In the past, bioinformatics was often regarded as a difficult and rather remote field, practiced only by computer scientists and not a practical tool available to biologists. However, the various on-going genome projects have had a serious impact on biological sciences in various ways and now there is little doubt that bioinformatics is an essential part of the research environment, with a wealth of biological information to analyze and predict. Fully sequenced genomes made us to have additional insights into the functional properties of the encoded proteins and made it possible to develop new tools and schemes for functional biology on a proteomic scale. Among those are the yeast two-hybrid system, mass spectrometry and microarray: the technology of choice to detect protein-protein interactions. These functional insights emerge as networks of interacting proteins, also known as "pathway informatics" or "interactomics". Without exception it is no longer possible to make advances in the signaling/regulatory pathway studies without integrating information technologies with experimental technologies. In this paper, we will introduce the databases of protein interaction worldwide and discuss several challenging issues regarding the actual implementation of databases.
Biological Science Disciplines ; Biology ; Computational Biology ; Genome ; Mass Spectrometry ; Two-Hybrid System Techniques

In the past, bioinformatics was often regarded as a difficult and rather remote field, practiced only by computer scientists and not a practical tool available to biologists. However, the various on-going genome projects have had a serious impact on biological sciences in various ways and now there is little doubt that bioinformatics is an essential part of the research environment, with a wealth of biological information to analyze and predict. Fully sequenced genomes made us to have additional insights into the functional properties of the encoded proteins and made it possible to develop new tools and schemes for functional biology on a proteomic scale. Among those are the yeast two-hybrid system, mass spectrometry and microarray: the technology of choice to detect protein-protein interactions. These functional insights emerge as networks of interacting proteins, also known as "pathway informatics" or "interactomics". Without exception it is no longer possible to make advances in the signaling/regulatory pathway studies without integrating information technologies with experimental technologies. In this paper, we will introduce the databases of protein interaction worldwide and discuss several challenging issues regarding the actual implementation of databases.
Biological Science Disciplines ; Biology ; Computational Biology ; Genome ; Mass Spectrometry ; Two-Hybrid System Techniques

Currently, various Nickel-Titanium rotary files are used in endodontic treatment, but there is no one perfect system that can be applied to any clinical situation. Therefore, the combined uses of various file systems which can emphasize the advantages of each system are introduced as hybrid instrumentation. The ProTaper system is efficient in body shaping and apical pre-enlargement but is reported to have more possibility of transportation and produce more aberrations and deformation in more or less severe curved canals. Recently, new ProTaper system (ProTaper Universal) with different configuration and cross-sectional design to overcome the week points of ProTaper have been marketed. The purpose of this study was to compare and evaluate the shaping abilities of ProTaper, ProTaper Universal system, and two hybrid methods using S-series of ProTaper Universal and Hero Shaper or ProFile. The time lapses for instrumentation were measured and the used files were inspected for distortion. The pre- and post-instrumented root canals were scanned and superimposed to evaluate the aberrations and reduction of root canal curvature and change of radius of canal curvature. The increased canal width and apical centering ratio were calculated at 1, 2, 3, 4 and 5 mm levels from apical foramen. Under the conditions of this study, the ProTaper Universal seems to have better shaping ability than ProTaper in terms of instrumented width and instrumentation time. It may be suggested that the ProTaper Universal system is efficient as much as hybrid instrumentation using ProTaper and other constant-tapered NiTi file systems in highly experienced operators.
Dental Pulp Cavity ; Radius ; Tooth Apex ; Transportation ; Two-Hybrid System Techniques

OBJECTIVE: To screen proteins interacting with ring finger protein 216(RNF216) through yeast two hybrid experiment, and further clarify the role of RNF216 in the pathogenesis of gonadotropin-releasing hormone deficiency. METHODS: A recombinant expression vector pGBKT7-RNF216 was constructed and transformed into yeast Y2HGold, which was hybridized with a human cDNA library in order to screen proteins interacting with RNF216. The interaction was verified in yeast Y2HGold. RESULTS: A recombinant expression vector pGBKT7-RNF216 was successfully constructed and expressed in yeast Y2HGold. Filamin B (FLNB) was identified by yeast two hybrid experiment, and their interaction was verified in yeast Y2HGold. CONCLUSION An interaction between FLNB and RNF216 was identified through yeast two hybrid experiment. RNF216 may affect the proliferation and migration of GnRH neurons by regulating FLNB or FLNB/FLNA heterodimers.
Gene Library ; Gonadotropin-Releasing Hormone/genetics* ; Humans ; Proteins ; Two-Hybrid System Techniques ; Ubiquitin-Protein Ligases/genetics*

The kinesin proteins (KIFs) make up a large superfamily of molecular motors that transport cargo such as vesicles, protein complexes, and organelles. KIF5 is a heterotetrameric motor that conveys vesicles and plays an important role in neuronal function. Here, we used the yeast two-hybrid system to identify the neuronal protein (s) that interacts with the tail region of KIF5 and found a specific interaction with betaIII spectrin. The amino acid residues between 1394 and 1774 of betaIII spectrin were required for the interaction with KIF5C. betaIII spectrin also bound to the tail region of neuronal KIF5A and ubiquitous KIF5B but not to other kinesin family members in the yeast two-hybrid assay. In addition, these proteins showed specific interactions, confirmed by GST pull-down assay and co-immunoprecipitation. betaIII spectrin interacted with GST-KIF5 fusion proteins, but not with GST alone. An antibody to betaIII spectrin specifically co-immunoprecipitated KIF5s associated with betaIII spectrin from mouse brain extracts. These results suggest that KIF5 motor proteins transport vesicles or organelles that are coated with betaIII spectrin.
Animals ; Brain ; Humans ; Immunoprecipitation ; Kinesin* ; Mice ; Microtubules ; Neurons ; Organelles ; Spectrin* ; Transport Vesicles ; Two-Hybrid System Techniques

KIF1B beta is a member of the Kinesin superfamily proteins (KIFs), which are microtubule-dependent molecular motors that are involved in various intracellular organellar transport processes. KIF1B beta is not restricted to neuronal systems, however, is widely expressed in other tissues, even though the function of KIF1B beta is still unclear. To elucidate the KIF1B beta-binding proteins in non-neuronal cells, we used the yeast two-hybrid system, and found a specific interaction of KIF1B beta and the sorting nexin (SNX) 17. The C-terminal region of SNX17 is required for the binding with KIF1B beta. SNX17 protein bound to the specific region of KIF1B beta (813-916. aa), but not to other kinesin family members. In addition, this specific interaction was also observed in the Glutathione S-transferase pull-down assay. An antibody to SNX17 specifically co-immunoprecipitated KIF1B beta associated with SNX17 from mouse brain extracts. These results suggest that SNX17 might be involved in the KIF1B beta-mediated transport as a KIF1B beta adaptor protein.
Animals ; Brain ; Glutathione Transferase ; Humans ; Kinesin ; Mice ; Microtubules ; Neurons ; Proteins ; Sorting Nexins ; Two-Hybrid System Techniques

Alcohol Oxidoreductases ; genetics ; isolation & purification ; Cloning, Molecular ; Hep G2 Cells ; Humans ; Two-Hybrid System Techniques

ADAM Proteins ; genetics ; ADAM17 Protein ; Animals ; Gene Library ; Genetic Vectors ; Male ; Mice ; Two-Hybrid System Techniques

The Kinesin superfamily proteins (KIFs) make up a large superfamily of molecular motors that transport cargo such as vesicles, protein complexes, and organelles. KIF1Balpha is a monomeric motor that conveys mitochondria and plays an important role in cellular function. Here, we used the yeast two-hybrid system to identify the proteins that interacts with KIF1Balpha and found a specific interaction with the mammalian LIN-7 (MALS)-3/vertebrate homology of LIN-7 (Veri) and synaptic scaffolding molecule (S-SCAM). MALS-3 protein bound to the tail region of KIF1Balpha but not to other kinesin family members in the yeast two-hybrid assay. The "T-X-V" motif at the C-terminal end of KIF1Balpha is essential for interaction with MALS-3. In addition, this protein showed specific interactions in the Glutathione S-transferase (GST) pull-down assay. An antibody to MALS-3 specifically coimmunoprecipitated KIF1Balpha associated with MALS-3 from mouse brain extracts. These results suggest that MALS-3, as KIF1Balpha receptor, is involved in the KIF1Balpha-mediated transport.
Animals ; Brain ; Glutathione Transferase ; Humans ; Kinesin* ; Mice ; Microtubules ; Mitochondria ; Organelles ; PDZ Domains* ; Two-Hybrid System Techniques

The kinesin proteins (KIFs) make up a large superfamily of molecular motors that transport cargo such as vesicles, protein complexes, and organelles. KIF1A is a monomeric motor that conveys synaptic vesicle precursors and plays an important role in neuronal function. Here, we used the yeast two-hybrid system to identify the neuronal protein (s) that interacts with the tail region of KIF1A and found a specific interaction with synaptotagmin XI. The amino acid residues between 830 and 1300 of KIF1A are required for the interaction with synaptotagmin XI. KIF1A also bound to the tail region of synaptotagmin IV but not to other synaptotagmin in the yeast two-hybrid assay. KIF1A interacted with GST-synaptotagim XI fusion proteins, but not with GST alone. An antibody to synaptotagmin XI specifically co-mmunoprecipitated KIF1A associated with synaptotagimin from mouse brain extracts. These results suggest that KIF1A motor protein transports of synaptotagmin XI-containing synaptic vesicle precursors along microtubule.
Animals ; Brain ; Kinesin* ; Mice ; Microtubules ; Neurons ; Organelles ; Protein Transport ; Synaptic Vesicles ; Synaptotagmins* ; Two-Hybrid System Techniques