Protein Matchmaking & Salt Bridges

On the C90, Tidor simulated the leucine zipper of a gene-regulating protein called GCN4 bathed in about 200 water molecules. He used the CHARMM molecular dynamics software, which tracks the movement of individual atoms over time. His simulations followed protein movement over a nanosecond (a billionth of a second) with a million snapshots during this time span.

Tidor substituted different amino acids in the water-avoiding core of the protein dimer, and the visualized results present a picture of how the substitutions affect the protein's stability. "It's really a short movie," says Tidor, "of how the molecule moves. Small changes were tolerated, but the zipper becomes less stable. The zipper still forms, but more weakly."

The research is still at an early stage, notes Tidor, but the picture emerging so far -- from a combination of laboratory and computer research -- suggests that the hydrophobic interactions at the coil interface provide much of the driving force that zips two protein coils together. These water-avoiding interactions, however, play only a minor role in determining which coils pair up. More important to this matchmaking are the amino acids on the outer surface of the coils, through their ability to repel and attract other amino acids (depending on whether they have like or different electronic charges).

Tidor's recent calculations have yielded an interesting insight into this picture. The bonds between opposite-charge amino acids on the surface of the zipper, called salt bridges, which help to dictate which coils pair, actually destabilize the dimer. In other words, these salt bridges add interactions that work against correct dimers. Nature, explains Tidor, has solved the problem of forming the right dimers at the right time by producing more than enough driving force -- through the hydrophobic effect -- to make both correct and incorrect dimers. At the same time, however, other interactions that work against the correct dimers -- but not enough to stop them forming -- produce strong repulsions that prevent incorrect dimers from forming at all.

Experiments are underway in the laboratories of Peter Kim at the Whitehead Institute and Tom Alber at the University of California, Berkeley on some of the mutated structures Tidor has modeled, research that will complement his computational results. "This project provides a unique collaboration among three groups," says Tidor, "each devoting its expertise toward a common aim of understanding protein structure and stability. The ultimate goal is designing molecules to mediate coil interactions, which may be useful cancer therapies."

The two helices of the leucine zipper, shown here in top (left) and front (right) views, are outlined as yellow-striped ribbons. The ribbons gently wrap around each other, apparent in the top view. The stick figure represents the molecular structure -- oxygen (red), nitrogen (blue), hydrogen (white) and carbon (green). The dotted surface shows the area of the molecule that can come into contact with surrounding water. As seen in the top view, the surface shields the interface between the helices so that water is not able to penetrate into this area, where leucine and other hydrophobic amino acids form the "teeth" of the zipper.

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