3D map depicts cell ‘wheel of death’ in action

It appears inside doomed cells when bidden, like a creature from a horror film: a seven-pronged, wheel-shaped structure that orders its minions to go on a killing spree. They obey, snipping away at critical parts of a cell until it implodes. The command structure is called “the wheel of death,” or the apoptosome.

But the process, called programmed cell death, or apoptosis—from the Greek words for leaves falling from a tree—is a normal part of life. Cells die in an orderly fashion so that during development, we’re not born with webbed hands, for example, and during adulthood we have a protective layer of dead skin cells on top of live ones. Apoptosis is perhaps best known for its role in cancer, either killing cancer cells as they start to proliferate or failing to kill them.

At the center of all this destruction is the apoptosome, the cellular structure that facilitates programmed cell death. Scientists knew it existed decades ago, and over time they have slowly, painstakingly, built models of its structure to better understand its function.

A team led by Christopher Akey, a Boston University School of Medicine professor of physiology and biophysics, has revealed the most detailed three-dimensional model of the apoptosome to date. The model, published in the journal eLife, answers some questions and raises others. Ultimately, a better understanding of how cell death occurs may lead to treatment options that can enhance or suppress the process.

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“The apoptosome was discovered more than 20 years ago, but now we have a much better idea of how it works,” says Tat Cheung Cheng, lead author of the eLife paper, a former postdoctoral fellow working with Akey, and now a postdoctoral associate at the Yale School of Medicine. “This lays groundwork for future drug development.”

How apoptosis works

Apoptosis is a complicated yet elegant process. When a wayward cell is marked for death, either by internal or external signals, proteins puncture the mitochondria—those jelly bean–shaped structures that supply cells with fuel—causing a small molecule called cytochrome c to leak out. The liberated cytochrome c, drifting through the cell, connects with another protein, called Apaf-1, causing it to assemble into the wheel-shaped apoptosome.

The central hub of the wheel then docks with a critical protein-cutting enzyme called procaspase-9, which, once activated, triggers other proteins to dismantle the cell.

“The proteins that become activated then go throughout the cell—not indiscriminately at all, they have a few hundred targets—they cleave these things, and it leads to cell destruction,” says Akey, corresponding author of the eLife paper. “The cell starts to collapse from the inside out.”

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Akey has been studying the structure of the apoptosome for 18 years, taking photographs at ever finer resolutions and thus answering ever more detailed questions about apoptosis. The particular question he sought to answer this time: how is procaspase-9 activated? “That is the crux of the matter,” says Cheng. “We know that the apoptosome exists, but we just don’t know how the apoptosome can induce the activation of this enzyme.”

Frozen fast

To find out, the team used a technique called cryo-electron microscopy, in which biological samples are cooled rapidly, before the water molecules within them can form damaging ice crystals. “The cooling rate is so high that the water molecules just stop moving. They don’t have time to crystallize,” says Akey. “You freeze-frame it, literally.”

This technique, along with better stabilizers, detectors, and computing power, has allowed Akey and his team to capture increasingly detailed photographs of the apoptosome. “Our first structure, which was published in 2002, was at about 25-angstrom resolution,” says Akey. An angstrom is a unit of length equal to one ten-billionth of a meter; a hydrogen atom measures about half an angstrom across. “We could see the wheel, we could see some details. But now we’re at 4-angstrom resolution. So that’s a huge difference.”

The new pictures allowed the team to solve—or at least partly solve—the procaspase-9 mystery. It appears that a disk on the central hub of the wheel of death—not the whole superstructure—is the key. Shaped like a spiral, the disk can dock three to four procaspase-9 enzymes, and each pair of enzymes can then activate itself. “It’s weird,” says Cheng. “It means the whole platform underneath is kind of not really necessary. It seems to be just to help form the disk, and that’s it.”

Ultimately, even higher resolution photos may give scientists ever more definitive answers. “If you get really high resolution, you can see the actual atoms. That requires something like two‑angstrom resolution,” says Akey. “We’re not at that stage yet, but eventually we might get there.”

“But the work is already telling us a lot about the basic biology,” he adds. “You have to first understand the fundamentals, and then after you have that, then you can start to understand disease.”

The National Institutes of Health supports Akey’s work.

Source: Boston University

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Source: Futurity