With their miniature parallel tracks twisting and turning and their connections in the middle, the structure looks like a winding ride. As it turns out, it is, although not for humans.
Using an 11-amino acid sled, viruses shuttle proteases along the double helical structure of DNA, enabling them to infect other cells.
Leading an international team of researchers, Walter Mangel, a biophysicist at Brookhaven National Laboratories, recently found the sled that slides along the phosphate spine of DNA. It carries a protease important in the activation of a virus to its destination.
When the protease and another protein collide on DNA, it begins a reaction that leads to the removal of clumps of proteins that support the construction of viral DNA.
Mangel likens the proteins that are cut away to the scaffolding builders use when they put together a cathedral. With the scaffolding in place, the viral DNA can’t become an effective invading genetic force.
“We took a model virus, one that was not dangerous to work with, and we wanted to understand how this protein functions,” Mangel said. “If we do, we can inhibit that protein.”
The researchers chose the adenovirus, which causes common colds, pink eye, blindness, weight gain and diarrhea.
The molecular sled moves by thermal (i.e. heat) energy and doesn’t use miniature wheels to move along the track, but rather has electrical charges that keep it stuck to the DNA. The sled has four positive charges that interact with the negatively charged phosphates in the major groove of the DNA.
“The sled enables the molecule to collide with another molecule on DNA,” he explained.
Once the protease removes the scaffolding, the virus can infect other cells. Mangel said the concept of a molecular sled came together in his mind when he was visiting a museum in Vermont that had farm equipment. He saw a large sled and realized this was likely how these proteins were navigating through the nucleus to their destination.
“Once we saw the 11-amino acid peptide slide by itself, we thought it might be a sled,” he said. This molecular sled not only could transport molecules to the right destination in the DNA, but could also ensure that they collided in a way that ensured a reaction would take place.
In a solution, molecules typically only bind to each other when they collide at a specific speed at particular sites on their surfaces. In most collisions, even those molecules with complementary functions recoil. If both molecules are stuck to DNA and one or both slide on the sled, the speed of the collisions is set by the speed of the sled.
“This could give rise to chemistry that is far more efficient, in which almost all collisions by sliding lead to binding,” Mangel said.
While researchers will try to disable or deactivate the sled — perhaps by attaching other blocker molecules to keep the protease from navigating down to its spot on the viral DNA — they may also find ways to use the sled.
“The sled is capable of carrying anything attached to it,” Mangel said. That means it could be used in transgenic therapy, where doctors and scientists may want to replace one genetic sequence for another, potentially correcting a genetic disorder.
Mangel explained that the experiments with the molecular sled took considerable collaborative coaxing. He wrote to 10 labs that had equipment that would allow him to do single molecule experiments. When he spoke to Sunney Xie at Harvard, a partnership began.
The first set of experiments in Massachusetts failed.
He had planned to return to Long Island the next day, but wanted to try one last experiment, in which he increased the acidity of the solution. Immediately, he saw considerable sliding.
Mangel lives in Shoreham with his wife Anne. They enjoy running together and visiting the beaches and parks in the area, especially along the east end.
Mangel is a fan of opera and classical music and has conducted his work while listening to classical music from a BBC station. He also is an avid artist and has sketched his colleagues in the lab.
The direction of his work and his artistic interested collided when he discovered the use of this molecular sled.
“What comes out of the work is rather simple,” he said, alluding to the sled. “The experiments are sophisticated to support that theory.”