• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1999년도 학술발표회 진행표 및 논문초록
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• pp.17-17
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• 1999

Almost half of the entire set of predicted genomic products from M ethanococcus jannaschii are classified as functionally unknown hypothetical proteins. We present a structure-based identification of the biochemical function of a protein with hitherto-unknown function from a M. jannaschii gene, Mj0226.(omitted)

• 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.123.2-123.2
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• 2003

The cellular mechanisms by which excess exposure to the excitatory neurotransmitter glutamate can produce neuronal injury are unknown. In this study, we found that glutamate induced cell death at IC (50) of 100 microM on the cultured human SH-SY5Y neuroblastoma cells. It has been hypothesized that glutamate excitotoxicity is related with the elevation of calcium (Ca) levels. To determine the dependence of glutamate neurotoxicity on Ca environment, extracellular (EDTA) and intracellular (BAPTA/AM) chelator were used. (omitted)

• 한국응용곤충학회지
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• 제50권2호
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• pp.131-139
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• 2011

본 연구는 음파 처리에 따른 아메리카잎굴파리(Liriomyza trifolii)의 생리 변화를 발육 시기별로 분석하였다. 유충의 섭식량은 섭식을 통해 형성된 잎 내부 갱도의 길이로 분석했다. 이때 5,000 Hz (95 dB)의 음파 처리는 섭식 행동을 크게 둔화시켰다. 이러한 스트레스 음파는 또한 용발육에 영향을 주어 315 - 5,000 Hz 음파 범위에서 발육 지연 효과를 나타냈고, 1,000 - 5,000 Hz 음파 범위에서 우화를 억제하였다. 스트레스 음파는 암컷의 산란 행동을 억제시켰으나 성충의 주광성 행동에는 영향을 주지 않았다. 스트레스 음파(5,000 Hz, 95 dB)를 받은 용은 이차원 전기영동 분석 결과 단백질 발현 양상에서 무처리구와 뚜렷한 차이를 보였다. 특정 단백질에 대한 MALDI-TOF 분석 결과는 trafficking protein particle complex I, triosephosphate isomerase, hypothetical protein TcasGA2_TC013388, polycystin-2, paraneoplastic neuronal antigen MA1 및 tropomyosin I (isoform M)의 단백질들이 무처리구에서 발견되고, 음파 처리구에서는 소멸되었다. 반면에 DOCK9, cytoskeletal keratin II 및 $F_0F_1$-ATP synthase beta subunit은 스트레스 음파 처리에 따라 새롭게 나타나는 단백질로 판명되었다. 이러한 스트레스 음파는 아메리카잎굴파리의 살충제에 대한 감수성을 크게 증가시켰다. 이상의 결과는 아메리카잎굴파리의 생리 과정을 교란하는 스트레스 음파가 작용한다는 것을 제시하고 있다. 또한 본 연구는 이러한 스트레스 음파를 이용하여 아메리카잎굴파리에 대한 새로운 물리적 해충 방제 기술 개발 가능성을 제시하고 있다.

• Genomics & Informatics
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• 제14권3호
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• pp.125-135
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• 2016

Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP). This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. After extensive analysis of all the 340 HPs, we found that 104 HPs are showing characteristic similarities with the proteins with known functions. Thus, on the basis of such similarities, we assigned probable functions to 104 HPs with high confidence and precision. All the predicted HPs contain representative members of diverse functional classes of proteins such as enzymes, transporters, binding proteins, regulatory proteins, proteins involved in cellular processes and other proteins with miscellaneous functions. Therefore, we classified 104 HPs into aforementioned functional groups. During the virulence factors analysis of the HPs, we found 11 HPs are showing significant virulence. The identification of virulence proteins with the help their predicted functions may pave the way for drug target estimation and development of effective drug to counter the activity of that protein.

• Genomics & Informatics
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• 제16권4호
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• pp.26.1-26.12
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• 2018

Shigella spp. constitutes some of the key pathogens responsible for the global burden of diarrhoeal disease. With over 164 million reported cases per annum, shigellosis accounts for 1.1 million deaths each year. Majority of these cases occur among the children of the developing nations and the emergence of multi-drug resistance Shigella strains in clinical isolates demands the development of better/new drugs against this pathogen. The genome of Shigella flexneri was extensively analyzed and found 4,362 proteins among which the functions of 674 proteins, termed as hypothetical proteins (HPs) had not been previously elucidated. Amino acid sequences of all these 674 HPs were studied and the functions of a total of 39 HPs have been assigned with high level of confidence. Here we have utilized a combination of the latest versions of databases to assign the precise function of HPs for which no experimental information is available. These HPs were found to belong to various classes of proteins such as enzymes, binding proteins, signal transducers, lipoprotein, transporters, virulence and other proteins. Evaluation of the performance of the various computational tools conducted using receiver operating characteristic curve analysis and a resoundingly high average accuracy of 93.6% were obtained. Our comprehensive analysis will help to gain greater understanding for the development of many novel potential therapeutic interventions to defeat Shigella infection.

• BMB Reports
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• 제42권6호
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• pp.387-392
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• 2009

Here, we report the first biochemical and structural characterization of the hypothetical protein HP0902 from Helicobacter pylori, in terms of structural genomics. Gel-permeation chromatography and dynamic light scattering indicated that the protein behaves as a dimer in solution. Circular dichroism spectroscopy showed that HP0902 primarily adopts a $\beta$-structure and the protein was highly thermostable with a denaturing temperature higher than $70^{\circ}C$. Finally, the backbone NMR assignments were obtained on the [$^{13}C,^{15}N$]HP0902 and the secondary structure was determined using the chemical shift data. Additionally, the local flexibility was assessed via a heteronuclear $^1H-^{15}N$ steady state NOE experiment. The results revealed that HP0902 would adopt a compactly folded, all-$\beta$ topology with 11 $\beta$-strands. All of the results clearly support the notion that HP0902 belongs to the cupin superfamily of proteins.

• Parasites, Hosts and Diseases
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• 제54권4호
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• pp.461-469
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• 2016

Giardia lamblia is a protozoan that causes diarrheal diseases in humans. Cytoskeletal structures of Giardia trophozoites must be finely reorganized during cell division. To identify Giardia proteins which interact with microtubules (MTs), Giardia lysates were incubated with in vitro-polymerized MTs and then precipitated by ultracentifugation. A hypothetical protein (GL50803_8405) was identified in the precipitated fraction with polymerized MTs and was named GlMBP1 (G. lamblia microtubule-binding protein 1). Interaction of GlMBP1 with MTs was confirmed by MT binding assays using recombinant GlMBP1 (rGlMBP1). In vivo expression of GlMBP1 was shown by a real-time PCR and western blot analysis using anti-rGlMBP1 antibodies. Transgenic G. lamblia trophozoites were constructed by integrating a chimeric gene encoding hemagglutinin (HA)-tagged GlMBP1 into a Giardia chromosome. Immunofluorescence assays of this transgenic G. lamblia, using anti-HA antibodies, revealed that GlMBP1 mainly localized at the basal bodies, axonemes, and median bodies of G. lamblia trophozoites. This result indicates that GlMBP1 is a component of the G. lamblia cytoskeleton.

• Bulletin of the Korean Chemical Society
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• 제31권12호
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• pp.3521-3524
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• 2010

MTH1880 is a hypothetical protein derived from Methanobacterium thermoautotrophicum, thermophilic methanogen. The solution structure determined by NMR spectroscopy showed that it has a novel $\alpha+\beta$-fold with a highly acidic ligand binding pocket. Since MTH1880 maintains its ultra-stable structural characteristics at both high temperature and pressure, it has been considered as an excellent model for studying protein folding. To initiate the structural and folding study of MTH1880 in proving its unusual stability, we performed the site directed mutagenesis and biochemical analysis of MTH1880 mutants. Data from circular dichroism and NMR spectroscopy suggest that the point mutations perturbed the structural stability of protein even though the secondary structure is retained. This study will provide the useful information in understanding the role of participating residues during folding-unfolding process and our result will be used in designing further folding experiments for hyper-thermopile proteins like MTH1880.

• Journal of Microbiology and Biotechnology
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• 제27권9호
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• pp.1692-1700
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• 2017

Ralstonia solanacearum causes bacterial wilt in a wide variety of host plant species and produces a melanin-like blackish-brown pigment in stationary phase when grown in minimal medium supplemented with tyrosine. To study melanin production regulation in R. solanacearum, five mutants exhibiting overproduction of melanin-like pigments were selected from a transposon (Tn) insertion mutant library of R. solanacearum SL341. Most of the mutants, except one (SL341T), were not complemented by the original gene or overproduced melanins. SL341T showed Tn insertion in a gene containing a conserved domain of eukaryotic transcription factor. The gene was annotated as a hypothetical protein, given its weak similarity to any known proteins. Upon complementation with its original gene, the mutant strains reverted to their wild-type phenotype. SL341T produced 3-folds more melanin at 72 h post-incubation compared with wild-type SL341 when grown in minimal medium supplemented with tyrosine. The chemical analysis of SL341T cultural filtrate revealed the accumulation of a higher amount of homogentisate, a major precursor of pyomelanin, and a lower amount of dihydroxyphenylalanine, an intermediate of eumelanin, compared with SL341. The expression study showed a relatively higher expression of hppD (encoding hydroxyphenylpyruvate dioxygenase) and lower expression of hmgA (encoding homogentisate dioxygenase) and nagL (encoding maleylacetoacetate isomerase) in SL341T than in SL341. SL341 showed a significantly higher expression of tyrosinase gene compared with SL341T at 48 h post-incubation. These results indicated that R. solanacearum produced both pyomelanin and eumelanin, and the novel hypothetical protein is involved in the negative regulation of melanin production.

• 한국환경농학회지
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• 제22권3호
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• pp.203-209
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• 2003

항진균 활성균주를 선발하는 과정에서 DM3 균주를 대천 바닷가에서 수집된 진흙 시료로부터 분리하였으며 API 50CHB kit를 이용하여 동정한 결과 Bacillus licheniformis로 동정되었다. 이 균주는 12종의 식물병원성 진균에 대해 항균활성을 나타내었다. 감마선($^{60}Co$)을 조사하여 항진균 활성 결핍 돌연변이체(mDMB)를 유도한 후, 이차원전기영동으로 단백질을 분석한 결과 DM3와 mDM3에만 존재하는 각각 4종과 3종의 단 단백질을 확인할 수 있었다. 2-DE 결과 B. licheniformis DM3에서 spot 1은 serine hydroxymethyltransferase(45.0kDa), spot 2는 hypothetical protein(40.7 kDa), spot 3는 NifU protein homolog(15.4 kDa), 그리고 spot 4는 resolvase(12.5 kDa)와 상동성을 지닌 단백질로 동정되었고 B. licheniformis mDM3에서만 발현된 spot 5는 lysozyme(18.1 kDa)과 spot 6, 7은 alkyl hydroperoxide reductase(15.6 kDa)으로 동정되었다. B. licheniformis DM3에서 이들 단백질들의 항진균 활성 관련 여부를 규명하기 위해서 더 연구가 진행되어야 할 것으로 사료된다.