Atrial fibrillation is a disruption of the heart’s rhythm that can lead to life-threatening conditions.
Simulations with Anton at PSC Show How Positive-Negative Pairing in Protein Is Broken, Opening A Membrane Channel Too Soon that May Contribute to Atrial Fibrillation
Atrial fibrillation happens when the atrial chambers of the heart begin beating out of sync, disrupting blood flow. This can lead to life-threatening conditions like strokes or heart failure. Over-activation of the small conductance calcium-activated potassium 2 channel (SK2 channel) can make heart muscle cells in the atrium recover too quickly and start contracting for the next heartbeat too early. Scientists at the University of California, Davis and University of Arizona used a second-generation Anton system developed by D. E. Shaw Research (DESRES) and hosted at PSC to simulate the molecular interactions that govern SK2 activation. This showed how breaking a positive-negative charge pairing opens the protein’s central channel — and how future drugs may hinder that opening, slowing down SK2 channel and the atrial contraction to restore a healthy heartbeat.
WHY IT’S IMPORTANT
Atrial fibrillation is a heartbeat disorder that affects more than 33 million people worldwide. Often causing palpitations, fainting, or shortness of breath, it also raises the risk of heart failure, stroke, and dementia.
A-fib happens when the heart’s upper chambers, called the atria, fire in a way that’s too fast and is uncoordinated with the rest of the heartbeat. Out of sync with the rest of the heart, the atria now are contracting when they should be relaxing, disrupting blood flow and causing symptoms.
The SK2 channel, which sits in the outer membane of heart muscle cells. plays an important role in A-fib. SK2 opens up after an electrical event in a muscle or nerve cell, letting potassium pass through and helping the cell to reset for the next contraction. In A-fib, SK2 gets over-expressed (too much SK2), leading to atrial cells recovering too quickly. But it’s complicated. Some potential drugs that shut down SK2 help slow the early recovery which underlies A-fib. Others can make it worse.
“During atrial fibrillation, SK2 is upregulated … When you have [this] upregulation … the recovery phase is too fast. … Our goal here is to figure out how SK2 is modulated, and if we can change that modulation [so that] the recovery period is long enough for the entire heart to recover.”
— Ryan Woltz, University of Arizona
Ryan Woltz and Yang Zheng, then postdoctoral scientists working in the lab of Nipavan Chiamvimonvat at the University of California, Davis, wanted to unravel the complicated activation of the SK2 channel. They did this with laboratory experiments guided by computer simulations. The sims made predictions for the experiments to test. This saved years of time and money in the laboratory experiments, since they didn’t have to test thousands of possible pairings within the SK2 protein.
A critical part of the computer work was molecular dynamics simulations performed on Anton, a special-purpose supercomputer for such simulations that was designed and constructed by D. E. Shaw Research (DESRES). The second-generation Anton machine they used was made available to scientists without cost by DESRES, and was hosted at PSC with operational funding support by the National Institutes of Health. (DESRES recently replaced that machine at PSC with a third-generation Anton, which also receives operational funding from the NIH.)
HOW PSC HELPED
Scientists had previously learned that calcium ions in the cell, which increase with the electrical firing of the muscle contraction, stick to the calmodulin protein. Calmodulin then adheres to SK2, helping to activate it.
Woltz, who is now at the University of Arizona, and Zheng knew from work elsewhere that, in nerve cells, an additional signal often speeds up SK-protein activation. That’s the fatty molecule phosphatidylinositol 4,5-bisphosphate (PIP2). Was PIP2 also needed in cardiac muscle cells? If so, how exactly do these molecules interact with each other to trigger SK2? And could the UC Davis team find a drug that disrupted those interactions in a way that reliably reduces A-fib?
To dissect the system’s activity, the scientists conducted a series of molecular dynamics simulations. The second-generation Anton at PSC specialized in these long, complex simulations. It could simulate large numbers of atoms in a complex protein molecule roughly 10 times faster than general-purpose supercomputers. While short by everyday standards, a microsecond is an eternity for many computer simulations. Anton put microsecond simulations of the entire SK2-calmodulin-PIP2 system within reach.
“There’s two very important findings [about the simulations with] Anton … One was [that the increased simulation time showed that] PIP2 is held by basic amino acids from floating away then passed down the line to neighboring basic amino acids [in SK2 on its way to R395], reminding us of a conveyor belt or venus fly trap pulling a fly into the center. Also, the main finding of PIP2 being able to break the salt bridge didn’t happen until the 4,000th nanosecond [fourth microsecond] of the simulation. So the 5,000 nanoseconds that we calculated with Anton 2 were really, really critical for this finding, and I don’t think we would be able to reproduce these findings using any other methods.”
— Ryan Woltz, University of Arizona
The Anton simulations pinpointed one of the 579 amino acids that make up SK2 as a critical lynchpin. That amino acid, arginine 395 (R395), is right at the gate that blocks the SK2 channel on the inside of the cell. Positively charged, or “basic,” R395 normally forms a salt bridge — an electrical attraction bond — with negatively charged “acidic” glutamate 398 (E398), effectively closing off the channel. These salt bridges act like rubber bands holding a bundle of sticks together when the channel is closed. In the simulations, PIP2, which is also negatively charged, breaks apart that salt bridge, sticking to R395 and letting E398 loose. This makes the gate part of the protein more flexible. This in turn opens the channel to potassium ions passing through. The group’s lab experiments agreed with the simulations, offering confidence that the simulations are capturing reality. The team reported their results in the Proceedings of the National Academy of Sciences U.S.A. in September 2024.
The UC Davis and University of Arizona team’s work on SK2 continues. Their simulated system can now be used as a testbed for drug candidates. A candidate that disrupts the PIP2 interaction so that the salt bridge remains can reduce SK2 activity, forcing over-fast atrial muscle cells to slow down and wait for the proper time in the heartbeat to recharge. The study’s timing couldn’t have been better: A number of pharmaceutical companies are ready to test SK2-based drugs, and such a simulation could help narrow down candidates so that only the most promising progress to real-world trials.