• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.103-113
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• 2014

Hydrophobicity is the key concept to understand the role of water in protein folding, protein self-assembly, and protein-ligand interaction. Conventionally, hydrophobicity of amino acids in a protein has been argued based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein. Here, we investigate how the hydrophobicity of constituent amino acids depends on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we compute and analyze the hydration free energy - free energy change upon hydration quantifying the hydrophobicity - of three short proteins based on the integral-equation theory of liquids. We find that the hydration free energy of charged amino acids is significantly affected by the protein total charge and exhibits contrasting behavior depending on the protein net charge being positive or negative. We also observe that amino acids in the central ${\beta}$-strand sandwiched by ${\beta}$-sheets display more enhanced hydrophobicity than free amino acids, whereas those in the ${\alpha}$-helix do not clearly show such a tendency. Our results provide novel insights into the hydrophobicity of amino acids, and will be valuable for rationalizing and predicting the strength of water-mediated interaction involved in the biological activity of proteins.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.163-166
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• 2016

Hydrophobicity is the key concept to understand the water plays in protein folding, protein aggregation, and protein-protein interaction. Traditionally, the hydrophobicity of protein is defined based on the scales of the hydrophobicity of residue, assuming that the hydrophobicity of free amino acids is maintained. Here, we explore how the hydrophobicity of constituting amino acids in protein rely on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we calculate and investigate the hydration free energy of three short proteins based on the integral-equation theory of liquids. We find that the hydration free energy of charged amino acids is significantly affected by the protein total charge and exhibits contrasting behavior depending on the protein total charge being positive or negative. We also observe that amino acids in the ${\beta}-sheets$ display more enhanced the hydrophobicity than amino acids in the loop, whereas those in the ${\alpha}-helix$ do not clearly show such a tendency. And the salt-bridge forming amino acids also exhibit increase of the hydrophobicity than that with no salt bridge. Our results provide novel insights into the hydrophobicity of amino acids, and will be valuable for rationalizing and predicting the strength of water-mediated interaction involved in the biological activity of proteins.

• Journal of Nutrition and Health
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• v.28 no.10
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• pp.976-985
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• 1995

Changes in free amino acid concentrations is blood and various tissues were evaluated in cats adapted to the low-protein diet(20% protein, LPD) or the high-protein diet(60% protein, HPD) for 5 weeks. Cumulative body weigth gain for the 5 week period was 463$\pm$43g, and -128$\pm$40g for cats fed HPD and LPD, respectively. Feeding HPD significantly increased the size of liver and kidney. Cats adapted to HPD for 5 weeks have significantly elevated plasma concrntrations of essential amino acids (branched-chain amino acides, threonine, trytophan, phenylalanine and methoionine), whereas plasma levels of non-essential amino acids(alanine, asparagine, glycine, glutamine and serine) were significantly reduced in animals adapted to HPD(p<0.01, or p<0.001) compared to the values for the cats fed LPD. Changes in free amino acid concentratioks in whole blood induced by the variations in dietary level of protein closely reflect the pattern seen in plasma. Amino acids such as branched-chain amino acids, proline and threonine were most difficult to maintain homeostasis and consistantly elevated in lever, kidney, skeletal muscle and brain, as well as in blood of cats adapted to HPD(p<0.01 or p<0.001). All of the free amino acids in jejunum, excluding taurine and ornithine, were significantly elevated in animals adapted to HPD, most probably due to the rapid absorption of large amount of amino acids across the epithelium of small intestine.

• Korean Journal of Poultry Science
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• v.42 no.1
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• pp.87-100
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• 2015

It is well known that dietary protein affects the growth performance and carcass composition of poultry. Over the last several decades, numerous studies have been carried out to investigate to optimize the level of dietary protein since the protein is an important and expensive constituent in poultry feed. It is generally accepted that dietary protein should represent a balance of amino acids supporting the requirements for growth and maintenance of birds. A protein with balanced essential amino acids that matches a bird's requirement and sufficient non-essential amino acid nitrogen to enable the synthesis of all of the non-essential amino acids, is referred to as an 'ideal protein'. Feeding of excess protein or amino acids may result in an amount of nitrogen emission. Most common method to reduce nitrogen emission is using diet formulation which has lower dietary crude protein level and higher concentration of amino acid supplements. However, there are conflicting reports whether low protein diets supplemented with synthetic amino acids can obtain the growth performance equal to high protein diets. Excessive nitrogen excretion caused by amino acid imbalance also may influence the environment of poultry house due to ammonia production from uric acid. These environmental conditions may increase the incidence of skin problem or respiratory diseases of chickens. Various strategies based on comprehensive understanding should be tested to optimize nitrogen utilization and reduce nitrogen emission while maintaining the performance in poultry production.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.3
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• pp.406-409
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• 2002

The effect of refeeding with various single essential amino acids on the recovery of plasma insulin-like growth factor-I (IGF-I) concentration in fasted young chickens was examined. Young chickens (29 days of age) were divided into 15 experimental groups. Chickens in one group were fed on the commercial diet ad libitum for 4 days. The remaining 56 chickens in 14 experimental groups were fasted. After 2 days of fasting, 52 chicks in 13 fasted groups were refed with one of the following experimental diets for 2 days. Eleven experimental diets were protein-free diets supplemented with one of 11 essential amino acids (Arg, Gly, His, Ileu, Leu, Met, Phe, Lys, Thr, Trp, Val). The remaining 2 experimental diets were a protein-free diet containing 11 essential amino acids and a protein-free diet not supplemented with amino acids. Birds in the remaining fasted group continued to be fasted for 2 days. Fasting for 2 days markedly reduced plasma IGF-I concentration. When fasted chickens were refed the protein-free diet containing either Gly alone or all essential amino acids, plasma IGF-I concentration was recovered to the level similar to that of fed chickens. Protein-free diet alone, however, failed to restore the reduced IGF-I concentration in plasma. Body weight loss modulated by feeding with protein-free diets supplemented with various single essential amino acids was associated with changes in plasma IGF-I concentrations. We concluded that body weight loss by feeding with a protein-free diet was lower than that of fasted chickens and that body weight loss associated with the decrease in plasma IGF-I concentration was modulated by feeding with protein-free diets containing various single essential amino acids.

• Journal of the Korean Society of Food Science and Nutrition
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• v.24 no.2
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• pp.336-340
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• 1995

Urinary excretion of total amino acids was measrued in normal and diabetic rats, streptozotocin-induced diabetic rats excreted increased amount of urinary total amino acids and nitrogen. This suggested increased degradation of body protein. Although excretion of total amino acids increased in the diabetic rats, the amino acid pattern of amino acids for both groups were very similar. The efficiency of dietary protein utilization was significantly lower in diabetic rats then that of normal rats. Streptozotocin injeciton affected the urinary excretion of 3-methylhistidine whereas diet did not. These findings suggest that the rate of urinary excretion of total amino acids can be empolyed as an index of protein metabolism, particulary as a simple index in the assesing the status of protein nutrition.

• Nutrition Research and Practice
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• v.3 no.1
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• pp.64-71
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• 2009

Amino acids are fundamental nutrients for protein synthesis and cell growth (increase in cell size). Recently, many compelling evidences have shown that the level of amino acids is sensed by extra- or intra-cellular amino acids sensor(s) and regulates protein synthesis/degradation. Mammalian target of rapamycin complex 1 (mTORC1) is placed in a central position in cell growth regulation and dysregulation of mTOR signaling pathway has been implicated in many serious human diseases including cancer, diabetes, and tissue hypertrophy. Although amino acids are the most potent activator of mTORC1, how amino acids activate mTOR signaling pathway is still largely unknown. This is partly because of the diversity of amino acids themselves including structure and metabolism. In this review, current proposed amino acid sensing mechanisms to regulate mTORC1 and the evidences pro/against the proposed models are discussed.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.1
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• pp.133-140
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• 2005

Although amino acids are substrates for the synthesis of proteins and nitrogen-containing compounds, it has become more and more clear over the years that these nutrients are also extremely important as regulators of body protein turnover. The branched-chain amino acids (BCAAs) together or simply leucine alone stimulate protein synthesis and inhibit protein breakdown in skeletal muscle. However, it was only recently that the mechanism(s) involved in the regulation of protein turnover by BCAAs has begun to be defined. The acceleration of protein synthesis by these amino acids seems to occur at the level of peptide chain initiation. Oral administration of leucine to food-deprived rats enhances muscle protein synthesis, in part, through activation of the mRNA binding step of translation initiation. Despite our knowledge of the induction of protein synthesis by BCAAs, there are few studies on the suppression of protein degradation. The recent findings that oral administration of leucine rapidly reduced $N^{\tau}$-methylhistidine (3-methylhistidine; MeHis) release from isolated muscle, an index of myofibrillar protein degradation, indicate that leucine suppresses myofiblilar protein degradation. The details of the molecular mechanism by which leucine inhibits proteolysis is just beginning to be elucidated. The purpose of this report was to review the current understanding of how BCAAs act as regulators of protein turnover.

• 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.

• 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.