• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.20-20
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• 2003

The success of genome project brought us a vast amount of sequence information about whole genes for some species. In order to get functional understanding of un-annotated genes, a number of frontiers in structural biology proposed a new paradigm for structural research on the basis of given information. Structural biologists believe that the whole characters of the living cells come from the protein functions, which could be regulated by three-dimensional protein structures.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.20 no.9
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• pp.1816-1821
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• 2016

Protein secondary structure is important for the study of protein evolution, structure and function of proteins which play crucial roles in most of biological processes. This paper try to effectively extract protein secondary structure information from the large protein structure database in order to predict the protein secondary structure of a query protein sequence. To find more remote homologous sequences of a query sequence in the protein database, we used PSI-BLAST which can perform gapped iterative searches and use profiles consisting of homologous protein sequences of a query protein. The secondary structures of the homologous sequences are weighed combined to the secondary structure prediction according to their relative degree of similarity to the query sequence. When homologous sequences with a neural network predictor were used, the accuracies were higher than those of current state-of-art techniques, achieving a Q3 accuracy of 92.28% and a Q8 accuracy of 88.79%.

• Journal of the Korean Vacuum Society
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• v.14 no.3
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• pp.138-142
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• 2005

We tested performance of the 4C1 beamline for analyzing structures of proteins in solution using small angle X-ray scattering (SAXS) at the Pohang Light Source(PLS). Structurally well-known proteins such as lysozyme and $Bcl-XL(\vartriangle TM/\vartriangle loop)$ were used for the study. Low resolution solution structures of lysozyme and $Bcl-XL(\vartriangle TM/\vartriangle loop)$ were obtained at a resolution of at least i.2 nm, and the structures were basically same as those calculated from the crystal structures of the proteins. We also used $Bcl-XL(\vartriangle TM/\vartriangle loop)$ with a long flexible loop attached [$Bcl-XL(\vartriangleTM))$] and obtained significantly different data from $Bcl-XL(\vartriangle TM/\vartriangle loop)$, although the electron density map of the loop is known to be invisible from the crystal structure of $Bcl-XL(\vartriangleTM))$. We confirm that SAXS experiment is a powerful tool for the structural study of proteins in solution and the 4Cl beamline at the PLS is well-equipped and suitable for the protein solution SAXS experiment.

• Korean Journal of Head & Neck Oncology
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• v.9 no.1
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• pp.74-87
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• 1993

Immunohistochemical studies on S-100 protein and lactoferrin were carried out to evaluate the existence and distribution pattern of S-100 protein and lactoferrin positive cells in salivary gland tumors. The specimens used were 25 cases of pleomorphic adenoma, 2 cases of monomorphic adenoma, 2 cases of mucoepidermoid tumor, 2 cases of acinic cell tumor, 3 cases of adenoid cystic carcinoma and 2 cases of adenocarcinoma occured in parotid and submandibular salivary gland. ABC kits(Dako corp. Copenhagen. Denmark) for S-100 protein and lactoferrin were used. The results obtained were summarized as follows: In the normal salivary gland. positive immunoreaction for S-100 protein was observed in myoepithelial cells of acini and intercalated ducts. Positive immunoreaction for lactoferrin was observed in serous acinic cells, epithelial cells of intercalated ducts, and excretory material in the ductal lumina. In the pleomorphic and monomorphic adenomas. most of tumor cells were positive for S-100 protein, while luminal tumor cells in gland-like or duct-like structures were rarely positive for lactoferrin. In mucoepidermoid tumor, most of squamous cells and a few of intermediate cells were positive for S-100 protein, but all of tumor cells were negative for lactoferrin. In acinic cell tumor, most of tumor cells were positive for lactoferrin, but all of tumor cells were negative for S-100 protein. In adenoid cystic carcinoma, basaloid tumor cells in trabecular structure were focally positive for S-100 protein. and in adenocarcinoma, many of tumor cells were posivive for both S-100 protein and lactoferrin. Thus, according to the embryonic stage of the development of the tumor cell origin, it was possible to classify the salivary gland tumor as followings: mucoepidermoid carcinoma which originated from the earliest stage, acinic cell tumor which originated from the end stage. Between these two extremes, there were pleomorphic adenoma, adenoid cystic carcinoma and adenocarcinoma which originated in the middle stage of the development of .the salivary glands. Based on the above results, it can be stated that S-100 protein is demonstrated in tumor cells orginated from myoepithelial cells and lactoferrin in glandular differentiated tumor cells.

• Journal of Pharmaceutical Investigation
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• v.31 no.3
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• pp.191-196
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• 2001

Biodegradable polymeric microspheres were studied for their usefulness as carriers for the delivery of vaccine antigens. However, protein antigen could be denatured during microencapsulation processes due to the exposure to the organic phase and stress condition of cavitation and shear force. Therefore this study was carried out to re-evaluate the degree of protein denaturation during microencapsulation with poly(lactide-co-glycolide) (PLGA) copolymer. PLGA microspheres containing ovalbumin (OVA), prepared by W/O/W multiple emulsification method, were suspended in pH 7.4 PBS and incubated with shaking at $37.5^{\circ}C$. Drug released medium was collected periodically and analyzed for protein contents by micro-BCA protein assay. In order to evaluate the protein integrity, release medium was subjected to the analyses of SDS-PAGE and size exclusion chromatography (SEC). And enzyme-linked immunosorbent assay (ELISA) was introduced to measure the immunoreactivity of entrapped OVA and to get an insight into the three-dimensional structure of epitope. The structures of entrapped protein were not affected significantly by the results of SDS-PAGE and SEC. However, immunoreactivity of released antigen was varied, revealing the possibility of protein denaturation in some microspheres when it was evaluate by ELISA method. Therefore, in order to express the degree of protein denaturation, antigenicity ratio (AR) was obtained as follows: amount of immunoreactivity of OVA/total amount of OVA released ${\times}100(%)$. ELISA method was an efficient tool to detect a protein denaturation during microencapsulation and the comparison of AR values resulted in more accurate evaluation for immunoreactivity of entrapped protein.

• BMB Reports
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• v.31 no.4
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• pp.307-327
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• 1998

Cytochrome c peroxidase (CcP) is a yeast mitochondrial enzyme which catalyzes the reduction of hydrogen peroxide to water using two equivalents of ferrocytochrome c. The CcP/cytochrome c system has many features which make it a very useful model for detailed investigation of heme protein structure/function relationships including activation of hydrogen peroxide, protein-protein interactions, and long-range electron transfer. Both CcP and cytochrome c are single heme, single subunit proteins of modest size. High-resolution crystallographic structures of both proteins, of one-to-one complexes of the two proteins, and a number of active-site mutants are available. Site-directed mutagenesis studies indicate that the distal histidine in CcP is primarily responsible for rapid utilization of hydrogen peroxide implying significantly different properties of the distal histidine in the peroxidases compared to the globins. CcP and cytochrome c bind to form a dynamic one-to-one complex. The binding is largely electrostatic in nature with a small, unfavorable enthalpy of binding and a large positive entropy change upon complex formation. The cytochrome c-binding site on CcP has been mapped in solution by measuring the binding affinities between cytochrome c and a number of CcP surface mutations. The binding site for cytochrome c in solution is consistent with the crystallographic structure of the one-to-one complex. Evidence for the involvement of a second, low-affinity cytochrome c-binding site on CcP in long-range electron transfer between the two proteins is reviewed.

• Korean Journal of Computational Design and Engineering
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• v.11 no.2
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• pp.97-106
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• 2006

Voronoi diagrams have been known for numerous important applications in science and engineering including CAD/CAM. Especially, the Voronoi diagram for 3D spheres has been known as very useful tool to analyze spatial structural properties of molecules or materials modeled by a set of spherical atoms. In this paper, we present two algorithms, the edge-tracing algorithm and the region-expansion algorithm, for constructing the Voronoi diagram of 3D spheres and applications to protein structure analysis. The basic scheme of the edge-tracing algorithm is to follow Voronoi edges until the construction is completed in O(mn) time in the worst-case, where m and n are the numbers of edges and spheres, respectively. On the other hand, the region-expansion algorithm constructs the desired Voronoi diagram by expanding Voronoi regions for one sphere after another via a series of topology operations, starting from the ordinary Voronoi diagram for the centers of spheres. It turns out that the region-expansion algorithm also has the worst-case time complexity of O(mn). The Voronoi diagram for 3D spheres can play key roles in various analyses of protein structures such as the pocket recognition, molecular surface construction, and protein-protein interaction interface construction.

• Journal of IKEEE
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• v.13 no.3
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• pp.18-23
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• 2009

FEATURE is a computational method to recognize functional and structural sites for automatic protein function prediction. By profiling physicochemical properties around residues, FEATURE can characterize and predict functional and structural sites in 3D protein structures in a high-throughput manner. Despite its effectiveness, it has been challenging to apply FEATURE to novel protein data due to limited customization support. To address this problem, we thoroughly analyze the internal modules of FEATURE and propose a methodology to customize FEATURE so that it can be used for new protein data for automatic functional annotations.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.65-65
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• 2003

After many genome projects, algorithms and software to process explosively growing biological information have been developed. To process huge amount of biological information, high performance computing equipments are essential. If we use the remote resources such as computing power, storages etc., through a Grid to share the resources in the Internet environment, we will be able to obtain great efficiency to process data at a low cost. Here we present the performance improvement of the protein secondary structure prediction (PSIPred) by using the Grid platform, distributing protein sequence data on the Grid where each computer node analyzes its own part of protein sequence data to speed up the structure prediction. On the Grid, genome scale secondary structure prediction for Mycoplasma genitalium, Escherichia coli, Helicobacter pylori, Saccharomyces cerevisiae and Caenorhabditis slogans were performed and analyzed by a statistical way to show the protein structural deviation and comparison between the genomes. Experimental results show that the Grid is a viable platform to speed up the protein structure prediction and from the predicted structures.

• Transactions of the Society of Information Storage Systems
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• v.9 no.1
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• pp.28-31
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• 2013

We proposed a method to fabricate label-free protein sensor with sub-wavelength nanograting structures to be used for diagnosing acute myocardial infarction. A nickel stamp for the injection molding of nanograting integrated protein sensor was fabricated by electroforming process with high fidelity. By using metallic stamp, we replicated label-free protein sensor via injection molding, which is an outstanding method for low-cost and mass production of polymer products. Finally, we performed a feasibility test, examining cardiac troponin T (cTnT) and anti-cTnT interactions. From the results, we demonstrated that the fabricated protein sensor can provide information for the early and accurate detection of cardiac diseases such as acute myocardial infarction.