Globular Proteins Have a Variety of Tertiary Structures

With elucidation of the tertiary structures of hundreds of other globular proteins by x-ray analysis, it became clear that myoglobin illustrates only one of many ways in which a polypeptide chain can be folded. In Figure 4-18 the structures of cytochrome c, lysozyme, and ribonuclease are compared. These proteins have different amino acid sequences and different tertiary structures, reflecting differences in function. All are relatively small and easy to work with, facilitating structural analysis. Cytochrome c is a component of the respiratory chain of mitochondria (Chapter 19). Like myoglobin, cy-tochrome c is a heme protein. It contains a single polypeptide chain of about 100 residues (Mr 12,400) and a single heme group. In this case, the protoporphyrin of the heme group is covalently attached to the polypeptide. Only about 40% of the polypeptide is in a-helical segments, compared with 70% of the myoglobin chain. The rest of the cytochrome c chain contains 3 turns and irregularly coiled and extended segments.

Lysozyme (Mr 14,600) is an enzyme abundant in egg white and human tears that catalyzes the hydrolytic cleavage of polysaccharides in the protective cell walls of some families of bacteria. Lysozyme, because it can lyse, or degrade, bacterial cell walls, serves as a bactericidal agent. As in cytochrome c, about 40% of its 129 amino acid residues are in a-helical segments, but the arrangement is different and some 3-sheet structure is also present (Fig. 4-18). Four disulfide bonds contribute stability to this structure. The a helices line a long crevice in the side of the molecule, called the active site, which is the site of substrate binding and catalysis. The bacterial polysaccharide that is the substrate for lysozyme fits into this crevice. ^ Protein Architecture-Tertiary Structure of Small Globular Proteins, III. Lysozyme

Ribonuclease, another small globular protein (Mr 13,700), is an enzyme secreted by the pancreas into the small intestine, where it catalyzes the hydrolysis of certain bonds in the ribonucleic acids present in ingested

Cytochrome c

FIGURE 4-18 Three-dimensional structures of some small proteins.

Shown here are cytochrome c (PDB ID 1CCR), lysozyme (PDB ID 3LYM), and ribonuclease (PDB ID 3RN3). Each protein is shown in surface contour and in a ribbon representation, in the same orientation. In the ribbon depictions, regions in the fi conformation are

Lysozyme Ribonuclease represented by flat arrows and the a helices are represented by spiral ribbons. Key functional groups (the heme in cytochrome c; amino acid side chains in the active site of lysozyme and ribonuclease) are shown in red. Disulfide bonds are shown (in the ribbon representations) in yellow.

Cytochrome c

FIGURE 4-18 Three-dimensional structures of some small proteins.

Shown here are cytochrome c (PDB ID 1CCR), lysozyme (PDB ID 3LYM), and ribonuclease (PDB ID 3RN3). Each protein is shown in surface contour and in a ribbon representation, in the same orientation. In the ribbon depictions, regions in the fi conformation are

Lysozyme Ribonuclease represented by flat arrows and the a helices are represented by spiral ribbons. Key functional groups (the heme in cytochrome c; amino acid side chains in the active site of lysozyme and ribonuclease) are shown in red. Disulfide bonds are shown (in the ribbon representations) in yellow.

food. Its tertiary structure, determined by x-ray analysis, shows that little of its 124 amino acid polypeptide chain is in an a-helical conformation, but it contains many segments in the fi conformation (Fig. 4-18). Like lysozyme, ribonuclease has four disulfide bonds between loops of the polypeptide chain.

In small proteins, hydrophobic residues are less likely to be sheltered in a hydrophobic interior—simple geometry dictates that the smaller the protein, the lower the ratio of volume to surface area. Small proteins also have fewer potential weak interactions available to stabilize them. This explains why many smaller proteins such as those in Figure 4-18 are stabilized by a number of covalent bonds. Lysozyme and ribonuclease, for example, have disulfide linkages, and the heme group in cytochrome c is covalently linked to the protein on two sides, providing significant stabilization of the entire protein structure.

Table 4-2 shows the proportions of a helix and fi conformation (expressed as percentage of residues in each secondary structure) in several small, single-chain, globular proteins. Each of these proteins has a distinct structure, adapted for its particular biological function, but together they share several important properties. Each is folded compactly, and in each case the hydro-

phobic amino acid side chains are oriented toward the interior (away from water) and the hydrophilic side chains are on the surface. The structures are also stabilized by a multitude of hydrogen bonds and some ionic interactions.

TABLE 4-2 Approximate Amounts of a Helix and P Conformation in Some Single-Chain Proteins

TABLE 4-2 Approximate Amounts of a Helix and P Conformation in Some Single-Chain Proteins

Protein (total residues)

a Helix

ß Conformation

Chymotrypsin (247)

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  • daisy
    Does glucose have a tertiary structure?
    7 years ago

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