• Journal of the Korean Data and Information Science Society
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• v.15 no.4
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• pp.1019-1031
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• 2004

This paper describes a new modeling method for the prediction of transmembrane protein topology. The structural regions of the transmembrane protein have been modeled by means of a multiple state hidden Markov model that has provided for the detailed modeling of the heterogeneous amino acid distributions of each structural region. Grammatical constraints have been incorporated to the prediction method in order to capture the biological order of membrane protein topology. The proposed method correctly predicted 76% of all membrane spanning regions and 92% sidedness of the integration when all membrane spanning regions were found correctly.

• Journal of Life Science
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• v.29 no.9
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• pp.949-954
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• 2019

Membrane topology is a key characteristic of membrane proteins. We previously reported the cloning of the chromosome 4 open-reading frame 32 (C4orf32) gene as a potential membrane protein; however, the cellular localization and membrane topology of C4orf32 was as yet unknown. In this study, we found that green fluorescent protein (GFP) fused to the C-terminus of C4orf32 (C4orf32-GFP) was localized to the endoplasmic reticulum (ER). We applied three tools to identify determinants of C4orf32 topology: protease protection, fluorescence protease protection (FPP), and an inducible system using the ternary complex between FK506 binding protein 12 (FKBP), rapamycin, and the rapamycin-binding domain of mTOR (FRB) (the FRB-rapamycin-FKBP system). Using protease protection and FPP assays, we found that the GFP tag in C4orf32-GFP was localized to the cytoplasmic surface of the ER membrane of HeLa cells. Protease protection and FPP assays are useful and complimentary tools for identifying the topology of GFP fusion membrane proteins. The FRB-rapamycin-FKBP system was also used to study the topology of C4orf32. In the absence of rapamycin, a monomeric red fluorescent protein-FKBP fusion (mRFP-FKBP) and C4orf32-GFP-FRB were localized to the cytoplasm and the ER membrane, respectively. However, in the presence of rapamycin, the mRFP-FKBP was shifted from the cytoplasm to the ER and colocalized with the C4orf32-GFP-FRB. These results indicate that the FRB moiety is facing the cytoplasmic surface of ER membrane. Overall, our results clearly suggest that C4orf32 belongs to the family of type I ER resident membrane proteins.

• BMB Reports
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• v.42 no.11
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• pp.697-704
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• 2009

Membrane proteins play important roles in the biology of the cell, including intercellular communication and molecular transport. Their well-established importance notwithstanding, the high-resolution structures of membrane proteins remain elusive due to difficulties in protein expression, purification and crystallization. Thus, accurate prediction of membrane protein topology can increase the understanding of membrane protein function. Here, we provide a brief review of the diverse computational methods for predicting membrane protein structure and function, including recent progress and essential bioinformatics tools. Our hope is that this review will be instructive to users studying membrane protein biology in their choice of appropriate bioinformatics methods.

• Proceedings of the Korean Biophysical Society Conference
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• 1998.06a
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• pp.28-28
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• 1998

RbsC of Escherichia coli is the integral membrane component of the high-affinity ribose transport system classified as the AraH family. To understand the function and structure of RbsC, the topology of RbsC was investigated by alkaline phosphatase fusion. Characterization of a total of 64 RbsC-PhoA fusions revealed that RbsC is composed of six transmembrane helixes and has three periplasmic and two cytoplasmic loops.(omitted)

• Journal of the Korean Magnetic Resonance Society
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• v.13 no.1
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• pp.1-6
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• 2009

Syndecan-4 cytoplasmic domain was tested to confirm the interactions with the bilayer membrane using $^{31}P$ solid-state NMR measurements. Syndecan-4 was known as a coreceptor with integrins in the cell adhesion. The syndecan-4 V region is not understood of its functional roles and tested its ability of the interaction with multilamellar vesicles. The $^{31}P$ powder pattern was dramatically changed and showed isotropic peak which imply the bilayer membrane changed its topology to the micelle-like structure. Especially, phosphatidylcholine membrane was affected this effect more than phosphatidylethanolamine membrane.

• Genomics & Informatics
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• v.7 no.2
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• pp.111-121
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• 2009

Cell membrane proteins play crucial roles in the cell's molecular interaction with its environment and within itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, and enzymes. Membrane proteomes of cellular organisms reveal some characteristics in their global topological distribution according to their evolutionary positions, and show their own information transfer complexity. Predicted transmembrane segments (TMSs) in membrane proteomes with HMMTOP showed near power-law distribution and frequency characteristics in 6-TMS and 7-TMS proteins in prokaryotes and eukaryotes, respectively. This reaffirms the important roles of membrane receptors in cellular communication and biological evolutionary history.

• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1090-1094
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• 2008

In this article, we show that the orf slr1471 from Synechocystis sp. PCC 6803 codes for a functional member of the YidC/Alb3/Oxa1 protein family, and the encoded protein has a transmembrane topology with a common core structure. Using specific antibodies raised against the Synechocystis YidC homologous protein, we further show that the Synechocystis YidC protein appears to be predominantly localized in the cyanobacterial cytoplasmic membrane. The impact of the described findings for synthesis of membrane proteins and for protein sorting within cyanobacterial cells is discussed.

• Journal of Korean Association for Spatial Structures
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• v.20 no.4
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• pp.53-62
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• 2020

This study examines the optimum shape of a trolley, the driving device of the retractable membrane roof. The closed-type trolley was determined as the model of the study, and a trolley composed of cylindrical-shaped inner and outer holders was selected as the basic model. Based on this model, a cylindrical-based optimal trolley model was proposed. In the basic trolley model, steel was used for the outer holder, and steel, titanium, and aluminum were used for the inner holder. In each case, the most economical shape for the external load of the basic model was newly proposed through the topology optimization process, and the finite element analysis results of the proposed model were compared to define the durability and economics. Here, topology optimization analysis and finite element analysis used the commercial software ANSYS. As a result of optimization, the volume of the outer holder of the trolley was reduced by 58.2% and the volume of the inner holder was reduced by 25.0% compared to the basic model. In the case of stress, a stress increase of 43.2 to 79.2% occurred depending on the material of the inner holder, but it was found to be significantly lower than the yield strength, thereby ensuring safety.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1996.04a
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• pp.181-181
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• 1996

The (Na, K) ATPase is a membrane ion transporting ATPase composed of an ${\alpha}$ catalytic subunit and a ${\beta}$ glycoprotein subunit. The topology of the rat ${\alpha}$1 and ${\beta}$1 subunits has been studied by insertion of epitope(s) : at the NH2-terminus and COOH-terminus and between Glu117 and Glul18, Lys828 and Arg829, Gln900 and Trp901, and Va1939 and Phe940 of the ${\alpha}$ subunit; and at the NH2-terminus and COOH-terminus and between Glu228 and Tyr229 of the ${\beta}$ subunit. The epitope-tagged ${\alpha}$l, constructs were expressed in HeLa cells to select for stable cell lines expressing a functional (Na, K)ATPase. All constructs, except for the one tagged between Gln900 and Trp901, resulted in ouabain-resistant colonies indicating that modified proteins retained functional integrity. The epitope-tagged ${\beta}$ constructs were transiently expressed in Cos-7 cells. The orientation of the epitopes with respect to the cell membrane was revealed by indirect immunofluorescence performed on permeabilized and non-permeabilized cells expressing the (Na, K)ATPase chains. The results indicate that the ${\alpha}$ subunit has 4 transmembrane segments in the COOH terminal membrane bound domain between residues 760 and 938, and that both the NH2-terminus and the COOH-terminus are in the cytosol; it was not determined whether there are more transmembrane segments between residue 938 and the COOH-terminus. The ${\beta}$ subunit has only one transmembrane spanning region with the NH2-terminus in the cytosol and the COOH-terminus on the extracytoplasmic surface of the plasma membrane.

• Transactions of the Korean hydrogen and new energy society
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• v.28 no.5
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• pp.465-470
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• 2017

Sulfonated fluorinated block copolymers having diphenyl units were mixed with the sulfonated cationic conductive polymers at an optimum mixing ratio to form hybrid membranes for fuel cells and their characteristics were studied. 2D and 3D AFM topology analysis confirmed that the number of hydrophilic units in the hybrid membrane was improved. Through the FE-SEM, the microstructure of the hybrid membrane implied hydrogen bonding and pi-pi interactions, and EDAX confirmed carbon, oxygen, sulfur, and fluorine. The thermogravimetric analysis showed that the hybrid membrane was thermally stable and the hydrophilicity of the hybrid membrane was increased by the contact angle of water droplets. As a result, it was confirmed that the cation conductivity increased by a factor of 1.8 times as the number of acidic domains in the hybrid film increased.