• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.742-744
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• 2003

PDB로부터 얻은 51개의 단백질-RNA 복합체를 대상으로 기존 연구에서 얻은 단백질과 RNA의 결합 성향성 값과 본 논문에서 새로 구한 단백질의 표면 노출정도에 따른 결합 성향성 값을 이용하여 단백질의 결합 기대치를 구한다. 또한 구한 결합 기대치를 활용하여 새로운 단백질-RNA 복합체를 대상으로 단백질의 결합 부위 예측을 시도하였다. 결합 기대치는 0.240 이상인 경우 결합할 가능성이 높은 것으로 판별하였고, 그 결과 단백질의 결합 후보지를 전체 단백질의 25% 정도로 줄일 수 있었다.

• Proceedings of the Korea Information Processing Society Conference
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• 2016.10a
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• pp.583-586
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• 2016

단백질과 RNA의 상호작용 데이터가 대량으로 늘어남에 따라, 단백질과 RNA의 결합부위를 예측하는 계산학적인 방법들이 많이 개발되고 있다. 하지만, 많은 계산학적인 방법들은 단백질에서 단백질과 RNA 결합부위를 예측한다는 한계점이 있었다. 본 논문에서는 RNA와 단백질의 서열정보를 모두 사용하여, 단백질과 결합하는 RNA 결합부위를 예측하는 기법과 그 결과를 논한다. WEKA random forest(http://www.cs.waikato.ac.nz/ml/weka/)를 이용하여 예측 모델을 개발하였고, RNA 서열의 서열 프로파일, 서열 composition, 결합 상대방의 단백질의 특성 등을 특정으로 표현하였다. Random forest 기법을 사용한 cross validation의 결과로서 1:1 모델에서 제일 높은 성능인 92.4% sensitivity, 92.0% specificity, 92.2% accuracy를 보였고, independent test에서는 72.5% sensitivity, 90.0% specificity, 2.1% accuracy를 보였다.

• Korean journal of applied entomology
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• v.34 no.2
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• pp.100-105
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• 1995

A whole body extract (WBE), a crude nuclear fraction, of aphids was prepared and used to identify the proteins which bound specifically to 5'-upstream regions of the transcription initiation site of the aphid ribosomal RNA gene (rDNA). While DNA fragment (-263/-195) was bound by only one specific 53 kDa protein, two DNA fragments, A(-194/23) and B(-393/-264), were commonly bound by three proteins (52 kDa, 50 kDa and 40 kDa). It was also revealed that the formation of he DNA-protein complex requires a cation.

• Journal of Applied Biological Chemistry
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• v.58 no.3
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• pp.201-208
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• 2015

The role of RNA-binding proteins (RBPs) to regulate expression of genes seems to be very important. RBPs play important roles in RNA related bioprocess such as transcription, pre-mRNA splicing, polyadenylation, transport, localization, translation, turn over and maintenance of structure. Despite of many researches on RNA binding proteins, detailed mechanisms of these proteins have not been fully understood. It seems that many parts of RBPs remains unknown and should be characterized for the better understanding of gene expression. Recently, genetic, biochemical, and bioinformatic analysis of genomes revealed a vast array of RBPs and many parts are interesting to understand bioprocessing including gene expression.

• Journal of Life Science
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• v.8 no.2
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• pp.119-125
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• 1998

Column-purified double-stranded RNA binding factor (RBF) protein was tested for its binding affinity for the different forms of nucleic acids structure such as single-stranded(ss) and double-stranded(ds)RNA and ss- and dsDNA. The RBF protein was incubated with each of these nucleic acid structures in separate reactions and its comparative binding affnity was visualized by SDS-polyacrylamide gel electrophoresis. The RBF protein bound to the dsRNA molecule to form a tight RNA:protein complex in agreement with previous studies, but not to the other nucleic acid molecules confirming its distinctive affinity for the dsRNA structure. In phosphorylation assay in vito, the purified RBF protein significantly inhibited the autophosphorylation of the PKR derived from not only human but mouse source in the presence of poly(I):poly(C). It is suggesting that PKR vs. RBF is similarly under a competitive interaction among different eukaryotic organisms during protein synthesis.

• Journal of Life Science
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• v.23 no.11
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• pp.1311-1316
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• 2013

Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a major pre-mRNA binding protein and it is an abundant nuclear protein that shuttles between the nucleus and the cytoplasm. hnRNP L is known to be related to many cellular processes, including chromatin modification, pre-mRNA splicing, mRNA export of intronless genes, internal ribosomal entry site (IRES)-mediated translation, mRNA stability, and spermatogenesis. In order to identify the cellular proteins interacting with hnRNP L, this study performed a yeast two-hybrid screening, using a human liver cDNA library. The study identified insulin-like growth factor binding protein-4 (IGFBP-4) as a novel interaction partner of hnRNP L in the human liver. It then discovered, for the first time, that hnRNP L interacts specifically with IGFBP-4 in a yeast two-hybrid system. The authenticity of this two-hybrid interaction of hnRNP L and IGFBP-4 was confirmed by an in vitro pull-down assay.

• Journal of Life Science
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• v.21 no.9
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• pp.1226-1233
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• 2011

In neurons, kinesin is the molecular motor that transport cargos along microtubules. KIF5s (alias kinesin-I), are heterotetrameric motor conveying cargos, but the mechanism as to how they recognize and bind to a specific cargos has not yet been completely elucidated. To identify the interaction proteins for KIF5C, yeast two-hybrid screening was performed, and specific interaction with the $\underline{S}$am68-$\underline{l}$ike $\underline{m}$ammalian protein $\underline{2}$ (SLM-2), a member of the $\underline{s}$ignal $\underline{t}$ransducers and $\underline{a}$ctivators of $\underline{R}$NA (STAR) family of RNA processing proteins, was found. SLM-2 bound to the carboxyl (C)-terminal region of KIF5C and to other KIF5 members. The C-terminal domain of Sam68, SLM-1, SLM-2 was essential for interaction with KIF5C in the yeast two-hybrid assay. In addition, glutathione S-transferase (GST) pull-downs showed that SAM68, SLM-1, and SLM-2 specifically interacted to Kinesin-I complex. An antibody to SAM68 specifically co-immunoprecipitated SAM68 associated with KIF5s and coprecipitated with a specific set of mRNA. These results suggest that Kinesin-I motor protein transports RNA-associated protein complex in cells.

• The Journal of Natural Sciences
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• v.14 no.2
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• pp.83-91
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• 2004

Recently phage K11 lysozyme was cloned and characterized in our lab. The K11 lysozyme was identified to have dual functions. It not only cuts a peptidoglycan bond in bacterial cell wall but also acts as an inhibitor of K11 RNA polymerase. It has been known that the T7 lysozyme binds specifically to T7 RNA polymerase and inhibits transcription. The dual activities of K11 lysozyme are atreeable to the case of T7 phage lysozyme and RNA polymerare. In order to identify the binding magnitude of K11 lysozyme with K11 RNA polymerase, yeast two-hybrid system was used. K11 phage lysozyme gene was introduced into pLexA plasmid and used as a prey. Also, K11 phage RNA polymerase gene was introduced into pJG4-5 and used as a bait. The binding between K11 lysozyme and K11 RNA polymerase was demonstrated by expression of reporter genes such as lacZ and leu2.

• Journal of Life Science
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• v.6 no.4
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• pp.234-240
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• 1996

A double-stranded RNA binding factor (RBF), characterized as an inhibitor of PKR kinase in our previous study, was evaluated for its RNA binding specificities by RNA gel electrophoretic mobility shift analysis and membrane filter binding assay, RBF displayed affinities for a broad range of RNAs including viral RNAs and synthetic RNAs consiting of stem and loop structures. GC-rich RNA stem helices as short as 11 bp are suggested to represent the minimal binding motif for RBF. RBF binding to all the natural RNAs tested was reversible by poly(I): poly(C) addition, but E. coli 5S RNA was inefficient.

• Proceedings of the Korea Contents Association Conference
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• 2011.05a
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• pp.341-342
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• 2011

선행연구에서 우리는 암과 관련된 단백질-단백질 상호작용 네트워크와 단백질-질병 네트워크를 통해서 핵심 단백질 60개를 추출했다. 이 단백질들을 조절하여 암을 제어하기 위한 방법으로 miRNA(microRNA)를 이용하기위해 단백질과 상호작용하는 miRNA와 miRNA 서열정보를 추출하였다. 한 단백질과 상호작용하는 miRNA의 수가 많았기 때문에 각각의 miRNA에 대해 우선순위를 주어서 가중치를 부여했는데, 기준으로는 miRNA 서열길이, 수소결합 수 등으로 잡아주었다. 이 방법을 사용함으로써 밝혀지지 않은 단백질과 miRNA의 상호작용 서열을 찾는데 이용가능 할 것이다.