Dna

binding domain

Active CAP is a dimer of two identical a helix-turn-helix DNA-binding proteins, one shown in green, one in gray.

Figure 9.18. Active catabolite activator protein is a dimer.

Example 9.2

Recognition by Binding

Many of the jobs proteins do depend on recognition and binding. Proteins vary greatly in the specificity with which they bind other substances. Histones are at one extreme. About 25% of their amino acids are lysine or arginine, whose side chains are positively charged. Histones therefore bind to DNA—any DNA—through an electrostatic attraction to the negative charges on the phosphates of the DNA backbone.

The glucocorticoid receptor also binds DNA, but it is at the very other extreme of specificity. After binding glucocorticoid hormone, the hormone-receptor complex enters the nucleus and binds to the base sequence 5' AGAACA 3'. The protein does this using a zinc finger domain (page 200), which inserts an a helix into the major groove of DNA. The receptor works as a dimer so the sequence 5' AGAACA 3' must appear twice in the DNA, separated by three nucleotides (page 203). Once bound the receptor binds other proteins that in turn stimulate transcription.

Figure 9.19. (a) Two zinc finger motifs in the glucocorticoid receptor. Each circle is one amino acid residue. Amino acid residues that are important in binding Zn2+ or DNA are specified. (b) Cartoon representation of the zinc finger domains of a dimerized pair of glucocorticoid hormone receptors interacting with DNA.

Figure 9.19. (a) Two zinc finger motifs in the glucocorticoid receptor. Each circle is one amino acid residue. Amino acid residues that are important in binding Zn2+ or DNA are specified. (b) Cartoon representation of the zinc finger domains of a dimerized pair of glucocorticoid hormone receptors interacting with DNA.

IN DEPTH 9.2 Hydropathy Plotting—The PDGF Receptor_

One of the central problems in structural biology is the prediction of the structure of a protein from the primary structure or indeed from the DNA sequence once the gene has been found. Although we have come some way in understanding protein folding, the problem remains unsolved. It is possible, however, to identify proteins that will have similar structures. One of the simpler things that can be looked for is regions of hydrophobic amino acids: if these are 21-22 amino acids long, they are likely to be membrane spanning a helices. The figure shows a hydropathy plot for the platelet-derived growth factor (PDGF) receptor. Each amino acid in the protein has a hydrophobicity allotted to it, so that ionized groups like those on aspartate and arginine get a big negative score while groups like those on phenylalanine and leucine get a big positive score. The plot is a running average of the hydrophobicity along the polypeptide chain. The protein begins with a somewhat hydrophobic region: this is the signal sequence (page 215) that directs the growing protein to the endoplasmic reticulum. The rest

of the protein is neutral or somewhat hydrophilic except for a prominent short hydrophobic region in the center. We can therefore predict that this protein will cross the membrane once at this location. Figure 9.15 shows the full predicted structure of this protein.

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