Oddly enough, it might seem, among all the hydrophobic amino acids that bind leucine zippers in pairs, there is one water-loving amino acid that is found in virtually every leucine zipper helix: the amino acid asparagine. ''So it's a really important thing for function," says Alber. Since such an entity could only weaken the zipper, the researchers were mystified as to what its purpose might be. To answer the question, they substituted in turn four different amino acids for asparagine and then determined the structure and bonding strength variant. Chavela Carr, a graduate student in Kim's lab, studied the stabilities, and Russ Brown, a postdoctoral student with Alber in Utah, deciphered the structures. Two things happened. First, the new helices bonded so strongly that even boiling didn't sunder the zipper. Second, these asparagine-free leucine zippers formed both pairs and triplets, and Alber speculates that they may have formed skewed dimers as well (see Figure 10.8).
In hindsight, it was easy to deduce what the purpose of the destabilizing asparagine might be. Any biological switching device must be capable both of holding on to and letting go of its substrate. For example, hemoglobin must bind oxygen strongly enough to pull it from the lungs as blood cells pass through the alveolar tissue but weakly enough to release it throughout the rest of the body. Carbon monoxide molecules are poison because they adhere so tightly to blood cells that they rarely let go, thereby preempting oxygen. Similarly, a leucine zipper would be useless if it bound so tightly to one partner that it could never let go. Furthermore, too strong a propensity to bond would allow the helices to pair in an improper alignment. An improperly aligned leucine dimer would be unable to bind to the DNA because the DNA binding ends of the leucine zippers would be askew.
For biological switches to function, then, the strength of the binding must be finely tuned: Strong enough to come together but weak enough to do so without misaligning the molecules and weak enough to break apart when the time comes. In the leucine zipper, asparagine accomplishes this fine tuning.
Most coiled coils are not as regular as leucine zippers, and frequently another hydrophobic amino acid occupies the "leucine position." Harbury hopes to develop a set of rules for predicting the structures and bonding arrangements of this variety of coiled coils, and he is asking such questions as how many substitutions of leucine by isoleucine, one of the so-called beta-branching hydrophobes that fail to fit in the knob-in-hole