Figure 717

Hemoglobin—An Example of a Heterotetramer

Two a-subunits and two p-subunits form the hemoglobin tetramer. The two a-subunits are identical as are the two p-subunits. However, the a-subunits differ from the p-subunits, although both types of chain are related in amino acid sequence and have a similar overall shape.

prefixes homo- (same) and hetero- (different) are sometimes used to indicate whether the subunits are the same or different. Thus the lactose repressor is a homo-tetramer, whereas hemoglobin is a hetero-tetramer.

The same hydrophobic forces largely responsible for tertiary structure are involved in the assembly of multiple subunits. Soluble proteins, with only a single polypeptide chain, fold so that almost all of their hydrophobic residues are hidden in the interior. In the case of subunit proteins, the polypeptide chains are folded, leaving a cluster of hydrophobic residues exposed to the water at the protein surface (Fig. 7.18). This is an unfavorable arrangement and when two polypeptide chains with exposed hydrophobic patches come into contact with each other, they tend to stick together, rather like hook-and-loop fasteners. As noted above, the hydrophobic force

FIGURE 7.18 Hydrophobic Force Drives Assembly of Subunits

Two proteins with hydrophobic regions will often bind together so that their hydrophobic regions become internalized, away from the surrounding water, in the dimer.

is weaker at lower temperatures, hence many subunit proteins tend to come apart at low temperatures.

Higher Level Assemblies and Self-Assembly

Subunits that are designed with more than one bonding region can be used to build rings or chains. Long chains of identical protein subunits are often twisted helically, as in bacterial flagella or in human collagen. If a helix of protein subunits has wide coils that are packed close together, it will form a hollow cylinder (Fig. 7.19). The protein shell of certain viruses (e.g. tobacco mosaic virus) and the microtubules that are found in eukaryotic cells are both constructed in this manner. In some cases, merely mixing the subunits allows the final structure to form. This is known as self-assembly and is true of the coat of tobacco mosaic virus, for example. In other cases, these higher level structures require other proteins and cofactors to help assembly.

Cofactors and Metal Ions Are Often Associated with Proteins

To function properly, many proteins need extra components, called cofactors or prosthetic groups, which are not themselves proteins. Many proteins use single metal atoms as cofactors; others need more complex organic molecules. Strictly speaking, prosthetic self-assembly Automatic assembly of protein subunits without need of any outside assistance

FIGURE 7.18 Hydrophobic Force Drives Assembly of Subunits

Two proteins with hydrophobic regions will often bind together so that their hydrophobic regions become internalized, away from the surrounding water, in the dimer.

FIGURE 7.19 Protein Assemblies: Rings, Chains and Cylinders

A) Joining protein subunits in a circle forms a ring. B) A helical chain, like that of actin, allows assembly of a very long thin structure from globular subunits. C) Winding protein subunits into a helix forms a cylinder, like that found in microtubules.

groups are fixed to a protein, whereas cofactors are free to wander around from protein to protein. However, this classification breaks down because the same organic co-factor may be covalently attached to one enzyme but non-covalently associated with another. Consequently, the terms are often used loosely. A protein without its prosthetic group is referred to as an apoprotein.

For example, oxygen carrier proteins such as hemoglobin have a cross-shaped organic cofactor called heme that contains a central iron atom. The heme is bound in the active site of the apoprotein, in this case globin, and so hemoglobin results. Oxygen binds to the iron atom at the center of the heme and the hemoglobin carries it around the body. Prosthetic groups are often shared by more than one protein; for example, heme is shared by hemoglobin and by myoglobin, which receives oxygen and distributes it inside muscle cells.

Most bacteria and plants are able to synthesize their own cofactors. However, many organic enzyme cofactors cannot be made by animals and consequently they or their immediate precursors must be provided in the diet. Such cofactors and/or their precursors are then referred to as vitamins (Table 7.02).A few cofactors, such as heme, can be synthesized by animals and are therefore not vitamins. Conversely, not all vitamins are cofactors or their precursors. For example, vitamin D gives rise to a hormone. Vitamin A confuses the classification scheme as it is partly converted to retinalde-hyde—a protein cofactor—and partly to retinoic acid—a hormone. Vitamin C does not act directly as a cofactor but is needed to keep metal ions (such as Cu and Fe) that do act as cofactors in their reduced states. A further complication is that certain cofactors apoprotein That portion of a protein consisting only of the polypeptide chains without any extra cofactors or prosthetic groups

X-Ray Crystallography is Used to Solve 3D Structures

X-ray crystallography, also known as X-ray diffraction, is used to solve the 3-D structure of molecules, in particular proteins and nucleic acids. It was X-ray diffraction that first revealed that DNA was twisted into a double helix. Knowing their 3-D shapes allows us to understand better how biological molecules fit together and interact.

When a beam of X-rays is shone through a substance, the X-rays are scattered by the atoms they encounter. If the target substance is a crystal with a regular structure, the scattering of the X-rays will give rise to a regular, though complex, diffraction pattern (Fig. 7.20). In practice, the crystal is rotated into a variety of positions on a computer-controlled stage.The diffraction patterns are recorded and, after computer analysis, are used to generate a 3-D atomic map of the protein molecule.

X-ray crystallography needs large well-formed crystals of highly purified protein. Nowadays, molecular cloning and over-expression of the gene encoding it allow us to obtain plenty of the protein under investigation. However, getting nice crystals is often difficult for such massive complex molecules as proteins, especially those whose 3-D shapes are irregular. X-ray crystallography is sophisticated and time consuming and each protein must be purified and examined individually. Nonetheless, X-ray structures are available for a significant number of proteins. As of early 2004, the Protein Data Bank (www.rcsb.org/pdb/) lists approximately 24,000 structures of which 19,000 were provided by X-ray analysis and 3,000 by NMR. Since many proteins are members of related families, once a 3-D structure is available for one, it provides insight into the conformation of a whole series of related molecules.

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