant human SH2 ...Domain database is essential for domain property research. Eliminatingredundant information in database query is very important for database quality. Here we report themanual construction of a non-redundant human SH2 domain database. There are 119 human SH2 domains in110 SH2-containing proteins. Human SH2s were aligned with ClustalX, and a homologous tree wasgenerated. In this tree, proteins with similar known function were classified into the same group.Some proteins in the same group have been reported to have similar binding motifs experimentally.The tree might provide clues about possible functions of hypothetical proteins for furtherexperimental verification.展开更多
HtrA2/Omi is a mammalian mitochondrial serine protease, and was found to have dual roles in mam- malian cells, not only acting as an apoptosis-inducing protein but also maintaining mitochondrial ho- meostasis. PDZ dom...HtrA2/Omi is a mammalian mitochondrial serine protease, and was found to have dual roles in mam- malian cells, not only acting as an apoptosis-inducing protein but also maintaining mitochondrial ho- meostasis. PDZ domain is one of the most important protein-protein interaction modules and is in- volved in a variety of important cellular functions, such as signal transduction, degradation of proteins, and formation of cytoskeleton. Recently, it was reported that the PDZ domain of HtrA2/Omi might regulate proteolytic activity through its interactions with ligand proteins. In this study, we rapidly characterized the binding properties of HtrA2/Omi PDZ domain by validation screening of the PDZ ligand library with yeast two-hybrid approach. Then, we predicted its novel ligand proteins in human proteome and reconfirmed them in the yeast two-hybrid system. Finally, we analyzed the smallest networks bordered by the shortest path length between the protein pairs of novel interactions to evaluate the confidence of the identified interactions. The results revealed some novel binding proper- ties of HtrA2/Omi PDZ domain. Besides the reported Class II PDZ motif, it also binds to Class I and Class III motifs, and exhibits restricted variability at P?3, which means that the P?3 residue is selected according to the composition of the last three residues. Seven novel ligand proteins of HtrA2/Omi PDZ domain were discovered, providing significant clues for further clarifying the roles of HtrA2/Omi. Moreover, this study proves the high efficiency and practicability of the newly developed validation screening of candidate ligand library method for binding property characterization of peptide-binding domains.展开更多
Objective Formation of the endophilin II-Ca 2＋ channel complex is Ca 2＋ -dependent in clathrin-mediated endocytosis. However, little is known about whether the other two endophilin isoforms have the same features. T...Objective Formation of the endophilin II-Ca 2＋ channel complex is Ca 2＋ -dependent in clathrin-mediated endocytosis. However, little is known about whether the other two endophilin isoforms have the same features. The present study aimed to investigate the characteristics of the interactions of all three isoforms with Ca 2＋ channels and dynamin I. Methods N-type Ca 2＋ channel C-terminal fragments （NCFs） synthesized with a 3 H-leucine-labeled kit, were incubated with endophilin-GST fusion proteins, followed by pull-down assay. Results were counted on a scintillation counter. In addition, the different endophilin isoforms were each co-transfected with dynamin I into 293T cells, followed by flow cytometry and co-immunoprecipitation assay. Immunostaining was performed and an image analysis program was used to evaluate the overlap coefficient of cells expressing endophilin and dynamin I. Results All three isoforms interacted with NCF. Endophilins I and II demonstrated clear Ca 2＋ -dependent interactions with NCF, whereas endophilin III did not. Co-immunoprecipitation showed that, compared to endophilin I/II, the interaction between endophilin III and dynamin I was significantly increased. Similar results were obtained from flow cytometry. Furthermore, endophilin III had a higher overlap coefficient with dynamin I in co-transfected 293T cells. Conclusion Endophilin isoforms have distinct characteristics in interactions with NCF and dynamin I. Endophilin III binding to NCF is Ca 2＋ -independent, implying that it plays a different role in clathrin-mediated endocytosis.展开更多
基金This work was partly supported by grants from Na-tional Natural Science Foundation of China (No.3037030 30270657 and 30230150)+2 种基金 Major State Basic Research Development Program of China(2004CB520804) Pilot Study for Key Basic Re-search Project of China (2002CCA04100) and Key Project for International Cooperation of China (2002AA229031).
文摘Domain database is essential for domain property research. Eliminatingredundant information in database query is very important for database quality. Here we report themanual construction of a non-redundant human SH2 domain database. There are 119 human SH2 domains in110 SH2-containing proteins. Human SH2s were aligned with ClustalX, and a homologous tree wasgenerated. In this tree, proteins with similar known function were classified into the same group.Some proteins in the same group have been reported to have similar binding motifs experimentally.The tree might provide clues about possible functions of hypothetical proteins for furtherexperimental verification.
基金the National Basic Research Program (Grant No. 2004CB520804)the National High Technology Research and Development Program (Grant No. 2006AA02Z308)+1 种基金the National Natural Science Foundation of China (Grant Nos. 30270657, 30230150, and 3037030)Beijing Natural Science Foundation (Grant No. 5072037)
文摘HtrA2/Omi is a mammalian mitochondrial serine protease, and was found to have dual roles in mam- malian cells, not only acting as an apoptosis-inducing protein but also maintaining mitochondrial ho- meostasis. PDZ domain is one of the most important protein-protein interaction modules and is in- volved in a variety of important cellular functions, such as signal transduction, degradation of proteins, and formation of cytoskeleton. Recently, it was reported that the PDZ domain of HtrA2/Omi might regulate proteolytic activity through its interactions with ligand proteins. In this study, we rapidly characterized the binding properties of HtrA2/Omi PDZ domain by validation screening of the PDZ ligand library with yeast two-hybrid approach. Then, we predicted its novel ligand proteins in human proteome and reconfirmed them in the yeast two-hybrid system. Finally, we analyzed the smallest networks bordered by the shortest path length between the protein pairs of novel interactions to evaluate the confidence of the identified interactions. The results revealed some novel binding proper- ties of HtrA2/Omi PDZ domain. Besides the reported Class II PDZ motif, it also binds to Class I and Class III motifs, and exhibits restricted variability at P?3, which means that the P?3 residue is selected according to the composition of the last three residues. Seven novel ligand proteins of HtrA2/Omi PDZ domain were discovered, providing significant clues for further clarifying the roles of HtrA2/Omi. Moreover, this study proves the high efficiency and practicability of the newly developed validation screening of candidate ligand library method for binding property characterization of peptide-binding domains.
基金supported by grants from the National Natural Science Foundation of China (30870785)the Natural Science Foundation of Guangdong Province, China (9351008901000003)
文摘Objective Formation of the endophilin II-Ca 2＋ channel complex is Ca 2＋ -dependent in clathrin-mediated endocytosis. However, little is known about whether the other two endophilin isoforms have the same features. The present study aimed to investigate the characteristics of the interactions of all three isoforms with Ca 2＋ channels and dynamin I. Methods N-type Ca 2＋ channel C-terminal fragments （NCFs） synthesized with a 3 H-leucine-labeled kit, were incubated with endophilin-GST fusion proteins, followed by pull-down assay. Results were counted on a scintillation counter. In addition, the different endophilin isoforms were each co-transfected with dynamin I into 293T cells, followed by flow cytometry and co-immunoprecipitation assay. Immunostaining was performed and an image analysis program was used to evaluate the overlap coefficient of cells expressing endophilin and dynamin I. Results All three isoforms interacted with NCF. Endophilins I and II demonstrated clear Ca 2＋ -dependent interactions with NCF, whereas endophilin III did not. Co-immunoprecipitation showed that, compared to endophilin I/II, the interaction between endophilin III and dynamin I was significantly increased. Similar results were obtained from flow cytometry. Furthermore, endophilin III had a higher overlap coefficient with dynamin I in co-transfected 293T cells. Conclusion Endophilin isoforms have distinct characteristics in interactions with NCF and dynamin I. Endophilin III binding to NCF is Ca 2＋ -independent, implying that it plays a different role in clathrin-mediated endocytosis.
