• 한국컴퓨터정보학회논문지
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• 제14권3호
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• pp.193-207
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• 2009

세포 내에서 일어나는 단백질 신호 전달 과정은 단백질간의 상호작용을 통해 수행되고 조절된다. Yeast 상호작용 정보와 녹색형광단백질(GFP)을 이용하여 밝혀진 약 5,000여 개의 Yeast 단백질 위치정보를 이용하여 가중치를 부여하고 신호 전달경로 추출 및 예측을 위한 고성능 LocSPF 알고리즘을 최초로 제안하였다. 가중치 알고리즘에 의해 산출된 결과 중 의미 상관도가 높은 것을 채택한 후 KEGG에서 제공하는 신호전달 경로와 같은 신호전달 경로를 추출하는지 유사도 비교를 하였다. 한편 더 나아가 아직 실험을 통해 밝혀지지 않은 단백질 신호전달 경로를 예측하여 결과를 제시함으로써 본 연구를 통해서 알려지지 않은 새로운 신호전달 경로를 발견하거나 이전 경로에 참여하지 않은 단백질들을 발견할 수 있는 가능성을 제시 하였다.

• Journal of Microbiology and Biotechnology
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• 제33권12호
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• pp.1681-1691
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• 2023

Flavin mononucleotide-binding proteins or domains emit cyan-green fluorescence under aerobic and anaerobic conditions, but relatively low fluorescence and less thermostability limit their application as reporters. In this work, we incorporated the codon-optimized fluorescent protein from Chlamydomonas reinhardtii with two different linkers independently into the redox-responsive split intein construct, overexpressed the precursors in hyperoxic Escherichia coli SHuffle T7 strain, and cyclized the target proteins in vitro in the presence of the reducing agent. Compared with the purified linear protein, the cyclic protein with the short linker displayed enhanced fluorescence. In contrast, cyclized protein with incorporation of the long linker including the myc-tag and human rhinovirus 3C protease cleavable sequence emitted slightly increased fluorescence compared with the protein linearized with the protease cleavage. The cyclic protein with the short linker also exhibited increased thermal stability and exopeptidase resistance. Moreover, induction of the target proteins in an oxygen-deficient culture rendered fluorescent E. coli BL21 (DE3) cells brighter than those overexpressing the linear construct. Thus, the cyclic reporter can hopefully be used in certain thermophilic anaerobes.

• 생명과학회지
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• 제18권3호
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• pp.318-322
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• 2008

단백질 상호작용 관련 데이터들이 기하급수적으로 증가하고 있는데 그러한 데이터들을 수동으로 갱신하고 관리하는 작업은 엄청나게 많은 시간과 노력을 요구한다. 뿐만 아니라 개발자가 아닌 비전문가인 생물학자들이 시스템 구성 데이터베이스들을 갱신하고 관리하며 분석 시스템을 운영한다는 것은 현실적으로 거의 불가능하다. 이러한 측면에서 단백질 상호작용 정보를 이용한 효율적인 단백질 기능분석 시스템인 WASPIFA에 대해 자동적으로 데이터를 갱신하고 관리할 수 있는 시스템을 설계하고 개발하였다. WASPIFA 시스템은 단백질의 상호작용 관련 데이터들을 통합하여 사용자가 편리하게 데이터를 검색할 수 있으며 단백질 상호작용에 관련된 정보 즉, 기능 및 주석 정보, 도메인 정보, 도메인 간의 상호 작용 정보 등을 제공해 주는 유용한 단백질 기능분석 시스템이다.

• 대한기계학회논문집A
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• 제28권12호
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• pp.1997-2003
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• 2004

This paper presents a new method and an associated device, capable of detecting protein presence and size from the shift of the mechanical stiffness changing points due to the presence and size of proteins in a nano-gap actuator. Compared to the conventional resonant detection method, the present nanomechanical stiffness detection method shows higher precision for protein detection. The present method also offers simple and inexpensive protein detection devices by removing labeling process and optical components. We design and fabricate the nanomechanical protein detector using an electrothermal actuator with a nano-gap. In the experimental study, we measure the stiffness changing points and their coordinate shift from the devices with and without target proteins. The fabricated device detects the protein presence and the protein size of 14.0$\pm$7.4nm based on the coordinate shift of stiffness changing points. We experimentally verify the protein presence and size detection capability of the nanomechanical protein detector for applications to high-precision biomolecule detection.

• ETRI Journal
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• 제37권4호
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• pp.813-823
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• 2015

Because protein is a primary element responsible for biological or biochemical roles in living bodies, protein function is the core and basis information for biomedical studies. However, recent advances in bio technologies have created an explosive increase in the amount of published literature; therefore, biomedical researchers have a hard time finding needed protein function information. In this paper, a classification system for biomedical literature providing protein function evidence is proposed. Note that, despite our best efforts, we have been unable to find previous studies on the proposed issue. To classify papers based on protein function evidence, we should consider whether the main claim of a paper is to assert a protein function. We, therefore, propose two novel features - protein and assertion. Our experimental results show a classification performance with 71.89% precision, 90.0% recall, and a 79.94% F-measure. In addition, to verify the usefulness of the proposed classification system, two case study applications are investigated - information retrieval for protein function and automatic summarization for protein function text. It is shown that the proposed classification system can be successfully applied to these applications.

• Advances in nano research
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• 제13권6호
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• pp.561-574
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• 2022

The stability of protein tissues and protein fibers in the human muscle is investigated in the presented paper. The protein fibers are modeled via tube structures embedded in others proteins fibers like the elastic substrate. Physical sport and physical exercise play an important role in the stability of synthesis and strength of the protein tissues. In physical exercise, the temperature of the body increases, and this temperature change impacts the stability of the protein tissues, which is the aim of the current study. The mathematical simulation of the protein tissues is done based on the mechanical sciences, and the protein fibers are modeled via wire structures according to the high-order theory beams. The thermal stress due to the conditions of the sport is applied to the nanoscale protein fibers, then the stability regarding the frequency analysis is investigated. Finally, the impact of temperature change, physical exercise, and small-scale parameters on the stability of the protein tissues are examined in detail.

• 대한전기학회:학술대회논문집
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• 대한전기학회 2006년도 제37회 하계학술대회 논문집 C
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• pp.1629-1630
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• 2006

This paper describes a micro total analysis system ($\mu$ TAS) for detecting and digesting the target protein which includes a bead based temperature controllable microchip and computer based controllers for temperature and valve actuation. We firstly combined the temperature control function with a bead based microchip and realized the on-chip sequential reactions using two kinds of beads. The PEG-grafted bead, on which RNA aptamer was immobilized, was used for capturing and releasing the target protein. The target protein can be chosen by the type of RNA aptamer. In this paper, we used the RNA aptamer of HCV replicase. The trypsin coated bead was used for digesting the released protein prior to the matrix assisted laser desorption ionization time of flight mass spectrometer (MALDI TOF MS). Heat is applied for release of the captured protein binding on the bead, thermal denaturation and trypsin digestion. PDMS microchannel and PDMS micro pneumatic valves were also combined for the small volume liquid handling. The entire procedures for the detection and the digestion of the target protein were successfully carried out on a microchip without any other chemical treatment or off-chip handling using $20\;{\mu}l$ protein mixture within 20 min. We could acquire six matched peaks (7% sequence coverage) of HCV replicase.

• Asian-Australasian Journal of Animal Sciences
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• 제11권4호
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• pp.391-397
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• 1998

The present study was conducted to examine the effects of dietary protein (20, 22, 24%) with a constant protein-to-energy ratio on clenbuterol-induced performance in broilers. The protein-to-energy ratio was based on adequate level (22% protein, 3,100 kcal of energy). Female broiler chickens were used for a $3{\times}2$ factorial arrangement and fed diets with or without 1 ppm clenbuterol from 14- to 32-days of age. Feed efficiency improved with increasing dietary protein level, regardless of clenbuterol treatment. The dietary clenbuterol increased weights of breast and leg muscles (gastrocnemius and peroneus longus), and clenbuterol markedly reduced protein content of leg muscles in chickens fed the 20% protein diet, but did not in chickens fed the 22 and 24% protein diets. Feeding the 24% protein diet with clenbuterol improved the protien accretion (peroneus longus) by 8.4%. Clenbuterol decreased DNA content and increased the protein/DNA ratio in breast muscle regardless of dietary protein intake. Clenbuterol had no effect on RNA content in both breast and leg muscles. The present results demonstrated that various protein levels which retain the same protein-to-energy ratio in the diet markedly alter the protein accretion induced by ${\beta}$-agonist in broilers.

• Genomics & Informatics
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• 제2권2호
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• pp.99-106
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• 2004

In this paper we introduce PubMiner, an intelligent machine learning based text mining system for mining biological information from the literature. PubMiner employs natural language processing techniques and machine learning based data mining techniques for mining useful biological information such as protein­protein interaction from the massive literature. The system recognizes biological terms such as gene, protein, and enzymes and extracts their interactions described in the document through natural language processing. The extracted interactions are further analyzed with a set of features of each entity that were collected from the related public databases to infer more interactions from the original interactions. An inferred interaction from the interaction analysis and native interaction are provided to the user with the link of literature sources. The performance of entity and interaction extraction was tested with selected MEDLINE abstracts. The evaluation of inference proceeded using the protein interaction data of S. cerevisiae (bakers yeast) from MIPS and SGD.

• BMB Reports
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• 제52권5호
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• pp.324-329
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• 2019

Recent progress in cellular reprogramming technology and lineage-specific cell differentiation has provided great opportunities for translational research. Because virus-based gene delivery is not a practical reprogramming protocol, protein-based reprogramming has been receiving attention as a safe way to generate reprogrammed cells. However, the poor efficiency of the cellular uptake of reprogramming proteins is still a major obstacle. Here, we reported key factors which improve the cellular uptake of these proteins. Purified red fluorescent proteins fused with 9xLysine (dsRED-9K) as a cell penetrating peptide were efficiently delivered into the diverse primary cells. Protein delivery was improved by the addition of amodiaquine. Furthermore, purified dsRED-9K was able to penetrate all cell lineages derived from mouse embryonic stem cells efficiently. Our data may provide important insights into the design of protein-based reprogramming or differentiation protocols.