• KSBB Journal
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• v.16 no.1
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• pp.11-14
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• 2001

Techniques for protein refolding from inclusion body are discussed in view of its engineering application to large scale protein purification. Among the techniques, dilution and dialysis are mainly utilized due to simple operation. Membrane reactor, gel filtration chromatography, and continuous tank operation are emerging tools for their process-scale possibility in refolding. Reaction engineering approaches could be used to analyze the kinetic behaviour in the process scale refolding reactor. The kinetic analysis is helpful in the optimization of refolding yield in the refolding reactor.

• Journal of Microbiology and Biotechnology
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• v.18 no.5
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• pp.885-888
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• 2008

In this work, we demonstrate that glycolytic intermediates can serve as efficient energy sources to regenerate ATP during continuous-exchange cell-free (CECF) protein synthesis reactions. Through the use of an optimal energy source, approximately 10 mg/ml of protein was generated from a CECF protein synthesis reaction at greatly reduced reagent costs. Compared with the conventional reactions utilizing phosphoenol pyruvate as an energy source, the described method yields 10-fold higher productivity per unit reagent cost, making the techniques of CECF protein synthesis a more realistic alternative for rapid protein production.

• Genomics & Informatics
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• v.2 no.2
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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.

• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.37-40
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• 2001

We showed the result that an appreciable difference of secondary structures in the intracrystlline protein was observed between Normal and Deform shells. In order to understand the exact secondary structure of proteins, we investigated the changes in protein conformation from the specific layers via Fourier Self-Deconvolution(FSD) techniques, using ATR(Attenuated Total Reflection) information.

• Applied Chemistry for Engineering
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• v.32 no.3
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• pp.253-259
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• 2021

Colorectal cancer (CRC) is one of the most prevalent diseases in modern society, constituting a serious threat to global health. Currently, routine clinical screening and early removal of precancerous polyps are the most successful methods for reducing CRC incidence and mortality. However, the high cost and invasive detection of sigmoidoscopy and colonoscopy limited the CRC-screening participation and prevention. The emergence of biosensors provides an inexpensive, sensitive, less invasive tool for detecting CRC disease biomarkers. This review highlights some of recent efforts made on developing biosensors with electrochemical and optical techniques targeting CRC specific protein biomarkers for early diagnosis and prognosis, potential applications, and future perspectives.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.128-133
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• 2006

This paper compares domain combination based protein-protein interaction prediction method with domain based protein-protein interaction method. The prediction accuracy and reliability of the methods are compared using the same prediction technique and interaction data. According to the comparison, domain combination based prediction method has showed superior prediction accuracy to domain based prediction method for protein pairs with fully overlapped domains with protein pairs in learning sets. When we consider that domain combination based method has the effects of assigning a weight to each domain interaction, it implies that we can improve the prediction accuracies of currently available domain or domain combination based protein interaction prediction methods further by developing more advanced weight assignment techniques. Several significant facts revealed from the comparative studies are also described in this paper.

• Journal of Dairy Science and Biotechnology
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• v.41 no.3
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• pp.149-156
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• 2023

Milk protein is often fractionated/concentrated by using various techniques in dairy industries. Among these techniques, ultrafiltration (UF) is particularly efficient at concentrating the casein fraction of milk protein. The objectives of this study were to produce casein hydrolysates by concentrating the casein fraction in skim milk using the UF technique and to investigate the chemical composition of the casein hydrolysates. The skim milk was concentrated using a UF laboratory test unit equipped with 10 kDa and 30 kDa membranes. After UF, the protein content of the milk was concentrated up to ~7.2% and the Ca was concentrated up to ~196 mg/100 g of milk. Trypsin was then added to the concentrated skim milk to produce the casein hydrolysates. The results of sodium dodecyl sulphate-polyacrylamide gel electrophoresis showed that the casein fraction was not present after hydrolysis, indicating that casein in the milk had been hydrolyzed. The Ca content in the casein hydrolysates was much higher (p<0.05) compared to Ca content in commercial casein phosphopeptides (CPP) indicating that was acidified during the manufacture of commercial CPP. In conclusion, it seems that casein hydrolysates containing large concentrations of protein and Ca can also be made from concentrated UF milk without acidification or renneting.

• Macromolecular Research
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• v.17 no.3
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• pp.192-196
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• 2009

Recently, the multi-screening of target materials has been made possible by the development of the surface plasmon resonance (SPR) imaging method. To adapt this method to biochemical analysis, the multi-patterning technology of protein microarrays is required. Among the different methods of fabricating protein microarrays, the microfluidic platform was selected due to its various advantages over other techniques. Microfluidic devices were designed and fabricated with polydimethylsiloxane (PDMS) by the replica molding method. These devices were designed to operate using only capillary force, without the need for additional flow control equipment. With these devices, multiple protein-patterned sensor surfaces were made, to support the two-dimensional detection of various protein-protein interactions with SPR. The fabrication technique of protein microarrays can be applied not only to SPR imaging, but also to other biochemical analyses.

• Journal of Microbiology and Biotechnology
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• v.16 no.1
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• pp.141-144
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• 2006

An antibody layer was fabricated to detect Escherichia coli O157:H7. The micropattern of 16-mercaptohexadecanoic acid (16-MHDA) as alkylthiolate was formed on the gold surface by using the PDMS stamp with microcontact printing $({\mu}CP)$ techniques. In order to form antibody patterns on the template, protein G was chemically bound to the 16-MHDA patterns, and antibody was adsorbed on a self-assembled protein G layer. The formation of the 16-MHDA micropattern, self-assembled protein G layer and antibody pattern on Au substrate was confirmed by surface plasmon resonance (SPR) spectroscopy. Finally, the micropatterning method was applied to fabricate the antibody probe for detection of E. coli O157:H7, and monitoring of antigen by using this probe was successfully achieved.

• Genomics & Informatics
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• v.21 no.1
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• pp.7.1-7.11
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• 2023

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazF-like toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.