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In search of the basis of life

20 September 2017

Egbert Boekema has spent almost his entire academic career working on a single problem – and he came across it by chance: elucidating the structure of the proteins responsible for photosynthesis. ‘The photosynthesis system has worked for billions of years and it forms the basis of life on earth.’ His official farewell was on 27 September and his last day at work will be two weeks later.

Old electron microscope | Photo Science LinX
Old electron microscope | Photo Science LinX

An old, traditional electron microscope still stands in a corridor of the Linnaeusborg. We pass it on our way to the latest version of the device that has served science for so long. Manufactured by our very own Philips. ‘Production moved to a separate company years ago. They still manufacture electron microscopes that mainly go to China now. There are dozens of the latest ones there. In the Netherlands, there are two in Leiden, one in Maastricht and now one here in Groningen.’

It can be found in a special vibration-free part of the building. A box taller than a man, with a control panel and the technology neatly concealed behind panels. This is to keep it as stable as possible, and to hide trade secrets while it’s at work. This type of device makes it possible to study the structure of proteins in very fine detail. ‘This has gained momentum in the last five years, thanks to spectacular improvements in technology’, Boekema explains.

Gert Oostergetel (l) and Egbert Boekema by the new electron microscope | Photo Science LinX.
Gert Oostergetel (l) and Egbert Boekema by the new electron microscope | Photo Science LinX.

His colleague Gert Oostergetel lets us take a quick look behind the panels. He is responsible for adjusting and aligning the new microscope . It is important to know how such an advanced piece of equipment works. Oostergetel points to the tube that emits the beams of electrons, the magnetic lenses. ‘Twelve specimens fit in the device at a time. You can study them from a distance’, he explains. The machine cost about EUR three million – not the most expensive model, but enough to keep up with your international neighbours. The Faculty Board made the purchase possible. Boekema: ‘The Faculty is demonstrating that they also find this research important.’

Green stuff

Boekema began his career with very different equipment with which he made several groundbreaking discoveries. His object of study was the large protein complexes responsible for converting sunlight into a stable form of energy, photosystem I and II (abbreviated to PSI and PSII). This interest came about by chance when Boekema was working as a postdoc in Berlin on the structure of an enzyme that is involved in metabolism, ATPase. ‘There was another Dutch postdoc there. He had this green stuff that he wanted me to take a look at.’

Trimer structure of PSI (1987) | Photo E. Boekema
Trimer structure of PSI (1987) | Photo E. Boekema

That ‘stuff’ was PSI, and Boekema discovered that this complex consisted of three identical proteins that form a ‘trimer’. The images that he shows look a bit like the Mercedes logo. ‘I discovered later that there is a ring of “antennae” on this trimer, which collect photons and lead them to the complex. There even proved to be a second ring of antennae.’

Boekema recently published a structure of PSII at high-resolution, one of the breakthroughs that gives him the most satisfaction. ‘It’s also nice to think that I laid the foundations by being the first to describe the trimer structure, and to discover the antennae rings. The names of the large complexes in the photosynthesis system that I developed with the help of my Amsterdam colleague Jan Dekker have also been adopted worldwide.’

Photons

Studying protein structures with an electron microscope was a lengthy process, which was mainly used for very large proteins. Boekema: ‘It could take years before you had a good specimen of your protein.’ Traditional electron microscopes work in more or less the same way as standard light microscopes but the ‘light source’ is a beam of electrons. Electrons have a shorter wavelength than visible light, so they can reveal the structure of smaller objects. Detectors collect the electrons after they have passed through the protein, thus creating an image.

‘Until a few years ago, the detectors were still CCD, which can only count photons. But they weren’t very efficient. A lot of information was lost when the electrons were converted into light.’ New types of detector can detect every single electron and thus provide many more details. The ‘illumination time’ for an image is shorter, so modern microscopes can produce a few images per second – more like a film than a series of photos.

Structure of PSI at a resolution of 2.5 angstroms (2001) | Photo Witt et al.
Structure of PSI at a resolution of 2.5 angstroms (2001) | Photo Witt et al.

‘The advantage is that you can take the average of a series of images. You thus remove small vibrations in the sample.’ Details to about 3 angstroms in length, or 0.3 nanometres, are now visible. ‘You can see the amino acids that make up a protein.’ Boekema has been able to elucidate the structure of PSII to about 4 angstroms. Then there is the structure of a separate form of PSI, which sometimes occurs as a tetramer (four parts). ‘My last PhD student will continue to work here for a bit longer before moving to the Czech Republic, to a former postdoc from my group. And my last postdoc stops when I do on 13 October.’

Computer cluster

The new research method is a real ‘big data’ approach. Smart software in the microscope scans a sample of purified protein, recognizes the correct protein and makes films of it. Analysis software takes the thousands of images of the proteins arranged in all kinds of ways in the specimen and creates a single three-dimensional model. ‘We use a computing cluster at CIT for this, although we do have our own small cluster for the initial rough analysis.’

The number of structures that have been elucidated in the last five years has grown almost exponentially. Isn’t it a shame to stop at this point? ‘Definitely, but once you turn 60 it’s almost impossible to secure research funding. And I don’t want to get in the way of my successor, Cristina Paulino.’ She will not be focusing on photosynthesis. ‘It’s a bit of a pity really, because it will then practically disappear from the University of Groningen. And photosynthesis is the basis of life on earth!’

Last modified:04 October 2017 12.04 p.m.
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