• 한국멀티미디어학회논문지
• /
• 제15권6호
• /
• pp.794-804
• /
• 2012

단백질 분자에 대해 공간 상의 한 점으로부터의 최소 거리를 계산하거나, 임의의 점에 대한 충돌을 감지하는 등의 proximity query는 분자에 대한 기하학적 연산을 수행하기 위해 매우 중요한 기본 연산이다. Proximity query의 계산 시간 효율성은 분자가 어떤 자료구조로 표현되는가에 따라 크게 달라질 수 있다. 본 논문에서는 GPU 가속을 이용하여 효율적으로 proximity 연산을 수행하기 위한 기법을 제안하고자 한다. 분자에 대응하는 구의 집합에 대해 복셀 맵 (voxel map)과 스피어 트리 (sphere tree) 를 사용한 자료구조를 제안하며 각 자료구조에 대응되는 알고리즘을 제시한다. 또한, 1,000개~15,000개의 원자를 포함하는 분자에 대한 실험을 통해 두 자료구조의 성능이 기존 자료구조에 비해 최소 3배에서 최대 633배 향상되었음을 보인다.

• Archives of Pharmacal Research
• /
• 제26권12호
• /
• pp.1047-1054
• /
• 2003

Molecular chaperones have a crucial role in the folding of nascent polypeptides in endoplasmic reticulum. Some of them are known to be sensitive to the modification by electrophilic metabolites of organic pro-toxicants. In order to identify chaperone proteins sensitive to alkyators, ER extract was subjected to alkylation by 4-acetamido-4 -maleimidyl-stilbene-2,2 -disulfonate (AMS), and subsequent SDS-PAGE analyses. Protein spots, with molecular mass of 160, 100, 57 and 36 kDa, were found to be sensitive to AMS alkylation, and one abundant chaperon protein was identified to be protein disulfide isomerase (PDI) in comparison with the purified PDI. To see the reactivity of PDI with cysteine alkylators, the reduced form ($PDI_{red}$) of PDI was incubated with various alkylators containing Michael acceptor structure for 30 min at $38^{\circ}C$ at pH 6.3, and the remaining activity was determined by the insulin reduction assay. Iodoacetamide or N-ethylmaleimide at 0.1 mM remarkably inactivated $PDI_{red}$ with N-ethylmaleimide being more potent than iodoacetamide. A partial inactivation of $PDI_{oxid}$ was expressed by iodoacetamide, but not N-ethylmaleimide (NEM) at pH 6.3. Of Michael acceptor compounds tested, 1,4-benzoquinone ($IC_{50}, 15 \mu$ M) was the most potent, followed by 4-hydroxy-2-nonenal and 1,4-naphthoquinone. In contrast, 1,2-naphthoquinone, devoid of a remarkable inactivation action, was effective to cause the oxidative conversion of $PDI_{red}$ to $PDI_{oxid}$. Thus, the action of Michael acceptor compounds differed greatly depending on their structure. Based on these, it is proposed that POI, one of chaperone proteins in ER, could be susceptible to endogenous or xenobiotic Michael acceptor compounds in vivo system.

• Bulletin of the Korean Chemical Society
• /
• 제28권5호
• /
• pp.730-736
• /
• 2007

The interaction of a polyoxometal (POM), K6SiW11Co(H2O)O39.10H2O (K6) as a Keggin, with human serum albumin (HSA) was studied by different methods and techniques. Binding studies show two sets of binding sites for interaction of POM to HSA. Binding analysis and isothermal calorimetery revealed that, the first set of binding site has lower number of bound ligand per mole of protein (ν), lower Hill constant (n), higher binding constant (K), more negative entropy (ΔS) and more electrostatic interaction in comparison to the second set of binding site. In addition, differential scanning calorimetery (DSC) and spectrophotometery data showed that, there are two energetic domains. The first domain is less stable (lower Tm and Cp) which corresponds to the tail segment of HSA and another with more stability is related to the head segment of HSA. Polyoxometal also decreases the stability of protein as Tm, secondary and tertiary structure as well as quenching of the fluorescence decrease. On other hand, perturbations in tertiary structure are more than secondary structure.

• 생명과학회지
• /
• 제28권10호
• /
• pp.1140-1146
• /
• 2018

이중탈인산화효소(DUSP)는 성장인자활성 단백질키나제(MAPK)를 조절해서 세포성장과 분화에 관여하며 암, 당뇨병, 면역질환, 신경질환의 신약개발표적이다. DUSP 단백질군에 속하는 DUSP19는c-Jun N-말단 키나제(JNK)를 조절하며 골관절염의 질환화과정에 관여한다. 우리는 야생형 DUSP19 에 비하여 상당히 활성이 증가된 cavity 형성 돌연변이인 DUSP19-L75A의 결정구조를 규명하였다. 결정구조는 Leu75의 곁가지가 없어진 결과로 cavity가 잘 형성되어 있는 것을 보여주며, 활성부위에 결합한 황이온이 회전된 형태로 존재하는 것을 보여준다. Cavity 형성에도 불구하고 cavity를 둘러싸고 있는 잔기들은 그다지 재조정되지 않은 것으로 나타나며 그 대신에 멀리 떨어진 트립토판 잔기가 소수성결합을 강화하고 있는 것으로 나타나서 L75A 돌연변이의 접힘은 cavity 부위의 재조정이 아니라 글로벌 접힘 에너지 최소화 기작에 의해 안정화 되었음을 발견할 수 있었다. 회전된 활성화부위 황이온의 구조는 인산화티로신 잔기와 유사함이 발견되어 L75A 돌연변이가 최적의 활성화형태를 유도했다는 것을 알 수 있었다. 내부 cavity에 의한 활성증가현상과 이에 대한 구조적 정보는 DUSP19의 알로스테릭 조절과 치료제 개발에 정보를 제공한다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제15권3호
• /
• pp.421-426
• /
• 2002

The pyruvate dehydrogenase complex (PDC), a member of $\alpha$-keto acid dehydrogenase complex, catalyzes the oxidative decarboxylation of pyruvate with the formation of $CO_2$, acetyl-CoA, NADH, and $H^+$. This complex contains multiple copies of three catalytic components including pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Two regulatory components (E1-kinase and phospho-E1 phosphatase) and functionally less-understood protein (protein X, E3BP) are also involved in the formation of the complex. In this study, we have partially cloned the gene for E3BP in human. Nine putative clones were isolated by human genomic library screening with 1.35 kb fragment of E3BP cDNA as a probe. For investigation of cloned genes, Southern blot analysis and the construction of the restriction map were performed. One of the isolated clones, E3BP741, has a 3 kb-SacI fragment, which contains 200 bp region matched with E3BP cDNA sequences. The matched DNA sequence encodes the carboxyl-terminal portion of lipoyl-bearing domain and hinge region of human E3BP. Differences between yeast E3BP and mammalian E3BP coupled with the remarkable similarity between mammalian E2 and mammalian E3BP were confirmed from the comparison of the nucleotide sequence and the deduced amino acid sequence in the cloned E3BP. Cloning of human E3BP gene and analysis of the gene structure will facilitate the understanding of the role(s) of E3BP in mammalian PDC.

• 한국식물병리학회:학술대회논문집
• /
• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
• /
• pp.113.1-113
• /
• 2003

A potexvirus, Hosta virus X (HVX-Kr), causing mosaic and mottle symptoms was isolated from hosta plants (Hosta spp.), and its entire genome RNA sequence was determined. in Korea using cDNA library and RACE methods. The genome of HVX encodes five open reading frames coding for viral replicase, triple gene block (TGB), and viral coat protein (CP) from the 5'to 3' ends, which is a typical genome structure of potexviruses. The 3-terminal region of the virus includes the TGBI (26 kDa), TGB2 (13 kDa), TGB3 (8 kDa), and 23 kDa coat protein (CP) and the 3-nontranslated region (NTR). The CP gene of the type isolate of HVX (HVX-U) was amplified by RT-PCR and its nucleotide sequence was determined. The CPs of HVX-Kr and HVX-U had 100％ and 98.9％ identical amino acids and nucleotides, respectively. Most of the regions of the genome HVX had over 50％ nucleotide identical to other sequenced potexviruses. This is the first report of complete genome sequence information of HVX and molecular evidence supporting the virus as a distinct species of the genus Potexvirus.

• Parasites, Hosts and Diseases
• /
• 제51권3호
• /
• pp.327-334
• /
• 2013

Vaccination is considered a promising alternative for controlling tick infestations. Haemaphysalis longicornis midgut proteins separated by SDS-PAGE and transferred to polyvinylidene difluoride (PVDF) membrane were screened for protective value against bites. The western blot demonstrated the immunogenicity of 92 kDa protein (P92). The analysis of the P92 amino acid sequence by LC-MS/MS indicated that it was a H. longicornis paramyosin (Hl-Pmy). The full lenghth cDNA of Hl-Pmy was obtained by rapid amplification of cDNA ends (RACE) which consisted of 2,783 bp with a 161 bp 3' untranslated region. Sequence alignment of tick paramyosin (Pmy) showed that Hl-Pmy shared a high level of conservation among ticks. Comparison with the protective epitope sequence of other invertebrate Pmy, it was calculated that the protective epitope of Hl-Pmy was a peptide (LEEAEGSSETVVEMNKKRDTE) named LEE, which was close to the N-terminal of Hl-Pmy protein. The secondary structure analysis suggested that LEE had non-helical segments within an ${\alpha}$-helical structure. These results provide the basis for developing a vaccine against biting H. longicornis ticks.

• Journal of Plant Biotechnology
• /
• 제4권1호
• /
• pp.7-15
• /
• 2002

Eight cDNAs corresponding to fruit-specific genes were isolated from ripened melon through differential screening. Sequence comparison indicated that six of these cDNAs encoded proteins were previously characterized into aminocyclopropane-1-carboxylate (ACC) oxidase, abscisic acid, stress and ripening inducible (ASR) gene, RINC-H2 zinc finger protein, pyruvate decarboxylase, or polyubiquitin. RFS2 and RFS5 were the same clone encoding polyubiquitin. The other cDNAs showed no significant homology with known protein sequences. The ASR homologue (Asr1) gene was further characterized on the cDNA and genomic structure. The deduced amino acid sequence had similar characteristics to other plant ASR. The Asr1 genomic DNA consisted of 2 exons and 1 intron, which is similar to the structure of other plants ASR genes. The promoter region of the Asr1 gene contained several putative functional cis-elements such as an abscisic acid responsive element (ABRE), an ethylene responsive element (ERE), a C-box or DPBf-1 and 2, Myb binding sites, a low temperature responsive element (LTRE) and a metal responsive element (MRE). The findings imply that these elements may play important roles in the response to plant hormones and environmental stresses in the process of fruit development. The results of this study suggest that the expressions of fruit specific and ripening-related cDNAs are closely associated with the stress response.

• Journal of Microbiology and Biotechnology
• /
• 제17권8호
• /
• pp.1249-1253
• /
• 2007

A hyperthermostable endoglucanase from Pyrococcus horikoshii with the capability of hydrolyzing crystalline cellulose was analyzed. A protein engineering study was carried out to obtain a reduced-size mutant. Five amino acid residues at both the N- and C-terminus were found to be removable without any loss of activity or thermal stability. Site-directed mutagenesis was also performed on R102, N200, E201, H297, Y299, E342, and W377, residues possibly involved in the active center or in the recognition and binding of a cellulose substrate. The activity of the resulting mutants was considerably decreased, confirming that the mutated residues were all important for activity. A reduced-size enzyme, as active as the wild-type endoglucanase, was successfully obtained, plus the residues critical for its activity and specificity were confirmed. Consequently, an engineered enzyme with a reduced size was obtained, and the amino acids essential for activity were confirmed by site-directed mutagenesis and comparison with a known three-dimensional structure.

• Bulletin of the Korean Chemical Society
• /
• 제34권9호
• /
• pp.2640-2644
• /
• 2013

The all-hydrocarbon i,i+4 stapling system using an oct-4-enyl crosslink is one of the most widely employed chemical tools to stabilize an ${\alpha}$-helical conformation of a short peptide. This crosslinking system has greatly extended our ability to modulate intracellular protein-macromolecule interactions. The helix-inducing property of the i,i+4 staple has shown to be highly dependent on the length and the stereochemistry of the oct-4-enyl crosslink. Here we show that changing the double bond position within the i,i+4 staple has a considerable impact not only on the formation of the crosslink but also on ${\alpha}$-helix induction. The data further increases the understanding of the structure-activity relationships of this valuable chemical tool.