• Journal of the Korea Institute of Information and Communication Engineering
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• v.22 no.1
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• pp.26-32
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• 2018

The protein secondary structures are important information for studying the evolution, structure and function of proteins. Recently, deep learning methods have been actively applied to predict the secondary structure of proteins using only protein sequence information. In these methods, widely used input features are protein profiles transformed from protein sequences. In this paper, to obtain an effective protein profiles, protein profiles were constructed using protein sequence search methods such as PSI-BLAST and HHblits. We adjust the similarity threshold for determining the homologous protein sequence used in constructing the protein profile and the number of iterations of the profile construction using the homologous sequence information. We used the protein profiles as inputs to convolutional neural networks and recurrent neural networks to predict the secondary structures. The protein profile that was created by adding evolutionary information only once was effective.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.7
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• pp.974-978
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• 2001

The effect of three varying ratios (high, medium and low) of Rumen Degradable Protein (RDP) to Undegradable Dietary Protein (UDP) of 37:63, 52:48 and 70:30 in iso-nitrogenous and iso-caloric concentrate mixtures on rumen fermentation profile was studied using rumen fistulated Jersey crossbred cows. Rumen pH and ammonia nitrogen concentration were found to be lower with a concentrate mixture containing a higher UDP level of 63.38% when compared with those having medium and low UDP levels of 47.55 and 29.75%, respectively, at all post feeding intervals. Total volatile fatty acid concentration as well as concentrations of individual fatty acids viz., acetate, propionate and butyrate were also found higher in animals fed concentrate mixture with the highest UDP level.

• Bioinformatics and Biosystems
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• v.1 no.1
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• pp.82-87
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• 2006

The most popular protein structure prediction method is comparative modeling. To guarantee accurate comparative modeling, the sequence alignment between a query protein and a template should be accurate. Although choosing the best template based on the protein sequence alignments is most critical to perform more accurate fold-recognition in comparative modeling, even more critical is the sequence alignment quality. Contrast to a lot of attention to developing a method for choosing the best template, prediction of alignment accuracy has not gained much interest. Here, we develop a method for prediction of the shift score, a recently proposed measure for alignment quality. We apply support vector regression (SVR) to predict shift score. The alignment between a query protein and a template protein of length n in our own library is transformed into an input vector of length n +2. Structural alignments are assumed to be the best alignment, and SVR is trained to predict the shift score between structural alignment and profile-profile alignment of a query protein to a template protein. The performance is assessed by Pearson correlation coefficient. The trained SVR predicts shift score with the correlation between observed and predicted shift score of 0.80.

• Journal of Applied Biological Chemistry
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• v.55 no.2
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• pp.79-83
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• 2012

It has been known that the proteome profiles in the period of growth and development of rice are changed by the growth conditions including temperature, soil, and fertilization. In this study, the proteome profiles of Odae polished white rice grown in Chulwon and Chilgog were compared on 2-dimensional(D) gels. The differentially expressed proteins were selected from the 112 identified total proteins and classified into functional groups. The most significantly differentially expressed proteins were stress responsive proteins; Ent-kaur-16-ene synthase, which is responsible for synthesizing a plant hormone gibberellin, was expressed in Chulwon rice and heat shock proteins were in Chilgog rice, respectively. Xylanase inhibitor protein, which inhibits the enzyme xylanase produced by pathogenic fungi and Bacilli, was expressed significantly high in Chilgog rice grown at high temperature. Differential expressions of transporter proteins were observed both in Chulwon and Chilgog rice. Regarding the facts that Chilgog rice contained relatively higher amount of proteins than Chulwon rice and Chulwon rice showed large number of proteins were differentially expressed, it can be concluded that different cultivation conditions could change the protein expression profiles in rice in various ways, including elevation of protein amount or differential expressions of specific proteins, etc. The results suggest that the characteristics of the profiles of the proteome in the polished white rice are definitely changed by the environmental factors including high temperature. The results can be utilized for the development of the proper cultivation conditions for the production of high quality rice with good palatability.

• Journal of the Korean Society of Food Science and Nutrition
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• v.35 no.4
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• pp.470-475
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• 2006

In order to elucidate the differences of protein profiles among soybean cultivars, the protein composition of three conventional domestic soybean cultivars and two imported ones including glyphosate-tolerant HS2906 was analyzed by total nitrogen measurement, amino acid analysis and PAGE/densitometry. There were no statistically significant differences in the levels of any amino acid, including aromatic amino acids, between glyphosale-tolerant soybean and the conventional soybean WS82. In the extraction of protein, the SDS/buffer system was more efficient than the defatting/water system. The SDS-PAGE/densitometry analysis showed that there was a similar profile of proteins among cultivars, although the amount of total protein ranged from 380.2 mg/g to 423.9 mg/g. In addition, there was no discernable difference of protein profile between glyphosate- tolerant soybean (total protein amount, 380.2 mg/g) and the conventional soybean WS82 (390.2 mg/g), although the amount of ${\beta}$-conglycinin (55 kDa) was lower in glyphosate-tolerant soybean. Meanwhile, the amount of 25 kDa protein was greater in domestic soybean cultivars than imported ones. Thus, normal PAGE/ densitometry method would be useful to analyze the difference in protein profiles of soybean proteins, and furthermore Evaluate the protein profile of proteins between GMO and conventional soybean.

• IMMUNE NETWORK
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• v.4 no.3
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• pp.184-189
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• 2004

Background: Hu syndrome, a neurological disorder, is characterized by the remote effect of small cell lung cancer on the neural degeneration. The suspicious effectors for this disease are anti-Hu autoantibodies or Hu-related CD8+ T lymphocytes. Interestingly, the same effectors have been suggested to act against tumor growth and this phenomenon may represent natural tumor immunity. For these diagnostic and therapeutic reasons, the demand for antibodies against Hu protein is rapidly growing. Methods: Polyclonal and monoclonal antibodies were generated using recombinant HuR protein. Western blot analyses were performed to check the specificity of generated antibodies using various recombinant proteins and cell lysates. Extracellular stimuli for HuR expression had been searched and HuR-associated proteins were isolated from polysome lysates and then separated in a 2-dimensional gel. Results: Polyclonal and monoclonal antibodies against HuR protein were generated and these antibodies showed HuR specificity. Antibodies were also useful to detect and immunoprecipitate endogenous HuR protein in Jurkat and BJAB. This report also revealed that TNF-${\alpha}$ treatment in BJAB up-regulated HuR expression. Lastly, protein profile in HuR-associated mRNAprotein complexes was mapped by 2-dimensional gel electrophoresis. Conclusion: This study reported that new antibodies against HuR protein were successfully generated. Currently, project to develop a diagnostic kit is in process. Also, this report showed that TNF-${\alpha}$ up-regulated HuR expression in BJAB and protein profile associated with HuR protein was mapped.

• Journal of Applied Biological Chemistry
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• v.51 no.3
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• pp.88-94
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• 2008

Three different protein extraction methods-phenol extraction, trichloroacetic acid (TCA) precipitation, and desalting/TCA precipitation-were compared to determine the optimal reproducible high resolution 2-dimensional (2-D) electrophoresis for each chungkugjang, doenjang, and kochujang samples. The soluble proteins from Chungkugjang extracted by phenol were separated with high reproducibility and resolution, and gained 1.75- to 3-fold more protein spots on 2-D gel than those from the other methods. On the contrary, the extracted proteins from doenjang and kochujang treated by desalting/TCA precipitation method showed about 1.5- to 3.3-fold more protein spots on 2-D gel. Using the established methods, the changes in the protein profiles of the fermented soy foods were monitored during the fermentation period by 2-DE. One of the major proteins in soy, $\beta$-conglycinin $\alpha$-subuint, and some proteins with unknown functions were localized on 2-D gel as the protease-resistant proteins throughout the fermentation period of doenjang. Changes in the protein profile monitored by the established methods can provide basic information on unfolding the mechanisms of the generation of biofunctional activity in the fermented soy foods.

• Animal cells and systems
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• v.4 no.2
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• pp.145-150
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• 2000

Retinoic acid (RA) evokes pattern duplication in the regenerating salamander limb. Interestingly, it also enhances dedifferentiation in the regenerate by the morphological, histological and biochemical criteria. To examine whether there is any correlation between the RA-evoked pattern duplication and de novo protein synthetic profile in the regenerating salamander limb, especially during dedifferentiation, we analyzed stage-specific protein synthesis pattern in the normal and RA-treated regenerating limbs by metabolic labeling followed by two-dimensional gel electrophoresis. In the regenerating limbs without RA treatment, a few hundred kinds of proteins were found to be synthesized at the stage of wound healing and the total number of protein synthesized increased greatly as regeneration proceeded. The same trend was also observed in the RA-treated regenerating limbs. Interestingly, some protein spots were noted to be either newly synthesized or highly expressed by the RA treatment especially at the stage of dedifferentiation. The results shows that the enhancement of dedifferentiation state after the RA treatment correlates well with the protein synthesis profile, and suggest that those proteins are important for the RA-evoked pattern duplication in the regenerating limbs of salamander.

• Korean Journal of Animal Reproduction
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• v.16 no.4
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• pp.289-299
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• 1993

The polypeptide patterns of cellular and follicular components were analysed by SDS-PAGE and two dimensional(2-D)electrophoresis combined with isoelectric focusing (IEF) to establish protein profiles in each of the components in porcine follicles. Oocyte-cumulus complexes were cultured in M16+FCS+Gn at 39 in an atmosphere of 5% CO$_2$, in air for 35 h. At the end of the culture, the zona-free oocyte, ZP alone and cumulus cells were prepared and analysed either on 10% SDS-PAGE for the protein profile at the first dimensional gel or 2-D protein pattern. The amounts of each samples were determined for the visualization with Coomasie brilliant blue (CBB) or silver staining, thus giving useful information for the identification of specific proteins in the components or appropriate amount of samples for proper visualization. Oocyte showed 25 and 114 kd major protein band. Other minor components were additionally visualized with CBB on the same gel after silver staining procedure. Cumulus cells also showed specific proteins which is not present in the oocytes. The number of cumulus cell was proper to give major bands with CBB and additional minor bands with silver staining. To establish the degree of contamination from the remnant of the corona radiata to the ZP, zonae were differently prepared or analysed by SDS-PAGE.The preparation of the ZP in this study did not showed any contamination judged by the protein profile of the components. Also follicular fluid showed its specific protein profile without any significant differences among the different sizes of follicles. The established protein profile of each follicular component should be helpful for the identification and elimination of contaminated components, i. e., antigen preparation or immunological studies. The results also suggest that the preparation of each components in the study was appropriate and can be used for a further sensitive biochemical analysis in mammalian oocytes and early embryos.

• Korean Journal of Veterinary Research
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• v.50 no.4
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• pp.285-295
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• 2010

Protein expression patterns in Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) strains with diverse phenotypes, such as phage type, antibiotic resistance pattern and plasmid profiles were examined. For detailed analysis of proteins expressed by different S. Typhimurium strains, protein fractions were divided into detergent-rich phase (DP) and aqueous phase (AP) using triton X-114 detergent. The two phases were subjected to two-dimensional gel electrophoresis (2-DE), followed by protein identification using peptide mass fingerprinting (PMF). In the results, PMF showed that DP fractions consisted mainly of outer membrane proteins, whereas the AP fractions included cytosolic proteins. Comparison of 2-DE profiles of DP did not show any distinct protein spots which could be correlated with phage type, antibiotic resistance pattern or plasmid profile. However, comparisons of 2-DE profiles of the AP revealed differences in the protein spots, which could be correlated with the plasmid profile and phage types. Among these protein spots, flagellin was specific for strains containing a 90 kb plasmid. Compared to DT193 phage type, three protein spots in the range of pI 5.0-5.5 and MW 8-15 kDa of AP 2-DE profiles were absent in the DT104 phage types. Additionally, a protein spot with PI in the range of 4.5-5.0 and molecular weight (MW) between 51-69 kDa was specific for phage type DT104, while a protein spot with pI in the range of 4.0-4.8 and MW between 18-20 kDa was specific for DT193 phage type. These protein spots may be useful for discriminating phage types of S. Typhimurium.