• BMB Reports
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• v.35 no.1
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• pp.61-66
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• 2002

The TNF receptor-associated factor (TRAF) family is a group of adapter proteins that link a wide variety of cell surface receptors. Including the TNF and IL-1 receptor superfamily to diverse signaling cascades, which lead to the activation of NF-${\kappa}B$ and mitogen-activated protein kinases. In addition, TRAFs interact with a variety of proteins that regulate receptor-induced cell death or survival. Thus, TRAF-mediated signals may directly induce cell survival or interfere with the death receptor-induced apoptosis.

• Journal of Life Science
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• v.12 no.2
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• pp.43-46
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• 2002

Kinesin Superfamily Protein 1A (KIF1A) is an anterograde monomeric motor transporting a subset of synaptic vesicle precursors and plays an important role in neuronal function and survival. Here, f have used the yeast two-hybrid system to identify the proteins that interacts with the tail region of KIF1A. Calmodulin was found to interact specifically with the tail region of KIF1A. Calmodulin regulates many diverse cellular functions by modulating the activity of the proteins that interact with it. KIF1A interacts with calmodulin in the yeast two-hybrid assay, which is proved by immunoprecipitation with calmodulin in brain fraction. These results indicate that KIF1A is associated with calmodulin, suggesting that calmodulin may be a key role in the regulation of anterograde transport of synaptic 1 vesicle precursors.

• Biomolecules & Therapeutics
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• v.8 no.4
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• pp.285-292
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• 2000

The effects of the members of the same nuclear receptor superfamily (all-trans retinoic acid (RA), thyroid hormone(T3) or hydrocortisone) on proliferation and differentiation in the SK-N-SH neuroblastoma (NB) cell lines were studied. NB cells were treated with RA, T3, or hydrocortisone at concentration of 10$^{-6}$ M or 10$^{-8}$ M for 3 days or 7 days. RA induced concentration- and time-dependent morphologic differentiation(neurite outgrowth and microtubule-associated protein expression) and growth inhibition in NB cells. Treatment of 10$^{-7}$ M T3 for 7 days increased viability and differentiation of NB cells. Treatment of 10$^{-6}$ M hydrocortisone for 7 days increased viability of NB cells. Although these three effectors are members of the same receptor superfamily, the regulation of brain development may be carried out in a different manner.

• YAKHAK HOEJI
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• v.47 no.3
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• pp.180-183
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• 2003

Crystal structure of TRAF6 in complex with TRAF6-binding sites from CD40 was previously determined. The structure revealed a distinct TRAF6-binding groove of CD40, the key structural determinant of interaction. The structural information leads to a proposed TRAF6-binding motif. This allows the identification of TRAF6-binding sequences in the hIRAK protein, whose functional requirement in IL-1/Toll-like receptor superfamilies-mediated signal transduction is further demonstrated using site-directed mutagenesis. The mutational effects of hIRAK on the down-stream NF-kB signaling shows the importance of the TRAF6 interface for signaling by IL-1/Toll-like receptor superfamilies.

• Molecules and Cells
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• v.42 no.1
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• pp.56-66
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• 2019

Histidine triad nucleotide-binding protein (HINT) is a member of the histidine triad (HIT) superfamily, which has hydrolase activity owing to a histidine triad motif. The HIT superfamily can be divided to five classes with functions in galactose metabolism, DNA repair, and tumor suppression. HINTs are highly conserved from archaea to humans and function as tumor suppressors, translation regulators, and neuropathy inhibitors. Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albicans (CaHINT) in complex with zinc ions at a resolution of $2.5{\AA}$. Based on structural comparisons, the monomer of CaHINT overlaid best with HINT protein from the protozoal species Leishmania major. Additionally, structural comparisons with human HINT revealed an additional helix at the C-terminus of CaHINT. Interestingly, the extended C-terminal helix interacted with the N-terminal loop (${\alpha}1-{\beta}1$) and with the ${\alpha}3$ helix, which appeared to stabilize the dimerization of CaHINT. In the C-terminal region, structural and sequence comparisons showed strong relationships among 19 diverse species from archea to humans, suggesting early separation in the course of evolution. Further studies are required to address the functional significance of variations in the C-terminal region. This structural analysis of CaHINT provided important insights into the molecular aspects of evolution within the HIT superfamily.

• Journal of Life Science
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• v.18 no.8
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• pp.1059-1065
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• 2008

KIF21A is a member of the Kinesin superfamily proteins (KIFs), which are microtubule-dependent molecular motors, anterograde axonal transporters of cargoes. Recently, congenital fibrosis of the extraocular muscles 1 (CFEOM1) has been shown to result from a small number of recurrent heterozygous missense mutations of KIF21A. CFEOM1 results from the inability of mutated KIF21A to successfully deliver cargoes to the development of the occulo-motor neuron or neuromuscular junction. Here, we used an yeast two-hybrid system to identify a protein that interacts with the WD-40 repeat domain of KIF21A and found a specific interaction with Purkinje cell protein-2 (Pcp-2), a small protein also known as L7. Pcp-2 protein bound to the WD-40 domain of KIF21A and KIF21B but not to other KIFs in yeast two-hybrid assays. In addition, this specific interaction was also observed in the glutathione S-transferase pull-down assay. An antibody to Pcp-2 specifically co-immunoprecipitated KIF21A associated with Pcp-2 from mouse brain extracts. These results suggest that Pcp-2 may be involved in the KIF21A-mediated transport as a KIF21A adaptor protein.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• Korean Journal of Microbiology
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• v.51 no.4
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• pp.319-328
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• 2015

The $sdu1^+$ gene encodes Sdu1, a PPPDE superfamily member of deubiquitinating enzymes (DUBs) in Schizosaccharomyces pombe. Sdu1 was previously shown to contain an actual ubiquitin C-terminal hydrolase (UCH) activity using the recombinant plasmid pYSTP which harbors the $sdu1^+$ gene. This work was designed to assess a thermotolerant role of Sdu1 against high incubation temperatures. In the temperature-shift experiments, the S. pombe cells harboring pYSTP grew much better after the shifts to $37^{\circ}C$ and $42^{\circ}C$, when compared with the vector control cells. After being shifted to $37^{\circ}C$ and $42^{\circ}C$ for 6 h, the S. pombe cells harboring pYSTP contained lower reactive oxygen species (ROS) levels, compared with the vector control cells. The nitric oxide (NO) levels of the S. pombe cells harboring pYSTP were slightly lower than those of the vector control cells in the absence or presence of the temperature shifting. The total glutathione (GSH) levels of the S. pombe cells harboring pYSTP were significantly higher than those of the vector control cells. Total superoxide dismutase (SOD) and GSH peroxidase activities were also higher in the S. pombe cells harboring pYSTP after the temperature shifts than in the vector control cells. In brief, the S. pombe Sdu1 plays a thermotolerant role against high incubation temperature through the down-regulation of ROS and NO and the up-regulation of total GSH content, total SOD and GSH peroxidase activities.

• Korean Journal of Poultry Science
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• v.47 no.3
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• pp.127-133
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• 2020

Chibby family member 2 (CBY2), also known as SPERT or NURIT, is a gene with Chibby-like super family domain, whose function is not well known. In this study, the quail CBY2 gene was cloned, its sequences were analyzed, and its role in the myogenesis of QM7 quail muscle cells was characterized. Quail CBY2 has 978 nucleotides, which are translated into 325 amino acids, and the amino acid sequences are highly similar to those of chicken CBY2. Avian CBY2 diverted from mammalian CBY2 during early evolutionary history. According to the protein domain prediction analysis, quail CBY2 has a Chibby-like superfamily domain consisting of 83 amino acids at the N-terminal of the protein, although compared to mammalian CBY2, many of the amino acids were different. CBY2 was highly expressed in the adipose tissue and moderately expressed in the liver, heart, and kidney, whereas rarely expressed in the muscle tissue in quail. To characterize the role of CBY2 in myogenesis, CBY2 was overexpressed in QM7 cells. The overexpression of CBY2 inhibited myotube formation as shown that the myotube area was approximately only 25% that of the control. Taken together, quail CBY2 has a Chibby-like superfamily domain and inhibits myogenesis. Further studies should focus on the identification of the inhibitory mechanism of CBY2 on myogenesis.

• Toxicological Research
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• v.13 no.1_2
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• pp.1-21
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• 1997

염증반응이란 우리 신체에 외부 물질이 침입했을 경우 대처하는 정상적인 현상이다. 외부에서 물리, 화학, 생물학적 물질에 노출되었을 경우 혈관이 팽창하고, 비특이적 면역반응이 시작된다. Selectin, integrin, immunoglobulin superfamily와 같은 adhesion molecule에 의해 macrophage 및 neutrophil과 같은 leukocyte의 반응을 촉진하기 위해 exudation이 일어나고 침입 부위에 모여 hyperemia가 발생된다.(Govan 등, 1995)