Amino acids hydrophobic interactions between

Folding of a peptide probably occurs coincident with its biosynthesis (see Chapter 38). The physiologically active conformation reflects the amino acid sequence, steric hindrance, and noncovalent interactions (eg, hydrogen bonding, hydrophobic interactions) between residues. Common conformations include a-helices and P pleated sheets (see Chapter 5). 

Figure 10.7 The EGF receptor. The N-terminal, extracellular region of the receptor contains 622 amino acids. It displays two cysteine-rich regions, between which the ligand-binding domain is located. A 23 amino acid hydrophobic domain spans the plasma membrane. The receptor cytoplasmic region contains some 542 amino acids. It displays a tyrosine kinase domain, which includes several tyrosine autophosphorylation sites, and an actin-binding domain that may facilitate interaction with the cell cytoskeleton...

Peripheral proteins are loosely associated with the membrane through electrostatic interactions and hydrogen bonds or by covalently attached lipid anchors. Integral proteins associate firmly with membranes by hydrophobic interactions between the lipid bilayer and their nonpolar amino acid side chains, which are oriented toward the outside of the protein molecule. 

Hydrophobic interactions between amino acids with nonpolar side chains. 

Location of polar and nonpolar amino acid residues The interior of the myoglobin molecule is composed almost entirely of nonpolar amino acids. They are packed closely together, forming a structure stabilized by hydrophobic interactions between these clustered residues (see p. 19). In contrast, charged amino acids are located almost exclusively on the surface of the molecule, where they can form hydrogen bonds, with each other and with water. 

Hydrophobic interaction chromatography relies on hydrophobic interactions between apolar amino acid residues in the proteins and a resin containing hydrophobic groups, such as /7-octyl or phenyl groups. After the protein mixture is applied to the column, an elution buffer with decreasing ionic strength is used. Hydrophilic proteins will elute first, whereas hydrophobic proteins elute last. 

It is believed that proteins and tannins interact via hydrogen bonding and hydro-phobic effects. Hydrogen bonds can be formed between the hydroxyl groups of phenolic compounds and carbonyl and amide groups of proteins. Hydrophobic interaction can occur between the benzenic nuclei of phenolic compounds and the apolar side-chains of amino acids such as leucine, lysine, or proline in proteins. Several authors have observed the occurrence of hydrophobic interactions between proteins and tannins [16-20]. 

After adsorption one side of the protein molecule is oriented towards the sorbent surface, turned away from the aqueous solution. As a consequence, hydrophobic parts of the protein that are buried in the interior of the dissolved molecule may become exposed to the sorbent surface where they are still shielded from contact with water. Because hydrophobic interaction between apolar amino acid residues in the protein s interior support the formation of secondary structures as a-helices and P-sheets, a reduction of this interaction destabilizes such structures. Breakdown of the a-helices and/or P-sheets content is, indeed, expected to occur if peptide units released from these ordered structures can form hydrogen bonds with the sorbent surface. This is the case for polar surfaces such as oxides, e.g. silica and metal oxides, and with sorbent retaining residual water at their surfaces. Then the decrease in ordered secondary structures leads to an increased conformational entropy of the protein. This may favour the protein adsorption process considerably.13 It may be understood that proteins having an intrinsically low structural stability are more prone to undergo adsorption-induced structural changes. 

The compact, asymmetric structure that individual polypeptides attain is called tertiary structure. The tertiary structures of water-soluble proteins have features in common (1) an interior formed of amino acids with hydrophobic side chains and (2) a surface formed largely of hydrophilic amino acids that interact with the aqueous environment. The driving force for the formation of the tertiary structure of water-soluble proteins is the hydrophobic interactions between the interior residues. Some proteins that exist in a hydrophobic environment, in membranes, display the inverse distribution of hydrophobic and hydrophilic amino acids. In these proteins, the hydrophobic amino acids are on the surface to interact with the environment, whereas the hydrophilic groups are shielded from the environment in the interior of the protein. 

The hydrophobic effect is a driving force in the formation of clathrate hydrates and the self-assembly of lipid bilayers. Hydrophobic interactions between lipids and proteins are the most important determinants of biological membrane structure. The three-dimensional folding pattern of proteins is also determined by hydrophobic interactions between nonpolar side chains of amino acid residues. 

---