30-year eye mystery solved – ion channel structure understood

The researchers understood the structure of an ion channel from the rod cells of the eye (shown in blue) when it interacts with the protein calmodulin (purple). This interaction is important for ion channel function in the eye, but also for ion channel function in other parts of the body, such as the heart. Credit: Paul Scherer Company / Tina Schuster

Exciting new findings shed light on interactions between the protein calmodulin and an ion channel in the eye, unlocking the secret behind our eyes’ exceptional sensitivity to low light conditions.

Using cryo-electron microscopy and mass spectrometry, a team of researchers at PSI has successfully unraveled the structure of an ion channel in the eye that interacts with the protein calmodulin—a puzzle that has stumped scientists for 30 years. This correlation may explain how our eyes can achieve such remarkable sensitivity to dim light. The findings are published in the journal PNAS.

When you look at a bright screen on your phone or computer, the ion channels in your eyes react to the light by closing. This action marks the culmination of a biochemical chain reaction initiated by light exposure. As a result, calcium ions can no longer pass through the channels located in the cell membrane, which leads to the conversion of the biochemical signal into electricity. This signal then travels through the nervous system and eventually reaches your brain for processing.

The same process happens when you stand outside at night and look at the sky. Now, rod cells do the trick. These are the cells that sensitize our eyes to low levels of light, enabling us to see the night sky and detect a few photons of light from a distant star. We take this for granted, but it is a remarkable achievement.

A team led by PSI scientist Jacopo Marino has now advanced our understanding of how a small protein called calmodulin helps achieve this by interacting with ion channels in wire cells. Calmodulin is a calcium sensor. It is one of the cell’s global communication mechanisms – helping the cell respond to calcium fluctuations. This group, in collaboration between groups at PSI, ETH Zurich and the University of Bonn, has for the first time elucidated the three-dimensional structure of a rod cyclic nucleotide-gated (CNG) ion channel with calmodulin binding.

An important function of calmodulin in the eye

A year ago, researchers succeeded in understanding the structure of this same ion channel, which is found in the rod cells of a cow’s retina and is similar to the ion channel found in the rod cells of our eyes. Rod CNG consists of four subunits that are shared with several ion channels. A unique feature of the channel, however, is that three subunits, called subunit A, are identical, while the fourth—subunit B—is different.

Scientists have long known that this subunit binds calmodulin. Throughout the animal kingdom, this feature is seen. However, the exact nature of its role remains unclear. „If something is conserved through evolution, that’s a very strong indicator that it’s important in some way,” Marino explains. „We know that calmodulin modulates channel activity through subunit B, but what kind of structural changes occur has been a big mystery for about thirty years, mainly because people haven’t been able to solve the structure of the ion channel.”

Now, researchers can provide a three-dimensional view of what is actually happening. Through a combination of cryo-electron microscopy and mass spectrometry, they could observe that the ion channel becomes slightly more compact as calmodulin binds.

Researchers believe this is nature’s way of keeping the channels closed. What would be the purpose of this? „We think this is a way to reduce the spontaneous channel openings that cause background noise, so that our eyes can perceive dim light,” says Marino.

Mass spectrometry helps researchers resolve a bent structure

Deriving the structure of calmodulin and ion channel binding is not easy. The interaction between calmodulin and rod CNG occurs in the most flexible part of the channel, where it freely oscillates. In cryo-electron microscopy, this makes obtaining high-resolution structural information very difficult. Here, Marino offers an analogy, “Imagine you have a dance room. You take a photo and want to know what the human body shape is from it. You can make out what a head looks like, but moving the limbs all over the place will blur the legs and arms.

Thanks to a chance meeting, the team was able to narrow down this agile framework. Ph.D. Student Tina Schuster listened to Marino’s explanation. „We were ready to publish based on the cryo-electron microscopy data alone, which left most of the interactions vague, and Dina approached me and said, 'I think I can help you,'” he recalls.

Schuster is developing novel mass spectrometry-based techniques to study protein interactions. These techniques use enzymes to cut proteins into pieces while they are chemically cross-linked or within parts of the retinal membrane. Protein fragments, some of which are linked together, are identified by mass spectrometry. This reveals information about which parts of the protein were close together in three-dimensional space—akin to piecing together a 3D jigsaw puzzle. „These techniques allowed us to narrow down some of the possibilities obscured by cryo-electron microscopy,” explains Schuster, joint first author of the publication with PhD student Diane Barrett.

From the wonder of vision to the implications for human health

Calmodulin regulates ion channels not only in the eye but throughout the body, controlling electrical signals that are essential for the proper functioning of various muscles and organs. In recent years, when this communication goes wrong due to mutations in the calmodulin gene, serious health effects such as heart failure can occur: something that is still not fully understood.

The findings and methods used in this study may help our understanding of the interactions of calmodulin with ion channels in other parts of the body, in addition to helping our understanding of a very fundamental miracle.

Reference: Diane CA Barrett, Tina Schuster, Matthew J. Rodriguez, Alexander Leitner, Paola Pigotti, Gebhardt FX Schertler, U. Benjamin Kaupp, Volodymykov, Volodymyrov, Diane C.A. Jacopo Marino, 3 April 2023, Proceedings of the National Academy of Sciences.
DOI: 10.1073/pnas.2300309120

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