Cooh

' Reverse turn

FIGURE 7.09 Modular Arrangement of a-Helices and |3-Sheets

A stylized polypeptide chain. Both a-helical regions and a b-sheet segment are shown in this folded polypeptide chain. These modular segments are linked by reverse turns and regions of random coil.

reverse turns. Those regions of protein that do not form secondary structures are referred to as "random coil" although they are, of course, not truly random, but merely irregular.

The Tertiary Structure of Proteins

Further folding of the polymer chain constitutes the tertiary structure. In a nucleic acid this would be the supercoiling. In a protein, the polypeptide chain, with its preformed a-helix and b-sheet regions, is folded to give the final 3-D structure. In general, polypeptide chains with similar amino acid sequences fold to give similar 3-D structures. Tertiary folding depends on interactions between the side chains of the individual amino acids. Since there are 20 different amino acids, a large variety of final 3-D conformations is possible, although most polypeptides are roughly spherical.

The a-helix and b-sheet modules form the basic structural units of the protein (Fig. 7.09). They are linked by loops of random coil of various lengths. Many of these loops are at the surface of the protein, exposed to a solvent and contain predominantly charged or polar amino acid residues. The rigid ring structure of proline causes an approximately 90° change in direction of the polypeptide backbone. Consequently, random coil Region of polypeptide chain lacking secondary structure

FIGURE 7.10 Arrangement of an a/b-Barrel Domain

Schematic diagram of the a/b barrel domain of the enzyme methylmalonyl CoA mutase. Alpha helices are red and beta strands are blue. The inside of the barrel is lined by small hydrophilic side chains (Ser and Thr) which allows space for the substrate coenzyme A (green) to bind along the axis of the barrel. From: Introduction to Protein Structure by Brandon & Tooze, 2nd ed., 1999. Garland Publishing, Inc., New York and London.

FIGURE 7.10 Arrangement of an a/b-Barrel Domain

Schematic diagram of the a/b barrel domain of the enzyme methylmalonyl CoA mutase. Alpha helices are red and beta strands are blue. The inside of the barrel is lined by small hydrophilic side chains (Ser and Thr) which allows space for the substrate coenzyme A (green) to bind along the axis of the barrel. From: Introduction to Protein Structure by Brandon & Tooze, 2nd ed., 1999. Garland Publishing, Inc., New York and London.

FIGURE 7.11 The Oil Drop Model of Protein Structure

A simplified model to illustrate that hydrophilic groups are exposed to the water environment and that most hydrophobic groups are centrally positioned. Note that in real life many of the hydrophilic groups will form hydrogen bonds to the surrounding water molecules. In addition some hydrophilic groups will ionize, forming charged ions.

proline disrupts secondary structures and contributes to overall folding by forming bends. Examination of their 3-D structures has shown that the thousands of known proteins are in fact built from relatively few structural motifs. Such motifs generally consist of several a-helices and/or b-sheets joined to form a useful and recognizable structure (Fig. 7.10).

This 3-D folding is largely driven by two factors acting in concert. Many of the amino acids have R-groups that are very water-soluble (hydrophilic).These side chains prefer to be on the surface of the protein so they can dissolve in the water surrounding the protein and make hydrogen bonds to water molecules. In contrast, R-groups that are water repellent (hydrophobic) huddle together inside the protein away from the water (Fig. 7.11). Since hydrophobic molecules are greasy and insoluble, this

hnoc

2 Hydrophilic

H,O

H,O

, H,O

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