From protein to medicine

Five animations created for the Berlin Science Week Talk by Manfred Weiss, Helmholtz Zentrum Berlin on November 4th 2020.


What is a protein?

Proteins consist of 20 different building blocks, the amino acids. They all have different properties. Amino acids are linked together by a peptide bond, forming a linear chain with a defined sequence. Rotation around these bonds allows for spatial flexibility. Depending on the amino acid sequence, higher order structures such as helices or sheets are formed. These then come together and form a defined three-dimensional structure. Ultimately, it is this structure that determines the function of the protein.


How do proteins form crystals?

Protein molecules in a super-saturated solution can assemble and form regular crystals. It all starts from a small seed of a few molecules and continues with regular growth in all three dimensions. This process can last several days and results in crystals which are up to one millimeter in size. The regular arrangement of the molecules in the crystal lattice is essential for the use in an X-ray diffraction experiment.


What is a synchrotron?

This is a top view of the Bessy II synchrotron in Berlin. A synchrotron is a particle accelerator in which electrons are sped up to nearly the speed of light. When these electrons are forced around a curve, they produce very strong radiation. This so-called synchrotron radiation includes all sorts of rays, from Infrared to hard X-rays. For our experiment, rays of just one energy are filtered out of the entire spectrum and then focused on our protein crystal.


How to obtain a protein structure

Protein crystals are exposed to X-rays. Due to the periodic arrangement of the molecules inside the crystals, the X-rays are deflected in a characteristic way. They produce a so-called diffraction pattern. By rotating the crystal, different peaks can be recorded on the detector until a complete data set is measured. From this, the three-dimensional structure of the protein can be calculated.


Finding binding partners for a protein

If we want to know which chemical compounds bind to a given protein, we need to bring them all together. Many of these compounds will not bind and bounce right off the surface of the protein. Some will bind loosely but leave again. And then there are a few compounds that bind tightly to the protein and stick to it. They may even bind more tightly than the protein’s natural binding partner. In such a situation, the protein cannot fulfil its natural function anymore: it is inhibited. If the protein happens to be involved in a disease, we may have found a drug against this disease!



above: transcripts of the voiceover; speaker is Deborah Friedman (Cologne) 


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