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Brain Cell Linker Dependence Shown by XSEDE/TACC Supercomputer Simulations

Published on September 22, 2014 by Jorge Salazar



It all begins in the brain as a flood, tens of millions of neurotransmitters handed off from one neuron to another in just a fraction of a second.

"TACC has provided us with some very reliable resources, in a fast and well-organized environment to carry out those large-scale simulations." — Jian Dai, Post Doctoral Researcher, Institute of Molecular Biophysics, Florida State University
Memories, dreams and learning share a common thread in this exchange of electrical and chemical signals by the nearly 100 billion spindly neurons of the brain, each cell networked to 10,000 others.

Stubborn walls that enclose our neurons keep out the signal flow of one cell to another needed for brain activity. Chemists call this gatekeeper of our thoughts an ion channel, which takes a key in the form of a chemical neurotransmitter, unlocking the channel and opening it.

The discovery of how ion channels work earned chemist Roderick MacKinnon the Nobel Prize in 2003. Now scientists are making new discoveries of the inner workings of ion channels that function as brain receptors.

Neuroscientists at Stony Brook University in New York teamed up with computational biophysicists at Florida State University and found that the function of a key brain cell receptor critically depends on a short polypeptide segment, which they call a linker, to function. Parkinson's disease, Alzheimer's disease, and a number of psychiatric disorders such as schizophrenia are associated with malfunctions of this brain receptor, called the NMDA (N-methyl-D-aspartate) receptor. They published their results in May 2014 in the journal Nature Neuroscience. The National Institutes of Health (NIH) funded the research.

The scientists performed modeling and molecular dynamics simulations with the programs NAMD and MODELLER of the full NMDA receptor molecule. They used computational resources provided by XSEDE, the Extreme Science and Engineering Discovery Environment, a single virtual system that scientists use to interactively share computing resources, data and expertise. The code ran on Stampede, the nearly 10 petaflop Dell/Intel Linux supercomputer at the Texas Advanced Computing Center (TACC).

"TACC has provided us with some very reliable resources, in a fast and well-organized environment to carry out those large-scale simulations," said computational biophysicist Jian Dai, a post doctoral researcher at the Institute of Molecular Biophysics at Florida State University. Dai used Stampede to conduct several independent computational simulations of the NMDA receptor system of more than 300,000 atoms. "Normally, people don't reach that kind of scale," Dai added.

The NMDA receptor acts like a gate that sits on the membrane of a neuron, or nerve cell. The terminal end of a neuron releases the human brain's main neurotransmitter, glutamate, and unlocks the gate of another neuron, opening a channel that allows calcium ions into the cell.

"This can have a variety of downstream effects, including affecting how we learn and how we can remember events in our lives," said study lead Lonnie Wollmuth, a professor in the Department of Neurobiology and Behavior and at the Center for Nervous System Disorders at Stony Brook University.

Previous studies, said Wollmuth, had shown that the clamshell-shaped part of the NMDA receptor that accepts the neurotransmitter key is mechanically coupled by a linker region to another part that forms the ion channel embedded in the cell. The linker region is made of a string of amino acids that act like a rope to pull on the gate of the ion channel and open it.

"If this gets impeded even slightly you completely lose the efficiency of the signaling process…The basic idea is that there's this mechanical coupling. And without that, the ability of the NMDA receptor to convert this transient glutamate into a robust and efficient signal is lost," Wollmuth said.

In the lab, an MD/PhD student Rashek Kazi and a medical student Cameron Sweeney of Stony Brook tested the function of the brain receptor by using what's called a patch clamp, essentially an electrode on the membrane of a neuron in a technique called single molecule electrophysiology. It's like taking an EEG of a single brain receptor. Squiggles on a graph record a jump in electrical activity from the passage of ions through the gate triggered by glutamate.

"The basic idea is that there's this mechanical coupling. And without that, the ability of the NMDA receptor to convert this transient glutamate into a robust and efficient signal is lost." — Lonnie Wollmuth Professor, Department of Neurobiology and Behavior and at the Center for Nervous System Disorders at Stony Brook University
What Wollmuth's team did was insert just one amino acid between the linker and the clamshell region. The effect was to make the 'rope' longer and create a tiny bit of slack. In the laboratory and in computer simulations, the tug of the clamshell failed to take up the slack and the gate of the ion channel didn't open like it was supposed to. No squiggles.

"What we found, and this was really the most fascinating part of it, is that the ability of the transient glutamate to cause the ion channel to open was largely lost," said Wollmuth. "That suggested that it was critical to how the NMDA receptor functions at a synapse, how it's able to convert that transient glutamate into a signal."

"These experiments demonstrate the critical role that the linker region plays in the functioning of NMDARs and suggests that this pivotal junction may be an important target for additional work to explore for the development of neuromodulatory drugs," commented Chiiko Asanuma, the program chief of the Signal Transduction Program with the National Institutes of Health and the program officer of the research grant.

"The resources that are present in the Stampede and XSEDE facilities go far beyond what can be obtained in one single lab, or even an institution." — Huan-Xiang Zhou Professor, Department of Physics, Florida State University
The idea to go to the lab and test the linker of the NMDA receptor initially came out of computer simulations, said study co-designer and author Huan-Xiang Zhou, a computational biophysicist at Florida State University.

"One of the things that we constantly ask ourselves is, how can our predictions be tested by functional studies," Zhou said. "That's something that we constantly think about, with regards to the NMDA receptor in particular."

Zhou said that integration of computation and experiment reflects a general trend of science today. "I think computation in general has now matured to a point where integration with experimental studies has become possible and has become very fruitful," Zhou said.

Zhou referred to the 2013 Nobel prize in chemistry, which recognized three scientists in developing computer models of the complexity of the chemistry of nature.

Scales of time and space, said Zhou, are really starting to open up for researchers as computers get more powerful and can handle the data.

"The resources that are present in the Stampede and XSEDE facilities go far beyond what can be obtained in one single lab, or even an institution. It's a very important piece of the computational infrastructure that's going to be required to push the frontier of computational research. Having this national infrastructure is really critical for us to move science forward and to maintain the leading position of the United States in terms of computational research," Zhou said.

"The approach used in this study further demonstrates the power that multi-disciplinary strategies involving computational analysis and dynamic simulations can bring to solving a challenging neuroscience puzzle," said Dr. Asanuma of the NIH. "We anticipate an increase in collaborations in the future involving experimental neuroscientists with experts from statistics, physics, mathematics, engineering and computer science leading to similar important findings."

"Indeed, fostering collaborations of this type is one of the goals of the President's BRAIN initiative," said Asanuma, referring to a massive multi-year multi-agency effort launched with an initial $100 million in 2014 to develop new tools to study the human brain's billions of nerve cells, networks, and pathways in real time.

What's Next?

In terms of next steps in this research of the NMDA receptor, Wollmuth wants to further study the subtleties of how it functions. Additional linkers abound, tiny structures ripe for investigation that sit around the core gating element.

"We think by targeting these more peripheral structures and understanding how they contribute to the opening of the ion channel, that maybe compounds can be developed that target those and modulate the receptor in a more subtle, more refined way," Wollmuth said. "Rather than turning on or off the receptor, we now can make it work only 10 percent as well, or 20 percent as well, or 50 percent. We can modulate it more."

When asked about his personal tie to researching brain receptors, Wollmuth said that he like millions of others has family affected by neurodegenerative diseases. "I have a brother who has multiple sclerosis and a mother who had Parkinson's disease. So I'm very interested in brain diseases."

Wollmuth sustains his interest with a deep curiosity of how molecular machines work and their importance to brain function. " They're just absolutely fascinating. That's why you have to bring a number of approaches, x-ray crystallography, functional approaches, cryo-EM computational approaches to tackle how they work and how they carry out their basic biological function, and how that might be disrupted in disease state," Wollmuth said.


Story Highlights

A key brain receptor for NMDA depends on a linker subunit to function.

The XSEDE-allocated Stampede system was used to perform modeling and molecular dynamics of 300,000 atom NMDA receptor system.

Research advances potential drug targets to treat neurological illnesses such as Alzheimer's disease, Parkinson's disease, depression, and schizophrenia.

The University of Texas System Research Cyberinfrastructure (UTRC) facilitated the computing resources used by the research group.

Stampede is funded by the National Science Foundation (NSF) through award ACI-1134872. XSEDE is funded by the National Science Foundation (NSF) through award ACI-1053575.


Contact

Faith Singer-Villalobos

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faith@tacc.utexas.edu | 512-232-5771

Aaron Dubrow

Science And Technology Writer
aarondubrow@tacc.utexas.edu

Jorge Salazar

Technical Writer/Editor
jorge@tacc.utexas.edu | 512-475-9411