Side chains amino acid composition

The packing interactions between a helices and p strands are dominated by the residues Val (V), He (I), and Leu (L), which have branched hydrophobic side chains. This is reflected in the amino acid composition these three amino acids comprise approximately 40% of the residues of the P strands in parallel P sheets. The important role that these residues play in packing a helices against P sheets is particularly obvious in a/P-barrel structures, as shown in Table 4.1. 

Complete hydrolysis alone is not sufficient for an exact analysis of amino acid composition, however, because some side reactions occur during the procedure. For example, the amide bonds in the side chains of asparagine and glutamine are cleaved by acid treatment, yielding aspartate and glutamate, respectively. The side chain of tryptophan is almost completely degraded by acid hydrolysis, and small amounts of serine, threonine,... 

In a similar manner to a helices, extended structures can be held together by hydrogen bonds with the hydrogen bonds running perpendicular to the chain axis. Silk is an example of a protein that is found in the p structure. The amino acid composition of silk is rich in glycine (44.5%), alanine (29.3%), and serine (12.1%) amino acids with small hydrocarbon side chains that form sets of antiparallel hydrogen bonds between molecular chains. Models of polypeptide chains with sequences of poly(gly-ala) and poly(ala-gly-ala-gly-ser-gly) show that the most probable structure contains all the gly residues on one side of the chain and all the ala residues on the other side of the chain, and therefore by packing the chains in... 

The conformation of a protein in a particular environment affects its functional properties. Conformation is governed by the amino acid composition and their sequence as influenced by the immediate environment. The secondary, tertiary and quaternary structures of proteins are mostly due to non-covalent interactions between the side chains of contiguous amino acid residues. Covalent disulfide bonds may be important in the maintenance of tertiary and quaternary structure. The non-covalent forces are hydrogen bonding, electrostatic interactions, Van der Waals interactions and hydrophobic associations. The possible importance of these in relation to protein structure and function was discussed by Ryan (13). 

Amino Acid Composition of Antigenic Site. Structurally, each antigenic site on the surface of a protein antigen is composed of a number of side chains of amino acids. To date, the exact boundaries of a single... 

Simmonds comments (1958b) that the ready uptake of dyes by mohair, which Dusenbury and Menkart class as orthocortex, may be due to the presence of a high content of ionizable side-chain groups. As remarked earlier, however, the correlation of differences in amino composition with microfibril/matrix and ortho/para ratios is complicated by the fact that both the low- and high-sulfur fractions are complex groups of proteins with variable over-all amino acid compositions (see Section II,D,4). 

If the amount of acid required for titration of the "acidic side chains of wool is calculated from the amino acid composition of the fiber (Table X), the theoretical acid-binding capacity of the fiber is from 0.63 meq per gram for Merino 70 s to 0.69 meq per gram for Lincoln. The apparent discrepancy can be attributed largely to excessive values for the amide content of wool. These errors arise from the formation of ammonia by degradation of amino acids such as serine and threonine during hydrolysis. If the values of Leach and Parkhill (1956) for amide content are accepted (Table IX), the expected titration value becomes approximately 0.8 meq per gram. 

The site-specific modification of native proteins is not one of the routine procedures in protein chemistry. It cannot be placed in the same category as end-group labelling or determination of amino acid composition and sequence. The specific chemical modification of a native protein can never be guaranteed because the reactivity of amino acids in a native protein is rarely predictable even if the three-dimensional structure of the protein is known. Unusual pK s of side chains, steric and solvent effects and the proximity of the amino acid residue to a ligand-binding site all influence its reactivity, frequently in opposite directions. However certain well-defined avenues of in-... 

The protein is completely hydrolyzed by acid (6 N HCl, 24 hours or longer at 110°C, under vacuum or inert gas) to its constituent amino acids and the resultant hydrolysate is evaporated to dryness. The amino acid composition is determined on protein hydrolysates obtained after 24,48, and 72 hours of acid treatment. The content of amino acids with bulky aliphatic side chains such as isoleucine, leucine, and valine, which undergo slow hydrolysis, is calculated from an extrapolation of the hydrolysate data to infinite time. The content of hydroxyl-containing amino acids, which are slowly destroyed during hydrolysis, is obtained by a corresponding extrapolation to zero time. Since cysteine, cystine, and methionine residues are somewhat unstable to hydrolysis, these residues are oxidized to cysteic acid and methionine sulfone, respectively, with performic acid before quantitative analysis. Cysteine, or half-cystine, is quantitated as a derivative such as carboxymethyl cysteine after reduction and alkylation, a necessary prerequisite to subsequent sequence analysis. Tryptophan... 

Figure 3.16 Determination of amino acid composition. Different amino acids in a peptide hydrolysate can be separated by ion-exchange chromatography on a sulfonated polystyrene resin (such as Dowex-SO). Buffers (in this case, sodium citrate) of increasing pH are used to elute the amino acids from the column. The amount of each amino acid present is determined from ihe absorbance. Aspartate, which has an acidic side chain, is first to emerge, whereas arginine, which has a basic side chain, is the last. The original peptide is revealed to be composed of one aspartate, one alanine, one phenylalanine, one arginine, and two glycine residues.

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