• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.133-138
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• 2003

The prediction of protein secondary structure has been an important bioinformatics tool that is an essential component of the template-based protein tertiary structure prediction process. It has been known that the predicted secondary structure information improves both the fold recognition performance and the alignment accuracy. In this paper, we describe several novel ideas that may improve the prediction accuracy. The main idea is motivated by an observation that the protein's structural information, especially when it is combined with the evolutionary information, significantly improves the accuracy of the predicted tertiary structure. From the non-redundant set of protein structures, we derive the 'potential' parameters for the protein secondary structure prediction that contains the structural information of proteins, by following the procedure similar to the way to derive the directional information table of GOR method. Those potential parameters are combined with the frequency matrices obtained by running PSI-BLAST to construct the feature vectors that are used to train the support vector machines (SVM) to build the secondary structure classifiers. Moreover, the problem of huge model file size, which is one of the known shortcomings of SVM, is partially overcome by reducing the size of training data by filtering out the redundancy not only at the protein level but also at the feature vector level. A preliminary result measured by the average three-state prediction accuracy is encouraging.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• 한국자기공명학회논문지
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• 제19권3호
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• pp.149-155
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• 2015

Acyl carrier protein is related with fatty acid biosynthesis in which specific enzymes are involved. Especially, acyl carrier protein (ACP) is the key component in the growing of fatty acid chain. ACP is the small, very acidic protein that covalently binds various intermediates of fatty acyl chain. Acylation of ACP is mediated by holo-acyl carrier protein synthase (ACPS), which transfers the 4'PP-moiety of CoA to the 36th residue Ser of apo ACP. Acyl carrier protein P (ACPP) is one of ACPs from Helicobacter plyori. The NMR structure of ACPP consists of four helices, which were reported previously. Here we show how acylation of ACPP can affect the overall structure of ACPP and figured out the contact surface of ACPP to acyl chain attached during expression of ACPP in E. coli. Based on the chemical shift perturbation data, the acylation of ACCP seems to affect the conformation of the long loop connecting helix I and helix II as well as the second short loop connecting helix II and helix III. The significant chemical shift change of Ile 54 upon acylation supports the contact of acyl chain and the second loop.

• Bulletin of the Korean Chemical Society
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• 제28권6호
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• pp.1010-1014
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• 2007

M1 RNA is the catalytic component of RNase P, a tRNA-processing enzyme in Escherichia coli. M1 RNA is produced in the cell by transcription of the rnpB gene and subsequent processing at the 3' end. The 3' flanking region of rnpB contains repeated sets of overlapping sequences coding for small proteins. The issue of whether these proteins are expressed remains to be established. In this study, we showed the expression of a small protein encoded by the first repeat within the 3' flanking region of rnpB. Interestingly, protein expression was increased at lower temperatures. The termination efficiency of rnpB terminators was decreased at lower temperatures, suggesting that antitermination is responsible for enhanced protein expression. Moreover, the purified small protein contained M1 RNA, implying a role as a specific RNA-binding protein.

• 약학회지
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• 제44권4호
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• pp.347-353
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• 2000

To examine influence of artificial digestive juice on the antitumor activity of Ganoderma lucidum-A(GL-A), protein-bound polysaccharide from Ganoderma lucidum, we compared the digested protein-bound polysaccharide with undigested one both on immunopotentiating activity and influence of digestive juices. Protein-bound polysaccharide GL-B was obtained by digesting the antitumor component GL-A with artificial digestive Juices in vitro. When GL-A was administered orally to sarcoma 180 tumor-bearing ICR mice, the life prolonging effect was exhibited in a dose dependent manner Not only GL-A but GL-B increased the production of colony forming unit (CFU) to 10- and 8-fold of that of the control, respectively. Both of the protein-bound polysaccharides also showed the secretion of nitric oxide in RAW 264.7 cell lines to 3.5-and 3.7-fold of that of the control, respectively: GL-A activated components of the alternative complement pathway, whereas GL-B did not. In humoral immunity GL-A increased the activity of alkaline phosphatase in differentiated B cells to 3 times and GL-B to 4 times of that of the control. These results showed that the artificial digestive juices had no influence on the antitumor activity of the protein-bound polysaccharide from Ganoderma lucidum and that its immunomodulating activity retained after treatment with artificial digestive juice. And this provides a basis of the protein-bound polysaccharide of Ganoderma lucidum as an peroral anticancer drug.

• 한국가축번식학회지
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• 제16권4호
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• pp.289-299
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• 1993

돼지 난포내의 각 구성분들에 대해 10% SDS-PAGE와 IEF를 이용한 이차원 전기영동을 실시하여 세포 및 난포액 구성분의 구조단백질상을 분석하였다. 난자-난구세포 복합체를 호르몬과 15%의 FCS가 포함된 M16 배양액으로 39$^{\circ}C$, 5% CO2 상태에서 35시간 동안 체외배양하였다. 배양 전후의 난자, 투명대 및 난구세포와 난포 크기별로 회수된 난포액들을 각각 분리 회수하여 구조단백질상을 분석하였으며, Silver 염색과 CBB 염색으로 분석이 가능한 각 구성분의 적정 시료량을 조사하였다. 한편 난포 구성분들에 있어서 난자는 분자량이 25와 114kd, 난구세포는 20, 33, 58, 78 및 112kd, 투명대는 65kd, 그리고 난포액은 18, 76, 92, 152 및 187kd 단백질을 세포특이단백질로 가지고 있음이 확인되었다. 특히 난자의 경우 성숙에 따라 구조단백질상의 변화가 확인된 반면, 난구세포에서는 차이가 없었다. 또한 난포액은 난포의 크기에 따라서는 단백질상의 차이가 없었으나 호르몬 처리 여부에 따라서는 이차원 전기영동상에서 몇가지 단백질에서 차이가 확인되었고, 난포세포들도 폐쇄 여부에 따라 단백질 조성에 차이를 보였다. 따라서 본 실험에서는 전기영동에 필요한 시료의 양과 준비 방법을 확립하여 각 난포 구성분들의 단백질상 분석에 대한 기초자료를 확립하였으며, 이상의 결과는 앞으로 진행될 단백질의 생합성 분석이나 면역화학학적 분석에 유용하게 이용될 수 있을 것이다.

• 미생물학회지
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• 제39권3호
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• pp.141-147
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• 2003

여러 항진균 활성 관련 유전자들의 발현 수준을 동시에 연구하기 위하여 DNA microarray를 이용하여 유전자들의 발현 패턴을 비교 분석하였다. 본 연구에서는 항진균활성을 가지는Bacillus lentimorbus WJ5의 genomic DNA를 무작위 하게 제한효소로 절단하여 2,000개의 DNA단편을 microarray하였으며, 감마선($^{60}Co$)조사로 유도된 7종의 항진균 활성 결핍 돌연변이체와 발현양상을 정량적으로 비교하였다. Gene Cluster (Michael Risen, Stanford Uniy.)를 이용한 DNA microarray의 분석 결과, 총 408개의 DNA 단편이 발현되는 것을 확인할 수 있었으며, 이들 중 20개의 DNA단편이 항진균 활성 결핍 돌연변이체에서 발현이 억제되는 것으로 나타났다. 특히,pbuX (xanthine permease, K222), ywbA (phosphotransferase system enzyme II, K393), ptsG (PTS glucose specific enzyme II ABC component, K877), yufO (ABC transporter(ATP-binding protein), K1301), 그리고 ftsY (signal recognition particle (docking protein), K868)는 모든 돌연변이체에서 동시에 발현되는 down-regulation된 유전자들로서 물질 이동과 관련된 것으로 보고되어 있으며, 항진균 활성 관련 신호 및 물질의 이동에 관여할 것으로 사료되어진다.

• 미생물학회지
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• 제55권2호
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• pp.112-116
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• 2019

Thp1/PCID2 단백질은 전사와 연계되어 mRNA를 핵에서 세포질로 방출하는데 필요한, 진화적으로 보존된 TREX-2 복합체의 구성요소이다. 분열효모인 Schizosaccharomyces pombe에는 Thp1/PCID2 단백질의 이종상동체가 2개 존재한다. pci2(SPBC1105.07c) 유전자 이외에, SPAC1B3.08 유전자는 PCI 영역을 갖고 있으며 TREX-2 복합체의 구성요소로 추정되는 단백질을 암호화하고 있다. SPAC1B3.08을 과발현하면, 생장이 약간 느려지고 mRNA 방출에 결함을 보였다. Yeast two-hybrid와 공동침전 분석 실험에서 SPAC1B3.08 단백질은 TREX-2 복합체의 다른 구성요소인 Sac3, Dss1 단백질들과 상호작용하였다. 이와 같은 관찰들은 S. pombe의 SPAC1B3.08 단백질도 TREX-2 복합체의 구성요소로서 mRNA 방출에 관여할 가능성을 지지한다.

• Molecules and Cells
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• 제47권1호
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• pp.100001.1-100001.8
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• 2024

In eukaryotes, a primary protein quality control (PQC) process involves the destruction of conformationally misfolded proteins through the ubiquitin-proteasome system. Because approximately one-third of eukaryotic proteomes fold and assemble within the endoplasmic reticulum (ER) before being sent to their destinations, the ER plays a crucial role in PQC. The specific functions and biochemical roles of several E3 ubiquitin ligases involved in ER-associated degradation in mammals, on the other hand, are mainly unknown. We identified 2 E3 ligases, ubiquitin protein ligase E3 component N-recognin 1 (UBR1) and ubiquitin protein ligase E3 component N-recognin 2 (UBR2), which are the key N-recognins in the N-degron pathway and participate in the ER stress response in mammalian cells by modulating their stability. Cells lacking UBR1 and UBR2 are hypersensitive to ER stress-induced apoptosis. Under normal circumstances, these proteins are polyubiquitinated through Lys48-specific linkages and are then degraded by the 26S proteasome. In contrast, when cells are subjected to ER stress, UBR1 and UBR2 exhibit greater stability, potentially as a cellular adaptive response to stressful conditions. Although the precise mechanisms underlying these findings require further investigation, our findings show that cytoplasmic UBR1 and UBR2 have anti-ER stress activities and contribute to global PQC in mammals. These data also reveal an additional level of complexity within the mammalian ER-associated degradation system, implicating potential involvement of the N-degron pathway.

• Journal of Korean Dental Science
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• 제4권1호
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• pp.6-13
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• 2011

Purpose: Craniosynostosis (CS), one of the most common congenital craniofacial deformities, is the premature closure of cranial sutures. NELL-1 is a novel molecule overexpressed during premature cranial suture closure in human CS. From a functional perspective, NELL-1 has been reported to accelerate chondrocyte maturation and modulate calvarial osteoblast differentiation and apoptosis pathways. The mechanism through which NELL-1 induces these phenomena, however, remains unclear. The purpose of this study is to identify the NELL-1 binding protein(s) through which the biologic mechanism of NELL-1 can be further investigated. Materials and Methods: Far-Western and Immunoprecipitation (IP) assays were performed, independently and in sequence, followed by mass spectrometry to identify the NELL-1 binding proteins. Reverse IP was used to verify and confirm candidate binding protein. Results: The only confirmative protein from current experimentation was vimentin. Vimentin is the major structural component of the intermediate filaments. Conclusion: The present study identified and confirmed vimentin as a NELL-1 binding protein, which opened up a new window to mechanistically facilitate studies on this CS-associated molecule.