Aromatic groups, hydrophobic

Cosurfactant requirements can be minimized usiag a surfactant having a short-branched hydrophobe or a branched-alkyl substituent on an aromatic group (232,234) and a long ethoxy group chain (234). Blends of surfactants optimized for seawater or reservoir brine salinity include linear alkyl xylene sulfonate—alcohol ether sulfate mixtures (235). 

Residue 189 is at the bottom of the specificity pocket. In trypsin the Asp residue at this position interacts with the positively charged side chains Lys or Arg of a substrate. This accounts for the preference of trypsin to cleave adjacent to these residues. In chymotrypsin there is a Ser residue at position 189, which does not interfere with the binding of the substrate. Bulky aromatic groups are therefore preferred by chymotrypsin since such side chains fill up the mainly hydrophobic specificity pocket. It has now become clear, however, from site-directed mutagenesis experiments that this simple picture does not tell the whole story. 

In order for folded helices to assemble into tertiary structures in water, they need to be amphipathic (e.g. where one hehcal face is hydrophobic and the other is hydrophilic). Because the first hehcal peptoids contained very hydrophobic chiral residues, ways to increase the water solubihty and side-chain diversity of the hehx-indudng residues were investigated [49]. It was found that a series of side chains with chiral-substituted carboxamides in place of the aromatic group could stiU favor hehx formation, while dramatically increasing water solubility. 

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. 

In a similar way the effect of alkylation of DNA by an activated PAH may be drastic, as the hydrophobic aromatic group of the alkylating agent tries to avoid the aqueous environment of the nucleic acid. 

Figure 4.4 Placement of the hERG blocker pharmacophore in the inner cavity of the channel. The Cavalli pharmacophore [83] is placed within the pore illustrating its main features N (positively charged central nitrogen), CO (aromatic group), Cl and C2 (hydrophobic groups). The N feature is thought to form...

Small molecules that act as collisional quenchers may penetrate into the internal structure of proteins, diffuse, and cause quenching upon collision with the aromatic groups. Lakowicz and Weber(53) have shown that the interaction of oxygen molecules with buried tryptophan residues in proteins leads to quenching with unexpectedly high rate constants—from 2 x 109 to 7 x 109 M l s 1. Acrylamide is also capable of quenching the fluorescence of buried tryptophan residues, as was shown for aldolase and ribonuclease 7V(54) A more hydrophobic quencher, trichloroethanol, is a considerably more efficient quencher of internal chromophore groups in proteins.(55)... 

While models suggest the P 3 residue is directed at solvent and the FXa thrombin cleavage sites have polar residues at this position (Thr, Glu), the BPTI mutant results show a clear preference for a hydrophobic group. It is possible that aromatic groups can pack to Phe41 of the enzyme. Mutant results show lie is favored over Phe, His, which in turn is selected over Tyr. 

Microbial proteinases can be classified by mechanism of action. Hartley (1960) divided them into four groups serine proteinases, thio proteinases, metalloproteinases, and acid proteinases. Morihara (1974) classified enzymes within these groups according to substrate specificity. Enzymes which split peptide substrates at the carboxyl side of specific amino acids are called carboxyendopeptidases, and those which split peptide substrates at the amino side of specific amino acids are called aminoendopeptidases. Acid proteinases, such as rennin and pepsin, split either side of specific aromatic or hydrophobic amino acid residues. The action of proteolytic enzymes on milk proteins has been reviewed by Visser (1981). 

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