Computers+and+Chemistry+Discovers+aPart+of+Cell+Division

In a paper published in the 24 November issue of //Biochemistry//, Rudolph and his team described the hypothesized orientation necessary for two enzymes to come together and form a complex that regulates cell division. In certain types of cancers, this enzyme complex overreacts, leading to uncontrollable cell division. The model shows an intricate design, with the enzymes coming together like puzzle pieces. The enzymes contain appendages that must be orientated so that the two interlock. These appendages only occur at certain areas of the enzymes, areas referred to as “hot spots” by Rudolph. The hot spots must be correctly orientation with respect to both enzymes before the complex is able to regulate cell division, according to Rudolph. The problem in mapping the binding process came from the large sizes and number of hot spots for both enzymes, says Rudolph

“Somehow these two large complicated molecules had to also interact specifically somewhere other than the site where the chemistry occurs, but it was literally a guessing game trying to find which residues might be important in this interaction,” he says.

Traditionally, researchers tested the location of the binding sites by producing multiple mutated strains of the enzymes and analyzing any changes in the functioning of the enzymes. This can be tedious work as only a single change is made in the enzyme per mutant.

When those tests came back negative, Rudolph looked to a team of computer scientists led by Herbert Edelsbrunner, a professor of computer science and mathematics at Duke University. Using custom programs Edelsbrunner developed for modeling and analyzing complex molecular shapes, one-thousand trillion match-ups between the molecules was narrowed down to 1000 possible fits.

These fits were further narrowed to a single possibility with the help of Waitao Yang, professor of chemistry at Duke University. Wang used a different computational technique that simulated how the enzymes would fit together while they were moving and rotating. This replicated how the enzymes act in real life, an important factor in considering how two molecules would fit together.

“Tiny little shifts can change these things,” Rudolph says.

The fit was then confirmed through biochemical evaluations of both hot spots on the two enzymes.

With the hypothesized model of how the enzyme complex is formed, anticancer drugs can be developed with the goal of blocking the two enzymes from binding together, says Rudolph.