Phenylalanine relative hydrophobicity

Figure 9.10 Specificity pocket of chymotrypsin. Notice that this pocket is lined with relatively hydrophobic residues and is relatively deep, favoring the binding of residues with long hydrophobic side chains such as phenylalanine (shown in green). Also notice that the active-site serine residue (serine 195) is positioned to cleave the peptide backbone between the residue bound in the pocket and the next residue in the sequence. The key amino acids that constitute the binding site are labeled.

In our first example (Fig. 1.13), the first in which a coenzyme was linked to a cyclodextrin, we synthesized compound 25, with a pyridoxamine covalently linked to a C-6 of /3-cyclodextrin. We saw transaminations of pyruvic acid, of phenylpyruvic acid, and of indolepyruvic acid to form alanine, phenylalanine, and tryptophan, respectively, and with high selectivity for the hydrophobic phenyl and indole derivatives relative to simple pyruvic acid. Relative to its reaction with simple pyridoxamine in solution, without an attached or unattached cyclodextrin, the indolepyruvate reacted 50 times faster with compound 25. Also, we saw a 5 1 preference for the formation of the L-phenylalanine relative to the d enantiomer in transamination by compoimd 25. ... 

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. 

The results of kinetic and X-ray crystallographic experiments on mutant carbonic anhydrases II, in which side-chain alterations have been made at the residue comprising the base of the hydrophobic pocket (Val-143), illuminate the role of this pocket in enzyme-substrate association. Site-specific mutants in which smaller hydrophobic amino acids such as glycine, or slightly larger hydrophobic residues such as leucine or isoleucine, are substituted for Val-143 do not exhibit an appreciable change in CO2 hydrase activity relative to the wild-type enzyme however, a substitution to the bulky aromatic side chain of phenylalanine diminishes activity by a factor of about 10 , and a substitution to tyrosine results in a protein which displays activity diminished by a factor of about 10 (Fierke et o/., 1991). 

Aromatic R Groups Phenylalanine, tyrosine, and tryptophan, with their aromatic side chains, are relatively nonpolar (hydrophobic). All can participate in hydrophobic interactions. The hydroxyl group of tyrosine can form hydrogen bonds, and it is an important func-... 

When switching from water to an organic solvent, or switching between organic solvents, the substrate specificity can change. In the example of the standard reaction, transesterification of N-acetyl-i-phenylalanine ethyl ester with n-propanol by Subtilisin Carlsberg, which has been mentioned several times in this chapter already, the relative specificity between the rather hydrophobic phenylalanine compound and its more hydrophilic analog N-acetyl-L-serine ethyl ester varies with the solvent (Table 12.8) (Wescott, 1993). 

Irreversible insolubilization of proteins may occur mainly through formation of both intermolecular disulfide and hydrophobic bonds. The product can be quite different depending on the relative contribution of these two types of bonds. The hydrophobic bonds are formed among the hydrophobic amino acid side chains contributed by valine, leucine, isoleucine, phenylalanine, etc. 

The term lyophobic interactions is intended to generalize the expres sion hydrophobic interactions to other solvents than water. Hydro-phobic interactions have been prominently implicated in determining the native configuration of proteins in aqueous solution. These interactions are actually not of a single relatively well-defined character, as are electrostatic or hydrogen bond interactions, but are rather a set of interactions responsible for the immiscibility of nonpolar substances and water. Proteins contain a substantial proportion of amino acids such as phenylalanine, valine, leucine, etc., with nonpolar side-chain residues. These nonpolar groups should tend, therefore, other factors permitting, to cluster on the... 

Effects of amino acids The effects of 18 kinds of amino acids on crystal appearance are summarized in table 4. Among these amino acids tested, only leucine and tryptophan affected the change in crystal form from pillars to thin plates at concentrations relative to Lmore than 3%. These two amino acids are hydrophobic, so they might interact with the Lrphenylalanine skeleton in the crystal structure of di-L-phenylalanine sulfate monohydrate and are supposed to suppress growth in the a-axis direction. Isoleucine, valine and tyrosine which are analogous... 

Effect of Different Pentamer Sequence Arrangements of the Same 30-mer Composition. Chemically synthesized polytricosapeptides, poly (30-mers), were prepared with compositions of 1 aspartic acid residue (Asp, D) and 5 more-hydrophobic phenylalanine (Phe, F) residues replacing valine (Val, V) residues per repeat of 30 residues, but with different relative locations of D and F residues. These compositions are written ... 

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