Progress in the x-ray crystallography of membrane proteins has enabled the determination of the three-dimensional structure of many of them. The structures confirm that it is often possible to predict from the protein’s amino acid sequence which parts of the polypeptide chain extend across the lipid bilayer. Segments containing about 20–30 amino acids, with a high degree of hydrophobicity, are long enough to span a lipid bilayer as an α helix, and they can often be identified in hydropathy plots (Figure 10–20). From such plots, it is estimated that about 30% 0 50 100 0 100 200 Rev. Biochem. 53:595–624, 1984. With amino acid number amino acid number permission from Annual reviews.) localize potential α-helical membrane-spanning segments in a polypeptide chain. the free energy needed to transfer successive segments of a polypeptide chain from a nonpolar solvent to water is calculated from the amino acid composition of each segment using data obtained from model compounds. this calculation is made for segments of a fixed size (usually around 10–20 amino acids), beginning with each successive amino acid in the chain. the “hydropathy index” of the segment is plotted on the Y axis as a function of its location in the chain. A positive value indicates that free energy is required for transfer to water (i.e., the segment is hydrophobic), and the value assigned is an index of the amount of energy needed. peaks in the hydropathy index appear at the positions of hydrophobic segments in the amino acid sequence. (A and B) hydropathy plots for two membrane proteins that are discussed later in this chapter. glycophorin (A) has a single membrane-spanning α helix, and one corresponding peak in the hydropathy plot. Bacteriorhodopsin (B) has seven membrane-spanning α helices and seven corresponding peaks in the hydropathy plot. (A, adapted from D. eisenberg, Annu.
of an organism’s proteins are transmembrane proteins, emphasizing their importance. Hydropathy plots cannot identify the membrane-spanning segments of a β barrel, as 10 amino acids or fewer are sufficient to traverse a lipid bilayer as an extended β strand and only every other amino acid side chain is hydrophobic.
The strong drive to maximize hydrogen-bonding in the absence of water means that a polypeptide chain that enters the lipid bilayer is likely to pass entirely through it before changing direction, since chain bending requires a loss of regular hydrogen-bonding interactions. But multipass transmembrane proteins can also contain regions that fold into the membrane from either side, squeezing into spaces between transmembrane α helices without contacting the hydrophobic core of the lipid bilayer. Because such regions interact only with other polypeptide regions, they do not need to maximize hydrogen-bonding; they can therefore have a variety of secondary structures, including helices that extend only part way across the lipid bilayer (Figure 10–21). Such regions are important for the function of some membrane proteins, including water channel and ion channel proteins, in which the regions contribute to the walls of the pores traversing the membrane and confer substrate specificity on the channels, as we discuss in Chapter 11. These regions cannot be identified in hydropathy plots and are only revealed by x-ray crystallography or electron crystallography (a technique similar to x-ray diffraction but performed on two-dimensional arrays of proteins) of the protein’s three-dimensional structure.
transmembrane α helices Often Interact with One Another