• Proceedings of the PSK Conference
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• 2002.10a
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• pp.275.1-275.1
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• 2002

It has been proposed that G protein interacts with receptor via multiple interaction sites. With regard to this, C-terminus of the G${\alpha}$ subunit is clearly not the only structural determinant on the G proteins that is critical for receptor coupling selectivity, but the extreme N-terminus of Ga subunit and other structural elements were proposed to be responsible for dictating the interaction with receptors. (omitted)

• Proceedings of the Korean Magnetic Resonance Society Conference
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• 2001.02a
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• pp.32-32
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• 2001

• Proceedings of the PSK Conference
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• 2001.04a
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• pp.169.1-169.1
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• 2001

• 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.

• BMB Reports
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• v.39 no.5
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• pp.560-570
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• 2006

Mistletoe (Viscum album) lectins, which are classified as a type II ribosome-inactivating protein (RIP) due to their unique biological function and the potential medical and therapeutic application in cancer cells, receive a rising attention. The heterodimeric glycoproteins contain the A-chain with catalytic activity and the B-chain with sugar binding properties. In recent years, studies involving the lectins from the white berry European mistletoe (Viscum album) and the yellow berry Korean mistletoe (Viscum album coloratum) have been described. However, the detailed mechanism in exerting unique cytotoxic effect on cancer cells still remains unclear. Here, we aim to understand and define the molecular basis and biological effects of the type II RIPs, through the studies of the recombinant Korean mistletoe lectin. To this end, we expressed, purified the recombinant Korean mistletoe lectin (rKML), and investigated its molecular characteristics in vitro, its cytotoxicity and ability to induce apoptotic cell death in cancer cells. To gain structural basis for its catalytic activity and sugar binding properties, we performed homology modeling studies based on the high degree of sequence identity and conserved secondary structure prediction between Korean and European, Himalayan mistletoe lectins, and Ricin.

• 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.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.212-216
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• 2015

Oseltamivir, also known as Tamifu, is an inhibitor of neuraminidase protein which plays an essential role in proliferation and replication of influenza virus. Binding to the active site of neuraminidase, the oseltamivir prevents the protein from enzyme reaction. Conformational change of the protein(neuraminidase) should be accompanied by the enzyme reaction, but the drug inhibits the protein to deform. In this study, we examine the influence of oseltamivir on protein's conformational change in the structural and mechanical point of view. Finite element analysis of the protein can be an useful approach to investigate the influence of oseltamivir on the deformation of a protein. We suggest the finite element based protein model, and then perform the linear static analysis with the displacement loading condition based on the first two largest motion which can be obtained from the normal mode analysis. The results show that it takes more energy to change shape of the protein with an oseltamivir attached than the protein without an oseltamivir.

• Proceedings of the Korean Biophysical Society Conference
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• 1999.06a
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• pp.17-17
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• 1999

Almost half of the entire set of predicted genomic products from M ethanococcus jannaschii are classified as functionally unknown hypothetical proteins. We present a structure-based identification of the biochemical function of a protein with hitherto-unknown function from a M. jannaschii gene, Mj0226.(omitted)

• Korean Journal of Microbiology
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• v.21 no.3
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• pp.115-126
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• 1983

The results that the effect of 6 detergents on the structural changes and biochemical composition of bacterial membrane of Escherichia coli and Bacillus cereus are as follows ; 1. Population growth of the bacteria was increased in case of the treatment with palmitoyl carnitine and sodium deoxy cholate but was increased in case of the treatment with palmitoyl carnitine and sodium deoxy cholate but was decreased by sodium dodecyl sulfate and palmitoyl choline, in E.coli and was decreased by palmitoyl carnitine and palmitoyl choline at the low concentration, in B. cereus. 2. The electron micrograph showed that cell wall lysis or cell collapse were observed in the treatment of sodium dodecyl sulfate and palmitoyl choline, and also cell wall was condensed by triton X-100 and sodium deoxy cholate, in E.coli. And in B. cereus, endospore formation of the bacteria was stimulated by palmitoyl choline, and cell lysis or structural changes of the membrane were observed in the treatment of sodium dodecyl sulfate, sodium cholate, and triton X-100, respectively. 3. As to the effect of detergent on the biochemical composition of biomembrane, the content of carnitine, in E.coli, and B.cereus, the content of structural protein and phospholipid were decreased by treatment of sodium dodecyl sulfate and structural protein was denatured by palmitoyl choline. 4. The profile of membrane protein revealed that the bacterial membrane were composed of various proteins. By dint of this result, some of membrane proteins were solubilized or changed to small molecules by the treatment of sodium dodecyl sulfate and palmitoyl choline, in E.coli and membrane protein of the biomembrane by treatment of sodium dodecyl sulfate, sodium deoxy cholate, palmitoyl choline, and palmitoyl carnitine were confirmed to be different profile as compared with those of the control, in B. cereus. Therefore, it is suggested that sodium dfodecyl sulfate and palmitoyl choline soulbilized biomembranes or inhibited membrane transport and that palmitoyl carnitine and sodium deoxy cholate were used as an energy source or stimulating the membrane transport, in E.coli. And, it is suggested that all of detergents were inhibited biomembrane synthesis, expet saponin, in B.cereus.

• Molecules and Cells
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• v.38 no.9
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• pp.789-795
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• 2015

A chromosome territory is composed of chromosomal subdomains. The internal structure of chromosomal subdomains provides a structural framework for many genomic activities such as replication and DNA repair, and thus is key to determining the basis of their mechanisms. However, the internal structure and regulating proteins of a chromosomal subdomain remains elusive. Previously, we showed that the chromosome territory expanded after BAF53 knockdown. Because the integrity of chromosomal subdomains is a deciding factor of the volume of a chromosome territory, we examined here the effect of BAF53 knockdown on chromosomal subdomains. We found that BAF53 knockdown led to the disintegration of histone H2B-GFP-visualized chromosomal subdomains and BrdU-labeled replication foci. In addition, the size of DNA loops measured by the maximum fluorescent halo technique increased and became irregular after BAF53 knockdown, indicating DNA loops were released from the residual nuclear structure. These data can be accounted for by the model that BAF53 is prerequisite for maintaining the structural integrity of chromosomal subdomains.