Amino acid aromatic, hydrophobic

Fig. 2. The standard amino acids, (a) Hydrophobic, aliphatic R groups, (b) hydrophobic, aromatic R groups. The molecular weights of the amino acids are given in Topic B2, Table 1.

These amino acids form hydrophobic (water-repelling) nonpolar regions in proteins. There are three more of this kind with special roles. Phenylalanine and tryptophan have aromatic rings and, though they are still hydrophobic, they can form attractive 7t-stacking interactions with other aromatic molecules. Enzyme-catalysed hydrolysis of proteins often happens next to one of these residues. Proline is very special. It has its amino group inside a ring and has a different shape from all the other amino acids. It appears in proteins where a bend or a twist in the structure is needed. 

Many kinds of interactions are possible for aromatic amino acids. Aromatic aromatic (n - - n) interactions and cation n interactions [33] are well known. Weak hydrogen-bonding interactions such as CH n, NH n, OH n, and CH O play important roles in biological systems [31]. In effect aromatic amino acids can recognize a variety of structures. Moreover, as mentioned above, the high hydrophobicity of aromatic amino acids enhances binding interactions. 

Also the arene-arene interactions, as encountered in Chapter 3, are partly due to hydrophobic effects, which can be ranked among enforced hydrophobic interactions. Simultaneous coordination of an aromatic oc amino acid ligand and the dienophile to the central copper(II) ion offers the possibility of a reduction of the number of water molecules involved in hydrophobic hydration, leading to a strengthening of the arene-arene interaction. Hence, hydrophobic effects can have a beneficial influence on the enantioselectivity of organic reactions. This effect is anticipated to extend well beyond the Diels-Alder reaction. 

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

Mammals, fungi, and higher plants produce a family of proteolytic enzymes known as aspartic proteases. These enzymes are active at acidic (or sometimes neutral) pH, and each possesses two aspartic acid residues at the active site. Aspartic proteases carry out a variety of functions (Table 16.3), including digestion pepsin and ehymosin), lysosomal protein degradation eathepsin D and E), and regulation of blood pressure renin is an aspartic protease involved in the production of an otensin, a hormone that stimulates smooth muscle contraction and reduces excretion of salts and fluid). The aspartic proteases display a variety of substrate specificities, but normally they are most active in the cleavage of peptide bonds between two hydrophobic amino acid residues. The preferred substrates of pepsin, for example, contain aromatic residues on both sides of the peptide bond to be cleaved. 

The structures predicted for the fast and slow Ca -ATPase (Fig. 1) are 84 /o identical [8], There are 164 differences in the amino acid sequences between the two isoenzymes, 66 of which are conservative replacements, involving substitution of serine for threonine, aspartic for glutamic, lysine for arginine, or interchanges between aromatic or hydrophobic amino acids [8],... 

In polar solvents, the structure of the acridine 13 involves some zwitterionic character 13 a [Eq. (7)] and the interior of the cleft becomes an intensely polar microenvironment. On the periphery of the molecule a heavy lipophilic coating is provided by the hydrocarbon skeleton and methyl groups. A third domain, the large, flat aromatic surface is exposed by the acridine spacer unit. This unusual combination of ionic, hydrophobic and stacking opportunities endows these molecules with the ability to interact with the zwitterionic forms of amino acids which exist at neutral pH 24). For example, the acridine diacids can extract zwitterionic phenylalanine from water into chloroform, andNMR evidence indicates the formation of 2 1 complexes 39 such as were previously described for other P-phenyl-ethylammonium salts. Similar behavior is seen with tryptophan 40 and tyrosine methyl ether 41. The structures lacking well-placed aromatics such as leucine or methionine are not extracted to measureable degrees under these conditions. 

Transport of amino acids across a chloroform liquid membrane with these carriers also revealed a high specificity (Scheme 2). For efficient transport, an aromatic side chain must be present and the distance between the aryl and ammonium functions is optimal in the P-aryl systems. Neither oe-phenyl-glycine 42 nor y-phenyl-butyrine 43 are transported to significant extents 25a>. These results are shown in Table 2. The selectivity with 13 contrasts sharply for that observed with typical detergents wherein side chain hydrophobicity determines the relative transport rates. 

Aromatic side chains of amino acids such as phenylalanine, tryptophan, and tyrosine are found in general in the interior of proteins, in hydrophobic regions. In some proteins they mediate helix-helix contacts. It is to be expected that agents containing aromatic groups could interact with proteins via aromatic-aromatic interactions, as for instance, proven by X-ray studies of biphenyl compounds which inhibit sickle-cell hemoglobin gelation. 

Phenylalanine and tryptophan contain aromatic side chains that, like the aliphatic amino acids, are also relatively non-polar and hydrophobic (Figure 1.4). Phenylalanine is unreactive toward common derivatizing reagents, whereas the indolyl ring of tryptophan is quite reactive, if accessible. The presence of tryptophan in a protein contributes more to its total absorption at 275-280nm on a mole-per-mole basis than any other amino acid. The phenylalanine content, however, adds very little to the overall absorbance in this range. 

Hydrocarbons (both aromatic and aliphatic) do not have many (or any) groups that can participate in the hydrogen-bonding network of water. They re greasy and prefer to be on the interior of proteins (away from water). Note that a couple of the aromatics, Tyr and Trp, have O and N, and Met has an S, but these amino acids are still pretty hydrophobic. The hydrophobic nature usually dominates however, the O, N, and S atoms often participate in hydrogen bonds in the interior of the protein. 

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