As described in Chapter 8, because of the powerful techniques of x-ray crystallography and nuclear magnetic resonance (NMR), we now know the three-dimensional shapes, or conformations, of more than 100,000 proteins. By carefully comparing the conformations of these proteins, structural biologists (that is, experts on the structure of biological molecules) have concluded that there are a limited number of ways in which protein domains fold up in nature—maybe as few as 2000, if we consider all organisms. For most of these so-called protein folds, representative structures have been determined.
The present database of known protein sequences contains more than twenty million entries, and it is growing very rapidly as more and more genomes are sequenced—revealing huge numbers of new genes that encode proteins. The encoded polypeptides range widely in size, from 6 amino acids to a gigantic protein of 33,000 amino acids. Protein comparisons are important because related structures often imply related functions. Many years of experimentation can be saved by discovering that a new protein has an amino acid sequence similarity with a protein of known function. Such sequence relationships, for example, first indicated that certain genes that cause mammalian cells to become cancerous encode protein kinases (discussed in Chapter 20).
As previously stated, most proteins are composed of a series of protein domains, in which different regions of the polypeptide chain fold independently to form compact structures. Such multidomain proteins are believed to have originated from the accidental joining of the DNA sequences that encode each domain, creating a new gene. In an evolutionary process called domain shuffling, many large proteins have evolved through the joining of preexisting domains in new combinations (Figure 3–14). Novel binding surfaces have often been created at the juxtaposition of domains, and many of the functional sites where proteins bind to small molecules are found to be located there.
A subset of protein domains has been especially mobile during evolution; these seem to have particularly versatile structures and are sometimes referred to as protein modules. The structure of one, the SH2 domain, was illustrated in Figure 3–6. Three other abundant protein domains are illustrated in Figure 3–15.
Each of the domains shown has a stable core structure formed from strands of β sheets, from which less-ordered loops of polypeptide chain protrude. The loops are ideally situated to form binding sites for other molecules, as most clearly demonstrated for the immunoglobulin fold, which forms the basis for antibody molecules. Such β-sheet-based domains may have achieved their evolutionary success because they provide a convenient framework for the generation of new binding sites for ligands, requiring only small changes to their protruding loops (see Figure 3–42).
Figure 3–14 Domain shuffling. An extensive shuffling of blocks of protein sequence (protein domains) has occurred during protein evolution. Those portions of a protein denoted by the same shape and color in this diagram are evolutionarily related. Serine proteases like chymotrypsin are formed from two domains (brown). In the three other proteases shown, which are highly regulated and more specialized, these two protease domains are connected to one or more domains that are similar to domains found in epidermal growth factor (EGF; green), to a calcium-binding protein (yellow), or to a “kringle” domain (blue). Chymotrypsin is illustrated in Figure 3–12.
Figure 3–15 The three-dimensional structures of three commonly used protein domains. In these ribbon diagrams, β-sheet strands are shown as arrows, and the Nand C-termini are indicated by red spheres. Many more such “modules” exist in nature. (Adapted from
M. Baron, D.G. Norman and I.D. Campbell, Trends Biochem. Sci. 16:13–17, 1991, with permission from Elsevier, and D.J. Leahy et al., Science 258:987–991, 1992, with permission from AAAS.)