• 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.

• Preventive Nutrition and Food Science
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• v.1 no.1
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• pp.16-22
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• 1996

Amino acids and ribonucleotides were measured for boiled-dried anchovy to determine the effect of 5 kGy γ-irradiation on its quality stability during storage at ambient and cooling (5∼10℃) temperatures for 12 months in a laminated-film package(Polyethylene 10㎛). The anchovy samples contained about 55%(d.b) of total amino acids and about 1%(d.b) of free amino acids. Although there found a significant change(p<0.01) in the content of leucine and lysine immediately sfter irradiation, the overall content of toral amino acids was little changed in stored anchovy even six months after irradiation at cooling conditions. γ-Irradiation caused a significant reduction(p<0.01) in the total content of free amino acids, showing a similar tendency by storage conditions. However, the ribonucleotides. which were 12.00mg/g(d.b) in inosine-5'-monophosphate and 0.38mg/g(d.b) in guanosine-5'-monophospate, were resistant to 5kGy-irradiation. With the lapse of storage time, it was also shown that storage temperature was more influential than irradiation on the contents of amino acids and taste compounds of dried anchovy.

• Journal of Plant Biotechnology
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• v.41 no.4
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• pp.229-235
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• 2014

Gastrodia elata Blume, an achlorophyllous orchid plant, has been used in traditional medicine and harvests in spring and fall. Here we investigated the quantitative changes of amino acids in G. elata by harvest times and seed tubers. In the results, we found that there was not big difference in contents of total amino acids but the distribution of amino acids differed depending on harvest times. 19% of total amino acids were asparagin and valine, an essential amino acid, occupied 10% within total amino acids in the tubers harvested in October. Among amino acids in the tubers harvested in April, serine occupied 23% and arginine, an essential amino acid, occupied 10% within total amino acids in tuber. Interestingly, the use of sexually propagated seed tubers produced high concentration of total amino acids compared to vegetatively propagated seed tubers. As for sexually propagated seed tubers, essential amino acids contents similar to the tubes harvested in October and nonessential amino acids contents similar to the tubers harvested in April. In this study, we found that amino acids contents in G. elata tubers altered depending on various cultivation practices. Therefore if these results can be applied to food industry, the value of G. elata as a natural food resource will be enhanced to a great extent.

• Environmental Mutagens and Carcinogens
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• v.24 no.2
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• pp.67-72
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• 2004

To find active components in Ganoderma lucidum, their free amino acid and free amino acid derivatives were analyzed. After extracting with hot water, the extracts were filtrated by three steps. So, supernatants below 10,000 dalton were obtained. Filtrates were derivativated with PITC (phenylthiocarbamyl) derivative reagent and PITC amino acid was obtained. Then, they were analyzed by RP-HPLC. 13 amino acids were analyzed in cultured Korean Nok-kak ji (one of Ganoderma lucidum), 15 amino acids in cultured Korean Ganoderma lucidum, 12 amino acids wild Ganoderma lucidum, 16 amino acids in cultured Taiwan Ganoderma lucidum.

• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2542-2548
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• 2009

Direct methylation behaviors of 20 amino acids with tetramethylammonium hydroxide (TMAH) were studied under diluted conditions with silica. Amino acid concentration was controlled by dilution with silica ($SiO_2$) and the molar ratios of amino acid/silica were 0.20, 0.50, and 2.0. The molar ratios of amino acid/TMAH (0.51 - 4.64) also varied. It was found that arginine, asparagine, aspartic acid, cysteine, glutamic acid, and glutamine did not generate any directly methylated pyrolysis products, whereas alanine, glycine, isoleucine, leucine, methionine, phenylanaline, valine, and proline generated all the directly methylated pyrolysis products. Tri- and tetra methylated products of lysine consisted of two types. Histidine and threonine hardly generated the partly methylated products. Mono- and dimethylated products of serine, tryptophan, and tyrosine were not observed. Relative intensities of the methylated products varied with the amino acid concentration, TMAH concentration, and pyrolysis temperature. Direct methylation behaviors of amino acids were explained by the structural characteristics of amino acids.

• Journal of the Korean Home Economics Association
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• v.20 no.4
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• pp.99-105
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• 1982

Changes of free amino acids as taste compunds during the fermentation of cod-roe, Gadus marcrocephlus, were analyzed by a amino acid autoanalyzer. Leucine, lysine, valine, isoleucine and arginine were dominent amino acids in fresh cod-roe extracts, and the amounts of leucine (797.3mg%, on moisture and salt free base), lysine (577.7mg%) and valine(487.4mg%0 were 54.9% of total free amino acids. The contents of methionine, histidine, tyrosine and phenylanine were lower, and aspartic acid, glycine, threonine, glutamic acid and serine were detected trace amount. The free amino acids analyzed in this experiment were not changed in composition but changed in the amounts during 80 days of the fermentation. Total free amino acids were increased until 59 days of fermentation and than decreased gradually.

• Journal of Plant Biology
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• v.4 no.1
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• pp.9-11
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• 1961

A comparative investigation of free amino acids content in healthy check and virus diseased leaves of Chinese date tree, Zyzyphus jujuqa Mill var. inermis Rhed, was carried out by authors throughout the growing season of 1959 and 1960 from June to October. The methods of qualitative analysis of free amino acids aplied in this experiment is followed by Moore and Stein. Free amino acids determined in this experiment are shown in Fig. 1 and Table 1. As the figure and the table are shown, three more amino acids such as glutamine, asparagine and histidine are detected in the diseased material. The additional amino acids which are known as diamines in diseased leaves are conspicuous. It is presumed that the diamine might be incresed by the self-reproduction of the virus in cooporation with certain enzymes which are carrying out the protein metabolism in the host protoplast in contrast with the healthy checks which is carrying out normal protein metabolism. From the histological poing of view, the facts of phloem degeneration or necrosis in diseased leaves, it seems to interrupt to move free amino acids from roots to leaves and it possibly takes place an excessive production of NH3 which is diaminated by the metabolism of nitrogen compounds in such conditioned leaves. Therefore, it is also presumed that additional diamino acids are accumulated in diseased leaves. There are no change of amino acids are accumulated in diseased leaves. There are no change of amino acids in both materials of this plant throughout the growing season qualitatively, and this result agress with the paper of Knight.

• Journal of Plant Biology
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• v.6 no.4
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• pp.5-10
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• 1963

KWON, Oh Yong (Chunju Teacher's Coll.) Partern of the amino acids influedced on nitrogen metabolism of edible bamboo sprouts. Kor. Jour. Bot. VI (4) : 5-10, 1963. It had been scarcely reported by any worker that the essential amino acids to be indispensable in our daily life contained in edible bamboo sprouts and that they had various pattern of free amino acids. For this reason, especially two species of Korean bamboo sprouts collected from the surburb of Chunju, in April, 1963 were used for researching the essential amino acids and free amino acids appeared on paper chromatography. The most suitable part for our edibles was investigated as a part of bio-chemical studies on Korean bamboo sprouts. The free amino acids contained in two species were found as 5-15 kinds and there were a few of difference according to it's growing parts. Many kinds of free amino acids were found in the end parts more than the tip parts and mid parts of bamboo sprouts. Besides, the essential amino acids in each species were found to 3-9 kinds. From the characteristics and the experiments marked above, it was suggested to the author that many kinds of free amino acids in the end part accelerated the formation of nitrogen comounds more than the other parts.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.139-147
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• 1999

Peptides are formed in the rumen as the result of microbial proteinase activity. The predominant type of activity is cysteine ptoteinase, but others, such as serine proteinases, are also present. Many species of protozoa, bacteria and fungi are involved in ptoteolysis; large animal-to-animal variability is found when proteinase activities in different animals are compared. The peptides formed from proteolysis are broken down to amino acids by peptidases. Different peptides are broken down at different rates, depending on their chemical composition and particularly their N-terminal structure. Indeed, chemical addition to the N-terminus of small peptides, such as by acetylation, causes the peptides to become stable to breakdown by the rumen microbial population; the microorganisms do not appear to adapt to hydrolyse acetylated peptides even after several weeks exposure to dietary acetylated peptides, and the amino acids present in acetylated peptides are absorbed from the small intestine. The amino acids present in some acetylated peptides remain available in nutritional trials with rats, but the nutritive value of the whole amino acid mixture is decreased by acetylation. The genus Prevotella is responsible for most of the catabolic peptidase activity in the rumen, via its dipeptidyl peptidase activities, which release dipeptides rather than free amino acids from the N-terminus of oligopeptides. Studies with dipeptidyl peptidase mutants of Prevotella suggest that it may be possible to slow the rate of peptide hydrolysis by the mixed rumen microbial population by inhibiting dipeptidyl peptidase activity of Prevotella or the rate of peptide uptake by this genus. Peptides and amino acids also stimulate the growth of rumen microorganisms, and are necessary for optimal growth rates of many species growing on tapidly fermented substrates; in rich medium, most bacteria use pre-formed amino acids for more than 90% of their amino acid requirements. Cellulolytic species are exceptional in this respect, but they still incorporate about half of their cell N from pre-formed amino acids in rich medium. However, the extent to which bacteria use ammonia vs. peptides and amino acids for protein synthesis also depends on the concentrations of each, such that preformed amino acids and peptides are probably used to a much lesser extent in vivo than many in vitro experiments might suggest.

• The Korean Journal of Ecology
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• v.18 no.4
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• pp.433-440
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• 1995

The constituents and proportions of non-protein free amino acids including canavanine were measured in roots and leaves of legumes, Robinia pseudo-acacia L., Wistaria floribunda L., and Canavalia lineata L. by using high performance liquid chromatography during dormant and fertilizing seasons. in all the three plant species, asparagine was the most abundant amino acid occurring 30％ of total free amino acids, and canavanine was the second most abundant amino acid contributing 10％ of total free amino acids throughout dormant and fertilizing seasons. In dormant season, roots contained 2 to 3 folds of free amino acids including canavanine and asparagine compared to those in fertilizing season. When proportions of asparagine and canavanine to total gree amino acids in various parts of C. lineata were examined in fertilizinng season, the level of asparagine was the highest in roots while that of canavanine was in seeds. On the basis of these results, it is assumed that canavanine appears and functions as a nitrogen-storing compound in roots and leaves throughout the whole life cycle of the investigated plants.