• BMB Reports
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• 제40권5호
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• pp.749-756
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• 2007

Phosphorylation on serine/threonine or tyrosine residues of target proteins is an essential and significant regulatory mechanism in signal transduction during many cellular and life processes, including spermatogenesis, oogenesis and fertilization. In the present work, we reported the isolation and characterization of mouse testis-specific serine/threonine kinase 5 (Tssk5), which contains four alternatively spliced variants including, Tssk5$\alpha$, Tssk5$\beta$, Tssk5$\gamma$ and Tssk5$\delta$. Moreover, the locus of Tssk5 is on chromosome 14qC3 and the four variants had a similar high expression in the testis and the heart; however, had a low expression in other tissues, except for Tssk5$\alpha$ which also had comparably high expression in the spleen. Each variant of Tssk5 expression began in the testis 16 days after birth. Aside from TSSK5$\alpha$, the other isoforms have an insertion of ten amino acid residues (RLTPSLSAAG) in region VIb (HRD domain) (His-Arg-Asp). Moreover, only TSSK5$\alpha$ exhibited kinase activity and consistently, a further Luciferase Reporter Assay demonstrated that TSSK5$\beta$, TSSK5$\gamma$ and TSSK5$\delta$ cannot be stimulated at the CREB/CRE responsive pathway in comparison to TSSK5$\alpha$. These findings suggest that TSSK5$\beta$, TSSK5$\gamma$, TSSK5$\delta$ may be pseudokinases due to the insertion, which may damage the structure responsible for active kinase activity. Pull-down assay experiments indicated that TSSK5$\beta$, TSSK5 $\gamma$ and TSSK5$\delta$ can directly interact with TSSK5$\alpha$. In summary, these four isoforms with similar expression patterns may be involved in spermatogenesis through a coordinative way in testis.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.325-330
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• 2005

We are generally interested in the analysis, detection and prediction of structural motifs in proteins, in order to infer compatibility of amino acid sequence to structure in proteins of known three-dimensional structure available in the Protein Data Bank. In this context, we are analyzing some of the well-characterized structural motifs in proteins. We have analyzed simple structural motifs, such as, ${\beta}$-turns and ${\gamma}$-turns by evaluating the statistically significant type-dependent amino acid positional preferences in enlarged representative protein datasets and revised the amino acid preferences. In doing so, we identified a number of ‘unexpected’ isolated ${\beta}$-turns with a proline amino acid residue at the (i+2) position. We extended our study to the identification of multiple turns, continuous turns and to peptides that correspond to the combinations of individual ${\beta}$ and ${\gamma}$-turns in proteins and examined the hydrogen-bond interactions likely to stabilize these peptides. This led us to develop a database of structural motifs in proteins (DSMP) that would primarily allow us to make queries based on the various fields in the database for some well-characterized structural motifs, such as, helices, ${\beta}$-strands, turns, ${\beta}$-hairpins, ${\beta}$-${\alpha}$-${\beta}$, ${\psi}$-loops, ${\beta}$-sheets, disulphide bridges. We have recently implemented this information for all entries in the current PDB in a relational database called ODSMP using Oracle9i that is easy to update and maintain and added few additional structural motifs. We have also developed another relational database corresponding to amino acid sequences and their associated secondary structure for representative proteins in the PDB called PSSARD. This database allows flexible queries to be made on the compatibility of amino acid sequences in the PDB to ‘user-defined’ super-secondary structure conformation and vice-versa. Currently, we have extended this database to include nearly 23,000 protein crystal structures available in the PDB. Further, we have analyzed the ‘structural plasticity’ associated with the ${\beta}$-propeller structural motif We have developed a method to automatically detect ${\beta}$-propellers from the PDB codes. We evaluated the accuracy and consistency of predicting ${\beta}$ and ${\gamma}$-turns in proteins using the residue-coupled model. I will discuss results of our work and describe databases and software applications that have been developed.

• Molecules and Cells
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• 제39권6호
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• pp.495-500
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• 2016

We have solved the crystal structure of a predicted fructose-specific enzyme $IIB^{fruc}$ from Escherichia coli ($EcEIIB^{fruc}$) involved in the phosphoenolpyruvate-carbohydrate phosphotransferase system transferring carbohydrates across the cytoplasmic membrane. $EcEIIB^{fruc}$ belongs to a sequence family with more than 5,000 sequence homologues with 25-99% amino-acid sequence identity. It reveals a conventional Rossmann-like ${\alpha}-{\beta}-{\alpha}$ sandwich fold with a unique ${\beta}$-sheet topology. Its C-terminus is longer than its closest relatives and forms an additional ${\beta}$-strand whereas the shorter C-terminus is random coil in the relatives. Interestingly, its core structure is similar to that of enzyme $IIB^{cellobiose}$ from E. coli ($EcIIB^{cel}$) transferring a phosphate moiety. In the active site of the closest $EcEIIB^{fruc}$ homologues, a unique motif CXXGXAHT comprising a P-loop like architecture including a histidine residue is found. The conserved cysteine on this loop may be deprotonated to act as a nucleophile similar to that of $EcIIB^{cel}$. The conserved histidine residue is presumed to bind the negatively charged phosphate. Therefore, we propose that the catalytic mechanism of $EcEIIB^{fruc}$ is similar to that of $EcIIB^{cel}$ transferring phosphoryl moiety to a specific carbohydrate.

• 한국미생물·생명공학회지
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• 제46권3호
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• pp.234-243
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• 2018

남극해에는 산업적으로 유용한 신규 효소촉매를 생산하는 미생물들이 들어 있다. 우리는 로스해(Ross Sea)로부터 분리한 여러 저온성 박테리아를 조사하였으며, 그 중에서 지방분해 능력이 뛰어난 Croceibacter atlanticus (No. 40-F12)를 찾았다. Shotgun 클로닝 방법으로 리파아제 유전자(lipCA)를 찾았으며 Escherichia coli 균에서 LipCA 효소를 발현하였다. Spain Arreo metagenome alpha/beta hydrolase를 기준으로 LipCA 상동구조모델을 만들어서 분석한 결과, ${\alpha}/{\beta}$ hydrolase fold, Gly-X-Ser-X-Gly motif, 그리고 lid 구조를 갖고 있기 때문에 전형적인 리파아제 효소임이 밝혀졌다. Ammonium sulfate 침전법과 겔여과 크로마토그래피를 통해서 세포추출액으로부터 LipCA 효소를 순수하게 분리한 후, 최적 온도, pH, 안정성, 기질특이성, 유기용매 안정성 등의 효소특성을 규명하였다. LipCA를 cross-linked enzyme aggregate (CLEA) 방법으로 고정화하고 효소특성을 조사, 비교하였다. 고정화를 통해 온도, pH, 유기용매에 대한 안정성이 증가하였고 기질특이성의 변화는 관찰되지 않았다. $LipCA^{CLEA}$는 원심분리 방법으로 쉽게 회수되었고 4번의 재사용 후에 40% 이상의 활성이 잔재하였다. 이 논문은 C. atlanticus 리파아제의 발현, 특성규명, Cross-linked Enzyme Aggregated 고정화를 바탕으로 안정성을 높여 산업적 활용 가능성을 제시한 최초의 보고이다.

• Laboraroty Animal Research
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• 제34권4호
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• pp.295-301
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• 2018

Nucleotide-binding domain 1 (Nod1) is a cytosolic receptor that is responsible for the recognition of a bacterial peptidoglycan motif containing meso-diaminophimelic acid. In this study, we sought to identify the role of Nod1 in host defense in vivo against pulmonary infection by multidrug resistant Acinetobacter baumannii. Wildtype (WT) and Nod1-deficient mice were intranasally infected with $3{\times}10^7CFU$ of A. baumannii and sacrificed at 1 and 3 days post-infection (dpi). Bacterial CFUs, cytokines production, histopathology, and mouse ${\beta}$-defensins (mBD) in the lungs of infected mice were evaluated. The production of cytokines in response to A. baumannii was also measured in WT and Nod1-deficient macrophages. The bacterial clearance in the lungs was not affected by Nod1 deficiency. Levels of IL-6, $TNF-{\alpha}$, and $IL-1{\beta}$ in the lung homogenates were comparable at days 1 and 3 between WT and Nod1-deficient mice, except the $TNF-{\alpha}$ level at day 3, which was higher in Nod1-deficient mice. There was no significant difference in lung pathology and expression of mBDs (mBD1, 2, 3, and 4) between WT and Nod1-deficient mice infected with A. baumannii. The production of IL-6, $TNF-{\alpha}$, and NO by macrophages in response to A. baumannii was also comparable in WT and Nod1-deficient mice. Our results indicated that Nod1 does not play an important role in host immune responses against A. baumannii infection.

• 한국자기공명학회논문지
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• 제11권1호
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• pp.10-23
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• 2007

A new disintegrin protein named saxatilin was purified from Korean snake venom (Gloydius saxatilis). Saxatilin is a 73 residue small ploypeptide, which has a primary recognition motif in extracellular matrix, Arg-Gly-Asp (RGD) sequence. Data from inhibition activity assay for the ${\alpha}_v{\beta}_3$ integrin showed that saxatilin showed about 5000-fold higher activity than those of RGD peptides, suggesting that RGD sequence may not be sufficient to induce full cellular function of this site. The solution structures calculated from NMR data were well converged for backbone atoms except RGD loop. The structure revealed that most of tight turns are stabilized by medium range NOE contacts and the RGD motif is located far from the rigid core of the C-terminal domain. The three-dimensional fold and biological function of saxatilin are discussed with those of salmosin, which is a disintegrin protein derived from Agkistrodon halys brevicaudus.

• 한국식품영양과학회지
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• 제42권10호
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• pp.1552-1559
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• 2013

본 연구에서는 미숙과와 성숙과의 복분자 섭취에 의한 쥐복강 대식세포의 염증반응을 조사하였다. 8주간 농도별 미숙과와 성숙과 복분자 식이를 섭취시킨 후 복강대식세포를 분리한 다음, LPS로 염증반응을 유도하여 염증매개 cytokines인 TNF-${\alpha}$, IL-$1{\beta}$, IL-6의 분비와 PGE2의 분비량을 측정하였으며, cDNA microarray 방법으로 유전자 발현을 측정하였다. 미숙과와 성숙과 복분자 섭취는 TNF-${\alpha}$의 생성을 유의적으로 억제하였으나, IL-$1{\beta}$, IL-6는 미숙과 복분자 섭취에 의해서만 감소하였으며 $PGE_2$의 분비에는 영향을 주지 않았다. 본 연구결과, 미숙과와 성숙과 복분자 섭취에 의해 8개의 유전자 발현이 감소된 것으로 확인되었는데, 이중 세포의 면역반응과 관련된 5-LOX, iNOS, IL-11의 발현이 유의적으로 감소되었으며, 만성질환 특히 심혈관계 질환을 유발하는 인자인 tPA, thrombospondin 1, ceruloplasmin과 암의 성장 및 전이와 관련된 VEGF A의 발현을 유의적으로 억제하였다. 한편 혐기성 관련 유전자의 발현을 억제하는 HIF3A의 발현을 유의적으로 증가시켰다. 또한 미숙과 복분자의 섭취만이 CCL8, CXCL14, PLA2의 발현을 감소시키는 것으로 나타났다. 따라서 복분자의 섭취, 특히 미숙과 복분자의 섭취는 항염증 효과를 보일 뿐 아니라 만성염증성 질환 관련 인자의 발현을 유의적으로 감소시키므로 이와 관련된 기능성 식품 개발에 활용될 수 있을 것으로 사료되며, 추후 복분자내 항염증 효능을 갖는 생리활성 성분에 대한 연구가 더 진행되어야 할 것으로 판단된다.

• Molecules and Cells
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• 제25권2호
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• pp.253-257
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• 2008

Acrolein is a highly electrophilic ${\alpha},{\beta}$-unsaturated aldehyde present in a number of environmental sources, especially cigarette smoke. It reacts strongly with the thiol groups of cysteine residues by Michael addition and has been reported to inhibit nuclear $factor-{\kappa}B$ ($NF-{\kappa}B$) activation by lipopolysaccharide (LPS). The mechanism by which it inhibits $NF-{\kappa}B$ is not clear. Toll-like receptors (TLRs) play a key role in sensing microbial components and inducing innate immune responses, and LPS-induced dimerization of TLR4 is required for activation of downstream signaling pathways. Thus, dimerization of TLR4 may be one of the first events involved in activating TLR4-mediated signaling pathways. Stimulation of TLR4 by LPS activates both myeloid differential factor 88 (MyD88)- and TIR domain-containing adapter inducing $IFN{\beta}$ (TRIF)-dependent signaling pathways leading to activation of $NF-{\kappa}B$ and IFN-regulatory factor 3 (IRF3). Acrolein inhibited $NF-{\kappa}B$ and IRF3 activation by LPS, but it did not inhibit $NF-{\kappa}B$ or IRF3 activation by MyD88, inhibitor ${\kappa}B$ kinase $(IKK){\beta}$, TRIF, or TNF-receptor-associated factor family member-associated $NF-{\kappa}B$ activator (TANK)-binding kinase 1 (TBK1). Acrolein inhibited LPS-induced dimerization of TLR4, which resulted in the down-regulation of $NF-{\kappa}B$ and IRF3 activation. These results suggest that activation of TLRs and subsequent immune/inflammatory responses induced by endogenous molecules or chronic infection can be modulated by certain chemicals with a structural motif that enables Michael addition.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2002년도 가을 학술발표논문집 Vol.29 No.2 (3)
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• pp.613-615
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• 2002

단백질의 3차원 공간상의 구조는 단백질 기능을 파악하는데 중요한 정보를 제공하고 있다. 단백질간 구조 비교 방법은 기능적 또는 구조적으로 연관된 단백질 분류 및 단백질 모티프(motif)를 찾는데 유용하게 사용되고 있다. 본 논문에서는 단백질 이차 구조($\alpha$-나선구조와 $\beta$-병풍구조)와 그들 사이의 관계(각도, 거리, 길이, 수소결합)를 기반으로 표현된 두 단백질 구조에서 유사한 부분 구조를 찾는 방법에 대하여 기술한다. 제안된 단백질간 구조 사이의 유사한 부분구조를 찾는 방법은 두 단백질 구조론 이차 구조와 그들 사이의 관계를 이용하여 그래프를 형성한 후, 최대 유사 서브 그래프를 찾는 방법을 이용하여 유사한 부분구조를 찾을 수 있다.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.2-2
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• pp.231.3-232
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• 2003

The biomedical applications of chitosan have been widely researched. FN mediates its biological effects through binding to the hetero-dimeric transmembrane glycoproteins, integrins, which physically couple the cytoskeleton to the ECM. FN binds to the integrin through a consensus site including the Arg-Gly-Asp (RGD) sequence within tenth type III module (Ruoslahti & Pierschbacher 1987). A short sequence Pro-His-Ser-Arg-Asn (PHSRN) has also been identified as a synergistic motif within ninth type III module for binding to ${\alpha}$5${\beta}$1 integrin (Aota et al. 1994). (omitted)