• Genomics & Informatics
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• 제19권4호
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• pp.43.1-43.12
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• 2021

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

• Genomics & Informatics
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• 제21권2호
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• pp.25.1-25.12
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• 2023

Adaptation of infections and hosts has resulted in several metabolic mechanisms adopted by intracellular pathogens to combat the defense responses and the lack of fuel during infection. Human tuberculosis caused by Mycobacterium tuberculosis (MTB) is the world's first cause of mortality tied to a single disease. This study aims to characterize and anticipate potential antigen characteristics for promising vaccine candidates for the hypothetical protein of MTB through computational strategies. The protein is associated with the catalyzation of dithiol oxidation and/or disulfide reduction because of the protein's anticipated disulfide oxidoreductase properties. This investigation analyzed the protein's physicochemical characteristics, protein-protein interactions, subcellular locations, anticipated active sites, secondary and tertiary structures, allergenicity, antigenicity, and toxicity properties. The protein has significant active amino acid residues with no allergenicity, elevated antigenicity, and no toxicity.

• BMB Reports
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• 제33권3호
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• pp.195-201
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• 2000

A human gene has been reported that may encode the enzyme acetohydroxyacid synthase. Previously this enzyme was thought to be absent from animals although it is present in plants and many microorganisms. In plants, this enzyme is the target of a number of commercial herbicides and the use of these compounds may need to be reassessed if the human enzyme exists and proves to be susceptible to inhibition. Here we report the construction of several plasmid vectors containing the cDNA sequence for this protein, and their expression in Escherichia coli. High levels of expression were observed, but most of the protein proved to be insoluble. The small amounts of soluble protein contained little or no acetohydroxyacid synthase activity. Attempts to refold the insoluble protein were successful insofar as the protein became soluble. However, the refolded protein did not gain any acetohydroxyacid synthase activity. In vivo complementation tests of an E. coli mutant produced no evidence that the protein is active. Incorrect folding, or the lack of another subunit, may explain the data but we favor the interpretation that this gene does not encode an acetohydroxyacid synthase.

• Asian-Australasian Journal of Animal Sciences
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• 제29권8호
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• pp.1159-1165
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• 2016

The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller's dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR) spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as ${\alpha}$-helices and ${\beta}$-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area) of feed proteins were correlated with their the in vitro digestibility and solubility ($p{\leq}0.003$); moreover, the relatively quantitative amounts of ${\alpha}$-helices, random coils, and ${\alpha}$-helix to ${\beta}$-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility ($p{\leq}0.004$). On the other hand, the percentage of ${\beta}$-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001) and solubility (p = 0.002). These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the ${\alpha}$-helix-to-${\beta}$-sheet ratio can be used to predict the nutritional value of feed proteins.

• 정보처리학회논문지D
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• 제12D권2호
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• pp.247-258
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• 2005

단백질의 구조는 단백질의 기능과 밀접한 연관을 가지고 있으며 단백질 구조비교는 단백질의 모티프와 패밀리를 결정하고 나아가서 그들의 기능을 파악하는데 매우 중요한 역할을 한다. 이 논문에서는 단백질 구조데이터 및 관련된 문헌 데이터의 통합된 데이터베이스를 구축하고 웹 환경에서 질의된 단백질과 유사성 비교를 진행하여 그 결과 및 연관된 문헌데이터를 검색하여 체계적으로 정보를 제공하는 단백질 분석시스템을 제안한다. 제안 시스템을 구축하기 위하여 현재까지 가장 큰 단백질 구조데이터의 저장소인 Protein Data Bank의 플랫파일 데이터에 대해 분석을 진행하고 여기에서 단백질의 구조비교 알고리즘에 필수적인 구조데이터정보를 추출하여 새로운 구조비교에 사용되는 엔트리 플랫 파일을 만들어서 데이터베이스를 구축한다 이러한 엔트리에 연관된 분석정보 데이터는 데이터베이스 스키마를 작성하여 문헌정보 데이터베이스를 구축한다. 따라서 사용자가 인터넷을 통하여 진행한 질의는 구조비교엔진을 통하여 유사부분과 RMSD값이 계산되고 이와 연관된 문헌정보의 검색이 진행된 후 체계적으로 출력화면에 보여준다. 제안 시스템은 기존의 구조비교시스템보다 빠른 검색을 지원하고 더 훌륭한 분석환경을 제공한다.

• Molecules and Cells
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• 제43권12호
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• pp.1035-1045
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• 2020

The Drosophila genome contains four low molecular weight-protein tyrosine phosphatase (LMW-PTP) members: Primo-1, Primo-2, CG14297, and CG31469. The lack of intensive biochemical analysis has limited our understanding of these proteins. Primo-1 and CG31469 were previously classified as pseudophosphatases, but CG31469 was also suggested to be a putative protein arginine phosphatase. Herein, we present the crystal structures of CG31469 and Primo-1, which are the first Drosophila LMW-PTP structures. Structural analysis showed that the two proteins adopt the typical LMW-PTP fold and have a canonically arranged P-loop. Intriguingly, while Primo-1 is presumed to be a canonical LMW-PTP, CG31469 is unique as it contains a threonine residue at the fifth position of the P-loop motif instead of highly conserved isoleucine and a characteristically narrow active site pocket, which should facilitate the accommodation of phosphoarginine. Subsequent biochemical analysis revealed that Primo-1 and CG31469 are enzymatically active on phosphotyrosine and phosphoarginine, respectively, refuting their classification as pseudophosphatases. Collectively, we provide structural and biochemical data on two Drosophila proteins: Primo-1, the canonical LMW-PTP protein, and CG31469, the first investigated eukaryotic protein arginine phosphatase. We named CG31469 as DARP, which stands for Drosophila ARginine Phosphatase.

• 한국자기공명학회논문지
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• 제20권4호
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• pp.102-108
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• 2016

With the rapid increase of data on protein-protein interactions, the need for delineating the 3D structures of huge protein complexes has increased. The protocols for determining nuclear magnetic resonance (NMR) structure can be applied to modeling complex structures coupled with sparse experimental restraints. In this report, I suggest the use of multiple rigid bodies for improving the efficiency of NMR-assisted structure modeling of huge complexes using CYANA. By preparing a region of known structure as a new type of residue that has no torsion angle, one can facilitate the search of the conformational spaces. This method has a distinct advantage over the rigidification of a region with synthetic distance restraints, particularly for the calculation of huge molecules. I have demonstrated the idea with calculations of decaubiquitins that are linked via Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, or Lys63, or head to tail. Here, the ubiquitin region consisting of residues 1-70 was treated as a rigid body with a new residue. The efficiency of the calculation was further demonstrated in Lys48-linked decaubiquitin with ambiguous distance restraints. The approach can be readily extended to either protein-protein complexes or large proteins consisting of several domains.

• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.347-351
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• 2008

Acetyl-CoA carboxylase (ACC) is an excellent candidate for antibiotics drug target, which mediates malonyl-CoA synthesis from acetyl-CoA through acetylation process. It is also involved in the committed step of fatty acid synthesis which is essential for living organisms. We have determined the three dimensional structure of C terminal domain of HP0371, biotin-carboxyl carrier protein of H. pyroli, in solution state using heteronuclear multi-dimensional NMR spectroscopy. The structure of HP0371 shows a flatten b-sheet fold which is similar with that of E. coli. However, the sequence and structure of protruding thumb are different with that of E. coli and the thumb shows different basis of structural rigidity based on backbone dynamics data.

• BMB Reports
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• 제38권5호
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• pp.591-594
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• 2005

One of the small proteins from Helicobacter pylori, HP1242, was investigated by the solution nuclear magnetic resonance (NMR) spectroscopy. HP1242 is known as a 76-residue conserved hypothetical protein and its function cannot be identified based on sequence homology. Here, the results of the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of the HP1242 are reported using double- and triple-resonance techniques. About 95% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances that cover 75 non- Proline residues of the 76 residues are clarified through sequential- and specific- assignments. In addition, three helical regions were clearly identified on the basis of the resonance assignments.

• 한국정보통신학회논문지
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• 제22권1호
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• pp.26-32
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• 2018

단백질의 이차구조는 단백질의 진화, 구조, 기능을 연구하는데 중요한 정보이다. 단백질 서열 정보만을 이용하여 단백질의 이차 구조를 예측하는 분야에 심층 학습 방법들이 최근 들어 활발히 적용되고 있다. 이러한 방법에서 널리 사용되는 입력은 단백질 서열을 변환하여 만들어진 단백질 프로파일이다. 본 논문에서는 효과적인 단백질 프로파일을 얻기 위하여 단백질 서열 탐색 방법으로 PSI-BLAST와 더불어서 HHblits를 사용하였다. 단백질 프로파일의 구성에 사용되는 상동 단백질 서열을 결정하기 위한 유사도 문턱치와 상동 단백질 서열 정보를 반복적으로 사용하는 회수를 조절하였다. 합성곱 신경망과 순환 신경망을 사용하여 단백질 이차구조를 예측하였는데, 진화적 정보를 한번만 추가하여 만들어진 단백질 프로파일이 효과적이었다.