• BMB Reports
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• v.38 no.5
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• pp.550-554
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• 2005

YKR049C is a mitochondrial protein in Saccharomyces cerevisiae that is conserved among yeast species, including Candida albicans. However, no biological function for YKR049C has been ascribed based on its primary sequence information. In the present study, NMR spectroscopy was used to determine the putative biological function of YKR049C based on its solution structure. YKR049C shows a well-defined thioredoxin fold with a unique insertion of helices between two $\beta$-strands. The central $\beta$-sheet divides the protein into two parts; a unique face and a conserved face. The 'unique face' is located between ${\beta}2$ and ${\beta}3$. Interestingly, the sequences most conserved among YKR049C families are found on this 'unique face', which incorporates L109 to E114. The side chains of these conserved residues interact with residues on the helical region with a stretch of hydrophobic surface. A putative active site composed by two short helices and a single Cys97 was also well observed. Our findings suggest that YKR049C is a redox protein with a thioredoxin fold containing a single active cysteine.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.12
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• pp.1743-1749
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• 2000

An experiment was conducted to investigate the effect of supplementation of commercial phytase and ${\beta}-glucanase$ to wheat-soybean meal based layer diets. Control (17% CP) and reduced protein (13.5% CP) diets were compared with and without phytase and/or ${\beta}-glucanase$. Reducing dietary crude protein levels reduced the amount of N excreted by laying hens with no adverse affect on egg production or overall feed conversion ratio. There was, however, a slight reduction in average egg weight. When phytase was added to the control protein diets it was possible to reduce the level of dicalcium phosphate in the diet without a loss in performance and daily P output was reduced significantly. When phytase was added to the reduced protein diets, however, there was a dramatic loss in performance in the last four weeks of the study. Supplementation of ${\beta}-glucanase$ to wheat based layer diet did not appear to have beneficial affects in terms of laying performance and reducing nitrogen or phosphorus excretion. Combination of phytase and ${\beta}-glucanase$ had no positive effects on laying performance or reduction of DM, N and P.

• Journal of Microbiology and Biotechnology
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• v.25 no.4
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• pp.503-510
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• 2015

The iLOV protein belongs to a family of blue-light photoreceptor proteins containing a light-oxygen-voltage sensing domain with a noncovalently bound flavin mononucleotide (FMN) as its chromophore. Owing to advantages such as its small size, oxygen-independent nature, and pH stability, iLOV is an ideal candidate over other reporter fluorescent proteins such as GFP and DsRed. Here, for the first time, we describe the feasibility of applying LOV domain-based fluorescent iLOV as a metal sensor by measuring the fluorescence quenching of a protein with respect to the concentration of metal ions. In the present study, we demonstrated the inherent copper sensing property of the iLOV protein and identified the possible amino acids responsible for metal binding. The fluorescence quenching upon exposure to Cu²⁺ was highly sensitive and exhibited reversibility upon the addition of the metal chelator EDTA. The copper binding constant was found to be 4.72 ± 0.84 µM. In addition, Cu²⁺-bound iLOV showed high fluorescence quenching at near physiological pH. Further computational analysis yielded a better insight into understanding the possible amino acids responsible for Cu²⁺ binding with the iLOV protein.

• Journal of Korean Biological Nursing Science
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• v.10 no.1
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• pp.1-10
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• 2008

Purpose: The purpose of this study was to investigate the cerebral infarction size, antioxidant enzyme activities and lipid peroxidation changes after 6 weeks of dietary soybean protein intake in a rat focal brain ischemia model. Method: Weaning Sprague-Dawley rats were fed with either modified AIN-93G diet containing casein 20% (control), 20% soybean protein isolate-based diet (S20), or 40% of soybean protein isolate-based diet (S40) for 6 weeks. The animals were subject to right middle cerebral artery occlusion for 2 hr. After 24 hr of recirculation, the rats were sacrificed. Antioxidant enzymes activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) and thiobarbituric acid reactive substance (TBARS) level in the right brain were also measured. Result: There were no significant differences in the right cortical infarction volume, TBARS level, SOD and CAT activities among the three groups whereas the GPx activities of the S20 group were significantly higher than those of the control group (p=.02). Conclusion: Our results suggest that 20% of soybean protein may have a modulating effect on GPx and possibly have some protective effect against oxidative stress although it may enough to decrease cerebral infarction volume in rat focal brain ischemia model.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.16 no.3
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• pp.771-791
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• 2022

Protein-protein interaction (PPI) extraction from original text is important for revealing the molecular mechanism of biological processes. With the rapid growth of biomedical literature, manually extracting PPI has become more time-consuming and laborious. Therefore, the automatic PPI extraction from the raw literature through natural language processing technology has attracted the attention of the majority of researchers. We propose a PPI extraction model based on the large pre-trained language model and adversarial training. It enhances the learning of semantic and syntactic features using BioBERT pre-trained weights, which are built on large-scale domain corpora, and adversarial perturbations are applied to the embedding layer to improve the robustness of the model. Experimental results showed that the proposed model achieved the highest F1 scores (83.93% and 90.31%) on two corpora with large sample sizes, namely, AIMed and BioInfer, respectively, compared with the previous method. It also achieved comparable performance on three corpora with small sample sizes, namely, HPRD50, IEPA, and LLL.

• Korean Journal of Exercise Nutrition
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• v.24 no.2
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• pp.6-10
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• 2020

[Purpose] Milk is a commonly ingested post-exercise recovery protein source. Casein protein, found in milk, is characterized by its slow digestion and absorption. Recently, several studies have been conducted with a focus on how pre-sleep casein protein intake could affect post-exercise recovery but our knowledge of the subject remains limited. This review aimed at presenting and discussing how pre-sleep casein protein ingestion affects post-exercise recovery and the details of its potential effector mechanisms. [Methods] We systematically reviewed the topics of 1) casein nutritional characteristics, 2) pre-sleep casein protein effects on post-exercise recovery, and 3) potential effector mechanisms of pre-sleep casein protein on post-exercise recovery, based on the currently available published studies on pre-sleep casein protein ingestion. [Results] Studies have shown that pre-sleep casein protein ingestion (timing: 30 minutes before sleep, amount of casein protein ingested: 40-48 g) could help post-exercise recovery and positively affect acute protein metabolism and exercise performance. In addition, studies have suggested that repeated pre-sleep casein protein ingestion for post-exercise recovery over a long period might also result in chronic effects that optimize intramuscular physiological adaptation (muscle strength and muscle hypertrophy). The potential mechanisms of pre-sleep casein protein ingestion that contribute to these effects include the following: 1) significantly increasing plasma amino acid availability during sleep, thereby increasing protein synthesis, inhibiting protein breakdown, and achieving a positive protein balance; and 2) weakening exercise-induced muscle damage or inflammatory responses, causing reduced muscle soreness. Future studies should focus on completely elucidating these potential mechanisms. [Conclusion] In conclusion, post-exercise ingestion of at least 40 g of casein protein, approximately 30 minutes before sleep and after a bout of resistance exercise in the evening, might be an effective nutritional intervention to facilitate muscle recovery.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.388-391
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• 2005

The Protein Structural and Functional Conservation need a common language for data definition. With the help of common language provided by Protein Ontology the high level of sequence and functional conservation can be extended to all organisms with the likelihood that proteins that carry out core biological processes will again be probable orthologues. The structural and functional conservation in these proteins presents both opportunities and challenges. The main opportunity lies in the possibility of automated transfer of protein data annotations from experimentally traceable model organisms to a less traceable organism based on protein sequence similarity. Such information can be used to improve human health or agriculture. The challenge lies in using a common language to transfer protein data annotations among different species of organisms. First step in achieving this huge challenge is producing a structured, precisely defined common vocabulary using Protein Ontology. The Protein Ontology described in this paper covers the sequence, structure and biological roles of Protein Complexes in any organism.

• Journal of Sensor Science and Technology
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• v.20 no.6
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• pp.434-438
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• 2011

A portable surface plasmon resonance(SPR) based immunosensor using thiolated protein G and protein G was developed for the detection of immunoglobulin G(IgG). The protein G has specific affinity with Fc fragment of IgG and was thiolated by 2-Iminothiolane for introduction of thiol groups. Anti-IgG, bovine serum albumin(BSA), and IgG have been sequently injected after surface modification of gold sensor chip with protein G and thiolated protein G. The output signal was increased with the injection of each protein and the actual signal was measured by subtracting signal of reference channel from signal of sample injected channel. The experimental results showed the higher detection capability of IgG using thiolated protein G compared with protein G. From these results, we can conclude that the current surface modification technique and the portable SPR sensor system can be applied to various immunosensors for diagnosis.

• Asian-Australasian Journal of Animal Sciences
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• v.5 no.1
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• pp.123-128
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• 1992

In Experiment 1, when fasted chicks were fed diets containing various sources of protein for 3 days, the activities of lipogenic enzymes (acetyl-CoA carboxylase, fatty acid synthetase, citrate cleavage enzyme and malic enzyme) in the liver of growing chicks were significantly lower in the soybean protein or gluten diet than in the casein or fish protein diet. Triglycride contents of the liver and plasma of chicks fed the casein or fish protein diet were significantly lower than that of those fed soybean protein or gluten diet. In Experiment 2, the effects of dietary amino acid mixture simulating casein or protein on the activities of hepatic lipogenic enzymes were examined. The activities of acetyl-CoA carboxylase and fatty acid synthetase in the liver of chicks fed the casein diet were significantly higher than that of those fed the soybean protein diet or two diets of amino acid mixtures. Furthermore, there were no significant differences between the two diets of amino acid mixture based on casein or soybean protein. However, the activities of malic enzyme and citrate cleavage enzyme tended to be lower in the soybean-type amino acid diet than in the casein-type amino acid diet. Thus, some effects can be ascribed to the protein itself and some to the amino acid composition of the protein sources.

• Journal of Nutrition and Health
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• v.12 no.4
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• pp.11-19
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• 1979

A numerical analysis of essential amino acid pattern of protein in daily Korean foods was conducted through computer programming based on the food intake data from 'Reports of national nutritional survey (1969, $1973{\sim}1979)'$ and food supply data from 'Food balance sheet $(1970{\sim}1977)'$. It was noted that the amounts of daily intake and supply of animal protein were gradually increased since 1973. In 1977, animal protein intake was 17.5g in total protein intake of 68g per person per day. Intake and supply of total essential amino acids were $20{\sim}28g$ per person per day in the both of urban and rural areas, and greater consumption of leucine, phenylalanine+tyrosine, isoleusine, lysine and valine was observed. Amino acids scores of consumed protein based on FAO provisional amino acid scoring pattern(1973) were around $75{\sim}90$ showing the scores of 77.9 in 1969 and 89.5 in 1977, and also lysine(1969, $1973{\sim}1976$) and threonine(1977) were considered as first limiting amino acid. On the other hand the scores of supply Protein $(1970{\sim}1977)$ rated in $82{\sim}88$, lysine$(1970{\sim}1971)$ or threonine $(1972{\sim}1977)$ was found as first limiting amino acid. Generally a protein quality of Korean daily food was improved since 1973 and a difference between urban and rural areas in terms of the nutritive quality of protein was considerably reduced in 1977.