• Journal of the Korean Institute of Intelligent Systems
• /
• v.25 no.6
• /
• pp.529-535
• /
• 2015

Biological networks have been handled with the static concept. However, life phenomena in cells occur depending on the cellular state and the external environment, and only a few proteins and their interactions are selectively activated. Therefore, we should adopt the dynamic network concept that the structure of a biological network varies along the flow of time. This concept is effective to analyze the progressive transition of the disease. In this paper, we applied the proposed method to Alzheimer's disease to analyze the structural and functional characteristics of the disease network. Using gene expression data and protein-protein interaction data, we constructed the sub-networks in accordance with the progress of disease (normal, early, middle and late). Based on this, we analyzed structural properties of the network. Furthermore, we found module structures in the network to analyze the functional properties of the sub-networks using the gene ontology analysis (GO). As a result, it was shown that the functional characteristics of the dynamics network is well compatible with the stage of the disease which shows that it can be used to describe important biological events of the disease. Via the proposed approach, it is possible to observe the molecular network change involved in the disease progression which is not generally investigated, and to understand the pathogenesis and progression mechanism of the disease at a molecular level.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
• /
• 2008.11a
• /
• pp.668-669
• /
• 2008

In this paper, we introduce various coarse-grained elastic network modeling (ENM) techniques as a novel computational method for simulating atomic scale dynamics in macromolecules including DNA, RNA, protein, and polymer. In ENM, a system is modeled as a spring network among representative atoms in which each linear elastic spring is well designed to replace both bonded and nonbonded interactions among atoms in the sense of quantum mechanics. Based on this simplified system, a harmonic Hookean potential is defined and used for not only calculating intrinsic vibration modes of a given system, but also predicting its anharmonic conformational change, both of which are strongly related with its functional features. Various nano and bio applications of ENM such as fracture mechanics of nanocomposite and protein dynamics show that ENM is one of promising tools for simulating atomic scale dynamics in a more effective and efficient way comparing to the traditional molecular dynamics simulation.

• BMB Reports
• /
• v.45 no.4
• /
• pp.213-220
• /
• 2012

Viruses have evolved to manipulate the host cell machinery for virus propagation, in part by interfering with the host cellular signaling network. Molecular studies of individual pathways have uncovered many viral host-protein targets; however, it is difficult to predict how viral perturbations will affect the signaling network as a whole. Systems biology approaches rely on multivariate, context-dependent measurements and computational analysis to elucidate how viral infection alters host cell signaling at a network level. Here we describe recent advances in systems analyses of signaling networks in both viral and non-viral biological contexts. These approaches have the potential to uncover virus- mediated changes to host signaling networks, suggest new therapeutic strategies, and assess how cell-to-cell variability affects host responses to infection. We argue that systems approaches will both improve understanding of how individual virus-host protein interactions fit into the progression of viral pathogenesis and help to identify novel therapeutic targets.

• IMMUNE NETWORK
• /
• v.9 no.6
• /
• pp.265-273
• /
• 2009

Foot-and-mouth disease virus (FMDV) is a small single-stranded RNA virus which belongs to the family Picornaviridae, genus Apthovirus. It is a principal cause of FMD which is highly contagious in livestock. In a wild type virus infection, infected animals usually elicit antibodies against structural and non-structural protein of FMDV. A structural protein, VP1, is involved in neutralization of virus particle, and has both B and T cell epitopes. A RNA-dependent RNA polymerase, 3D, is highly conserved among other serotypes and strongly immunogenic, therefore, we selected VP1 and 3D as vaccine targets. VP1 and 3D genes were codon-optimized to enhance protein expression level and cloned into mammalian expression vector. To produce recombinant protein, VP1 and 3D genes were also cloned into pET vector. The VP1 and 3D DNA or proteins were co-immunized into 5 weeks old BALB/C mice. Antigen-specific serum antibody (Ab) responses were detected by Ab ELISA. Cellular immune response against VP1 and 3D was confirmed by ELISpot assay. The results showed that all DNA- and protein-immunized groups induced cellular immune responses, suggesting that both DNA and recombinant protein vaccine administration efficiently induced Ag-specific humoral and cellular immune responses.

• Journal of Microbiology and Biotechnology
• /
• v.8 no.4
• /
• pp.325-332
• /
• 1998

In vitro phosphorylation experiments with a cell extract of Streptomyces coelicolor A3(2) M130 in the presence of ${\gamma}-[^32P]$]ATP revealed the presence of multiple phosphorylated proteins, including the AfsR/AfsK kinases which control the biosynthesis of A-factor, actinorhodin, and undecylprodigiosin. Phosphorylation of AfsR by a cell extract as an AfsK source was significantly inhibited by Ser/Thr protein kinase inhibitors, staurosporine and K-252a, at concentrations giving 50% inhibition ($IC_50$) of $1{\mu}M\;and\;0.1{\mu}M$, respectively. Further in vitro experiments with the cell extracts showed that phosphorylation of multiple proteins was inhibited by various protein kinase inhibitors with different inhibitory profiles. Manganese and calcium ions in the reaction mixture also modulate phosphorylation of multiple proteins. Manganese at 10 mM greatly enhanced the phosphorylation and partially circumvented the inhibition caused by staurosporine and K-252a. A calcium-activated protein kinase(s) was little affected by these inhibitors. Herbimycin and radicicol, which are known as tyrosine kinase inhibitors, did not show any significant inhibition of AfsR phosphorylation. Consistent with the in vitro effect of the kinase inhibitors, they inhibited aerial mycelium formation and pigmented antibiotic production on solid media. On the contrary, when assayed in liquid culture, the amount of actinorhodin produced was increased by staurosporine and K-252a and greatly decreased by manganese. All of these data clearly show that the genus Streptomyces possesses several protein kinases of eukaryotic types which are involved in the regulatory network for morphogenesis and secondary metabolism.

• IMMUNE NETWORK
• /
• v.4 no.1
• /
• pp.23-30
• /
• 2004

Background: A human orthologue of mouse S100A6-binding protein (CacyBP), Siah-1-interacting protein (SIP) had been shown to be a component of novel ubiquitinylation pathway regulating $\beta$-catenin degradation. The role of the protein seems to be important in cell proliferation and cancer evolution but the expression pattern of SIP in actively dividing cancer tissues has not been known. For the elucidation of the role of SIP protein in carcinogenesis, it is essential to produce monoclonal antibodies specific to the protein. Methods: cDNA sequence coding for ORF region of human SIP gene was amplified and cloned into an expression vector to produce His-tag fusion protein. Recombinant SIP protein and monoclonal antibody to the protein were produced. The N-terminal specificity of anti-SIP monoclonal antibody was conformed by immunoblot analysis and enzyme linked immunosorbent assay (ELISA). To study the relation between SIP and colon carcinogenesis, the presence of SIP protein in colon carcinoma tissues was visualized by immunostaining using the monoclonal antibody produced in this study. Results: His-tag-SIP (NSIP) recombinant protein was produced and purified. A monoclonal antibody (Korea patent pending; #2003-45296) to the protein was produced and employed to analyze the expression pattern of SIP in colon carcinoma tissues. Conclusion: The data suggested that anti-SIP monoclonal antibody produced here was valuable for the diagnosis of colon carcinoma and elucidation of the mechanism of colon carcinogenesis.

• IMMUNE NETWORK
• /
• v.2 no.3
• /
• pp.175-181
• /
• 2002

Background: S100A6 is a calcium-binding protein overexpressed in several tumor cell lines including melanoma with high metastatic activity and involved in various cellular processes such as cell division and differentiation. To detect S100A6 protein in patient' samples (ex, blood or tissue), it is essential to produce a monoclonal antibody specific to the protein. Methods: First, cDNA coding for ORF region of human S100A6 gene was amplified and cloned into the expression vector for GST fusion protein. We have produced recombinant S100A6 protein and subsequently, monoclonal antibodies to the protein. The specificity of anti-S100A6 monoclonal antibody was confirmed using recombinant S100A recombinant proteins of other S100A family (GST-S100A1, GST-S100A2 and GST-S100A4) and the cell lysates of several human cell lines. Also, to identify the specific recognition site of the monoclonal antibody, we have performed the immunoblot analysis with serially deleted S100A6 recombinant proteins. Results: GST-S100A6 recombinant protein was induced and purified. And then S100A6 protein excluding GST protein was obtained and monoclonal antibody to the protein was produced. Monoclonal antibody (K02C12-1; patent number, 330311) has no cross-reaction to several other S100 family proteins. It appears that anti-S100A6 monoclonal antibody reacts with the region containing the amino acid sequence from 46 to 61 of S100A6 protein. Conclusion: These data suggest that anti-S100A6 monoclonal antibody produced can be very useful in development of diagnostic system for S100A6 protein.

• Preventive Nutrition and Food Science
• /
• v.17 no.3
• /
• pp.223-227
• /
• 2012

This study examined the effects of corn gluten (CG), wheat gluten (WG), and soybean protein isolate (SPI), as well as their hydrolysates, on weight reduction in rats fed a high-fat diet. Eight-month-old male Sprague-Dawley rats (n=70) were fed a high-fat diet (40% of the calories were fat) for 4 weeks. Rats were then randomly divided into seven groups and were fed isocaloric diets with different protein sources for 8 weeks. The protein sources were casein (control group), intact CG (CG group), CG hydrolysate (CGH group), intact WG (WG group), WG hydrolysate (WGH group), intact SPI (SPI group), and SPI hydrolysate (SPIH group). Body weight gain, adipose tissue weights, lipid profiles in plasma and liver; and hepatic activities of carnitine palmitoyl transferase, fatty acid synthase (FAS), malic enzyme, and glucose-6-phosphate dehydrogenase were assessed. The CGH group showed significant weight reduction compared with the other groups. Epididymal fat pad and plasma triglycerides in the CGH group were the lowest and were significantly different than those in the control group. FAS activity in the CGH group was significantly lower than that in the other groups. In conclusion, the CGH diet of these experimental animals demonstrated a weight-reducing effect by lowering the adipose tissue weight and by affecting the activities of hepatic lipogenic enzymes.

• The KIPS Transactions:PartB
• /
• v.13B no.3 s.106
• /
• pp.323-328
• /
• 2006

Proteins in a cell appear as spots in a two dimensional gel image which is used in protein analysis. The spots from the same protein are in near position when comparing two gel images. Finding out the different proteins between a normal tissue and a cancer one is important information in drug development. Automatic matching of gel images is difficult because they are made from biological experimental processes. This matching problem is known to be NP-hard. Neural networks are usually used to solve such NP-hard problems. Hopfield neural network is selected since it is appropriate to solve the gel matching. An energy function with location and distance parameters is defined. The two spots which make the energy function minimum are matching spots and they came from the same protein. The energy function is designed to reflect the topology of spots by examining not only the given spot but also neighborhood spots.

• BMB Reports
• /
• v.35 no.2
• /
• pp.213-219
• /
• 2002

Malonyl-CoA decarboxylase (E.C.4.1.1.9) catalyzes the conversion of malonyl-CoA to acetyl-CoA. Although the metabolic role of this enzyme has not been fully defined, it has been reported that its deficiency is associated with mild mental retardation, seizures, hypotonia, cadiomyopathy, developmental delay, vomiting, hypoglycemia, metabolic acidosis, and malonic aciduria. Here, we isolated a cDNA clone for malonyl CoA decarboxylase from a rat brain cDNA library, expressed it in E. coli, and characterized its biochemical properties. The full-length cDNA contained a single open-reading frame that encoded 491 amino acid residues with a calculated molecular weight of 54, 762 Da. Its deduced amino acid sequence revealed a 65.6% identity to that from the goose uropigial gland. The sequence of the first 38 amino acids represents a putative mitochondrial targeting sequence, and the last 3 amino acid sequences (SKL) represent peroxisomal targeting ones. The expression of malonyl CoA decarboxylase was observed over a wide range of tissues as a single transcript of 2.0 kb in size. The recombinant protein that was expressed in E. coli was used to characterize the biochemical properties, which showed a typical Michaelis-Menten substrate saturation pattern. The $K_m$ and $V_{max}$ were calculated to be $68\;{\mu}M$ and $42.6\;{\mu}mol/min/mg$, respectively.