In case you missed my last post about structural biology, click here to read it!
In short, structural biology tries to determine the structure of biological molecules (mostly proteins). That's more difficult than it might sound, as the parts of these molecules are too small to be seen with a microscope.
Last time, I showed you the last steps in determining a protein's structure, which wasn't so super smart, because now I have nice pictures for the first steps. But what can I do, these things happen.
After all, it's good for you, you get to look at very pretty protein crystals! Or at least I think they're pretty. I'm a huge fan of things like that.
A protein crystal that's used to determine the structure is made out of the same protein, over and over again, arranged in a symmetric structure. But proteins don't just do that by themselves. There are several methods to make them crystallize.
In this experiment, we used the "hanging drop" method, where the protein is mixed with some other chemicals (that control variables like pH and salt concentration) and then 1 µl (yes, microliter!) is put on a tiny class, flipped around and put on a well plate, which contains the same liquid the protein was mixed with. The protein we used is called "lysozyme", which is important for the immune system.
A well plate looks like this:
The holes are the wells. In theory, you can have a different protein-liquid mix in every well to test different conditions, because every protein has its own perfect conditions for crystal formation.
Over the span of a week, water evaporated from the tiny drop, which increased the protein concentration slowly and allowed crystals to form.
Under one condition, that happend fast, we could see so-called microcrystals after 30 minutes!
But these were totally useless. Equally useless were the needles that had formed in a different drop with different conditions after a week:
But to our delight, there were already proper crystals in this drop!
But they were too tiny for us to use. Other drops that looked great but were pretty useless:
And finally, three drops that turned out great. If you look at them closely enough, you'll realize that they all have the same structure, we just captured them from different angles. That's because the protein was the same every time, which causes the same crystal structure, if there's a proper singular crystal.
Have you ever seen a salt crystal? Those look the same each time too, if you give them the correct conditions to develop!
The crystals, 400 µm to 900 µm big, were then fished out of the drop, using a tiny nylon loop and a microscope. Surgery is NOTHING against the precision needed here, because the crystals are very soft.
As soon as they're out of the drop, they're flash frozen in liquid nitrogen and kept at 100 degrees Kelvin. That serves to protect them, as they're put into this machine:
Where they're shot with x-rays. Those go through the crystal and are bent according to the protein's structure. A screen behind the crystal detects this, which creates the following pattern:
For this specific protein at least! If he had accidentally created a salt crystal (there's a lot of salt in the solution we used), the pattern would have looked more like this:
Why?
The more complex the molecule inside the crystal, the more complex is the pattern. The salt we used, NaCl (normal salt you eat) only has two different atoms. A protein consists of several amino acids which are all made up out of at least 4 different atoms (hydrogen, carbon, oxygen, nitrogen).
Not too long ago, a number of complicated calculations followed. Most of these can now be done by computers, which leaves us with the steps described in the post I published first and linked above. I really need to work on my timing!
I am licensing the pictures of the crystals under a Creative Commons 4.0 International License, as they're too pretty to not be shared!
