Key to a Good Fit: Flexibility

"Trp" is the abbreviation for tryptophan, one of the 20 amino acids essential for formation of proteins, and trp -repressor is what its name suggests -- a molecule that represses synthesis of tryptophan. Trp -repressor has been isolated from a common bacteria, E. Coli, and is not active in humans. Nevertheless, it is an important model for understanding how biosynthesis is regulated.

"It is the smallest complete regulatory system so far available," says Jardetzky, "and at this stage of knowledge, it is of great interest as a prototype of how these mechanisms work." When two molecules of tryptophan bind to the protein, it in turn binds to a DNA segment that controls tryptophan production. "It binds DNA in the presence of tryptophan and dissociates if the tryptophan level is low," explains Jardetzky. "In this way, tryptophan regulates its own synthesis."

A major finding of Jardetzky's calculations is that the region of the protein that binds with DNA is flexible and mobile. "What seems to be happening is that when the molecule binds, it doesn't dock as a rigid body. It adjusts the shape of the binding domain to the DNA, and the DNA also adjusts to create the best mutual fit. It is like getting a handshake. You cannot do it with rigid hands. You need some flexibility at the point of contact."

Calculations on the trp -repressor/DNA complex, furthermore, appear to have resolved a question about whether the protein actually contacts the DNA. The crystallographic structure suggested that interaction with DNA was mediated by water molecules. Other researchers, however, believed that the crystallized protein didn't reflect the reality of the natural environment, and several published studies concluded that direct contact was possible. "We have direct contact between the protein and DNA," says Jardetzky. "We do not see water-mediated contacts, and we expect that these results will settle the matter."

Trp Repressor and DNA
"Shaking Hands"

This graphic represents the structure of trp-repressor bound to DNA as determined from NMR data obtained by Oleg Jardetzky and colleagues at Stanford Magnetic Resonance Laboratory. Structurally, trp-repressor is a symmetric dimer, a molecule formed of two identical subunits (light blue and pink) intertwined with each other. The red atoms represent the two tryptophan ligands, molecules that bind with the represssor before it binds with DNA (light green).

Calculations at the Pittsburgh Supercomputing Center (conducted by Daqing Zhao) showed that the tryptophan ligands stabilize the otherwise more flexible DNA-binding region of the protein and hold it at an optimal configuration for binding with DNA.

The repressor regions directly above and below the tryptophan are the protein's "reading heads." They make direct contact with the DNA, wedging into DNA's "major groove" -- the opening that forms between DNA's two helical backbones. The DNA, in turn, bends at each end to wrap around the protein.

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