|
In describing the structure of a protein, it is helpful to distinguish various levels of organization. The amino acid sequence is called the primary structure of the protein. Regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices and beta sheets, which constitute the protein's secondary structure. Certain combinations of alpha helices and beta sheets pack together to form compactly folded globular units, each of which is called a protein domain. Domains are usually constructed from a section of polypeptide chain that contains between 50 and 350 amino acids, and they seem to be the modular units from which proteins are constructed (see below). While small proteins may contain only a single domain, larger proteins contain a number of domains, which are often connected by relatively open lengths of polypeptide chain. Finally, individual polypeptides often serve as subunits for the formation of larger molecules, sometimes called protein assemblies or protein complexes, in which the subunits are bound to one another by a large number of weak, noncovalent interactions; in extracellular proteins these interactions are often stabilized by disulfide bonds.
The three-dimensional structure of a protein can be illustrated in various ways. Consider the unusually small protein basic pancreatic trypsin inhibitor (BPTI), which contains 58 amino acid residues folded into one domain. BPTI can be shown as a stereo pair displaying all of its nonhydrogen atoms (Figure 3-34A) or as an accurate space-filling model, where most of the details are obscured (Figure 3-34B). Alternatively, it can be shown more schematically, with all of the side chains and actual atoms omitted so that it is easier to follow the course of the main polypeptide chain (Figures 3-34C, D, and E). An average-size protein contains about six times more amino acid residues than BPTI, and many proteins are more than 20 times its size. Schematic drawings are essential for displaying the structure of these larger proteins, and we use them throughout this text.
Figure 3-35 shows how the structure of a large protein can be resolved into several levels of organization, each level constructed from the one below it in a hierarchical fashion. These levels of increased organizational complexity may correspond to the steps by which a newly synthesized protein folds into its final native structure inside the cell.