Scientists don't know how this behemoth of an enzyme targets and degrades specific proteins but it's good that the enzyme is so selective. If it degraded every protein it comes across, the cell would quickly die.
"We want to know how it's regulated, how it selects proteins to degrade, and how it cuts them apart," says Jap.
To help answer these questions, his team determined the changes the molecular machine undergoes as it readies itself for action. Using x-ray crystallography, they obtained an atomic-scale resolution structure of the molecular machine in its inactive state. This work was conducted at Berkeley Lab's Advanced Light Source, a national user facility that generates intense x-rays to probe the fundamental properties of substances.
They also developed a lower-resolution, three-dimensional map of the molecular machine in its activated state, meaning it's poised to snip apart a protein. This structure was determined using cryo-electron microscopy.
They then merged these two structures together, one dormant and the other ready to pounce on a protein.
"When we dock these structures, we can begin to ascertain the changes the enzyme undergoes as it transitions from an inactive to an active state," says Peter Walian, a scientist in Berkeley Lab's Life Sciences Division who also contributed to the research.
This first molecular-scale vantage of the enzyme in action offers insights into how it works. For example, the scientists found that only very small proteins can fit in the chamber the enzyme uses to break down proteins.
"This sheds light on how the enzyme targets specific proteins," says Jap.
They also learned more about how the enzyme uses a molecular ruler to mince proteins into pieces that only span three residues.
"This work is yielding valuable clues as to how the giant enzyme carries out very fundamental biological processe
|Contact: Dan Krotz|
DOE/Lawrence Berkeley National Laboratory