Amino acid residue side chains properties

Another major effect, found in PGA, is optical inversion of L-glutamate to D-glutamate residues. One implication of the radiation-induced optical inversion in proteins is that some modification of amino acids may pass undetected by the usual chemical analyses which do not distinguish between l- and D-isomers. Furthermore, introducing a D-amino acid residue into a protein could have a far-reaching effect on the secondary and tertiary structures, and this could have a more serious effect on the functional properties of the molecule than changes in the side chains. One biological property of PGA which is affected by irradiation in solution is its hydrolysis by proteolytic enzymes. The conformation of the polymer has a marked effect on its susceptibility to hydrolysis by certain enzymes 27), and we have... 

The substrate specificity of an enzyme is determined by the properties and spatial arrangement of the amino acid residues forming the active site. The serine proteases trypsin, chymotrypsin and elastase cleave peptide bonds in protein substrates on the carboxyl side of positively charged, aromatic and small side-chain amino acid residues, respectively, due to complementary residues in their active sites. 

Reactions Analytical Methods. Alkaline treatments are used in the food and feeds technology for solubilization and purification of proteins, to destroy toxic contaminants, and to obtain functional properties. These alkaline treatments induce many chemical modifications on the side chains of the amino acid residues, which have been described by many workers. 

Recent research has suggested that short synthetic peptides containing different analogs of the first 19-23 amino acid residues of influenza hemaglutinin protein (HA) terminus may be attractive because of their pH-dependent lytic properties, with little activity at pH 7 but > 100-fold increase in transfection efficiency at pH 5. The lytic characteristics are revealed as the carboxyl groups of the aspartyl and glutamyl side chains are protonated, which allows the peptides to assume a a-helical conformation that can be inserted into the membrane bilayer. 

TABLE I Fundamental Properties of Amino Acid Residues in Terms of Occurrence in Proteins, Molecular Mass, Molecule Volume, Accessible Surface Area, Partial Specific Volume, pKa of Ionizing Side Chains, and Relative Hydrophobicity... 

Bitterness occurs as a defect in dairy products as a result of casein proteolysis by enzymes that produce bitter peptides. Bitter peptides are produced in cheese because of an undesirable pattern of hydrolysis of milk casein (Habibi-Najafi and Lee 1996). According to Ney (1979), bitterness in amino acids and peptides is related to hydrophobic-ity. Each amino acid has a hydrophobicity value (Af), which is defined as the free energy of transfer of the side chains and is based on solubility properties (Table 7-6). The average hydrophobicity of a peptide, Q, is obtained as the sum of the Af of component amino acids divided by the number of amino acid residues. Ney (1979) reported that bitterness is found only in peptides with molecular weights... 

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). 

Almost all peptides of hydrophobic L-amino acids elicit a bitter taste, which indicates that the bitterness of peptides is caused by the hydrophobic property of the amino acid side chain. Ney (12) has reported that whether a peptide has a bitter taste or not depends on its hydrophobic value Q. The value Q is obtained by adding the Af-values (Table 3) of each constituent amino acid residue of a peptide and dividing the sum by the number of amino acid residues (n). 

Proteins are made of twenty standard amino acid residues joined together through peptide bonds. Each of the twenty amino acids has unique physico-chemical properties stemming from the size of the side chain, and the possible presence of an acidic or basic ionizable group. Protein phosphorylation most... 

For the mutations on the surface of the protein, the classifications based on the chemical nature of amino acids, such as hydrophobic amino acids (Ala, Cys, Phe, Gly, He, Leu, Met, Val, Trp, and Tyr), amino acid side chains that can form hydrogen bonds (Asp, Cys, Glu, His, Lys, Met, Asn, Gin, Arg, Ser, Thr, Trp, and Tyr), and so forth, improved the correlation between amino acid properties and protein mutant stability. Furthermore, the inclusion of neighboring and surrounding residues remarkably improved the correlation in all the subgroups of mutations. This result indicates that the information from nearby polar/charged amino acid residues and/or the aliphatic and aromatic residues that are close in space is important for the stability of exposed mutations. 

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