• 한국전자통신학회논문지
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• 제13권6호
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• pp.1397-1404
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• 2018

입체적 단백질 구조를 이용한 단백질의 분석은 3차원 데이타를 생성하기 위한 기술적인 어려움과 요구되는 높은 비용으로 인해 크게 발전하지 못하였다. 모티프(motif)는 단백질이나 유전자 염기서열의 단편(segment) 정보로 정의된다. 단순성 때문에 모티프는 다양한 분야에서 활발하고 폭넓게 응용되고 있다. 그러나 모티프 자체에 대한 포괄적인 이해와 연구는 미미하다. 이 논문이 가지는 중요성은 인공지능 기법을 활용하여 인간 단백질을 분석하는 방법으로 3가지 측면에서 찾아볼 수 있다. (1) 현재 단백질 데이타 뱅크 (PDB)에 저장된 모든 인간의 단백질 구조를, 이에 상응하는 효소위원회 (EC)의 데이타베이스와 단백질의 구조적 특성에 따른 분류 데이타베이스 (SCOP)를 연동하여, 단백질이 가지는 고유의 특성을 모티프를 응용한 새로운 방법으로 컴퓨터를 이용하여, 분석한 최초의 종합적이고 심층적인 인간 단백질의 분석법이다. (2) 본 연구는 모티프에 의해 생성된 새로운 단백질의 특성을 계층적 클러스터링을 이용하여 단백질이 가지는 고유한 특징을 패턴 분석법과 통계 그리고 단백질 기능 분석의 세 가지 범주로 단백질의 특성을 분석한다. (3) 임의로 생성된 모티프가 단백질 내에서 가지는 빈도에 대해 빅 데이타를 활용하여 모티프의 길이를 다양화시킴과 동시에 접촉 염기와 단백질의 기능을 다각도로 분석할 수 있는 임의 모티프 빈도 (RMF)를 이용한 단백질 분석 방법론을 제안한다.

• 생명과학회지
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• 제30권12호
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• pp.1085-1091
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• 2020

본 연구에서는 고추(Capsicum annuum L.) 수확 후 버려지는 잔재물의 활용가치를 위해 이들로부터 추출한 발효추출물과 열수추출물의 생리활성과 세포독성을 분석하였다. 녹광고추 발효추출물에 함유된 질소, 인산, 칼륨, 칼슘, 마그네슘 성분의 총 함량은 청양고추 발효추출물 보다 2배 정도 높았고, 열수추출물에서는 유사한 함량을 보였다. 미량원소 중에는 붕산, 철, 규소 성분만 검출되고, 아연, 망간, 몰리브덴, 구리 성분은 두 추출물 모두에서 검출되지 않았다. 총 폴리페놀과 플라보노이드 함량은 청양고추와 녹광고추 모두에서 발효추출물이 열수추출물 보다 2배 이상 높게 나타내었다. DPPH radical 소거 능력은 발효추출물이 열수추출물 보다 항산화력이 높게 나타내었으나, ABTS radical 소거 능력은 열수추출물이 발효추출물 보다 항산화력이 높게 나왔다. MTT assay를 이용한 추출물의 세포독성 실험에서는 청양고추와 녹광고추 두 추출물의 모든 농도에서 세포독성이 미약한 것으로 확인되었다. 따라서 고추 수확 후 버려지는 잔재물이 천연 기능성 물질추출을 위한 소재로 이용되거나 또한 그 추출물이 각종 바이오 소재로 활용되어도 큰 문제가 없으리라 판단된다.

• IMMUNE NETWORK
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• 제21권6호
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• pp.38.1-38.8
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• 2021

Recently, a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (B.1.1.529) Omicron variant originated from South Africa in the middle of November 2021. SARS-CoV-2 is also called coronavirus disease 2019 (COVID-19) since SARS-CoV-2 is the causative agent of COVID-19. Several studies already suggested that the SARS-CoV-2 Omicron variant would be the fastest transmissible variant compared to the previous 10 SARS-CoV-2 variants of concern, interest, and alert. Few clinical studies reported the high transmissibility of the Omicron variant but there is insufficient time to perform actual experiments to prove it, since the spread is so fast. We analyzed the SARS-CoV-2 Omicron variant, which revealed a very high rate of mutation at amino acid residues that interact with angiostatin-converting enzyme 2. The mutation rate of COVID-19 is faster than what we prepared vaccine program, antibody therapy, lockdown, and quarantine against COVID-19 so far. Thus, it is necessary to find better strategies to overcome the current crisis of COVID-19 pandemic.

• Genomics & Informatics
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• 제6권4호
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• pp.173-180
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• 2008

The human genome has evolved as a consequence of evolutionary forces, such as natural selection. In this study, we investigated natural selection on the human genes by comparing the numbers of nonsynonymous (NS) and synonymous (S) mutations in individual genes. We initially collected all coding SNP data of all human genes from the public dbSNP. Among the human genes, we selected 3 different selection groups of genes: positively selected genes (NS/S${\geq}$3), negatively selected genes (NS/S${\leq}$1/3) and neutral selection genes (0.9

• Asian Pacific Journal of Cancer Prevention
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• 제14권6호
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• pp.3669-3676
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• 2013

Faithful transmission of genetic information depends on accurate chromosome segregation as cells exit from mitosis, and errors in chromosomal segregation are catastrophic and may lead to aneuploidy which is the hallmark of cancer. In eukaryotes, an elaborate molecular control system ensures proper orchestration of events at mitotic exit. Phosphorylation of specific tyrosyl residues is a major control mechanism for cellular proliferation and the activities of protein tyrosine kinases and phosphatases must be integrated. Although mitotic kinases are well characterized, phosphatases involved in mitosis remain largely elusive. Here we identify a novel variant of mouse protein tyrosine phosphatase containing domain 1 (Ptpcd1), that we named Ptpcd2. Ptpcd1 is a Cdc14 related centrosomal phosphatase. Our newly identified Ptpcd2 shared a significant homology to yeast Cdc14p (34.1%) and other Cdc14 family of phosphatases. By subcellular fractionation Ptpcd2 was found to be enriched in the cytoplasm and nuclear pellets with catalytic phosphatase activity. By means of immunofluorescence, Ptpcd2 was spatiotemporally regulated in a cell cycle dependent manner with cytoplasmic abundance during mitosis, followed by nuclear localization during interphase. Overexpression of Ptpcd2 induced mitotic exit with decreased levels of some mitotic markers. Moreover, Ptpcd2 failed to colocalize with the centrosomal marker ${\gamma}$-tubulin, suggesting it as a non-centrosomal protein. Taken together, Ptpcd2 phosphatase appears a non-centrosomal variant of Ptpcd1 with probable mitotic functions. The identification of this new phosphatase suggests the existence of an interacting phosphatase network that controls mammalian mitosis and provides new drug targets for anticancer modalities.

• Molecules and Cells
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• 제39권11호
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• pp.814-820
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• 2016

FtsZ, a tubulin homologue, is an essential protein of the Z-ring assembly in bacterial cell division. It consists of two domains, the N-terminal and C-terminal core domains, and has a conserved C-terminal tail region. Lateral interactions between FtsZ protofilaments and several Z-ring associated proteins (Zaps) are necessary for modulating Z-ring formation. ZapD, one of the positive regulators of Z-ring assembly, directly binds to the C-terminal tail of FtsZ and promotes stable Z-ring formation during cytokinesis. To gain structural and functional insights into how ZapD interacts with the C-terminal tail of FtsZ, we solved two crystal structures of ZapD proteins from Salmonella typhimurium (StZapD) and Escherichia coli (EcZapD) at a 2.6 and $3.1{\AA}$ resolution, respectively. Several conserved residues are clustered on the concave sides of the StZapD and EcZapD dimers, the suggested FtsZ binding site. Modeled structures of EcZapD-EcFtsZ and subsequent binding studies using bio-layer interferometry also identified the EcFtsZ binding site on EcZapD. The structural insights and the results of bio-layer interferometry assays suggest that the two FtsZ binding sites of ZapD dimer might be responsible for the binding of ZapD dimer to two protofilaments to hold them together.

• 대한의생명과학회지
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• 제23권1호
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• pp.8-16
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• 2017

p-Coumaric acid is an organic compound that is a hydroxyl derivative of cinnamic acid. Due to its multiple biological activities p-coumaric acid has been widely studied in biochemical and cellular systems and is also considered as a useful therapeutic candidate for various neuronal diseases. However, the efficacy of p-coumaric acid on zebrafish developmental regulation has not been fully explored. In this study, therefore, we first investigated the action mechanism of the p-coumaric acid on the zebrafish development in a whole-organism model. p-Coumaric acid treated group significantly inhibited the pigmentation of the developing zebrafish embryos compared with control embryos without any severe side effects. In addition, p-coumaric acid down-regulated more effectively in a lower concentration than the well-known zebrafish's melanogenic inhibitor, phenylthiourea. We also compared the molecular docking property of p-coumaric acid with phenylthiourea on the tyrosinase's kojic acid binding site, which is the key enzyme of zebrafish embryo pigmentation. Interestingly, p-coumaric acid interacted with higher numbers of the amino acid residues and exhibited a tight binding affinity to the enzyme than phenylthiourea. Taken all together, these results strongly suggest that p-coumaric acid inhibits the activity of tyrosinase, consequently down-regulating zebrafish embryo pigmentation, and might play an important role in the reduction of dermal pigmentation. Thus, p-coumaric acid can be an effective and non-toxic ingredient for anti-melanogenesis functional materials.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권3호
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• pp.218-224
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• 2005

Surface modification of glutaraldehyde fixed bovine pericardium (GFBP) was success­fully carried out with hyaluronic acid (HA) derivatives. At first, HA was chemically modified with adipic dihydrazide (ADH) to introduce hydrazide functional group into the carboxyl group of HA backbone. Then, GFBP was surface modified by grafting HA-ADH to the free aldehyde groups on the tissue and the subsequent HA-ADH hydrogel coating. HA-ADH hydrogels could be prepared through selective crosslinking at low pH between hydrazide groups of HA-ADH and crosslinkers containing succinimmidyl moieties with minimized protein denaturation. When HA­ADH hydrogels were prepared at low pH of 4.8 in the presence of erythropoietin (EPO) as a model protein, EPO release was continued up to $85\%$ of total amount of loaded EPO for 4 days. To the contrary, only $30\%$ of EPO was released from HA-ADH hydrogels prepared at pH=7.4, which might be due to the denaturation of EPO during the crosslinking reaction. Because the carboxyl groups on the glucuronic acid residues are recognition sites for HA degradation by hyaluronidase, the HA-ADH hydrogels degraded more slowly than HA hydrogels prepared by the crosslinking reaction of divinyl sulfone with hydroxyl groups of HA. Following a two-week subcutaneous implantation in osteopontin-null mice, clinically significant levels of calcification were observed for the positive controls without any surface modification. However, the calcification of surface modified GFBP with HA-ADH and HA-ADH hydrogels was drastically reduced by more than $85\%$ of the positive controls. The anti-calcification effect of HA surface modification was also confirmed by microscopic analysis of explanted tissue after staining with Alizarin Red S for calcium, which followed the trend as observed with calcium quantification.

• Plant Biotechnology Reports
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• 제3권1호
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• pp.95-101
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• 2009

Tea leaves are major source of catechins—antioxidant flavonoids. Dihydroflavonol 4-reductase (DFR, EC 1.1.1.219) is one of the important enzymes that catalyzes the reduction of dihydroflavonols to leucoanthocyanins, a key ''late'' step in the biosynthesis of catechins. This manuscript reports characterization of DFR from tea (CsDFR) that comprised 1,413 bp full-length cDNA with ORF of 1,044 bp (115-1,158) and encoding a protein of 347 amino acids. Sequence comparison of CsDFR with earlier reported DFR sequences in a database indicated conservation of 69-87% among amino acid residues. In silico analysis revealed CsDFR to be a membrane-localized protein with a domain (between 16 and 218 amino acids) resembling the NAD-dependent epimerase/dehydratase family. The theoretical molecular weight and isoelectric point of the deduced amino sequence of CsDFR were 38.67 kDa and 6.22, respectively. Upon expression of CsDFR in E. coli, recombinant protein was found to be functional and showed specific activity of 42.85 nmol $min^{-1}$ mg $protein^{-1}$. Expression of CsDFR was maximum in younger rather than older leaves. Expression was down-regulated in response to drought stress and abscisic acid, unaffected by gibberellic acid treatment, but up-regulated in response to wounding, with concomitant modulation of catechins content. This is the first report of functionality of recombinant CsDFR and its expression in tea.

• 대한바이러스학회지
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• 제28권4호
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• pp.303-316
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• 1998

An attenuated classical swine fever virus (CSFV), Suri strain, is a variant derived from a vaccine virus, LOM strain. This study was performed to elucidate the molecular biologcal properties of CSFV Suri strain, and to obtain the basic data for molecular epidemiological approaches for the disease. The truncated form of gp55 gene without the C-terminal transmembrane domain, in size of 1,023bp, was amplified by RT-PCR and sequenced by dye terminator cyclic sequencing method, and inserted into BamHI site of pAcGP67B baculovirus vector, establishing a cloned pAcHEG plasmid. By the nucleotide sequences determined, 341 amino acid sequences were predicted. As compared the nucleotide and amino acid sequences of gp55 of Suri with the various CSFV, Suri strain showed the high homology over 99.1% with ALD and LOM strains, but comparably the lower homology with Alfort and Brescia. In comparison of amino acid sequence in variable domain of gp55 protein, the similar tendency of homology was observed. In hydrophobicity analysis, all of four CSFV strains revealed the analogous patterns of hydrophobicity. The numbers and locations of N-glycosylation site and cysteine residues in gp55 were analyzed, those of Suri strain being coincident with ALD and LOM strains. The results suggest that gp55 in Suri strain has the high similarity to those in ALD and LOM strains in terms of the nucleotide and amino acid sequences and the functional properties of gp55 protein.