3D protein models developed to better understand diseases
Pioneering new microscopic techniques capable of achieving accurate 3D protein models could one day lead to new cancer therapies and treatments for diseases such as Alzheimer's. Developed by EU-funded researchers, the techniques have also been used to study how to improve antimalarial drugs.
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Proteins – complex molecules that carry out vital cell and organ functions – are so small that they can only be ‘imaged’ in electron microscopes. Until now, a major limitation of this method has been the fact that electrons – a form of radiation – can modify this image over time; observations must, therefore, be carried out quickly, before the picture becomes blurred.
To address this challenge, the EU-funded EM-FRAME project pioneered the use of new electron detectors to observe increasingly smaller particles, created ‘3D movies’ of proteins to offer sharper images, and developed techniques to create 3D images of proteins in different configurations.
Thanks to a Marie Curie Incoming International Fellowship grant, project coordinator Sjors Scheres from the Medical Research Council’s Laboratory of Molecular Biology, the UK was able to bring Xiaochen Bai, a post-doc researcher from China, into his lab. “We became a two-way team; Xiaochen would work on the electron microscope while I would work on the software,” Scheres explains.
Tapping the high-resolution revolution
The scientists began by freezing slides of super-thin layers of water, which protected the protein molecules inside and enabled the scientists to take a number of 2D images in an electron microscope. When fed into a computer, these 2D images can be turned into a stable and clear 3D image of the protein.
“In addition, we trialled new digital chips for photographing proteins – like the chips you might find in an iPhone – which proved more efficient in detecting electrons than traditional film,” says Scheres. “When electrons hit the proteins, they start moving about, and things can become blurry, but by being able to take lots of photos one after the other – like automatic burst shots from a digital camera of someone running – sharper pictures are possible.”
The project also opened the door to the development of complete 3D computer models of proteins carrying out specific functions. “Many proteins behave like machines,” explains Scheres. “They move around and have independent parts. Imaging these ‘machines’ at different stages also tends to generate blurry 3D images of the protein – imagine trying to capture a single image of a functioning appliance, like a rotating kitchen blender.”
The challenge is to isolate and capture many 3D pictures, creating a sort of 3D movie. “We can already separate these out quite well, which helps us to understand the dynamics of proteins,” says Scheres.
Achieving a clearer picture of how proteins behave could drastically improve cancer and disease research. “Gamma-secretase, one of the proteins in the membrane of cells that we have studied, for example, plays a key role in controlling signalling pathways, and its malfunction has been linked to cancer,” says Scheres. “Also, improper functioning of this protein can lead to aggregation of amyloid beta peptides, which have been found in large amounts in the brains of Alzheimer’s patients.”
For example, Scheres has since trialled the techniques pioneered through the EM-FRAME project to observe the ribosomes – machines that manufacture new proteins – of the parasites that cause malaria. Ribosomes from these parasites were isolated, and a 3D structure was built. Known inhibitors, which have been trialled as antimalarial drugs, were then introduced and also captured in 3D.
“The concept is that if you can stop the parasite from creating new proteins, it will die,” he explains. “By investigating 3D structures of drugs that bind with proteins, we can obtain mechanical information on how this works, and therefore improve the drug at the atomic level.”