Hydrophobic interactions, side chains

FIGURE 15.40 The polymerization of Hb S via the interactions between the hydrophobic Val side chains at position /36 and the hydrophobic pockets in the EF corners of /3-chains in neighboring Hb molecnles. The protruding block on Oxy S represents the Val hydrophobic protrusion. The complementary hydrophobic pocket in the EF corner of the /S-chains is represented by a sqnare-shaped indentation. (This indentation is probably present in Hb A also.) Only the /S9 Val protrusions and the /Si EF pockets are shown. (The /Si Val protrusions and the /S9 EF pockets are not involved, although they are present.)... 

This group of amino acids includes glycine, alanine, valine, leucine. Isoleucine and proline. The hydrocarbon R groups are non-polar and hydrophobic. The side chains of alanine, valine, leucine and isoleucine are important in promoting hydrophobic interactions within protein structures. On the other hand, the imino group of proline is held in a rigid conformation and reduces the structural flexibility of the protein. 

Clearly, thrombin binding data indicate that hydrophobicity is a major driving force for interaction. However, in the following we show that, beyond hydrophobicity, both side-chain orientation and electronic effects also play an important role in binding. 

The selectivity of the interaction of Nef with the Hck-SH3 domain is based on the interaction that the RT loop of the SH3 domain can form by extending over the surface of Nef. The RT loop is a remarkably variable and flexible structure, which in Src kinases can be differentially stabilized by networks of hydrogen-bonding interactions, according to its particular sequence (121). These differences may at least in part account for the selectivity of the Nef-SH3 interaction by stabilizing a particular conformation of the loop necessary for an optimal interaction with Nef. The character of this interaction is hydrophobic the side chain of Ile-96 of the Fyn-SH3 R—>I mutant inserts into an exposed, remarkably hydro-phobic crevice between the aA and aB helices of Nef. A correlation exists between the character of residues contributing to this specificity pocket and the ability of HIV-1, HIV-2, or SIV to interact with different Src family SH3 domains (124). The importance of this interaction is confirmed by the selection of RT-loop mutants of the Hck-SH3 domain that bind to Nef with affinities up to 40-fold higher than those of parental... 

To check whether these conclusions could be extended to copper(II) ternary systems of amino acids in which one of the possible interacting side chains is a hydrophobic cavity... 

Hydrogels with hydrophobic, crystallizable side chains formed by copolymerization of acrylic acid and stearyl acrylate crosslinked with methylenebisacrylamide (BIS) showed a strong temperature dependence in their mechanical properties [91-93]. Such shape-memory gels having Tians = 7m displayed a reversible order-disorder transition associated with the interactions between the alkyl side chains. While behaving like hard plastic below 25 °C, softening above 50 °C enabled the materials... 

A protein is a linear chain of amino acids that assumes a three-dimensional shape dictated by the primary sequence of the amino acids in the chain. The side chains of the amino acids play an important role in directing the way in which the protein folds in solution. The hydrophobic (nonpolar) side chains avoid interaction with water, while the hydrophilic (polar) side chains seek such interaction. This results in a folded globular structure with the hydrophobic side chains inside and the hydrophilic side chains outside [9]. The final shape of the protein (helix, planar or random coil ) is a product of many interactions which form a delicate balance [10,11]. These interactions and structural organizations are briefly discussed below. 

The packing interactions between a helices and p strands are dominated by the residues Val (V), He (I), and Leu (L), which have branched hydrophobic side chains. This is reflected in the amino acid composition these three amino acids comprise approximately 40% of the residues of the P strands in parallel P sheets. The important role that these residues play in packing a helices against P sheets is particularly obvious in a/P-barrel structures, as shown in Table 4.1. 

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