Now that you’re comfortable with carbon structures, let’s move on to the biological area ! In this tutorial, you will see the main secondary structures of most proteins.
First of all, click on the link : http://www.rcsb.org/ . You’ll be redirected on a website that lists different proteins. On the toolbar (top right), write “1EI0” (be careful it’s a capital i and a zero).
Download the file and select PDB format.
Now, go back on SAMSON and select “File”, “open” and select the molecule that you have downloaded. Now you have one of the main secondary structures of proteins wich is called the alpha helix ! At first glance, it may not look like the alpha helix you see when you search it on the internet : it’s because you only see the atoms, not the structure. In order to see it, go on “Visualization”, then “add visual model” and finally choose “secondary structure” in the menu “select visual model”. You can rename it “alpha helix” if you want too in order to make it clearer for you.
You can make visible the hydrogen bond by clicking on this icon : or on the menu in “app”, “all”, and “hydrogen bond finder” (select a max length threshold of 3 angstrom) :
Now you can see the secondary structure of what is in most of the proteins. Isn’t it great ?
The alpha helix has a step of 1,5 angstrom (10-10 meters) and 100 degres and a width of 5 angstrom. You can measure the length of a bond with the button :
There are two othes secondary structures that are interesting to see : the beta sheet and the beta turn. Now that you’ve understood how to see the secondary structure of a protein, it won’t be necessary to reiterate the process with these two (but you can definitely do it if you want ! You’ll just have to search on PDB the right molecule). So here is what these two moleculs look like :
The beta sheet and beta turn create hydrogen bonds (that you can see in red). The difference between these two is that a beta turn is at the end of a beta sheet and the begining of another one, so it can link the sheets between them.
The glucose oxidase protein
To see if you have understood the differences between those three secondary structures, let’s play a game : We’re going to find a complete protein and try to find which amino acid sequence matches which secondary structure !
Go on PDB and search on the toolbar “1CF3”. This molecule is named glucose oxidase. Download it and open it on SAMSON.
This is what the molecule is supposed to look like once opened in SAMSON :
Yes this one is way bigger than the others ! Many sequences of this molecul aren’t interesting for us, so we’ll just make visible the sequences that we need. Use the visual model “secondary structure” to see the tertiary structure of this molecul, which is just the assembly of the different secondary structures. On the window “document view”, click on the + sign next to the name of the molecule. Continue to click on the + sign when the other options appear until you see the names of the amino acids sequences (you can see where they are located on the glucose oxidase by clicking on them.) Now, keep all the elements from 388 to 429 and remove the others.
To do that : select the item point selection : then right click, “invert selection” after having selected all the moleculs you want to keep, then “remove”. You can select several amino acids at the same time by pressing the « maj » button while you choose the amino acids you want to keep.
Finally, use the secondary structure model as you’ve done with the alpha helix. Now, try to identify which parts matches which secondary structure. Here’s a tip : there is one alpha helix, two beta sheets and one beta turn ! Notice that their are no hydrogenes, so you can’t use “hydrogene bonding” option.
The DNA molecul
If you have finished this and have some time remaining, you can try to understand the bonding and the composure of the DNA. For that, download on the website PDB the molecul “6GPI” and open it on SAMSON.
Then visualize the hydrogen bond. Go on the “document view” menu in order to observe how the DNA molecul is composed. You should be able to make the link with your lessons and name the different parts.
As you saw, SAMSON is a simulator also use by biologists. We can, for instance, find the most adapted molecul for a drug. If you interested in it you can go on the PDB website, download different molecul to see them.
figure 1, 2 and 7: http://www.rcsb.org/
figure 5, 6 : pre-orientation Biomed courses of Phelma, 2019 (Weidenhaupt Marianne)