• Proceedings of the Korean Information Science Society Conference
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• 2004.10b
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• pp.256-258
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• 2004

단백질 상호작용에 대한 연구는 생명현상의 전반적인 원리를 규명하는데 필수적이다. 생물학 문헌 데이터베이스로부터 단백질 상호작용 정보를 찾는 것은 많은 시간과 노력이 필요하기 때문에 컴퓨터로 자동화시키는 방법이 요구된다. 문헌으로부터 단백질 상호작용 정보를 추출하는 작업은 단순 문자열 비교를 통한 정보검색으로는 한계가 있으므로 자연어 처리 기법을 적용해 문장의 문법 구조, 품사 정보 등을 이용하면 더 정확한 추출이 가능하다. 본 논문에서는 자연어 처리를 이용하여 문장을 트리로 표현한 뒤 가지치기, 병합 등을 통해 추상화된 트리를 패턴과 매칭하는 방법을 제안한다. 그리고 실제 데이터를 이용한 실험 결과를 통해 기존 방법에 비해 더 높아진 정확도를 확인하였다.

• Food Science and Preservation
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• v.22 no.6
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• pp.901-907
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• 2015

Genetically modified (GM) pepper H15 containing the gene for cucumber mosaic virus (CMV) coat protein (CP) and its control line non-GM pepper P2377 were investigated for their allergic risk. Amino acid sequence of the inserted gene product CMV-CP was compared with those of known allergens. No known allergen had greater than 35% amino acid sequence homology over an 80 amino acid window or more than 8 consecutive identical amino acids. Protein patterns of GM and non-GM pepper extracts were evaluated by SDS-PAGE, which showed similar distribution of protein bands for both GM and non-GM pepper. Antigen-antibody reactions were compared between GM and its non-transgenic parental control. ELISA and immunoblot analysis of sera from allergic patients showed some IgE reactivity; however, no differences were observed between GM pepper H15 and P2377. We therefore conclude that CMV-CP is less likely to be an allergen; the protein composition and allergenicity of the GM pepper H15 is not different from that of P2377 and safe as a commercial host.

• Korean Journal Plant Pathology
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• v.12 no.2
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• pp.176-181
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• 1996

Aster yomena로부터 분리한 오이 모자이크 바이러스(cucumber mosaic virus) (CMV-As)의 RNA4로부터 완전한 길이의 cDNA를 합성하고 그 전체적인 염기서열(1,043 nt`s)을 결정하였다. CMV-As RNA4는 73개의 염기로 구성된 5`말단의 leader 부위, 657개의 염기로 구성된 외피단백질(coat protein) 유전자 부위 및 312개의 염기로 구성된 3` 말단의 비번역 부위로 구성되어 있음을 확인하였다. 외피단백질 유전자 부위의 염기서열을 다른 계통의 CMV와 비교해 볼 때 그 염기서열이 보전적으로 존재하고 있으나 그 외의 부분은 다양함을 확인하였다. 특히 3` 말단부위의 61개의 염기로 구성된 부위(959-1019)는 다른 계통의 CMV에서는 상당히 유사하지만 CMV-As도 다른 CMV처럼 tRNA와 유사한 구조를 역시 형성함을 확인하였다. CMV-As의 RNA4 염기서열을 다른 계통의 CMV와 비교할 때 CMV-I17F와 가장 유사하였으며(91.9%) S형의 CMV-M과는 가장 낮은 동일성을 보였다(71.1%). 외와 같은 염기성열의 비교 결과와 EcoRI 제한효소 인식부위의 존재로 미루어 CMV-As는 WT형으로 분류된다.

• Proceeding of EDISON Challenge
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• 2017.03a
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• pp.158-164
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• 2017

암을 억제시키는 기능을 하는 단백질로 잘 알려진 p53은, 주로 종양세포에서 과도하게 발현되는 단백질인 HDM2와 복합체를 형성하여 비활성화되고 항암기능을 상실하게 됩니다. 때문에 종양세포에서의 p53-HDM2의 상호작용을 억제하기 위해 현재까지 많은 연구가 진행되어왔으며, 다양한 p53-HDM2 억제제가 개발된 바 있습니다. 최근 연구들에 따르면, HDM2와 결합친화도를 높이고 소수성 작용(hydrophobic interaction)에 기여하여 보다 안정한 구조를 만드는 탄화수소체인(staple)을 연결시킨 펩타이드 설계에 대한 관심이 높아지고 있는 추세입니다. 이에, 본 연구에서는 분자동역학 모의실험을 통해서 얻은 탄화수소체인-p53과 비탄화수소체인-p53 및 각각의 HDM2와 결합한 복합체를 기반으로 EDISON의 용매화 자유에너지(Solvation Free Energy) 프로그램을 이용하여 탄화수소체인의 특징 및 역할을 구조적인 측면과 열역학적인 측면으로 분석하여 비교하고자 합니다. 우리 연구에서 비탄화수소체인-p53의 구조는 분자동역학 시뮬레이션을 수행하는 동안 나선구조형태로 풀려 HDM2와 결합 유도 시에 주요결합 아미노산 잔기가 올바른 결합부위와 상호작용하지 못한 결과를 확인한 반면, 탄화수소체인이 형성된 구조는 시뮬레이션 동안에도 펩타이드의 나선구조를 유지시켜 HDM2와 주요 결합을 형성하는 아미노산 잔기들을 올바른 방향으로 배치시켜 HDM2와의 결합친화도를 높였습니다. 이 연구 결과는 탄화수소체인이 펩타이드의 나선성을 유지시키고, HDM2와의 상호작용을 통한 구조적인 안정성 유도 및 용매화 자유에너지에 큰 기여를 통해 p53-HDM2상호작용 억제제에서 긍정적인 역할을 할 가능성을 보여줍니다.

• The Journal of the Korea Contents Association
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• v.8 no.6
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• pp.74-81
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• 2008

Protein interaction network contains a small number of highly connected protein, denoted hub and many destitutely connected proteins. Recently, several studies described that a hub protein is more likely to be essential than a non-hub protein. This phenomenon called as a centrality-lethality rule. This nile is widely credited to exhibit the importance of hub proteins in the complex network and the significance of network architecture as well. To confirm whether the rule is accurate, we Investigated all protein interaction DBs of yeast in the public sites such as Uetz, Ito, MIPS, DIP, SGB, and BioGRID. Interestingly, the protein network shows that the rule is correct in lower scale DBs (e.g., Uetz, Ito, and DIP) but is not correct in higher scale DBs (e.g., SGD and BioGRID). We are now analyzing the features of networks obtained from the SGD and BioGRD and comparing those of network from the DIP.

• Journal of Sericultural and Entomological Science
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• v.34 no.2
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• pp.20-25
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• 1992

The location of the polyhedrin gene of Bmbyx mori nuclear polyhedrosis virus(BmNPV) was determined by using a cloned polyhedrin gene from the Autographa californica nuclear polyhedrosis virus(AcNPV) as a hybridization probe. The 7.4 Kb PstⅠ fragment DNA of Bm-NPV was cloned to plasmid pUC19 vector. A fragment containing this gene was mapped and sequenced in its entire polyhedrin reading frame. Nucleotide sequences comparison of the polyhedrin of the BmNPV to that of previously reported by Ⅰatrou(1985) revealed that the sequence varied in 10 base, Comparison of the amino acid sequence of the two structured gene revealed that coding sequence varied 74 valine to isoleucine, 76 aspargine to serine and 155 methionine to valine.

• Journal of Korea Multimedia Society
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• v.15 no.6
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• pp.794-804
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• 2012

For the geometric computations on the protein molecules, the proximity queries, such as computing the minimum distance from an arbitrary point to the molecule or detecting the collision between a point and the molecule, are essential. For the proximity queries, the efficiency of the computation time can be different according to the data structure used for the molecule. In this paper, we present the data structures and algorithms for applying proximity queries to a molecule with GPU acceleration. We present two data structures, a voxel map and a sphere tree, where the molecule is represented as a set of spheres, and corresponding algorithms. Moreover, we show that the performance of presented data structures are improved from 3 to 633 times compared to the previous data structure for the molecules containing 1,000~15,000 atoms.

• The Korean Journal of Food And Nutrition
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• v.15 no.4
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• pp.331-336
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• 2002

Conformation of soymilk protein was examined to obtain basic information for improved calcium intolerence of soymilk protein partially hydrolyzed with protease. Surface hydrophobicities of three proteins showed the order of SMP(soymilk protein) < SPI(soy protein isolate) < PT-SMP(protease treated soymilk protein). Total thiol group contents of SMP and PT-SMP were similar but larger than that of SPI. Reducing rate of disulfide bond in PT-SMP after 2-mercaptoethanol treatment was laster than that in SMP. And so, this result indicates that PT-SMP may be less compacting due to protease treatement. From circular dichroism result, PT-SMP showed different pattern from SMP and SPI suggesting change of secondary structure by hydrolysis. And analysis of heat denaturating property by DSC showed that denaturation enthalpy of three proteins were all small. Especially enthalpy of PT-SMP was least, and this result suggested that PT-SMP was denatured easily by heating due to less compacting structure.

• Journal of fish pathology
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• v.7 no.1
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• pp.13-22
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• 1994

To identify the immunogens of a PRT strain of Infectious Hematopoietci Necrosis Virus (IHNV) isolated from cultrued fish in Korea (Park et al, 1993). a panel of 4 monoclonal antibodies (MAbs) against IHNV-PRT strain and two polyclonal antisera from rainbow trout survived IHN disease were prepared. Proteins of purified IHNV-PRT strain were analysed on 10% SDS-PAGE and transferred onto NC paper and were incubated with the antibody solutions. With the polyclonal antibodies, four bands ($M_1$, $M_2$, G and 90Kd) were detected and the band density was in the order of $M_2$ > 90Kd > $M_1$ > G. However, with the MAbs, only two bands(G and 90Kd) were detected. The origin of 90Kd protein was not clear but maybe cell. All the results represented that among the five proteins of IHNV-PRT strain (Park et al., 1993), $M_2$, $M_1$ and G proteins were immunogens and $M_2$ protein was the strongest one.

• Journal of Life Science
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• v.22 no.1
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• pp.7-15
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• 2012

A polyguluronate-specific lyase from Streptomyces sp. strain M3 has been previously cloned and characterized. In this study, the M3 alginate lyase gene in the pColdI vector was mutated by site-directed mutagenesis and random mutagenesis to enhance the alginate degrading activity. Six mutants were obtained: Ser25Arg, Phe99Leu, Asp142Asn, Val163Ala, Lys191Glu, and Gly194Cys. Phe99Leu and Lys191Glu mutants completely lost their alginate lyase activity, whereas the alginate degrading activity of Gly194Cys mutant increased by nearly 10 fold. The 3-D protein structure of M3 alginate lyase, which was constructed using the Swiss-Model automodeler, was also compared to the crystal structure of another alginate lyase. A mutated glycine residue was positioned between Gly193 and Tyr195 of the C-terminal conserved sequence, YFKAGXYXQ. A phenylalanine residue (at position 99) and a glycine residue (at position 194) mutated in this study were distant from the active site, but the degrading activity was strongly affected by their mutation.