• Journal of the Korea Society of Computer and Information
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• v.14 no.7
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• pp.41-47
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• 2009

A solution to the problems of recognizing as one spot or detection failures for complex regions, in which many spots representing proteins are overlapped and saturated, is suggested. The accumulated gradients of each point in complex regions are calculated, and the resulting accumulated gradient image segmented using watershed technique. The suggested solution show better and efficient result than existing method for spot separation, detects more protein spots hidden in the image of 2-dimensional electrophoresis, and expands the scope of prediction.

• Journal of Photoscience
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• v.9 no.2
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• pp.102-105
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• 2002

Phoborhodopsin (pR or sensory rhodopsin II, sRII; the absorption maximum of ∼ 500 nm) is a retinoid protein and works as a photoreceptor of the negative phototaxis of Halobacterium salinarum. pharaonis phoborhodopsin (ppR or pharaonis sensory rhodopsin II, psRII) is a corresponding protein of Natronobacterium pharaonis. These sensory proteins form a complex with a cognate transducer protein in the membrane, and this complex transmits the light-signal to the cytoplasm to evoke avoidance reaction from blue-green light. Recently, the functional expression in Escherichia coli membrane of ppR was achieved, which can afford a large amount of the protein and enables mutant studies to clarify the role of various amino acid residues. A truncated transducer which can bind to ppR is also expressed in Escherichia. coli membrane. In this article, we will review properties of ppR mainly using observations of our laboratory; which contains photochemistry (photocycle), light-driven proton uptake, release and transport, F -helix titling during photocycle and association of the transducer.

• Journal of Food Hygiene and Safety
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• v.7 no.2
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• pp.77-82
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• 1992

In order to investigate the protein binding characteristics of braD6n and hematoxy6n to bovine semm albumin (BSA), the fluorescence probe method was adopted. Brazilin and hematoxy6n showed strong binding affinity for BSA. It was also confirmed that hematoxy6n was bound to BSA stronger than braDlin. The association constants were decreased by the elevation of concentrations of brazilin and hematoxylin. It might be due to the complex formation of the probe and both compounds or the interaction between the probe-protein complex and both compounds. The bindings between both compounds and BSA were dependent on pH and ionic strength. It seems that electrostatic force as weD as hydrophobic force is involved in the binding of braD6n and bematoxylin to BSA.

• Journal of Life Science
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• v.10 no.2
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• pp.218-227
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• 2000

Bone morphogenetic protein 1 (BMP-1) is part of a complex capable of inducing ectopic bone formation in mammals. Studies on TGF-β1 processing and Drosophila dorsal-ventral patterning have focused attention on BMP-1 as important in mediating the biological activity of this bone inducing complex. Herein, the bacterial expression, refolding, purification, and initial characterization of the BMP-1 proteolytic domain (BPD) are described. A semi-quantitative fluorescence-based thin layer chromatography assay was developed to assist in rapidly screening for optimal renaturation conditions. According to a preliminary screen for optimal conditions for the refolding of BPD , a detectable proteolytic activity against a high turnover substrate for astacin, a homologous protease from crayfish was observed. The conditions identified have allowed the expression of sufficient amounts of BPD for the characterization of the protein. Its proteolytic activity exhibits the same cleavage specificity as astacin against seven substrates that were previously synthesized for studying astacin. Furthermore, this activity is inhibited by the metal chelator 1,10-phenanthroline but not by its analogue 1,7-phenanthroline. The collagenase inhibitor Pro-Leu-Gly hydroxamate was found to inhibit both astacin and BPD activity. The results presented in this paper argue that BMP-1 does in fact possess an intrinsic proteolytic activity.

• Proceedings of the Korean Magnetic Resonance Society Conference
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• 2002.08a
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• pp.90-90
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• 2002

Syndecans, transmembrane heparan sulfate proteoglycans, are coreceptors with integrin in cell adhesion process. It forms a ternary signaling complex with protein kinase C and phosphatidylinositol 4,5 bisphosphate (PIP2) for integrin signaling. NMR data indicates that cytoplasmic domain of syndecan-4 (4L) undergoes a conformational transition in the presence of PIP2, forming oligomeric conformation. The structure based on NMR data demonstrated that syndecan-4L itself forms a compact intertwined symmetric dimer with an unusual clamp shape for residues Leu$^{186}$ -Ala$^{195}$ . The molecular surface of the syndecan-4L dimer is highly positively charged. In addition, no inter-subunit NOEs in membrane proximal amino acid resides (Cl region) has been observed, demonstrating that the Cl region is mostly unstructured in syndecan-4L dimmer. However, the complex structure in the presence of PIP2 induced a high order multimeric conformation in solution. In addition, phosphorylation of cytoplasmic domain induces conformational change of syndecan-4, resulting inhibition of PKC signaling. The NMR structural data strongly suggest that PIP2 promotes oligomerization of syndecan-4 cytoplasmic domain for PKC activation and further induces structural reorganization of syndecan for mediating signaling network in cell adhesion procedure.

• Molecules and Cells
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• v.43 no.9
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• pp.804-812
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• 2020

In cells, proteins form macromolecular complexes to execute their own unique roles in biological processes. Conventional structural biology methods adopt a bottom-up approach starting from defined sets of proteins to investigate the structures and interactions of protein complexes. However, this approach does not reflect the diverse and complex landscape of endogenous molecular architectures. Here, we introduce a top-down approach called Electron Microscopy screening for endogenous Protein ArchitectureS (EMPAS) to investigate the diverse and complex landscape of endogenous macromolecular architectures in an unbiased manner. By applying EMPAS, we discovered a spiral architecture and identified it as AdhE. Furthermore, we performed screening to examine endogenous molecular architectures of human embryonic stem cells (hESCs), mouse brains, cyanobacteria and plant leaves, revealing their diverse repertoires of molecular architectures. This study suggests that EMPAS may serve as a tool to investigate the molecular architectures of endogenous macromolecular proteins.

• BMB Reports
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• v.56 no.5
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• pp.302-307
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• 2023

Lyn, a tyrosine kinase that is activated by double-stranded DNA-damaging agents, is involved in various signaling pathways, such as proliferation, apoptosis, and DNA repair. Ribosomal protein S3 (RpS3) is involved in protein biosynthesis as a component of the ribosome complex and possesses endonuclease activity to repair damaged DNA. Herein, we demonstrated that rpS3 and Lyn interact with each other, and the phosphorylation of rpS3 by Lyn, causing ribosome heterogeneity, upregulates the translation of p-glycoprotein, which is a gene product of multidrug resistance gene 1. In addition, we found that two different regions of the rpS3 protein are associated with the SH1 and SH3 domains of Lyn. An in vitro immunocomplex kinase assay indicated that the rpS3 protein acts as a substrate for Lyn, which phosphorylates the Y167 residue of rpS3. Furthermore, by adding various kinase inhibitors, we confirmed that the phosphorylation status of rpS3 was regulated by both Lyn and doxorubicin, and the phosphorylation of rpS3 by Lyn increased drug resistance in cells by upregulating p-glycoprotein translation.

• Journal of Environmental Health Sciences
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• v.24 no.3
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• pp.26-34
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• 1998

Diethanolamine Dithiocarbamate containing OH groups which gave water-soluble [Pt(dtc)$_{2}$] (diethanolamine dithiocarbamate) were synthesized from the reaction of CS$_{2}$ with diethanolamine. The complex has been characterized by elemental analysis, electrical conductivity, and spectroscopic results. Diethanolamine dithiocarbamate is effective as rescue and inhibition of cis-[$Pt(NH_{3})_{2}Cl_{2}$] nephrotoxicity in rats. It is suggested that diethanolamine dithiocarbamare removes platinum(II) complex coordinated to -SH groups of protein of kidney tubule cells.

• KIPS Transactions on Software and Data Engineering
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• v.8 no.10
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• pp.421-426
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• 2019

In this paper, we propose a method to visualize the geometric features of the contact region between proteins in a protein complex. When proteins or ligands are represented as curved surfaces with irregularities, the property that the two surfaces contact each other without intersections is called shape compatibility. Protein-Protein or Protein-Ligand docking researches have shown that shape complementarity, chemical properties, and entropy play an important role in finding contact regions. Usually, after finding a region with high shape complementarity, we can predict the contact region by using residual polarity and hydrophobicity of amino acids belonging to this region. In the research for predicting the contact region, it is necessary to investigate the geometrical features of the contact region in known protein complexes. For this purpose, it is essential to visualize the geometric features of the molecular surface. In this paper, we propose a method to find the contact region, and visualize the geometric features of it as normal vectors and mean curvatures of the protein complex.

• Journal of Photoscience
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• v.9 no.2
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• pp.82-85
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• 2002

33kDa extrinsic protein, an important protein in oxygenic photosynthesis, was known to have no fixed configuration in solution. At 20$\^{C}$ and pH 6, 33kDa extrinsic protein showed changes of free energy of -14.6 kJ/mor$\^$-1/ and of standard volume of -120mL/mol, respectively, with increase of hydrostatic pressure, comparatively lower than for most proteins. NBS modification of Trp241 in 33kDa extrinsic protein dramatically changes the secondary protein structure, its affinity to photosystem II as well as photosynthetic oxygen evolution. The relationship between structural change and transport of oxygen, water and proton is deserved a further study.