Biological Micro Machines II: Inactivation Station

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Last month, we discussed the garage doors of the body’s ion channels, the millions of microscopic machines that control the heart’s beat and the nervous system’s communication. Benoît Roux and his colleagues employed 25 million computational hours to model the potassium channel voltage sensor, a kind of garage door control box that determines when the channel opens its gate. But the metaphor breaks down a bit when the channel is open, as the potassium channel does more than just wait to close again. Instead, there’s an in-between phase that keeps excessive potassium from stampeding through the open gate while the door prepares to close, a state called inactivation.

Determining the mechanism for inactivation has befuddled scientists for the same reason as the voltage sensor: how do you reverse-engineer a biological machine that works at the  nanoscale level, moving less than one-billionth of a meter at a time? One solution is to take pictures of the channel in motion, but doing so in the channel’s native habitat of the cell is beyond current technical means. Scientists have therefore resorted to a method called X-ray crystallography, a trick of chemistry and physics where the atomic structure of a protein can be determined.

X-ray crystallography has been used on potassium channels before – one such experiment even won the Nobel Prize for Chemistry in 2003. But each crystallographic portrait only catches the channel frozen at one particular moment of time, leaving scientists to make (educated) guesses about the movements that take place between each laboriously-obtained picture. The more pictures available, the less guesswork required.

More pictures and better theory are the result of two papers appearing in Nature today from the laboratory of Eduardo Perozo, professor of biochemistry and molecular biology at the University of Chicago Medical Center. Perozo’s group added to the potassium channel crystallography gallery by using a slightly mutated channel to keep the gate locked open and expose the elusive inactivation state to portraiture. From experiments conducted at Argonne National Laboratory, they hoped to get a new snapshot portraying a form of inactivation known as the C-type. But to their surprise and delight, they got 15 slightly different structures for the channel, which were determined to represent sequential stages between the open and inactivated state.

“By sheer luck, we happened to trap the channel in the process of opening, just like a movie,” Perozo said.

In one paper, Luis Cuello and colleagues found that C-type inactivation is mediated by the selectivity filter, the device on the inside of the channel pore that specifically allows potassium ions in and keeps everything else out. Normally while open, the selectivity filter lets potassium ions through via a sort of billiard ball effect (pictured above), with ions attracted into the channel and bumping those ahead of them further down the pore. But milliseconds after the channel opens, the selectivity filter collapses, creating both an energy barrier and a physical barrier to stop the flow of ions.

The sequence of this process – channel opens, then channel inactivates – was revealed in the second paper to be a clockwork cascade of moving parts. The gate of the channel and the selectivity filter are angstroms apart – small on any ruler, but a long distance on the ion channel’s tiny scale. Nevertheless, modeling and mutation experiments determined that the opening of the gate could physically trigger the collapse of the selectivity filter. Researchers found one single amino acid (F103) acting as a link between the two segments, changing conformation after the gate’s opening and starting a chain reaction that changes the shape of the selectivity filter. Experiments where this amino acid was mutated to a smaller or larger size accelerated or slowed inactivation, confirming the key role of the F103 coupling element.

Taken together, the two Nature papers make up the most complete animation of C-type inactivation ever constructed. The higher resolution could help scientists design better drugs for controlling the inactivation of potassium channels, which would be useful in treating diseases such as Long QT Syndrome – a cardiac disorder that can lead to sudden death. The work by Perozo’s group may be relevant to a potassium channel expressed in the heart called hERG, where C-type inactivation plays an important role in function and dysfunction.

“hERG is a nightmare for the pharmaceutical industry,” Perozo said. “Many drugs, no matter what they’re intended to do, appear to block hERG and produce pharmacologically-induced Long QT Syndrome. It turns out that when these drugs produce this blockage of hERG, they bind to the inactivated state, not the closed or the open. That’s why there is quite a bit of interest in knowing what the structure of the inactivated channel is – because if you know that, you could design better drugs.”


Cuello LG, Jogini V, Cortes DM, Pan AC, Gagnon DG, Dalmas O, Cordero-Morales JF, Chakrapani S, Roux B, & Perozo E (2010). Structural basis for the coupling between activation and inactivation gates in K(+) channels. Nature, 466 (7303), 272-5 PMID: 20613845

Cuello LG, Jogini V, Cortes DM, & Perozo E (2010). Structural mechanism of C-type inactivation in K(+) channels. Nature, 466 (7303), 203-8 PMID: 20613835

About Rob Mitchum (518 Articles)
Rob Mitchum is communications manager at the Computation Institute, a joint initiative between The University of Chicago and Argonne National Laboratory.

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