Question: I was reading you profile and I was wondering something. You said that once you knew the structure of a protein then you can see which shape chemical is needed to block it's active site; and once you have found that you can begin to make a medicine or vaccine against it. I would like to ask a few questions on this: 1) Could you please tell me what you you mean by 'active site'? 2) Can you tell me a bit more detail about the process between finding the structure of a protein and finding its shape chemical please? 3) How do you know/find out what to put in a medicine as well as the shape chemical? Thanks :)

Ailsa Powell answered on 17 Jun 2011:

Hi,
Great questions, thanks for reading my profile in such detail 🙂

The active site of a protein is the part of it that performs the chemical reaction that protein catalyses. It is usually a pocket or cleft in the protein and an experienced person can often spot it immediately once you have calculated the structure of the protein. I should add a disclaimer that not all proteins have active sites but only the ones that are enzymes which catalyse the many reactions that occur in living things – other proteins have a structural role and would have binding sites where they interact with other proteins.

Proteins are usually very specific in the reactions they catalyse – so they will only recognise one substrate and perform the chemical reaction on that. It’s pretty amazing how specific and accurate enzymes can be – certainly more so than any synthetic catalyst! The reason the proteins are so specific is because of the amino acids that are in the active site are both chemically and spatially in the correct configuration to recognise the specific substrates for that reaction – nothing else should bind in there and therefore no mistake reactions occur. You also have the specific amino acids that cause the reaction to occur in there too (otherwise I guess it wouldn’t be an active site 🙂 ).

I calculate the structure of my protein using X-ray crystallography (this is actually the trickiest bit and can take many years). X-ray crystallography is a technique where you get your protein to grow into a microscopic crystal and then you use X-rays to solve it’s atomic structure. It’s a similar idea to a microscope, but visible light doesn’t have the correct wavelength to be able to see atoms, X-rays do have the right wavelength which is why we use them. Unfortunately there are no lenses to re-focus X-rays after they have diffracted off the sample (as there is in a light microscope) so we use a series of computer algorithms to reconstitute the diffracted X-rays and locate (see) the positions of the atoms in the protein. We then have a 3D representation of the protein structure on the computer – it really is pretty cool and I’m always amazed by it. 🙂

After I have solved the protein structure I can see what the active site looks like and I know the exact position of all the atoms in the amino acids lining the active site. I will have been also been doing lots of biochemical experiments to characterise the protein so I know what it’s substrates are (and also read up on what other people have discovered too, an important part of research). So how do I find a chemical that isn’t the natural substrate to block up the active site and stop it working? Well I will have a good idea of the shape of the natural substrate and then over the years chemists have complied libraries of chemicals that mimic natural substrates. So I will start by looking at those types of chemical. I want it to stop the protein from working and because it is an enzyme I will have been able to check the protein is catalysing it’s reaction by setting up everything it needs to do the reaction in a in a test tube using the natural substrate – then if I add the test chemical it should stop the reaction – this is called enzyme inhibition. If the test chemical does stop the reaction then I will try and solve the structure of my protein with that test chemical bound to it, when I look at the structure I will be able to see how well it fits into the active site and if there are any little pockets available that I can use – as improving how the test chemical fits in the active site improves it’s binding and therefore it’s ability to block the natural reaction. If there is a pocket I can use I will get a chemist to add the right size chemical group onto the test chemical and go through the whole process again – both the enzyme reaction tests and looking at the structures.

I need to go through this process the get the best shape molecule with the best possible fit in the active site as that is what is needed to develop the test chemical into a medicine. And this is the point where my job is done. I pass on the work to scientists who will see if the medicine works on the malarial parasite and also that it isn’t toxic to human cells. Then other scientists need to make sure if we take a medicine that it can get to the part of our bodies that needs the treatment and they may need to add some bits to the test chemical to help it get to the right place and finally the medicine needs to be tested to make sure it does what it’s supposed to and isn’t toxic to people and has no nasty side effects. The whole process can take 20 years! So I would hope that some of my discoveries are good enough that they can be develop into new medicines eventually, but it will be a long time before they are 🙂

I hope that answers your question 🙂 If you want more explained just add a comment after this answer.