• 대한기계학회논문집A
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• 제30권7호
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• pp.841-848
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• 2006

Many researchers are developing computational prediction methods for protein tertiary structures to get much more information of protein. These methods are very attractive on the aspects of breaking technologies of computer hardware and simulation software. One of the computational methods for the prediction is a fragment assembly method which shows good ab initio predictions at several cases. There are many barriers, however, in conventional fragment assembly methods. Argues on protein energy functions and global optimization to predict the structures are in progress fer example. In this study, a new prediction method for protein structures is proposed. The proposed method mainly consists of two parts. The first one is a fragment assembly which uses very shot fragments of representative proteins and produces a prototype of a given sequence query of amino acids. The second one is a global optimization which folds the prototype and makes the only protein structure. The goodness of the proposed method is shown through numerical experiments.

• 농약과학회지
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• 제2권3호
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• pp.79-84
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• 1998

콩나물중 carbendazim 잔류분을 정량하고 확인할 수 있는 새로운 분석법을 확립하고자 tandem HPLC(UV & FL) 및 APcI를 source로 사용한 LC/MS를 이용하였다. 이를 위해 FL(fluorescence) 검출기를 UV(ultraviolet) 검출기와 나란히 연결하여 UV 검출기의 경우 280 nm 파장을 그리고 FL 검출기의 경우는 excitation파장과 emission파장을 각각 280 mn와 310 nm로 설정하였다. 분석결과 carbendazim의 검출한계는 $0.04{\mu}g/kg$이었다. 콩나물에 carbendazim을 0.5, 1.0 및 2.0 ppm 수준으로 첨가하여 회수율을 측정한 결과 그 평균값은 89.1%이었다. APcI source를 사용한 LC/MS 질량스펙트럼 방법은 콩나물중 carbendazim 잔류분을 최종 확인할 수 있었다. APcI LC/MS 방법은 전자충격에 의한 질량스펙트럼에 비해 훨씬 간단한 fragment를 형성할 뿐 만 아니라 carbendazim의 경우 m/z 133, m/z 159, m/z 191($M^{+}$)의 전형적인 fragment 이온을 형성하므로, 이 방법을 병행한다면 콩나물중 carbendazim 잔류분을 효과적으로 확인할 수 있을 것으로 사료되었다.

• 대한화학회지
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• 제34권3호
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• pp.288-296
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• 1990

GBⅠ-Ⅱ의 antielastic 고리과 LBI의 antitryptic 고리는 $P_1$ 위치의 아미노산 잔기만 차이가 있으며 나머지 모든 아미노산 잔기는 동일하다. Inhibitor의 $P_1$을 키모트립신에 효과적인 특이성이 있다고 알려진 Tyr 잔기로 치환시킨 cyclic nonapeptide와 저해작용에 필수적으로 생각되는 5개의 아미노산 잔기만으로 선정된 cyclic pentapeptide 유도체를 액상법으로 합성하였다. 이들 펩티드 유도체를 3종의 단백질 분해효소에 작용시켜 그 저해활성을 측정한 결과 cyclic nonapeptide는 키모트립신에는 저해작용이 없었고 의외로 에라스타제와 트립신에 저해활성이 있었다. 또한 cyclic pentapeptide는 키모트립신에만 저해활성이 있었다.

• Journal of Microbiology
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• 제45권2호
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• pp.158-167
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• 2007

In this study, we have cloned a novel cDNA encoding for a papain-family cysteine protease from the Uni-ZAP XR cDNA library of the polychaete, Periserrula leucophryna. This gene was expressed in Escherichia coli using the T7 promoter system, and the protease was characterized after partial purification. First, the partial DNA fragment (498 bp) was amplified from the total RNA via RT-PCR using degenerated primers derived from the conserved region of cysteine protease. The full-length cDNA of cysteine protease (PLCP) was prepared via the screening of the Uni-ZAP XR cDNA library using the $^{32}P-labeled$ partial DNA fragment. As a result, the PLCP gene was determined to consist of a 2591 bp nucleotide sequence (CDS: 173-1024 bp) which encodes for a 283-amino acid polypeptide, which is itself composed of an 59-residue signal sequence, a 6-residue propeptide, a 218-residue mature protein, and a long 3'-noncoding region encompassing 1564 bp. The predicted molecular weights of the preproprotein and the mature protein were calculated as 31.8 kDa and 25 kDa, respectively. The results of sequence analysis and alignment revealed a significant degree of sequence similarity with other eukaryotic cysteine proteases, including the conserved catalytic triad of the $Cys^{90},\;His^{226},\;and\;Asn^{250}$ residues which characterize the C1 family of papain-like cysteine protease. The nucleotide and amino acid sequences of the novel gene were deposited into the GenBank database under the accession numbers, AY390282 and AAR27011, respectively. The results of Northern blot analysis revealed the 2.5 kb size of the transcript and ubiquitous expression throughout the entirety of the body, head, gut, and skin, which suggested that the PLCP may be grouped within the cathepsin F-like proteases. The region encoding for the mature form of the protease was then subcloned into the pT7-7 expression vector following PCR amplification using the designed primers, including the initiation and termination codons. The recombinant cysteine proteases were generated in a range of 6.3 % to 12.5 % of the total cell proteins in the E. coli BL21(DE3) strain for 8 transformants. The results of SDS-PAGE and Western blot analysis indicated that a cysteine protease of approximately 25 kDa (mature form) was generated. The optimal pH and temperature of the enzyme were determined to be approximately 9.5 and $35^{\circ}C$, respectively, thereby indicating that the cysteine protease is a member of the alkaline protease group. The evaluation of substrate specificity indicated that the purified protease was more active towards Arg-X or Lys-X and did not efficiently cleave the substrates with non-polar amino acids at the P1 site. The PLCP evidenced fibrinolytic activity on the plasminogen-free fibrin plate test.

• 미생물학회지
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• 제40권3호
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• pp.226-229
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• 2004

염색질을 구성하는 histone 단백질 lysine 잔기에 histone acetylase에 의하여 결합된 acetyl기를 제거하는 histone deacetylase (HDAC)는 진핵세포 생물의 염색질 안정 파 및 유전자 발현에 매우 큰 영향을 미친다. 국내에서 분리된 영지의 HDAC 유전자를 클로닝 하고자 cDNA 및 genomic DNA를 대상으로 PCR을 수행한 결과 470bp의 cDNA유전자와, 585 bp, 589 bp 및 630 bp길이의 genomic DNA유전자 조각을 클로닝 하였다. 이들의 염기서열을 근거로 아미노산 서열을 다른 균류의 HDAC와 비교한 결과 59-72％의 상동성을 보였다.

• 생명과학회지
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• 제8권3호
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• pp.235-240
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• 1998

Matrix metalloproteinases(MMP)는 배발생 및 재조직화 등의 정상적인 생체형성과 관절염, 암전이, 치근막염, 골조송증 등의 질병과정에서 collagen이나 proteoglycan과 같은 세포외기질의 구성성분을 분해하는 아연(zinc)효소군이다. 지금까지 다양한 종에서 mmp의 유전자가 클로닝되고 그 기능이 연구되어 왔지만 아직 어류에서는 연구결과가 보고된 바가 없다. 본 연구에서는 한국의 부산연안에 많은 연골어유 투툽상어(Scylliorhinus toraxzame)로부터 RT-PCR(reverse transcriptase dependent polymerase chain reaction)의방법으로 mmp cDNA의 일부를 클로닝하였다. 이것은 염기서열에서 인간, 쥐 및 닭의 membrane type matrix matalloproteinase-3(mt3-mmps)의 염기서열과 74% 동일성을 보이며, 아미노산서열에서는 90%이상의 동일성을 갖고 있다. 또한 MMP에 나타나는 cysteine switch domain, zinc binding domain(HExGH motif), propeptide cleavage site, and RRKR motif등을 가지고 있다. 이러한 결과로부터 본 연구에서 클로닝된 RT-PCR단편은 두툽상어의 mt3-mmp 또는 이와 유사한 유전자의 cDNA이라 믿어진다.

• Journal of Microbiology and Biotechnology
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• 제9권3호
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• pp.255-259
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• 1999

A 6.9-kb DNA fragment including the minimal Bacillus pasteurii urease gene cluster was subcloned into a high-copy-number plasmid vector, pUC19, and the recombinant B. pasteurii urease was overexpressed in Escherichia coli. The recombinant urease was purified 25.9-fold by using combinations of anion-exchange and gel-filtration chromatography followed by Mono-Q chromatography on a FPLC. N-terminal peptide sequencing analyses revealed that two distinct smaller peptide bands resolved on a 10-18％ gradient SDS-PAGE corresponded to UreA and UreB peptides, respectively. It was also shown that the ureB gene was translated from a GUG codon and the first methionine residue was post-translationally cleaved off. The native molecular weight of the recombinant urease was 176,000 and 2 nickel atoms were present per catalytic unit. pH stability studies of the purified enzyme showed that the recombinant Bacillus pasteurii urease is stable in alkaline pH range, which is similar to the enzyme of the evolutionarily related bacterium, Sporosarcina ureae.

• Journal of Microbiology and Biotechnology
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• 제11권3호
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• pp.534-538
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• 2001

The xynA gene encoding an alikali-tolerant endo-1,4-${\beta}$-xylanase (XYN) was cloned from the alkalophilic Bacillus pumilus A-30. The nucleotide sequence of a 974-bp DNA fragment containing the xynA was determined. An ORF of 684 nucleotides that encoded a protein of 228 amino aicds was detected. Asparagine-71 of XYN from B. Pumilus A-30 showed to be highly conservative in alkaline xylanases of family G/11, upon comparing the amino acid sequences of 17 family G/11 xylanases. Site-directed mutation of N71D of the xynA gene resulted in a decrease of 12.4% in the specific acitivity and a significant decline in the enzyme activity in the alkaline pH range.

• 미생물학회지
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• 제31권4호
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• pp.279-285
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• 1993

p53 유전자의 변화는 인간의 여러 암에서 가장 흔하게 발견되며 종양세포내에서는 이러한 변형된 p53 단백질의 양의 증가가 초래된다. 세포내에 축적된 p53 단백질의 발견은 인간의 암증세를 판단할 유용한 기중이 되기도 한다. 본 연구에서는 이러한 면역조직화학 검사에 쓰일 수 있는 폴리클로날 항체를 만들기 위햐여 사람의 p53 유전자를 glutathione S-transferase 와의 융합 단백질의 형태로서 대장균내에서 발현시켰다. p53 의 아미노산 1-158번을 코딩하고 있는 NeoI fragment 와 아미노산 159-393 번을 코딩하는 NocI-BamHI fragment 를 BamHI linker 를 이용하여 in frame 으로 pGEX-2T 의 BamHI 자리에 삽입하여 재조합 플라스미드 pGTNS 와 pGTNL 을 각각 만들었다. 또 PCR 에 의한 증폭에 의햐여 아미노산 38-145번을 코딩하는 유전자 부위를 증폭하였으며 BamHI 과 PvuII 로 절단하여 pGEX-2T의 BamHI 과 SmaI 자리에 삽입함으로써 pGTBP 를 제조하였다. 이들 재조합 균주들을 IPTG 로 4시간 induction 한 후 세포 추출물로부터 glutathione Sepharose bead 를 이용하여 융합단백질을 분리하였다. Bead 에 결합된 단백질은 10% SDS-polyacrylamide gel 에서 전기영동하였으며, 각각의 분자량은 54 kDa, 53 kDa 와 40 kDa 였다. 이러한 방법으로 1리터 배양으로부터 약 1mg 의 단백질을 정제하였다.

• 한국환경농학회지
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• 제34권3호
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• pp.230-237
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• 2015

BACKGROUND: To identify the sources of inaccuracy in LC/MS/MS methods used in the routine quantitation of small molecules are described and discussed. METHODS AND RESULTS: Various UPLC coupled to triple quadrupole mass spectrometer and time of flight (TOF) were used to identify the potential sources of inaccuracy and inducing the pitfalls of qualification and quntitation during the veterinary drug residue analysis. Some of stable isotope labelled veterinary drugs, which were used as internal standards, presented "cross-talk", regardless of manufactures of mass spectrometer and types of spectrometer. Group of sulfonamides also presented inaccuracy qualification and quantitation due to the multi-residue analytical method with the same fragment ions at the close retention times. CONCLUSION: The phenomena of "cross-talk" occurring between subsequently monitored transition from stable isotope labelled and isotope non-labelled authentic chemical were identified. To prevent errors and achieve more accurate data during the analysis of small molecules by LC/MS/MS SRM method, Followings should be taken care of and kept checking; purity and concentration of stable isotope as an internal standard, prevention of carry-over during the separation in column, minimizing the ion suppression by matrix effect, identification of retention time, precursor ion and product ion, and full knowledge of data processing including smoothing and peak integration.