Tryptophan aromatic stacking interactions

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. 

There are also a few examples of interligand stacking interactions to give complexes of the form [M(L)(nucleotide)], where L is a tt-aromatic base such as bipy, phen, or tryptophanate (Trp ) (Figure 16) 3435,272 Metal-phosphate bonding, rather than bonding direct to the heterocyclic bases, becomes the dominant interaction in these complexes. 

Figure 23 Hypothesized structure of the [Zn"(16)(trp)] adduct. Tryptophane (trp) is recognized by the Zn" tetramine receptor through (i) the formation of a metal-carboxylate coordinative bond (ii) the establishing of 7t-stacking interactions between the aromatic part of the amino acid and one of the facing polyaromatic substituents of the tripodal tetramine framework.

Analysis of the coupling constants according to a Karplus-type equation revealed that the aromatic plane of phenylalanine and tryptophan is parallel to the porphyrin plane, suggesting that the Ti-rc-stacking interactions in water stabilize the complex. ... 

Binding of certain amino acids, as neutral (zwitterionic) substrates within the cleft of the acridine substrates has also been observed [14]. For such complexes, an additional element of recognition exists stacking interactions between the acridine surface and the aromatic side chains of tryptophan, phenylalanine and tyrosine are detected by NMR methods. This specific contact - which is also seen with other j -phenethylamines [15]-results in selective transport of the jS-aryl amino acids across liquid membranes with these carriers as 2 1 complexes (Scheme 7). 

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. 

Crystal and solution structures of SH3 domain-ligand complexes reveal that the SH3 region involved in the interaction with the proline-iich peptide is a surface patch formed by the side chains of a few well-conserved residues 1) one of the two aromatic residues in the ALY(F)DY(F) motif 2) the first tryptophan of the WW dipeptide 3) the PxxY motif. These residues are aligned to form a surface patch, quite hydrophobic, in which the aromatic side chains are stacked against each other (Figure 8). 

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