30 Oct 2014

Protein Nano-LEGO

From Our Changing World, 9:30 pm on 30 October 2014

By Ruth Beran

“We are really interested in making things smaller these days,” says PhD student Amy Yewdall from the University of Canterbury. “And we’re thinking of proteins as a nanomaterial that we can use as building blocks for future machines, so you’ve got nanomachines that we can make, or biosensors.”

In particular, Amy is working with proteins called peroxiredoxins that form “exciting structures”. These proteins are ring-shaped and self-assemble to form stacks or tubes.

A picture of Amy Yewdall and flasks of bacteria growing proteins

Amy Yewdall and flasks of bacteria growing proteins Photo: RNZ / Ruth Beran

“What I’m really interested in is looking at proteins with diverse structures so I can create big novel structures out of them, so think of them like nano LEGOs. I can try and fit these protein units together to make cool structures,” she says.

And they’re tiny. The rings they form are about 15 nanometres big. “Maybe 400 billion of these can fit on the top of a pin,” says Amy.

According to Amy, there are many potential future applications for these proteins that could be realised in the future. “If we can have tubes, say, we can maybe functionalise these tubes by creating nanowires," she says. "So if we can stick metal ions onto the inner surface of my tubes perhaps we can create conductible nanowires that can also be biocompatible."

These structures would be a similar size to carbon nanotubes, but are easier to generate, require less energy (so are cheaper to produce) and are potentially biocompatible, so could be used in medicine.

To create these stackable rings, Amy starts with DNA because it can be used as a program or code for the proteins that are produced from it. She uses circular DNA, or plasmids, which can be ordered commercially “Once we have these DNAs we can put them inside bacteria,” she says. “You can kind of think of them like workhorses, to produce proteins.”

Every living thing produces protein, from humans to plants, fungus to bacteria. “We choose bacteria because they’re really easy to grow and they’re quite simple creatures. So you put in the DNA and you just let it do its thing,” says Amy.

The bacteria can be used like machines or biofactories to make these proteins, which are grown in 2 litre flasks in a temperature controlled room of 26˚C. “Once we put the DNAs into the bacteria, we let the bacteria grow up a huge amount of this protein,” says Amy. "Then we break up the cells and extract this protein from the rest of the other stuff, like all the cellular walls and all the other proteins, and we purify it by using their special properties.” These special properties could be size, surface charge, or by beads which attach to an artificial tag on the protein.

Because the proteins are so small, they are incredible hard to see. Most of the time, what Amy deals with looks like water. So one way to “see” them is by manipulating light, and images need to be taken using an electron microscope.

Two electron microscope images showing rings (left) and rings stacked to form a tube (right)

Two electron microscope images showing rings (left) and rings stacked to form a tube (right) Photo: Amy Yewdall / University of Canterbury

Recently, it’s been discovered that pH can be used as a switch to create bigger structures out of these protein rings. Lowering the pH, or increasing the acidity, of the protein’s environment changes its surface charge, causing them to stick together and form longer tubes or stacks of rings. Making the surroundings more alkaline, causes the stacks to fall apart and go back into separate rings.

The next step for Amy is protein engineering. “I would like to add different units onto the outside of my proteins. So artificial units that can attach to different things,” says Amy.  And she’s thinking potentially clickable units that glow, to show that these proteins are really versatile building blocks that can be used in nanotechnology.