A typical ABC transporter contains a pair of membrane-spanning subunits linked to a pair of ATP-binding subunits located just below the plasma membrane. As in other examples we have discussed, the hydrolysis of the bound ATP molecules drives conformational changes in the protein, transmitting forces that cause the membrane-spanning subunits to move their bound molecules across the lipid bilayer (Figure 3–76).
Humans have invented many different types of mechanical pumps, and it should not be surprising that cells also contain membrane-bound pumps that
Figure 3–76 The abC (aTP-binding cassette) transporter, a protein machine that pumps molecules through a membrane. (A) How this large family of transporters pumps molecules into the cell in bacteria. As indicated, the binding of two molecules of ATP causes the two ATP-binding domains to clamp together tightly, opening a channel to the cell exterior. The binding of a substrate molecule to the extracellular face of the protein complex then triggers ATP hydrolysis followed by ADP release, which opens the cytoplasmic gate; the pump is then reset for another cycle.
(B) As discussed in Chapter 11, in eukaryotes an opposite process occurs, causing selected substrate molecules to be pumped out of the cell. (C) The structure of a bacterial ABC transporter (see Movie 11.5). (C, from R.J. Dawson and K.P. Locher, Nature 443:180–185, 2006. With permission from Macmillan Publishers Ltd;  PDB code: 2HYD).
function in other ways. Among the most notable are the rotary pumps that couple the hydrolysis of ATP to the transport of H+ ions (protons). These pumps resemble miniature turbines, and they are used to acidify the interior of lysosomes and other eukaryotic organelles. Like other ion pumps that create ion gradients, they can function in reverse to catalyze the reaction ADP + Pi → ATP, if the gradient across their membrane of the ion that they transport is steep enough.
One such pump, the ATP synthase, harnesses a gradient of proton concentration produced by electron-transport processes to produce most of the ATP used in the living world. This ubiquitous pump has a central role in energy conversion, and we shall discuss its three-dimensional structure and mechanism in Chapter 14.
Proteins Often Form Large Complexes That Function as Protein Machines
Large proteins formed from many domains are able to perform more elaborate functions than small, single-domain proteins. But large protein assemblies formed from many protein molecules linked together by noncovalent bonds perform the most impressive tasks. Now that it is possible to reconstruct most biological processes in cell-free systems in the laboratory, it is clear that each of the central processes in a cell—such as DNA replication, protein synthesis, vesicle budding, or transmembrane signaling—is catalyzed by a highly coordinated, linked set of 10 or more proteins. In most such protein machines, an energetically favorable reaction such as the hydrolysis of bound nucleoside triphosphates (ATP or GTP) drives an ordered series of conformational changes in one or more of the individual protein subunits, enabling the ensemble of proteins to move coordinately. In this way, each enzyme can be moved directly into position, as the machine catalyzes successive reactions in a series (Figure 3–77). This is what occurs, for example, in protein synthesis on a ribosome (discussed in Chapter 6)—or in DNA replication, where a large multiprotein complex moves rapidly along the DNA (discussed in Chapter 5).
Cells have evolved protein machines for the same reason that humans have invented mechanical and electronic machines. For accomplishing almost any task, manipulations that are spatially and temporally coordinated through linked processes are much more efficient than the use of many separate tools.
Scaffolds Concentrate Sets of Interacting Proteins