• 한국자기공명학회논문지
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• 제16권1호
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• pp.22-33
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• 2012

Tid1, belonging to the Hsp40/DnaJ family of proteins, functions as a cochaperone of cytosolic and mitochondrial Hsp70 proteins. In particular, the N-terminal J-domain of Tid1 (Tid1-JD) constitutes the major binding sites for proteinprotein interactions with client proteins, including p53, as well as its partner chaperone, Hsp70. In the present study, soluble, recombinant protein of Tid1-JD could be obtained by using the pCold vector system, and backbone NMR assignments were completed using the isotope $[^{13}C/^{15}N]$-enriched protein. Far-UV CD result implied that Tid1-JD is an ${\alpha}$-helical protein and the secondary structure determined using chemical shift data sets indentified four ${\alpha}$-helices with a loop region containing the HPD (conserved tripeptide of His, Pro and Asp) motif. Additionally, NMR spectra under different conditions implied that the HPD motif, which is a critical region for protein-protein interactions of Tid1-JD, would possess dynamic properties.

• 제어로봇시스템학회논문지
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• 제12권10호
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• pp.1044-1049
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• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.

• Journal of Microbiology and Biotechnology
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• 제16권9호
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• pp.1477-1480
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• 2006

The 63-amino-acid-encoding afsR2 is a global antibiotics-stimulating regulatory gene identified from the chromosome of Streptomyces lividans. To dissect a putative functional domain in afsR2, several afsR2-derivative deletion constructs were generated and screened for the loss of actinorhodin-stimulating capability. The afsR2-derivative construct missing a 50-bp C-terminal region significantly lost its actinorhodin-stimulating capability in S. lividans. In addition, site-directed mutagenesis on amino acid positions of #57-#61 in a 50-bp C-terminal region, some of which are conserved among known Sigma 70 family proteins, significantly changed the AfsR2's activity. These results imply that the C-terminal region of AfsR2 is functionally important for antibiotics-stimulating capability and the regulatory mechanism might be somehow related to the sigma-like domain present in the C-terminal of AfsR2.

• BMB Reports
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• 제41권12호
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• pp.881-885
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• 2008

Protein phosphatase 1 consists of a secondary structure arrangement, conserved in the serine/threonine protein phosphatase gene family, flanked by nonconserved N-terminal and C-terminal domains. The deletion mutant of PP1 with the 8 nonconserved N-terminal residues removed was designated PP1-(9-330). PP1-(9-330) had a higher activity and affinity than PP1 when assayed against four different substrates, and it also demonstrated a 6-fold higher sensitivity to the inhibitor okadaic acid. This suggested that the N-terminal domain suppresed the activity of PP1 and interfered with its inhibition by okadaic acid. The ANS fluorescence intensity of PP1-(9-330) was greater than that of PP1, which implies that the hydrophobic groove running from active site in the truncated PP1 was more hydrophobic than in PP1. Our findings provide evidence that the nonconserved N-terminus of PP1 functions as an important regulatory domain that influences the active site and its pertinent properties.

• 한국동물생명공학회지
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• 제36권4호
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• pp.314-322
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• 2021

Paired box protein, PAX7, is a key molecule for the specification, maintenance and skeletal muscle regeneration of muscle satellite cells. In this study, we identified and characterized the cDNA and amino acid sequences of PAX7 from black sea bream (Acanthopagrus schlegelii) via molecular cloning and sequence analysis. A. schlegelii PAX7 cDNA was comprised of 1,524 bp encoding 507 amino acids and multiple sequence alignment analysis of the translated amino acids showed that it contained three domains including paired DNA-binding domain, homeobox domain and OAR domain which were well conserved across various animal species investigated. Pairwise Sequence Alignment indicated that A. schlegelii PAX7 had the same amino acid sequences with that of yellowfin seabream (A. latus) and 99.8% identity and similarity with that of gilt-head bream (Sparus aurata). Molecular phylogenetic analysis confirmed that A. schlegelii PAX7 formed a monophyletic group with those of teleost and most closely related with those of the fish that belong to Sparidae family including A. latus and S. aurata. In the investigation of its tissue specific mRNA expression, the expression was specifically identified in skeletal muscle tissue and a weak expression was also shown in gonad tissue. The cultured cells derived from skeletal muscle tissues expressed PAX7 mRNA at early passage but the expression was not observed after several times of subculture.

• 한국자원식물학회지
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• 제24권5호
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• pp.584-590
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• 2011

의성종 마늘의 유묘로부터 상처(wound)에 특이적으로 발현되는 cytochrome P450 유전자군의 하나인 P450-Esg cDNA를 탐색하였다. P450-Esg는 1,419 bp의 open reading frame(ORF)을 가지고 473개의 아미노산을 가진 polypeptide를 코딩하는 것으로 나타났다. 국내와 몽골로부터 수집한 12개의 재배종으로 부터 P450-Esg 유사 유전자의 염기서열을 비교한 결과 시작코돈(ATG)에서 472~510 bp 및 1,210~1,240 bp 부위의 염기에서 재배종간에 차이를 보이는 염기서열을 다수 확인하였다. cDNA 1,210~1,240 bp의 부위는 P450 유전자에서 공통적으로 알려진 heme binding domain으로, 각 지역에서 수집된 재배종은 염기서열뿐만 아니라 아미노산 서열에 있어서도 특이적인 변이를 보였다. cDNA 472~510 bp 부위에서 코딩하는 13개 아미노산의 서열은 12개 재배종에서 모두 동일하였으나, 13개 아미노산 중 7개에서 재배종 마다 각각 다른 DNA 염기로 코딩하는 단일 염기다형성(single nucleotide polymorphism)을 보이는 서열을 확인하였다. 이 결과는 다양하게 존재하는 국내외 마늘 재배종을 구분하는 marker로 사용될 것이며, 외국산 마늘에 대한 유전적 우선권을 확보하는 수단으로 사용될 것이다.

• Journal of Applied Biological Chemistry
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• 제50권3호
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• pp.109-114
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• 2007

Sar1p is a ras-related GTP-binding protein that functions in intracellular protein transport between the endoplasmic reticulum (ER) and the Golgi complex. The effector domain of Ras family proteins is highly conserved and this domain is functionally interchangeable in plant, yeast and mammalian Sar1. Using a recombinant Brassica sar1 protein (Bsar1p) harboring point mutations in its effector domain, we here investigated the ability of Sar1p to bind and hydrolyze GTP and to interact with the two sar1-specific regulators, GTPase activating protein (GAP) and guanine exchange factor (GEF). The T51A and T55A mutations impaired Bsar1p intrinsic GTP-binding and GDP-dissociation activity. In contrast, mutations in the switch domain of Bsar1 did not affect its intrinsic GTPase activity. Moreover, the P50A, P54A, and S56A mutations affected the interaction between Bsar1p and GAP. P54A mutant protein did not interact with two regulating proteins, GEF and GAP, even though the mutation didn't affect the intrinsic GTP-binding, nucleotide exchange or GTPase activity of Bsar1p.

• 지구물리와물리탐사
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• 제7권1호
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• pp.45-50
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• 2004

This paper describes a method of detecting formation boundaries, and permeable fractures, from frequency-domain Stoneley wave logs. Field data sets were collected between the depths of 330 and 360 m in well EE-4 in the Higashi-Hachimantai geothermal field, using a monopole acoustic logging tool with a source central frequency of 15 kHz. Stoneley wave amplitude spectra were calculated by performing a fast Fourier transform on the waveforms, and the spectra were then collected into a frequency-depth distribution of Stoneley wave amplitudes. The frequency-domain Stoneley wave log shows four main characteristic peaks at frequencies 6.5, 8.8, 12, and 13.3 kHz. The magnitudes of the Stoneley wave at these four frequencies are affected by formation properties. The Stoneley wave at higher frequencies (12 and 13.3 kHz) has higher amplitudes in hard formations than in soft formations, while the wave at lower frequencies (6.5 and 8.8 kHz) has higher amplitudes in soft formations than in hard formations. The correlation of the frequency-domain Stoneley wave log with the logs of lithology, degree of welding, and P-wave velocity is excellent, with all of them showing similar discontinuities at the depths of formation boundaries. It is obvious from these facts that the frequency-domain Stoneley wave log provides useful clues for detecting formation boundaries. The frequency-domain Stoneley wave logs are also applicable to the detection of a single permeable fracture. The procedure uses the Stoneley wave spectral amplitude logs at the four frequencies, and weighting functions. The optimally weighted sum of the four Stoneley wave spectral amplitudes becomes almost constant at all depths, except at the depth of a permeable fracture. The assumptions that underlie this procedure are that the energy of the Stoneley wave is conserved in continuous media, but that attenuation of the Stoneley wave may occur at a permeable fracture. This attenuation may take place at anyone of the four characteristic Stoneley wave frequencies. We think our multispectral approach is the only reliable method for the detection of permeable fractures.

• BMB Reports
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• 제40권1호
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• pp.44-52
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• 2007

Kinesins, as a kind of microtubule-based motor proteins, have a conserved microtubule-binding site in their motor domain. Here we report that two homologous kinesins in Arabidopsis thaliana, KatB and KatC, contain a second microtubule-binding site in their tail domains. The prokaryotic-expressed N-terminal tail domain of the KatC heavy chain can bind to microtubules in an ATP-insensitive manner. To identify the precise region responsible for the binding, a serious of truncated KatC cDNAs encoding KatC N-terminal regions in different lengths, KatC1-128, KatC1-86, KatC1-73 and KatC1-63, fused to Histidine-tags, were expressed in E. coli and affinity-purified. Microtubule cosedimentation assays show that the site at amino acid residues 74-86 in KatC is important for microtubule-binding. By similarity, we obtained three different lengths of KatB N-terminal regions, KatB1-384, KatB1-77, and KatB1-63, and analyzed their microtubule-binding ability. Cosedimentation assays indicate that the KatB tail domain can also bind to microtubules at the same site as and in a similar manner to KatC. Fluorescence microscopic observations show that the microtubule-binding site at the tail domain of KatB or KatC can induce microtubules bundling only when the stalk domain is present. Through pull-down assays, we show that KatB1-385 and KatC1-394 are able to interact specifically with themselves and with each other in vitro. These findings are significant for identifying a previously uncharacterized microtubule-binding site in the two kinesin proteins, KatB and KatC, and the functional relations between them.

• International Journal of Industrial Entomology and Biomaterials
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• 제18권1호
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• pp.28-32
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• 2009

We describe here the cloning and characterization of a cDNA encoding the glutathione S-transferase (GST) from the bumblebee Bombus ignitus. The Delta-class B. ignitus GST (BiGSTD) gene spans 1668 bp and consists of four introns and five exons that encode 216 amino acid residues with a calculated molecular weight of approximately 24561 Da and a pI of 8.03. The N-terminal domain of BiGSTD has a conserved Ser residue, as well as conserved Lys, Pro, Glu, Ser and Tyr residues that are involved in the GSH-binding site of GST. The BiGSTD showed 60% protein sequence identity to the Bombyx mori GSTT1, 58% to Musca domestica GST, 57% to Drosophila melanogaster GST, and 55% to Anopheles gambiae GST1. BiGSTD was close to the insect-specific Delta class of GSTs in a phylogenetic tree. Northern blot analysis showed that BiGSTD is highly expressed in the fat body and midgut, and less so in the muscles of B. ignitus worker bees.