• Bulletin of the Korean Chemical Society
• /
• v.29 no.5
• /
• pp.1013-1017
• /
• 2008

Syndecan-3 is a cell-surface heparan sulfate proteoglycan, which performs a variety of functions during cell adhension process. It is also a coreceptor for growth factor, mediating cell-cell and cell-matrix interaction. Syndecan-3 contains a cytoplasmic domain potentially associated with the cytoskeleton. Syndecan-3 is specifically expressed in neuron cell and has related to neuron cell differentiation and development of actin filament in cell migration. Syndecans each have a unique, central, and variable (V) region in their cytoplasmic domains. And that region of syndecan-3 may modulate the interactions of the conserved C1 regions of the cytoplasmic domains by tyrosine phosphorylation. Cytoplasmic domain of syndecan-3 has been synthesized for NMR structural studies. The solution structure of syndecan-3 cytoplasmic domain has been determined by two-dimensional NMR spectroscopy and simulated-annealing calculation. The cytoplasmic domain of the syndecan proteins has a tendency to form a dimmer conformation with a central cavity, however, that of syndecan-3 demonstrated a monomer conformation with a flexible region near C-terminus. The structural information might add knowledge about the structure-function relationships among syndecan proteins.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.4
• /
• pp.1089-1095
• /
• 2013

The tumor necrosis factor-receptor 1 (TNFR1)-associated death domain protein (TRADD) contains an N-terminal TRAF binding domain and a C-terminal death domain. TRADD is known to interact directly with TNF receptor 2 (TNFR2) and the Fas-associated death domain protein (FADD), which are signal transducers that activate NF-${\kappa}B$ and induce apoptosis, respectively. To date, there has been no structural information on the TRADD and FADD death domain (DDs) complex. In this study, the death domains of TRADD and FADD were co-expressed and purified from Escherichia coli for structural characterization. We found that human TRADD (hTRADD) interacted strongly with mouse FADD (mFADD) via their DDs and interacted weakly with human FADD (hFADD)-DD. Moreover, the structures of the TRADD-DD:FADD-DD complexes were separately modeled from predicted structures in the protein data bank (PDB). The results of this study will have important applications in human diseases such as cancer, AIDS, degenerative and autoimmune diseases, and infectious diseases.

• Journal of Life Science
• /
• v.16 no.7 s.80
• /
• pp.1225-1228
• /
• 2006

Cyclic AMP receptor protein (CRP) complexed with cAMP binds to DNA and induces sharp DNA bending around ${\sim}90$ degree. Previous publication (5), however, reported that mutant CRP:cGMP complex showed high migration rate relative to mutant CRP:cAMP complex on native polyacrylamide gel. To confirm DNA structural change in the presence of CRP and cyclic nucleotide, molar cyclization factor $(j_M)$ [13] was measured with 6 constructed DNA fragments. Nonlinear regression analysis of $j_M$ data indicated that mutant CRP did not induce DNA bending in the presence of cGMP but bent DNA in the presence of cAMP without any helical twist change in DNA.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.5
• /
• pp.964-967
• /
• 2008

Two structural protein genes, VP19 and VP466, of white spot syndrome virus (WSSV) were cloned and expressed in Sf21 insect cells using a baculovirus expression system for the development of injection and oral feeding vaccines against WSSV for shrimps. The cumulative mortalities of the shrimps vaccinated by the injection of rVP19 and rVP466 at 15 days after the challenge with WSSV were 50.2% and 51.8%, respectively. For the vaccination by oral feeding of rVP19 and rVP466, the cumulative mortalities were 49.2% and 89.2%, respectively. These results show that protection against WSSV can be generated in the shrimp, using the viral structural protein as a protein vaccine.

• Journal of Life Science
• /
• v.17 no.3 s.83
• /
• pp.345-349
• /
• 2007

We wished to create a set of small molecular weight PDZ domain ligands that may be used in functional studies on the proteins AF6, PSD-95 and Shank. As a starting point, the Shank3 PDZ domain was cloned, purified, and characterized the structure of Shank3 PDZ domain by 1D $^1H-NMR$. The chemical shift dispersion of the proton signals indicates that the purified Shank3 PDZ protein is very pure and globally well folded. Currently, we are working on improving the yield of the protein production for complete NMR structural analysis of the Shank3 PDZ domain.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.10
• /
• pp.1366-1372
• /
• 2021

Bacterial nanocellulose (BNC) is a biocompatible material with a lot of potential. To make BNC commercially feasible, improvements in its production and surface qualities must be made. Here, we investigated the in situ fermentation and generation of BNC by addition of different cellulosic substrates such as Avicel and carboxymethylcellulose (CMC) and using Komagataeibacter sp. SFCB22-18. The addition of cellulosic substrates improved BNC production by a maximum of about 5 times and slightly modified its structural properties. The morphological and structural properties of BNC were investigated by using Fourier transform-infrared spectroscopy (FT-IR), scanning electron microscopy and X-ray diffraction. Furthermore, a type-A cellulose-binding protein derived from Clostridium thermocellum, CtCBD3, was used in a novel biological analytic approach to measure the surface crystallinity of the BNC. Because Avicel and CMC may adhere to microfibrils during BNC synthesis or crystallization, cellulose-binding protein could be a useful tool for identifying the crystalline properties of BNC with high sensitivity.

• Journal of Integrative Natural Science
• /
• v.9 no.2
• /
• pp.136-143
• /
• 2016

KiSS1-derived peptide receptor, a GPCR protein, binds with the hormone kiss peptin. They are important in the neuroendocrine regulation of reproduction and in the secretion of gonadotrophin-releasing hormone. Thus, analysing the structural features of the receptor becomes important. However, the three dimensional structure of the protein is unavailable. Hence in this study, we have performed the homology modelling of KiSS1-derived peptide receptor with 5 different templates. 30 models were constructed using two platforms - Easymodeller and ITasser. The optimal models were chosen based on the model validation. Two models were selected after validation. The developed models could provide useful for analysing the structural features of KiSS1-derived peptide receptor and their pathophysiological role in various disorders related to them.

• Applied Microscopy
• /
• v.47 no.3
• /
• pp.160-164
• /
• 2017

Electron crystallography has been used as the one of powerful tool for studying the structure of biological macromolecules at high resolution which is sufficient to provide details of intramolecular and intermolecular interactions at near-atomic level. Previously it commonly uses two-dimensional crystals that are periodic arrangement of biological molecules, however recent studies reported a novel technical approach to electron crystallography of three-dimensional crystals, called micro electron-diffraction (MicroED) which involves placing the irregular and small sized protein crystals in a transmission electron microscope to determine the atomic structure. In here, we review the advances in electron crystallography techniques with several recent studies. Furthermore, we discuss the future direction of this structural approach.

• BMB Reports
• /
• v.43 no.5
• /
• pp.319-324
• /
• 2010

Experimental bioinformatics data obtained from an E. coli cell-based eukaryotic protein purification experiment were analyzed in order to identify any bottleneck as well as the factors affecting the target purification. All targets were expressed as His-tagged maltose-binding protein (MBP) fusion constructs and were initially purified by immobilized metal affinity chromatography (IMAC). The targets were subsequently separated from the His-tagged MBP through TEV protease cleavage followed by a second IMAC isolation. Of the 743 total purification trials, 342 yielded more than 3 mg of target proteins for structural studies. The major reason for failure of target purification was poor TEV proteolysis. The overall success rate for target purification decreased linearly as cysteine content or isoelectric point (pI) of the target increased. This pattern of pI versus overall success rate strongly suggests that pI should be incorporated into target scoring criteria with a threshold value.

• BMB Reports
• /
• v.44 no.2
• /
• pp.102-106
• /
• 2011

Thermodynamic stability and refolding kinetics of firefly luciferase and three representative mutants with depletion of negative charge on a flexible loop via substitution of Glu by Arg (ER mutant) or Lys (EK mutant) as well as insertion of another Arg in ER mutants (ERR mutant) was investigated. According to thermodynamic studies, structural stability of ERR and ER mutants are enhanced compared to WT protein, whereas, these mutants become prone to aggregation at higher temperatures. Accordingly, it was concluded that enhanced structural stability of mutants depends on more compactness of folded state, whereas aggregation at higher temperatures in mutants is due to weakening of intermolecular repulsive electrostatic interactions and increase of intermolecular hydrophobic interactions. Kinetic results indicate that early events of protein folding are accelerated in mutants.