• Journal of the Korean Society for Industrial and Applied Mathematics
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• v.15 no.3
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• pp.191-199
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• 2011

In this paper, we adopt a position specific scoring matrix as an abstraction of amino acid type to derive two new statistical potentials for protein structure prediction, and investigated its effect on the quality of the potentials compared to that derived using residue specific amino acid identity. For stringent test of the potential quality, we carried out folding simulations of 91 residue A chain of protein 2gpi, and found unexpectedly that the abstract amino acid type improved the quality of the one-body type statistical potential, but not for the two-body type statistical potential which describes long range interactions. This observation could be effectively used when one develops more accurate potentials for structure prediction, which are usually involved in merging various one-body and many-body potentials.

• ALGAE
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• v.33 no.3
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• pp.279-290
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• 2018

Microalgae have been utilized in diverse industries including aquaculture. Among the microalgae, dinoflagellates are known to have various bioactive compounds, and thus the interest in their application to industry has increased. In order to test their potential as food materials for aquaculture animals, the crude protein contents and compositions of amino acids of six dinoflagellates Heterocapsa rotundata (family Heterocapsaceae), Ansanella granifera (Suessiaceae), Alexandrium andersonii (Ostreopsidaceae), Takayama tasmanica (Brachidiniaceae), Takayama helix, and Gymnodinium smaydae (Gymnodiniaceae) belonging to diverse families were analyzed. The percentage of the amount of the crude protein relative to dry weight of T. tasmanica was the highest (65%) and that of A. andersonii was the lowest (26%). However, the highest percentage of total detected amino acids in crude protein was found in A. andersonii (98.2%). In all six dinoflagellates, glutamic acid was the most dominant amino acid in crude protein. However, the second main amino acid was aspartic acid for H. rotundata, A. granifera, T. helix, and G. smaydae, but were arginine and leucine for A. andersonii and T. tasmanica, respectively. Furthermore, T. tasmanica and T. helix did not have taurine and gamma-aminobutyric acid, whereas the other dinoflagellates possessed them. The percentages of essential amino acid contents of the dinoflagellates met the requirement levels for juvenile shrimps. In addition, the dinoflagellates were not toxic to the brine shrimp Artemia salina. Compared with the other microalgae reported so far, H. rotundata and A. andersonii can be used for arginine-rich diets, T. tasmanica for valine and leucine-rich diets, A. granifera for histidine-rich diets, T. helix for threonine-rich diets, and G. smaydae for lysine-rich diets. Therefore, based on their biochemical composition and toxicity to Artemia, the dinoflagellates could be used as essential amino acid sources for cultivating animals in the aquaculture industry.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1616-1624
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• 2016

The aim of present experiment was to investigate the effect of protein reduction in commercial broiler chicken rations with incorporation of de-oiled rice bran (DORB) and supplementation of limiting amino acids (valine, isoleucine, and/or tryptophan) with ration formulation either on total amino acid (TAA) or standardized ileal digestible amino acids (SIDAA). The experimental design consisted of $T_1$, TAA control; $T_2$ and $T_3$, 0.75% and 1.5% protein reduction by 3% and 6% DORB incorporation, respectively by replacing soybean meal with supplemental limiting amino acids to meet TAA requirement; $T_4$, SIDAA control, $T_5$ and $T_6$, 0.75% and 1.5% protein reduction by DORB incorporation (3% and 6%) with supplemental limiting amino acids on SIDAA basis. A total of 360 dold fast growing broiler chicks (Vencobb-400) were divided into 36 homogenous groups of ten chicks each, and six dietary treatments described were allocated randomly with six replications. During 42 days trial, the feed intake was significantly (p<0.05) reduced by TAA factor compared to SIDAA factor and protein factor significantly (p<0.05) reduced the feed intake at 1.5% reduction compared to normal protein group. This was observed only during pre-starter phase but not thereafter. The cumulative body weight gain (BWG) was significantly (p<0.05) reduced in TAA formulations with protein step-down of 1.5% ($T_3$, 1,993 g) compared to control ($T_1$, 2,067 g), while under SIDAA formulations, BWG was not affected with protein reduction of 1.5% ($T_6$, 2,076 g) compared to $T_4$ (2,129 g). The feed conversion ratio (FCR) was significantly (p<0.05) reduced in both TAA and SIDAA formulations with 1.5% protein step-down ($T_3$, 1.741; $T_6$, 1.704) compared to respective controls ($T_1$, 1.696; $T_4$, 1.663). The SIDAA formulation revealed significantly (p<0.05) higher BWG (2,095 g) and better FCR (1.684) compared to TAA formulation (2,028 g; 1.721). Intake of crude protein and all limiting amino acids (SID basis) was higher in SIDAA group than TAA group with resultant higher nitrogen retention (4.438 vs 4.027 g/bird/d). The nitrogen excretion was minimized with 1.5% protein reduction (1.608 g/bird) compared to normal protein group (1.794 g/bird). The serum uric acid concentration was significantly reduced in $T_3$ (9.45 mg/dL) as compared to $T_4$ (10.75 mg/dL). All carcass parameters were significantly (p<0.05) higher in SIDAA formulation over TAA formulation and 1.5% protein reduction significantly reduced carcass, breast and thigh yields. In conclusion, the dietary protein can be reduced by 0.75% with TAA formulation and 1.5% with SIDAA formulation through DORB incorporation and supplementation of limiting amino acids and among formulations, SIDAA formulation was better than TAA formulation.

• Journal of Applied Biological Chemistry
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• v.44 no.3
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• pp.125-130
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• 2001

A putative protein encoded by Arabidopsis AtMTN3 gene, a homologue of Medicago truncatula MTN3, consists of 285 amino acid residues, and has a predicted molecular mass of 31.5 kDa and a calculated pI of 9.1. Primary amino acid sequence analyses have revealed that the protein contains seven putative transmembrane regions with N-terminus oriented to the outside of the membrane. The AtMTN3 protein shows overall 16.4% of amino acid identity with the rat GALR3 protein, known to be a G-protein-coupled receptor. The gene is present as a single copy in the Arabidopsis genome, and expressed in aerial parts but not in roots of Arabidopsis. Therefore, AtMTN3 appears not to be specifically involved in Rhizobium-induced nodule development, as was predicted for the MTN3 gene. These proteins possibly mediate signal transmission through G-protein-coupled pathways during general interactions between plants and symbiotic or pathogenic microbes.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.4
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• pp.543-560
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• 2000

The present paper gives a general overview on amino acid nutrition mainly focused on the concept of ideal protein and amino acid requirements in swine and poultry. Also, the nutritional, economic and environmental roles of synthetic amino acids are presented. A special emphasis has been given to the protein sparing effect by the supplementation of synthetic amino acids into diet and to the effect of this supplementation on growth performance and reduction of environmental pollutants in swine and poultry manure. It is concluded that the supplementation of limited amounts of synthetic amino acids (0.1 to 0.3%) to diets for swine and poultry could spare 2 to 3 percentage units of dietary protein and substantially reduce nutrient excretion, especially nitrogen. Immunocompetency as affected by amino acid nutrition is also introduced and the importance of threonine for the synthesis of immunoproteins in colostrum and milk to maintain piglets' health and intestinal integrity has been emphasized. Finally, some speculation on the future of global amino acids market is presented in conclusion.

• Journal of Microbiology and Biotechnology
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• v.7 no.2
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• pp.132-137
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• 1997

A novel protein (HEAAE, High Essential Amino Acid Encoding Protein), rich in essential amino acids ($75{\%}$ of total), was designed and constructed in our laboratory. The designed peptides were analyzed by SYBLE and stable secondary and tertiary structures were predicted. The monomeric form (HEAAE-1) of the protein consists of 20 amino acid residues with four additional amino acids comprising a potential ${\beta}$-turn (HEAAE-4). Size exclusion analysis demonstrated that the monomer is self-aggregates in aqueous solution to form higher ordered multimeric structures, which are very reminiscent of natural plant storage proteins. The DNA encoding this amino acid sequence was synthesized, and from this monomeric gene fragment (heaae-1), the stable tetrameric form of the gene (heaae-4) was generated by subcloning into the E. coli expression vector pKK223-3. A clear 6 kDa polypeptide band corresponding to the molecular weight of the dimeric form (HEAAE-2) was detected. The smeared band which appeared around the molecular weight corresponding to HEAAE-4 of 11 kDa suggested that the tetramer form of this protein might be processed into smaller size products.

• Applied Biological Chemistry
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• v.8
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• pp.11-20
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• 1967

In order to study the change of nitrogeneous compounds during the "Natto" preparation, the contents of insoluble protein, water soluble protein and amino nitrogen were determined and the pattern of peptides and amino acids was investigated by paper chromatography for the fractions resulting from molecular sieving. The results are summarized as follows: 1. Insoluble protein nitrogen which was increased to 84% by autoclaving the native soybean decreased to 44%, whereas the trichloroacetic acid soluble nitrogen increased from 8% to 45% during Natto preparation, But the soluble protein nitrogen showed a slight increase. 2. Fractionation of the peptides using Dowex-50 resins showed that they consisted mostly of lower molecular weight peptides which increased in accordance with the progress of fermentation, especially after 30-hour period. 3. Sixteen known and two unknown amino acids, and three peptides with different Rf values were identified during the Natto preparation. Their appearance showed some difference in that phenylalanine appeared after 10 hours, methionine, after 20 hours and proline, after 30 hours, respectively. The three peptides appeared at the different stage of fermentation.

• Journal of Dairy Science and Biotechnology
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• v.41 no.1
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• pp.34-43
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• 2023

Hydrolysis of whey-derived proteins using lactic acid bacteria (LAB) utilizes the mass culture method and fermentation of LAB to produce effective bioactive peptides. Whey protein has the biological potential of its precursors, but the active fragments may not be released depending on the hydrolysis method. As an alternative to these problems, the nutritional and bioactive functionality of the hydrolysis method have been reported to be improved using LAB for whey protein. Peptide fractions were obtained using a sample fast protein liquid chromatography device. Antioxidant activity was verified for each of the five fractions obtained. In vitro cell experiments showed no cytotoxicity and inhibited nitric oxide production. Cytokine (IL [interleukin]-1α, IL-6, tumor necrosis factor-α) production was significantly lower than that of lipopolysaccharides (+). As a result of checking the amino acid content ratio of the fractions selected through the AccQ-Tag system, 17 types of amino acids were identified, and the content of isoleucine, an essential amino acid, was the highest. These properties show their applicability for the production of functional products utilizing dietary supplements and milk. It can be presented as an efficient method in terms of product functionality in the production of uniform-quality whey-derived peptides.

• Asian-Australasian Journal of Animal Sciences
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• v.6 no.4
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• pp.619-622
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• 1993

Rumen bacterial amino acids in sheep on urea diet were monitored to assess a possible change in amino acid synthesis as a long term response to high rumen ammonia environment. A sheep was fed a semipurified diet with soybean meal, followed by a diet with urea as a main nitrogen source. Mixed rumen bacteria were harvested from ruminal fluid taken 3 h after feeding (twice in soybean meal feeding and 6 times in urea feeding) and fractionated as cell wall, proteins and protein-free cell supernatant of monitor amino acids in each fraction. Ruminal ammonia concentration at the sampling ranged from 5.7 to 39.5 mgN/dl. Cell wall and protein fractions of mixed rumen bacteria were stable in their amino acid composition regardless of nitrogen sources of diet and the feeding duration. However, protein-free cell supernatant fraction showed a higher alanine proportion with urea feeding (18.6 and 28.2 molar % of alanine for samples from sheep fed soybean meal and urea, respectively) and its duration (20.6 and 32.9 molar % for samples from sheep on urea diet for 1 and 65 days, respectively). Total free amino acid level of bacteria was depressed in the initial period of urea feeding but restored on 65th day of the feeding. These results suggest that an alanine synthesizing system may develop in rumen bacteria as urea feeding becomes longer.

• Korean Journal of Food Science and Technology
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• v.6 no.1
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• pp.12-16
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• 1974

The amino acid pattern of embryo and endosperm of brown rice different in specific gravity was investigated using Jinheung (local leading temperate variety) and IR667-Suweon 213 (high-yielding newly bred tropical variety). 1. Embryo of IR667 (higher protein rice) showed lower protein, and lower lysine or essential amino acid per protein than that of Jinheung (lower protein rice). 2. In both embryo and endosperm nitrogen recovery as amino acids was highest in middle class of specific gravity and lowest in low class indicating that abundancy of non-protein nitrogen in low class and decomposition of amino acids by starch in high specific gravity class. 3. In both embryo and endosperm IR667 showed abundancy in order of glutamic acid, aspartic acid while Jinheung showed glutamic acid, arginine, suggesting varietal difference in nitrogen metabolism. 4. In both IR667 and Jinheung least amino acid was histidine and next leucine in embryo but histidine and next threonine in endosperm, suggesting organ difference in nitrogen metabolism.