Tryptophane relative hydrophobicity

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 third class of host defense peptides, the extended peptide class, is defined by the relative absence of a defined secondary structure. These peptides normally contain high proportions of amino acids such as histidine, tryptophan, or proline and tend to adopt an overall extended conformation upon interaction with hydrophobic environments. Examples of peptides belonging to the extended class include indolicidin, a bovine neutrophil peptide, and the porcine peptide fragment, tritpticin. These structures are stabilized by hydrogen bonding and van der Waals forces as a result of contact with lipids in contrast to the intramolecular stabilization forces found in the former peptide classes. 

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-... 

Fluorescence may also be enhanced. Sometimes a compound has a low quantum yield in aqueous solution but a higher one in nonpolar media. The dyes tolu-idinyl- and anilinyl-naphthalene sulfonic acid fluoresce very weakly in water, but strongly when they are bound in the hydrophobic pockets of proteins. Interestingly enough, if they are bound next to a tryptophan residue, they may be excited by light that is absorbed by the tryptophan at 275 to 295 nm and whose energy is transferred to them. Tryptophan and NADH fluoresce relatively weakly in water, and their fluorescence may be enhanced in the nonpolar regions of proteins. 

Figure 19 shows the typical fluorescence transients of TBE from more than 10 gated emission wavelengths from the blue to the red side. At the blue side of the emission maximum, all transients obtained from four Trp-probes in the cubic phase aqueous channels drastically slow down compared with that of tryptophan in bulk water. The transients show significant solvation dynamics that cover three orders of magnitude on time scales from sub-picosecond to a hundred picoseconds. These solvation dynamics can be represented by three distinct decay components The first component occurs in about one picosecond, the second decays in tens of picoseconds, and the third takes a hundred picoseconds. The constmcted hydration correlation functions are shown in Fig. 20a with anisotropy dynamics in Fig. 20b. Surprisingly, three similar time scales (0.56-1.431 ps, 9.2-15 ps, and 108-140 ps) are obtained for all four Trp-probes, but their relative amplitudes systematically change with the probe positions in the channel. Thus, for the four Trp-probes studied here, we observed a correlation between their local hydrophobicity and the relative contributions of the first and third components from Trp, melittin, TME to TBE, the first components have contributions of 40%, 35%, 26%, and 17%, and the third components vary from 32%, to 38%, 43%, and 53%, respectively. 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... 

The possibility of HjO as the hydrogen donor is unlikely, because D is in all likelihood buried inside the strongly hydrophobic, membrane-spanning a-helix region of the Dj protein subunit. We therefore suggest that the proton donating species is an amino acid. The folding of the Dj polypeptide proposed in [14] results in four possiblities hisidine or serine in the second, or tryptophan or serine in the fifth intramembrane a-helix. A selection between these donors can only be made when a more precise location of the different a-helices relative to the tyrosyl donor is known. 

The reactivity of amino acids within a protein actually can vary considerably with regard to their reactivity for labeling due to variations in the microenvironment of the residues. These differences in reactivity are related to a number of factors including proximity to hydrophobic sequences or bulky amino acids such as tryptophan. Accessibility to solvent also must be considered. The relative amino acid reactivity of amino adds toward labeling has not been investigated on mAbs because of their complexity. However, studies with smaller proteins and peptides have documented, for example, that the rate of iodination of tyrosine residues in these molecules can vary by factors of 50-100 (Dube et al. 1966 Seon et al. 1970). 

Lipid peroxidation caused a decrease in phospholipid molecule mobility both in the region of polar heads and in the region of acyl chains till the depth of at least 1.7 nm from water-lipid interface (Panasenko et al. 1991). Under relative high levels of oxidation (>6 pmol malondialdehyde/g LDL phospholipid) the polarity of lipid phase increased. The decrease in efficiency of tryptophan fluorescence quenching by nitroxide fragments incorporated into hydrophobic regions at the depth of 2 nm from water-lipid interface indicated that lipid-protein interaction was disturbed as a result of oxidation of LDL lipids. 

This unexpected result was interpreted to mean that the reverse prenyl transferase presents the olefinic n-system of DMAPP in a manner in which both faces of the n-system are susceptible to attack by the 2-position of the indole moiety. The simplest explanation is to invoke binding of the DMAPP in an upside down orientation relative to normal prenyl transferases which permits a facially non-selective S attack on the rr-system as shown in Scheme 20. It was speculated that in this situation the pyrophosphate group is likely anchored in the enzyme active site with the hydrophobic isopropenyl moiety being presented in a conformationally flexible (A B) disposition with respect to the tryptophan-derived substrate (Scheme 20). This is in contrast to the normal mode of prenyl transfer where the nucleophilic displacement at the pyrophosphate-bearing methylene carbon occurs with inversion of stereochemistry at carbon with the hydrophobic tail of DMAPP buried in the enzyme active site. 

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