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Past Winner
2009 E.W.R. Steacie Memorial Fellowship

Peter Tieleman

Biochemistry

University of Calgary


Peter Tieleman
Peter Tieleman

Peter Tieleman’s lab at the University of Calgary isn’t your traditional biochemistry lab. There are no flasks of chemicals, no DNA sequencing machines, no iconic lab glassware — not even a beaker.

“The only piece of wetware in our lab is the coffee machine,” laughs the 36-year-old researcher.

But in a 21st century take on biochemistry he does have computing power — in spades.

“We use very big computers to calculate how molecules interact with cell membranes. By doing this we can accurately predict how biochemical processes occur in cells, for example how nutrients are actively transported across a cell membrane,” says Dr. Tieleman, the recipient of a 2009 NSERC E.W.R. Steacie Memorial Fellowship.

Dr. Tieleman’s research is the latest chapter in a centuries-long effort to understand the workings of life’s basic building blocks: cells. Three-and-a-half centuries ago, the Dutch scientist Antonie van Leeuwenhoek built one of the first microscopes. Exploring with it, he discovered the cellular nature of life. He was thus also the first to see cell membranes, the cellular organ that defines the inside from the outside of the cell.

But today, biologists want to understand cell membranes at the molecular level, beyond even the reach of light microscopes. At this level, it’s computational models that shed light on cellular happenings.

In the past decade, Dr. Tieleman, a Dutch native until his move to Calgary in 2000, has been at the forefront of making these computer models, or simulations, a central part of membrane biophysics.

His leading-edge research is a meeting of proteins and Pixar, as in the animated film company. His presently ten-person-strong lab group uses the same frame sequence technology as Hollywood animators to create digital simulations of membrane-molecule interactions.

What’s different between the box-office blockbusters and Dr. Tieleman’s research is the level of detail. While film animators create visuals that are believable, Dr. Tieleman and colleagues are creating computer simulations with atomic-level accuracy. It’s a level of precision at the intersection of biology, chemistry and physics that can lead scientists to a fundamental understanding of how cell membranes control what gets into and out of a cell.

As a graduate student at the University of Groningen, Dr. Tieleman helped develop Gromacs, one of the world’s leading biomolecular software packages. And he’s continued to develop world-leading computational techniques for membrane modeling.

“Two decades ago these models were general, but now they’re detailed enough that we can ask highly specific questions,” he says.

His lab group recently developed a simulation to show how buckyballs—hollow, soccer-ball-shaped carbon molecules—move through a cell membrane. It’s a critical question for the potential use of buckyballs in nanotechnology as transport vessels for sending materials, for example pharmaceuticals, into cells.

Some of the world’s most powerful computers are used in making animated movies, and the same goes for scientific simulations. Dr. Tieleman is a co-principal investigator of WestGrid, an academic computing consortium that is one of Canada’s most powerful computing resources. His lab group also has its own 700-processor strong computer cluster. This lab computational workhorse is in use 24/7, running simulations that can take months, even using hundreds of processors.

“We could use five thousand processors if we had them,” says Dr. Tieleman.

Making the most of limited computer resources is at the heart of his Steacie research. There’s an inevitable trade-off between the level of atomic detail and the time it takes to run a simulation. The more detail, the more computationally cumbersome the model. To get around this, Dr. Tieleman is developing an accurate “coarse grain” model.

“For these simulations we group together about four atoms in a single ‘bead,’” he explains. “By looking at the average interactions of these groups of atoms we create a course-grained molecular model. Although we lose a little atomic detail, we can still accurately model proteins and peptides, but it’s computationally much, much cheaper.”

Says Tieleman: “Our hope is that in the future, these simulations will help us understand the molecular basis of new antimicrobial agents, how specific proteins interact with cell membranes and even help in the design of new biocompatible materials for bioengineering.”