Molecules in 3-D movies by Janet Iwasa

Dr. Janet Iwasa is a molecular biologist and professional animator at Harvard Medical School. She uses her dual talents to create 3-D movies about protein molecules.

Janet Iwasa: Animating a protein can be as complicated as animating a human inside a Pixar movie. And a human, you can imagine, will need something to make the fingers and toes move, the knees and the head, and the eyes are blinking. I think proteins can be as complicated as that.

Janet Iwasa: Proteins are basically the workhorse of a cell, what makes the cell move around and divide.

To animate proteins, Iwasa works with the same kind of software used to make Hollywood films like Toy Story. Scientific data is Dr. Iwasa’s guide. Her movies show proteins that walk and seem to dance, dozens to hundreds of them at once, in an area smaller than a pinpoint. She added that films like hers can revolutionize the way scientists share ideas with each other.

Janet Iwasa: The way that many researchers still communicate about the molecular processes they study is by having these very crude drawings of, you know, circle one, a protein, interacts with square two, which is another protein, and there are a lot of arrows. It really doesn’t communicate the amount of knowledge we have these days.

EarthSky asked Iwasa exactly how she knows molecules move.

Janet Iwasa: There’s this wonderful resource called the Protein Data Bank which is basically a huge number of protein structures that have been contributed by thousands of scientists over many years. And so this is basically a sort of map, so you can get basically the image of a protein – the x+y coordinates – of your favorite protein. And that’s the starting point for a lot of my animation …

In other words, she gets a three-dimensional picture of proteins in numerical form.

Janet Iwasa: And we know that proteins start moving around, and they’re flexible. The structures in the protein bank don’t necessarily reflect that. So we can add that in with animation. Animation allows us to synthesize a lot more information in terms of what the proteins look like, how exactly they’re moving around, how exactly they’re interacting with other things. It brings it all together in this beautiful and engaging way.

She explained her favorite animated molecule, so far.

Janet Iwasa: My favorite animation is one that shows that process of clathrin-mediated endocytosis – the process by which a cell is able to internalize something that’s outside its membrane, so say a cell wants to internalize that, and process the protein that’s just landed there.

To do this, the cell actually has to make a bubble to grab the protein. And what she described as a “cage” forms in order to create that bubble.

Janet Iwasa: That was pretty challenging because there were 60 of these clathrin molecules that also had to be coordinated to form this very beautiful cage, and then it all falls apart at the end. We did the animation in real time. It took about a minute to form, and then a few seconds to fall apart. It was challenging because there were so many proteins involved, the timing of it, and including as many other proteins as we could.

As of late 2010, she could be found working with her Harvard colleagues to make a film starring dynein, a protein thought to walk inside cells in our body, including brain cells. It’s also known as a “motor” protein, because it shuttles molecules (or objects) from one part of a cell to another. But scientists still don’t know exactly how it works … or how it moves. Iwasa is hoping to change that.

Janet Iwasa: Just thinking about the cell as a small world, and that there are all these incredible things that are happening at this tiny, tiny scale, smaller than the wavelength of light. We’ll never be able to directly look at these incredible events, but they’re happening in our bodies every day. It’s just a beautiful thing to be able to see. And the only way we’ll be able to do it is by means like animation, and maybe other means in the future.