one turn of the helix, this places the other hydrophobic amino acids nearly in line with the leucines.
Harbury made certain changes in the sequence, substituting different hydrophobic amino acids at the positions of leucine and the other hydrophobe that forms the zipper mechanism. Then he asked how the amino acid substitutions changed the structure of the leucine zipper, the way it bonded, and its stability.
One set of substitutions barely altered the structure. But other changes caused the leucine zipper to form tetramers (quadruplets) or trimers (triplets) instead of dimers (see Figure 10.5). (To visualize the structure of these, imagine winding three and then four fibers around each other to form a rope). In the latter cases the main difference between the normally occurring hydrophobes and their replacements was shape. The substituting amino acids had side chains that branched at the first carbon atom; leucine does not.
It was surprising that a couple of substitutions could cause such drastic changes in bonding patterns, Alber said at the "Frontiers of Science" symposium, "because intuitively, you know that sequences that are similar generally form the same structure. That's a very big idea in protein structure. If you have two similar sequences, they have the same fold. This is an exception to that rule."
"These sequences are in fact 75 to 87 percent identical, and yet they form different arrangements," Alber continued. "Why is that? The only thing that we've changed in these sequences is the geometry of these [amino acids that connect the helices]. So it must be the packing of the interface that determines the number of strands. We've figured out how that can happen by determining by x-ray crystallography the three-dimensional structure of this tetrameric coil." (see Figure 10.6.)
The other reason the result seemed surprising is that researchers had