• Journal of KIISE:Computing Practices and Letters
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• v.11 no.2
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• pp.133-148
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• 2005

Since understanding of similarities and differences among protein structures is very important for the study of the relationship between structure and function, many protein structure comparison systems have been developed. Hut, unfortunately, these systems introduce their own protein data derived from the PDB(Protein Data Bank), which are needed in their algorithms for comparing protein structures. In addition, according to the rapid increase in the size of PDB, these systems require much more computation to search for common substructures in their databases. In this paper, we introduce a protein structure comparison system named WS4E(A Web-Based Searching Substructures of Secondary Structure Elements) based on a PSAML database which stores PSAML documents using the eXist open XML DBMS. PSAML(Protein Structure Abstraction Markup Language) is an XML representation of protein data, describing a protein structure as the secondary structures of the protein and their relationships. Using the PSAML database, the WS4E provides web services searching for common substructures among proteins represented in PSAML. In addition, to reduce the number of candidate protein structures to be compared in the PSAML database, we used topology strings which contain the spatial information of secondary structures in a protein.

• International Journal of Industrial Entomology and Biomaterials
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• v.4 no.2
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• pp.101-107
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• 2002

We describe here the cDNA sequence and mRNA expression of a novel family of the antioxidant protein, peroxiredoxin, from the firefly, Pyracoetia ruin. The 555 bp cDNA sequence codes for a 185 amino acid protein with a calculated molecular mass of approximately 21 kDa. The deduced protein of P. rufa peroxiredoxin gene contains two conserved cysteine residues. Alignment of the deduced protein of P. rufa peroxiredoxin gene showed 71.1% protein sequenceidentity to known insect Drosophila melanogaster peroxiredoxin. Northern blot analysis revealed that the P. rufa peroxiredoxin is specifically expressed in the fat body of P. rufa larvae.

• International Journal of Industrial Entomology and Biomaterials
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• v.8 no.2
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• pp.145-149
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• 2004

The expression of a fusion protein comprised of the B. thuringiensis crystal protein, Cry1Ac, and enhanced green fluorescent protein (EGFP) in Escherichia coli XLl-blue was examined. Three recombinant plasmids were transformed into E. coli XL1-blue and named as ProAc/Ec, MuEGFP/Ec and ProMu-EGFP/Ec, respectively. All transformants were observed by light and fluorescence microscopy at mid-log phase. The expression in E. coli transformants, ProMu-EGFP/Ec and MuEGFP/Ec, exhibited bright enough fluorescence to be observed. Furthermore, ProMu-EGFP/Ec produced fluorescent inclusions, which may have been recombinant crystals between EGFP and Cry1Ac while MuEGFP/Ec expressed soluble EGFP in cell. In SDS-PAGE, ProAc/Ec had 130 kDa crystal protein band and MuEGFP/Ec had thick 27 kDa EGFP band. However, ProMu-EGFP/Ec had about 150 kDa fusion protein band. Accordingly, these results indicated that a fusion protein between the B. thuringiensis crystal protein and a foreign protein under the lacZ promoter was successfully expressed as granular structure in E. coli. It is suggested that the E. coli expression system by N-terminal fusion of B. thuringiensis crystal protein may be useful as excellent means for fusion expression and characterization of B. thuringiensis fusion crystal protein.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.2
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• pp.241-249
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• 2016

The supplementation of livestock feed with animal protein is a present cause for public concern, and plant protein shortages have become increasingly prominent in China. This conflict may be resolved by fully utilizing currently available sources of plant protein. We estimated the rumen degradability and the small intestinal digestibility of the amino acids (AA) in rapeseed meal (RSM), soybean meal (SBM), sunflower seed meal (SFM) and sesame meal (SSM) using the mobile nylon bag method to determine the absorbable AA content of these protein supplements as a guide towards dietary formulations for the dairy industry. Overall, this study aimed to utilize protein supplements effectively to guide dietary formulations to increase milk yield and save plant protein resources. To this end, we studied four cows with a permanent rumen fistula and duodenal T-shape fistula in a $4{\times}4$ Latin square experimental design. The results showed that the total small intestine absorbable amino acids and small intestine absorbable essential amino acids were higher in the SBM (26.34% and 13.11% dry matter [DM], respectively) than in the SFM (13.97% and 6.89% DM, respectively). The small intestine absorbable Lys contents of the SFM, SSM, RSM and SBM were 0.86%, 0.88%, 1.43%, and 2.12% (DM basis), respectively, and the absorbable Met contents of these meals were 0.28%, 1.03%, 0.52%, and 0.47% (DM basis), respectively. Among the examined food sources, the milk protein score of the SBM (0.181) was highest followed by those of the RSM (0.136), SSM (0.108) and SFM (0.106). The absorbable amino acid contents of the protein supplements accurately reflected protein availability, which is an important indicator of the balance of feed formulation. Therefore, a database detailing the absorbable AA should be established.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.11
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• pp.1629-1634
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• 2008

A trial was conducted to determine the effect of low crude protein (CP) diets with constant metabolizable energy to crude protein (ME:CP) ratio on growth, body composition and nutrient utilization of broiler chicks from 1 to 26 days of age. Four dietary treatments having four levels of CP and ME as 23, 22, 21 and 20% and 3,036, 2,904, 2,772 and 2,640 kcal/kg, respectively, were formulated and a ME:CP ratio of 132 was maintained in all the diets. Digestible lysine was maintained at 1.10 of the diet. A total of 1,760 day-old Hubbard broiler chicks were randomly divided into 16 experimental units and each diet was offered to four experimental units at random. Feed intake was increased (p<0.05) while weight gain and feed conversion ratio were adversely affected (p<0.05) when the diets with low CP and ME were fed to broilers. Total protein intake and total ME intake were linearly decreased (p<0.05) and protein efficiency ratio and energy efficiency ratio were lower (p<0.05) than in the chicks fed dietary regimen with 22% CP and 2,904 kcal/kg ME. The whole body analysis of the birds revealed that chicks fed the lowest dietary regimens retained less (p<0.05) nitrogen and more ether extract than chicks fed the control diet, however, body dry matter, total body ash and fat free body protein were not affected. Similarly, protein and energy utilization were also unaffected by the dietary treatments. In summary, chicks fed low CP diets with constant ME:CP ratio grew slower, used feed less efficiently and retained less protein and more body fat than chicks fed the control diet.

• Nutritional Sciences
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• v.5 no.2
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• pp.53-59
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• 2002

This study was conducted to examine the effects of dietary sources of fatty acids and protein on serum protein profiles, hepatic functional enzyme activities, mammary tumor incidence and tumor weight in 7, 12-dimethylbenz($\alpha$)anthracene (DMBA)-treated rats. The sources of dietary fatty acids were 18n6 (rich in linoleic acid), 18n3 (rich in linolenic acid) and 22n3 (rich in DHA) : sources of dietary protein were casein (C) and soy protein isolate (S). mammary tumors (MTs) were chemically induced by DMBA (9 mg/100 g body weight) which was gastrically intubated at 7 weeks of age. Each experimental diet was given for the following 25 weeks. Casein-fed rats (group C) exhibited significantly higher levels of weight gain and FER (food efficiency ratio) than did group S. Group C showed higher levels of serum protein and globulin, and higher albumin/globulin (A/G) ratios than group S. Liver functional enzyme activities (GOT, GPT, ALP, LDH, $\gamma$-GT) and LDH/GOT ratios were not influenced by dietary protein. GPT activity was lower in the group given 18n3, and ALP activity was lower in the group given 18n6. The incidence and total number of MTs appeared to be lower in the group given 22n3 than in the group given 18n3 or 18n6, even though the average weight of MTs was highest in the group given 22n3, The average weight of MTs was higher in the C group than in the S group. MT incidence had a positive correlation with LDH activity and LDH/GOT ratio. The average weight of MTs had a negative correlation with serum albumin levels and A/G ratios, and a positive correlation with ALP activity. This research suggests that the measurement of serum protein profiles and liver functional enzyme activities may be utilized to monitor the development of mammary tumors.

• Korean Journal of Poultry Science
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• v.44 no.2
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• pp.67-73
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• 2017

The purpose of our study was to determine the effects of varying levels of energy, protein, and amino acids on the performances of laying hens. A total of 240 Hy-Line Brown laying hens at 36 weeks of age were used in this 4-week feeding trial. The hens were randomly allocated to five treatment diets, with eight replications of six hens in each replicate cage. The treatment diets were as follows: A- basal diet + 18% crude protein, metabolizable energy 2,800 kcal, total (methionine + cysteine) 0.65%; B- basal diet + 17% crude protein, metabolizable energy 2,700 kcal, total (methionine + cysteine) 0.59%; C- basal diet + 16.5% crude protein, metabolizable energy 2,700 kcal, total (methionine + cysteine) 0.59%; D- basal diet + 16.5% crude protein, metabolizable energy 2,700 kcal, total (methionine + cysteine) 0.54%; and E- basal diet + 16% crude protein, metabolizable energy 2,680 kcal, total (methionine + cysteine) 0.54%. The study results revealed that the hen-day egg production of hens that were fed with low-energy diets (B, C, and D) was comparable with that of hens fed with high-energy diet A, whereas average daily feed intake in hens fed treatment diet D and E was significantly higher (P<0.05) than that in hens fed treatment diet A. Overall, the eggshell thickness was unaffected by any of the treatment diets. Egg weight was comparable among the treatment diets, except for treatment diet E. Haugh unit improved with decreasing levels of dietary energy, protein, and methionine + cysteine in the diet. We can summarize that laying hens fed with low dietary energy and low crude protein treatment diets B, C, and D had satisfactory performance compared with those fed with high-energy treatment diet A. This indicates that there is the potential to reduce feed costs by formulating diets with lower energy and low protein levels.

• Journal of Life Science
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• v.17 no.2 s.82
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• pp.179-184
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• 2007

PTK6, an intracellular protein tyrosine kinase, is significantly overexpressed in a majority of breast cancers and has a role in promoting the proliferation of the cancer cells, but not of normal cells. Here, we report high-level production of the catalytic unit of PTK6 fused with Drosophila peptidoglycan recognition protein (PGRT)-LB, in the baculovirus system. We first found that the PGRP-LB was potentially useful as a fusion partner to increase the yield of heterologous protein in the baculovirus system. The purified recombinant protein exhibited a 1.5-fold activity with much higher yield than the bacterially-expressed protein. The protein expressed in the baculovirus system will be useful for the crystallization to determine its crystal structure helping understand the molecular mechanism of PTK6 and design its inhibitors.

• Journal of Life Science
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• v.21 no.1
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• pp.31-35
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• 2011

Dual-specificity protein phosphatases (DUSPs) constitute a family of protein phosphatase characterized by the ability to dephosphorylate phospho-tyrosyl and phospho-seryl/threonyl residues. Most DUSPs are involved in regulation of cell survival and differentiation. In this study, a human dual-specificity protein phosphatase, DUSP28, was isolated from a human kidney cDNA. The recombinant protein was successfully produed in E.coli and showed sufficient phosphatase activity toward DiFMUP (6,8-difluoro-4-methylumbelliferyl phosphate). Various phosphatase inhibitors and divalent metals were tested for their effects on the DUSP28 phosphatase activity. As a result, $Zn^{2+}$ was found to strongly inhibit DUSP28 phosphatase activity, suggesting DUSP28 is involved in Zn-related signal transduction pathway. Furthermore, the DUSP28 protein preferred phospho-tyrosyl residues to phospho-threonyl residues, implying its physiological roles in the cellular process.

• Genomics & Informatics
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• v.18 no.3
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• pp.28.1-28.9
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• 2020

Streptomyces coelicolor is a gram-positive soil bacterium which is well known for the production of several antibiotics used in various biotechnological applications. But numerous proteins from its genome are considered hypothetical proteins. Therefore, the present study aimed to reveal the functions of a hypothetical protein from the genome of S. coelicolor. Several bioinformatics tools were employed to predict the structure and function of this protein. Sequence similarity was searched through the available bioinformatics databases to find out the homologous protein. The secondary and tertiary structure were predicted and further validated with quality assessment tools. Furthermore, the active site and the interacting proteins were also explored with the utilization of CASTp and STRING server. The hypothetical protein showed the important biological activity having with two functional domain including POD-like_MBL-fold and rhodanese homology domain. The functional annotation exposed that the selected hypothetical protein could show the hydrolase activity. Furthermore, protein-protein interactions of selected hypothetical protein revealed several functional partners those have the significant role for the bacterial survival. At last, the current study depicts that the annotated hypothetical protein is linked with hydrolase activity which might be of great interest to the further research in bacterial genetics.