An unusually strong diffraction pattern from Mimivirus. The pattern can reveal both the size and shape of the virus.

Tomas uses images in almost everything he does

Svenska 2021-03-01

Six years ago, his picture of a giant virus was chosen as one of that year’s best scientific images by the journal Nature. Now, he and his colleagues have made a major breakthrough in the process of obtaining a picture of an individual protein.
“Images are unbeatable when it comes to communicating things such as the structure of proteins,” says Tomas Ekeberg, a biophysicist.

Tomas Ekeberg does research in biophysics at Uppsala University. His work relates primarily to developing methods for imaging small biological structures, such as viruses and proteins. Already several years ago, he was able to show clear images of viruses.

Recently, he and colleagues at Uppsala became the first in the world to obtain a ‘diffraction pattern’ from an individual protein. For the uninitiated, this just looks like a mass of yellow dots, which are clumped together so tightly in the centre that they form a yellow ball, but the image contains much more information than this.

“It exalts me to find a pattern from something as small as a protein. We are at a turning point now, where we are going from studying large things, such as viruses, to studying proteins, which are smaller than most viruses,” says Tomas Ekeberg.

Image with X-ray laser

In his work, he uses the free electron laser XFEL, a three-kilometre-long X-ray laser, located in Hamburg. This is a joint EU facility, which Sweden contributed to with funding. Swedish researchers are also among the most frequent users.

Viruses and proteins are sensitive, and the X-rays cause damage to them. The X-ray pulses in the free electron laser are so short, however, that the radiation damage does not have time to register. What the scientists see is the undamaged sample.

“The aim is to get better images than today, so that we can study the dynamics of proteins.” They skip between structures, open or closed. With the free electron laser, we can look at short-lived states, shorter than a millisecond.” In the world of proteins, lots can happen during this brief time.

In the experiment itself, a sample of the protein is sprayed into the X-ray laser beam in a thin stream. This causes the X-ray light to diffract, resulting in a light pattern that is captured by a detector.

Algorithms interpret raw data

Using algorithms, the pattern can then be transformed into a three-dimensional image showing the structure of a protein, for example. For Tomas Ekeberg, this means trying to work out what a protein looks like that gives rise to a certain pattern.

“My way of approaching the problem is largely about creating mental images. I sometimes draw them up, to discuss with colleagues.”

He uses some type of image in almost everything he does.

“It is almost unusual that raw data or research results are not expressed in this way. In principle, I almost exclusively use images when I give presentations,” says Tomas Ekeberg.

Visualising the result

He spends a lot of time on visualising the results the team discover.

“Perhaps it’s not always very artistic, but more educational. Images are unbeatable when it comes to communicating things such as structures. For me, the focus is one hundred per cent on trying to illustrate something clearly. I like to teach and explain things, so I end up there naturally.”

Tomas Ekeberg has won awards for this attitude. In 2015, he published a picture of a giant virus, which the journal Nature chose as one of that year’s best scientific images. “It was both surprising and wonderful,” he says, but now, five years later, he is not entirely satisfied with it.

“I like it in some ways, but certain aspects irritate me. There are things I would have done differently today. For one thing, I used a rather muddled colour scale. I would probably have placed the centre otherwise. The image doesn’t show what I want it to portray all that clearly,” says Tomas Ekeberg.

Text: Siv Engelmark
Photo: Tomas Ekeberg

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