What does the future hold? There are likely to be on the order of 10,000 different proteins in a typical human cell, each of which interacts with 5 to 10 different partners. Despite the enormous progress made in recent years, we cannot yet claim to understand even the simplest known cells, such as the small Mycoplasma bacterium formed from only about 500 gene products (see Figure 1–10). How then can we hope to understand a human? Clearly, a great deal of new biochemistry will be essential, in which each protein in a particular interacting set is purified so that its chemistry and interactions can be dissected in a test tube. But in addition, more powerful ways of analyzing networks will be needed based on mathematical and computational tools not yet invented, as we shall emphasize in Chapter 8. Clearly, there are many wonderful challenges that remain for future generations of cell biologists.
Proteins can form enormously sophisticated chemical devices, whose functions largely depend on the detailed chemical properties of their surfaces. Binding sites for ligands are formed as surface cavities in which precisely positioned amino acid side chains are brought together by protein folding. In this way, normally unreactive amino acid side chains can be activated to make and break covalent bonds. Enzymes are catalytic proteins that greatly speed up reaction rates by binding the high-energy transition states for a specific reaction path; they also can perform acid catalysis and base catalysis simultaneously. The rates of enzyme reactions are often so fast that they are limited only by diffusion. Rates can be further increased only if enzymes that act sequentially on a substrate are joined into a single multienzyme complex, or if the enzymes and their substrates are attached to protein scaffolds, or otherwise confined to the same part of the cell.
Proteins reversibly change their shape when ligands bind to their surface. The allosteric changes in protein conformation produced by one ligand affect the binding of a second ligand, and this linkage between two ligand-binding sites provides a crucial mechanism for regulating cell processes. Metabolic pathways, for example, are controlled by feedback regulation: some small molecules inhibit and other small molecules activate enzymes early in a pathway. Enzymes controlled in this way generally form symmetric assemblies, allowing cooperative conformational changes to create a steep response to changes in the concentrations of the ligands that regulate them.
The expenditure of chemical energy can drive unidirectional changes in protein shape. By coupling allosteric shape changes to ATP hydrolysis, for example, proteins can do useful work, such as generating a mechanical force or moving for long distances in a single direction. The three-dimensional structures of proteins have revealed how a small local change caused by nucleoside triphosphate hydrolysis is amplified to create major changes elsewhere in the protein. By such means, these proteins can serve as input–output devices that transmit information, as assembly factors, as motors, or as membrane-bound pumps. Highly efficient protein machines are formed by incorporating many different protein molecules into larger assemblies that coordinate the allosteric movements of the individual components. Such machines perform most of the important reactions in cells.
Proteins are subjected to many reversible, post-translational modifications, such as the covalent addition of a phosphate or an acetyl group to a specific amino acid side chain. The addition of these modifying groups is used to regulate the activity of a protein, changing its conformation, its binding to other proteins, and its location inside the cell. A typical protein in a cell will interact with more than five different partners. Through proteomics, biologists can analyze thousands of proteins in one set of experiments. One important result is the production of detailed protein interaction maps, which aim at describing all of the binding interactions between the thousands of distinct proteins in a cell. However, understanding these networks will require new biochemistry, through which small sets of interacting proteins can be purified and their chemistry dissected in detail. In addition, new computational techniques will be required to deal with the enormous complexity.
What are the functions of the surprisingly large amount of unfolded polypeptide chain found in proteins?
How many types of protein functions remain to be discovered? What are the most promising approaches for discovering them?