Tertiary protein structure hydrophilic interactions

The enrichments and depletions displayed in Figure 1 are concordant with what would be expected if disorder were encoded by the sequence (Williams et al., 2001). Disordered regions are depleted in the hydrophobic amino acids, which tend to be buried, and enriched in the hydrophilic amino acids, which tend to be exposed. Such sequences would be expected to lack the ability to form the hydrophobic cores that stabilize ordered protein structure. Thus, these data strongly support the conjecture that intrinsic disorder is encoded by local amino acid sequence information, and not by a more complex code involving, for example, lack of suitable tertiary interactions. 

In native state, proteins exist as either fibrous or globular form. Protein should be denatured and unfolded to produce an extended chain structure to form film. Extended protein chains can interact through hydrogen, ionic, and hydrophobic bonds to form a three-dimensional stmcture (24). Protein films are excellent gas barriers but poor moisture barriers because of their hydrophilic nature. Mechanical properties and gas permeability depend on the relative humidity (1). Al-ameri (25) smdied the antioxidant and mechanical properties of soy, whey and wheat protein, and carrageenan and carboxymethyl cellulose films with incorporated tertiary-butylhy-droquinone (TBHQ), butylated hydroxytoluene (BHT), fenugreek, and rosemary extracts. Armitage et al. (26) studied egg albumin film as a carrier of natural antioxidants to reduce lipid oxidation in cooked and uncooked poultry. 

Hydrophobic interactions among the amino acid side chains also determine tertiary structure. Most globular proteins have their hydrophobic side chains, for example, those of phenylalanine, valine, or tryptophan, located on the inside of the protein structure. Conversely, the hydrophilic amino acids, such as glutamic acid, serine, or asparagine, are generally found on the outside surface of the protein, where they are available for interaction with water. Alternatively, when these groups are found on the inside of soluble... 

What about tertiary structure Why does any protein adopt the shape it does The forces that determine the tertiary structure of a protein are the same forces that act on ail molecules, regardless of size, to provide maximum stability. Particularly important are the hydrophilic (water-loving Section 2.13) interactions of the polar side chains on acidic or basic amino acids. Those acidic or basic amino acids with charged side chains tend to congregate on the exterior of the protein, where they can be solvated by water. Those amino acids with neutral, nonpolar side chains tend to congregate on the hydrocarbon-like interior of a protein molecule, away from the aqueous medium. 

Most proteins contain more than one polypeptide chain. The manner in which these chains associate determines quaternary structure. Binding involves the same types of noncovalent forces mentioned for tertiary structure van der Waals forces, hydrophobic and hydrophilic attractions, and hydrogen bonding. However, the interactions are now interchain rather than infrachain (tertiary structure determination). The quaternary structure of hemoglobin (four almost identical subunits) will be discussed in Chapter 4, that of superoxide dismutase (two identical subunits) will be discussed in Chapter 5, and that of nitrogenase (multiple dissimilar subunits) will be discussed in Chapter 6. 

The van der Waals model of monomeric insulin (1) once again shows the wedge-shaped tertiary structure formed by the two chains together. In the second model (3, bottom), the side chains of polar amino acids are shown in blue, while apolar residues are yellow or pink. This model emphasizes the importance of the hydrophobic effect for protein folding (see p. 74). In insulin as well, most hydrophobic side chains are located on the inside of the molecule, while the hydrophilic residues are located on the surface. Apparently in contradiction to this rule, several apolar side chains (pink) are found on the surface. However, all of these residues are involved in hydrophobic interactions that stabilize the dimeric and hexameric forms of insulin. 

Hydrophilic attractions between a protein and an aqueous medium, such as cytoplasm or blood, also help maintain tertiary structure. In a protein dissolved in an aqueous medium, the polypeptide chain is folded so that nonpolar side groups are on the inside of the molecule and polar side groups are on the outside, where they interact with the water. 

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