• Journal of Dental Rehabilitation and Applied Science
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• v.26 no.3
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• pp.297-309
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• 2010

The objective of the present study was to perform a fracture analysis on fractured implant fixture after use in vivo and make clear the cause & mechanisms of failure. In case of fatigue fracture, the fractured surface represents fatigue striation. Fatigue striation indicate the progression of the crack front under cyclic loading, are characteristic of stage 2 crack growth. The site of crack initiation and stage 1 crack growth were not easily identified in any of the failure, presumably because of the complex microstructural features of the polycrystalline sample. In case of fractured by overload, dimpled or cleavage surface were observed. Using the interpretation of characteristic markings(ratchet mark, fatigue striation, dimple, cleavage et al) in fracture surfaces, failure events containing the crack origin, crack propagation, material deficiency could be understand.

• Journal of Microbiology and Biotechnology
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• v.27 no.11
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• pp.1999-2009
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• 2017

The secretion efficiency of a protein in a Sec-type secretion system is mainly determined by an N-terminal signal peptide and its combination with its cognate protein. Five signal peptides, namely, two synthetic Sec-type and three Bacillus licheniformis alpha-amylase-derived signal peptides, were compared for periplasmic expression of the human growth hormone (hGH) in E. coli. Based on in silico predictions on the signal peptides' cleavage efficiencies and their corresponding mRNA secondary structures, a number of amino acid substitutions and silent mutations were considered in the modified signal sequences. The two synthetic signal peptides, specifically designed for hGH secretion in E. coli, differ in their N-terminal positively charged residues and hydrophobic region lengths. According to the mRNA secondary structure predictions, combinations of the protein and each of the five signal sequences could lead to different outcomes, especially when accessibility of the initiator ATG and ribosome binding sites were considered. In the experimental stage, the two synthetic signal peptides displayed complete processing and resulted in efficient secretion of the mature hGH in periplasmic regions, as was demonstrated by protein analysis. The three alpha-amylase-derived signal peptides, however, were processed partially from their precursors. Therefore, to achieve efficient secretion of a protein in a heterologous system, designing a specific signal peptide by using a combined approach of optimizations of the mRNA secondary structure and the signal peptide H-domain and cleavage site is recommended.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2001.06a
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• pp.27-31
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• 2001

Previous biochemical assays and a structural model indicated that the dimer interface of the Hin recombinase is composed of the two a-helices. To elucidate the structure and function of the helix, amino acids in the N-terminal end of the helix, where the two helices contact most, were randomized, and inversion-incompetent mutants were selected. To investigate why the mutants lost their inversion activities, the DNA binding, hix-pairing, invertasome formation, and DNA cleavage activities were assayed using in vivo and in vitro methodologies. Results indicated that the mutants could be divided into 4 classes based on their DNA binding activity. We proposed that the a-helices might place a DNA binding motif of Hin properly to the minor DNA groove of the recombination site. All the mutants except the non-binders were able to perform hix-pairing and invertasome formation, suggesting that the dimer interface is not involved in the process of hix-pairing or invertasome formation. The inversion-incompetent phenotype of the binders was caused by the inability of mutants to perform the DNA cleavage activity. The less binders exhibited wild-type level of hix-pairing activity because the hix-pairing activity overcomes the DNA binding defect of the less binders. This phenotype of the less binders suggests that the binding domains of Hin could mediate Hin-Hin interaction during hix-pairing..

• KIISE Transactions on Computing Practices
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• v.22 no.1
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• pp.56-60
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• 2016

Peptide identification in tandem mass spectrometry is usually done by searching the spectra against target databases consisting of reference protein sequences. To control false discovery rates for high-confidence peptide identification, spectra are also searched against decoy databases constructed by permuting reference protein sequences. In this case, a peptide of the same sequence could be included in both the target and the decoy databases or multiple entries of a same peptide could exist in the decoy database. These phenomena make the protein identification problem complicated. Thus, it is important to minimize the number of such redundant peptides for accurate protein identification. In this regard, we examined two popular methods for decoy database generation: 'pseudo-shuffling' and 'pseudo-reversing'. We experimented with target databases of varying sizes and investigated the effect of the maximum number of missed cleavage sites allowed in a peptide (MC), which is one of the parameters for target and decoy database generation. In our experiments, the level of redundancy in decoy databases was proportional to the target database size and the value of MC, due to the increase in the number of short peptides (7 to 10 AA). Moreover, 'pseudo-reversing' always generated decoy databases with lower levels of redundancy compared to 'pseudo-shuffling'.

• The Korean Journal of Physiology and Pharmacology
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• v.17 no.3
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• pp.189-195
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• 2013

Amyloid-${\beta}$ peptide ($A{\beta}$), generated by proteolytic cleavage of the amyloid precursor protein (APP), plays a pivotal role in the pathogenesis of Alzheimer's disease (AD). The key step in the generation of $A{\beta}$ is cleavage of APP by beta-site APP-cleaving enzyme 1 (BACE1). Levels of BACE1 are increased in vulnerable regions of the AD brain, but the underlying mechanism is unknown. In the present study, we reported the effects of ferrous ions at subtoxic concentrations on the mRNA levels of BACE1 and a-disintegrin-and-metalloproteinase 10 (ADAM10) in PC12 cells and the cell responses to ferrous ions. The cell survival in PC12 cells significantly decreased with 0 to 0.3 mM $FeCl_2$, with 0.6 mM $FeCl_2$ treatment resulting in significant reductions by about 75%. 4,6-diamidino-2-phenylindole (DAPI) staining showed that the nuclei appeared fragmented in 0.2 and 0.3 mM $FeCl_2$. APP-${\alpha}$-carboxyl terminal fragment (APP-${\alpha}$-CTF) associations with ADAM10 and APP-${\beta}$-CTF with BACE1 were increased. Levels of ADAM10 and BACE1 mRNA increased in response to the concentrations of 0.25 mM, respectively. In addition, p-ERK and p-Bad (S112, S155) expressions were increased, suggesting that APP-CTF formation is related to ADAM10/ BACE1 expression. Levels of Bcl-2 protein were increased, but significant changes were not observed in the expression of Bax. These data suggest that ion-induced enhanced expression of AMDA10/BACE1 could be one of the causes for APP-${\alpha}/{\beta}$-CTF activation.

• Korean Journal of Microbiology
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• v.38 no.3
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• pp.153-161
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• 2002

Sox4, a transcription factor, consists of three functional domains: an HMG-box domain as a DNA binding domain, serine rich region as a transactivation domain and glycine rich region (GRR), an unknown functional domain. Although Sox4 is known to be functionally involved in heart, B-cell and reproductive system development, its physiological function remains to be elucidated. We used pGEX expression system to develop a simple and rapid method for purifying Sox4 protein in suitable forms for biochemical studies of their functions. Unexpectedly, we observed that full-length Sox4 appears to be protease-sensitive during expression and purification in E. coli. To map the protease-sensitive site in Sox4, we generated various constructs with each of functional domains of Sox4 and purified as the GST-Sox4 fusion proteins using glutathione beads. We found that the specific cleavage site for the proteolytic enzyme, which exists in E. coli, is localized within the novel GRR of Sox4. Our study suggest that the GRR of Sox4 may a target for the cellular protease action and this cleavage in the GRR may be involved in regulating physiological function of Sox4. Additionally, our study may provide a useful method for investigating the proteolytic cleavage of the target molecule in E. coli.

• Journal of Microbiology and Biotechnology
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• v.20 no.6
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• pp.1022-1026
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• 2010

The different cleavage patterns of pYBamy59 plasmid isolated from E. coli $DH5{\alpha}$ and B. longum MG1 by the cell extract of B. longum MG1 suggested that the main reason for its low transformation efficiency was related to the restriction modification (R-M) system. To confirm the correlation between the R-M system and transformation efficiency, in vitro methylation and site-directed mutagenesis were performed in pYBamy59. Sequence analysis of pYBamy59 fragments digested by the cell extract of B. longum MG1 revealed that all fragments were generated by restriction of the sequence recognized by SacII endonuclease. When pYBamy59 from E. coli was methylated in vitro by CpG or GpC methyltransferase, it was protected from SacII digestion. Site-directed mutagenesis, which removed SacII sites from pYBamy59, or in vitro methylation of pYBamy59 showed 8- to 15-fold increases in the transformation efficiency over intact pYBamy59. Modification of the SacII-related R-M system in B. longum MG1 and in vitro methylation in pYBamy 59 can improve the transformation efficiency in this strain. The results showed that the R-M system is a factor to limit introduction of exogenous DNA, and in vitro modification is a convenient method to overcome the barrier of the R-M system for transformation.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.62-62
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• 2003

The native form of serpin (serine protease inhibitor) is kinetically trapped in metastable state. Metastability in these proteins is critical to their biological function. Serpins inhibit target proteases by forming a stable covalent complex in which the cleaved reactive site loop of the serpin is inserted into $\beta$-sheet A of the serpin with concomitant translocation of the protease to the opposite of the initial binding site. Despite recent determination of the crystal structures of a Michaelis protease-serpin complex as well as a stable covalent complex, details on the kinetic mechanism remain unsolved. In this study we constructed several $\alpha$$_1$-antitrypsin variants and examined their kinetic mechanism of loop translocation and formation of protease-serpin complex by stopped-flow experiments of fluorescence resonance energy transfer as well as quenched-flow experiment. We report here the relationship of serpin's conformational switch mechanism with Inhibitory activity. There is little direct correlation between loop insertion rate and inhibitory activity. Rather, disrupting a salt bridge between R196 and E354 accelerates loop translocation even though it impairs the inhibitory activity. Moreover, the serpin's reactive site loop is translocated, at least partially, prior to loop cleavage.

• Journal of Microbiology
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• v.42 no.4
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• pp.340-345
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• 2004

To investigate the co-expression and crystallization of a fusion gene between the Bacillus thuringiensis crystal protein and a foreign protein in B. thuringiensis, the expression of the Cry1Ac fused with green fluorescent protein (GFP) genes in a B. thuringiensis $Cry^-B$ strain was examined. The cry1Ac gene was cloned in the B. thuringiensis-E. coli shuttle vector, pHT3101, under the control of the native cry1Ac gene promoter, while the GFP gene was inserted into the XhoI site upstream of the proteolytic cleavage site, in the middle region of the crylAc gene (pProAc-GFP). The B. thuringiensis $Cry^-B$ strain carrying pProAc-GFP (ProAc-GFP/CB) did not produce any inclusion bodies. However, the transformed strain expressed fusion protein forms although the expression level was relatively low. Furthermore, an immu­noblot analysis using GFP and Cry1Ac antibodies showed that the fusion protein was not a single spe­cies, but rather multiple forms. In addition, the N-terminal fragment of Cry1Ac and a non-fused GFP were also found in the B. thuringiensis $Cry^-B$ strain after autolysis. The sporulated cells before autolysis and the spore-crystal mixture after autolysis of ProAc-GFP/CB exhibited insecticidal activities against Plutella xylostella larvae. Accordingly, the current results suggest that a fusion crystal protein produced by the transfomant, ProAc-GFP/CB, can be functionally expressed but easily degraded in B. thuring­iensis.

• BMB Reports
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• v.40 no.4
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• pp.571-576
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• 2007

Three anti-apoptosis genes, Ls-iap2, iap3 and p49 were found in Leucania separata multiple nuclear polyhedrovirus. Amino acid sequence homology of Ls-IAP2 and Ls-IAP3 with Op-IAP2 and Op-IAP3 from Orgyia pseddotsugata MNPV were 20% and 42%, while that of Ls-P49 is 28% with Sl-P49 from Spodoptera littorolis MNPV. Ls-IAP2 contains one baculoviral IAP repeat (BIR) domain followed by a RING domain, while Ls-IAP3 contains two BIRs and a RING. Ls-P49 contains a reactive site loop, predicted cleavage site (KKLD$^{74}{\downarrow}$G) that is different from Sl-P49 (TVID$^{94}{\downarrow}$G). Expressed Ls-iap3 or Ls-p49 under presence of actinomycin D in SF9 cells, DNA ladder assayrevealed that Ls- IAP3 or Ls-P49 could block the apoptosis of SF9 cells induced by actinomycin D. Replication of p35 deficient-mutant Autographa californica MNPV in SF9 cells was also rescued when Ls-iap3 or Ls-p49 was expressed transiently. No anti-apoptotic activity was observed for Ls-IAP2. The results showed that both of Ls-IAP3 and Ls-P49 were functional apoptotic suppressors in SF9 cells.