Amino Acid Index

In the method by Schirmer and Cowan (1993), a kind of hydropho-bicity plot like the hydropathy plot of Kyte and Doolittle (1982) is used. The amino acid index representing hydrophobicity is modified to emphasize the effect of aromatic residues. Considering the structural feature of /3 strands, the averaged value of 4 positions (i — 2, i, i + 2, and i + 4 for position i) is taken, and the plot is drawn for both even- and odd-numbered positions. The peaks correspond well to the observed positions of the /3 strands. 

Figure 5.7. Amino acid index databases for physicochemical properties. The physicochemical properties, conformational parameters, and mutational indexes can be retrieved from AAindex database using keyword search.

Kawashima S, Ogata H, Kanehisa M. AAindex amino acid index database. Nucl. Acids Res. 1999 27 368-369. 

The protein concentration and amino acid composition of sunflower meal also vary with the source of seed, and high-temperature processing may have a deleterious effect on its lysine content. Generally, however, sunflower meal exhibits a well-balanced amino acid composition with an essential amino acid index of 68, compared to 79 for soybean meal and 100 for whole egg (35). 

One of the most comprehensive resources of amino acid properties freely available on line is the amino acid index database (AAindex), which includes numerical indices representing various physico-chemical, biochemical, and statistical properties of amino acids and pairs of amino acids. AAindex database has been made publicly available by the Japanese GenomeNet database service (http //www.genome.jp/aaindex/). 

In view of the low protein content of the diet in some countries, it is of paramount importance to be able to evaluate the biological efficiency of a given protein. To express this property mathematically for each protein, one can determine the essential amino acid index, which is the geometric mean of the ratio of the amino acid in the test protein versus the amino acid in a standard protein most efficiently utilized (egg protein). On the basis of the amino acid index, an equation was developed which expresses the biological value of the protein. 

Oser, B.L. An integrated essential amino acid index for predicting the biological value of proteins. In Protein and amino acid nutrition 66. (Albanese, A.A., ed.). New York Academic Press 1959... 

Biological value is stated as the proportion of the nitrogen intake that is actually retained and takes account of endogenous urinary and faecal nitrogen, whereas chemical score and the essential amino acid index are based on the proportion of the main limiting amino acid of the protein in relation to that in a standard protein. 

Proteins have different biological availabilities in the human body and a number of methods have been introduced to evaluate and measure protein utilisation and retention. Two types of measurements are used to estimate protein quality biological assays and chemical analysis. The most common measures of protein quality included Biological Value (BV), Protein Efficiency Ratio (PER), Net Protein Utilisation (NPU), Amino Acid Score (AAS also known as chemical score, CS), Essential Amino Acid Index (EAAl) and Protein Digestibility Corrected Amino Acids Score (PDCAAS), amongst other procedures and modifications. 

Figure C2.5.10. The figure gives tire foldability index ct of 27-mer lattice chains witli sets containing different number of amino acids. The sets are generated according to scheme described in [27], The set of 20 amino acids is taken as a standard sample. Each sequence witli 20 amino acids is optimized to fulfil tire stability gap [5]. The residues in tire standard samples are substituted witli four different sets containing a smaller number of amino acids [27]. The foldability of tliese substitutions is indicated by tire full circles. The open diamonds correspond to tire sequences witli same composition. However, tire amino acids are chosen from tire reduced representation and tire resultant sequence is optimized using tire stability gap [5].

Amino acid Three- letter code One- letter code Mass of residue in. b proteins Accessible surface area, 2 nm Hydrophobicity index ionizable side chain Occurrence in n/ proteins, /o Relative mutabihty... 

Enzymes are excellent catalysts for two reasons great specificity and high turnover rates. With but few exceptions, all reac tions in biological systems are catalyzed by enzymes, and each enzyme usually catalyzes only one reaction. For most of the important enzymes and other proteins, the amino-acid sequences and three-dimensional structures have been determined. When the molecular struc ture of an enzyme is known, a precise molecular weight could be used to state concentration in molar units. However, the amount is usually expressed in terms of catalytic activity because some of the enzyme may be denatured or otherwise inactive. An international unit (lU) of an enzyme is defined as the amount capable of producing one micromole of its reaction product in one minute under its optimal (or some defined) reaction conditions. Specific activity, the activity per unit mass, is an index of enzyme purity. 

Amino acids, carbohydrates and steroids not found below are in Chapter 4 (see also CAS Registry Numbers Index and General Index). 

Figure 12.23 Hydropathy plots for the polypeptide chains L and M of the reaction center of Rhodobacter sphaeroides. A window of 19 amino acids was used with the hydrophohicity scales of Kyte and Doolittle. The hydropathy index is plotted against the tenth amino acid of the window. The positions of the transmembrane helices as found by subsequent x-ray analysis by the group of G. Feher, La Jolla, California, ate indicated by the green regions.

The smdy of tissue protein breakdown in vivo is difficult, because amino acids released during intracellular breakdown of proteins can be extensively reutilized for protein synthesis within the cell, or the amino acids may be transported to other organs where they enter anabohc pathways. However, actin and myosin are methylated by a posttranslational reaction, forming d-methylliistidine. During intracellular breakdown of actin and myosin, 3-methylhistidine is released and excreted into the urine. The urinary output of the methylated amino acid provides a rehable index of the rate of myofibrillar protein breakdown in the musculature of human subjects. 

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