As we have described previously, genome sequences allow us to group many of the domains in proteins into families that show clear evidence of their evolution from a common ancestor. The three-dimensional structures of members of the same domain family are remarkably similar. For example, even when the amino acid sequence identity falls to 25%, the backbone atoms in a domain can follow a common protein fold within 0.2 nanometers (2 Å).
We can use a method called evolutionary tracing to identify those sites in a protein domain that are the most crucial to the domain’s function. Those sites that bind to other molecules are the most likely to be maintained, unchanged as organisms evolve. Thus, in this method, those amino acids that are unchanged, or nearly unchanged, in all of the known protein family members are mapped onto a model of the three-dimensional structure of one family member. When this is done, the most invariant positions often form one or more clusters on the protein surface, as illustrated in Figure 3–40A for the SH2 domain described previously (see Figure 3–6). These clusters generally correspond to ligand-binding sites.
The SH2 domain functions to link two proteins together. It binds the protein containing it to a second protein that contains a phosphorylated tyrosine side chain in a specific amino acid sequence context, as shown in Figure 3–40B. The amino acids located at the binding site for the phosphorylated polypeptide have been the slowest to change during the long evolutionary process that produced
Figure 3–39 an unusually reactive amino acid at the active site of an enzyme.
This example is the “catalytic triad” Asp-His-Ser found in chymotrypsin, elastase, and other serine proteases (see Figure 3–12). The aspartic acid side chain (Asp) induces the histidine (His) to remove the proton from a particular serine (Ser). This activates the serine and enables it to form a covalent bond with an enzyme substrate, hydrolyzing a peptide bond. The many convolutions of the polypeptide chain are omitted here.
the large SH2 family of peptide recognition domains. Mutation is a random process; survival is not. Thus, natural selection (random mutation followed by nonrandom survival) produces the sequence conservation by preferentially eliminating organisms whose SH2 domains become altered in a way that inactivates the SH2 binding site, destroying SH2 function.
Genome sequencing has revealed huge numbers of proteins whose functions are unknown. Once a three-dimensional structure has been determined for one member of a protein family, evolutionary tracing allows biologists to determine binding sites for the members of that family, providing a useful start in deciphering protein function.
Proteins Bind to Other Proteins Through Several Types of Interfaces
Proteins can bind to other proteins in multiple ways. In many cases, a portion of the surface of one protein contacts an extended loop of polypeptide chain (a “string”) on a second protein (Figure 3–41A). Such a surface–string interaction, for example, allows the SH2 domain to recognize a phosphorylated polypeptide loop on a second protein, as just described, and it also enables a protein kinase to recognize the proteins that it will phosphorylate (see below).
A second type of protein–protein interface forms when two α helices, one from each protein, pair together to form a coiled-coil (Figure 3–41B). This type of protein interface is found in several families of gene regulatory proteins, as discussed in Chapter 7.
The most common way for proteins to interact, however, is by the precise matching of one rigid surface with that of another (Figure 3–41C). Such interactions can be very tight, since a large number of weak bonds can form between two surfaces that match well. For the same reason, such surface–surface interactions can be extremely specific, enabling a protein to select just one partner from the many thousands of different proteins found in a cell.
Figure 3–40 The evolutionary trace method applied to the SH2 domain.