Designer Enzymes - Beyond Biology

14 August 2011

Interview with

Professor David Baker, University of Washington

One of the most important chemical players in nature is the protein.  The structure of a protein gives it specific chemical and mechanical properties.  Predicting the structures of proteins could allow us to design brand new proteins and enzyems, to help catalyse a range of reactions.  One man making significant headway in this direction is Professor David Baker from the University of Washington...

David -   Proteins carry almost all the basic functions in your body.  They're essentially like the machines.  They have very precise three-dimensional structures which are critical to them carrying out their function.  What we're working on is trying to make new machines, new protein machines that do new things.

Chris -   If we were to zoom in on an enzyme, and ask how does this thing actually work, what would be the answer to that?

David -   You see, on the outside, you see scaffolding that would hold certain groups in the enzyme in very precise positions to carry out the chemistry of the reaction.

Chris -   And what's the business end?  How does that scaffolding then make a chemical reaction happen in the way that enzymes do?

David -   It provides a very precise chemical environment in which the rate limiting step for the reaction is greatly sped up.  You have all the right types of positive and negative charges in the right places to speed up the reaction.

Chris -   So if we were looking at an enzyme active site, which is where it does the chemical reaction, you'd have a region of the protein which is just the right shape to fit a molecule into it. And then the right sorts of chemical groups are in the right places to transfer charge, or to distort, or move, a molecule around in order to make something happen.

David -   That's exactly right.

Chris -   So nature does this very well.  I mean, our bodies are a big bag of chemical reactions.  You're saying, we can take what nature does, work out how these things work, and make new ones?

David -   Exactly.  So we can take the basic principles for how the proteins in nature do things and then try to make new proteins that do new things that are of current use to the society, as we face a lot of problems that nature didn't face during biological evolution.

Chris -   Presumably, it's not trivial to do this though because if one takes a look at an enzyme, you've got something of several hundred amino acid building blocks in the protein, and there are many, many different amino acids existing in nature that could be in any of those positions.  So there are many possible combinations that could give the structure.  So how do you solve a problem like that?

David -   Yes, you're right.  There are an astronomical number of combinations, the number of possible amino acid sequences.  The way we approach this problem is by focusing on the active centre where the chemistry is going to happen and we build models of what the perfect active centre would be, that would catalyse the chemical reaction.  And once we've done that, we try to come up with a scaffold that will hold all of those key groups in position to carry out their reaction.Catalase

Chris -   How do you decide what chemical groups have got to go where though?

David -   We decide what chemical groups should go where based on quantum chemistry calculations and based on chemical intuition about how the reaction is likely to be sped up.  You actually commented on a couple of the ways we might do this.  For example, suppose you have a reaction in which there are two molecules that come together to be joined into one molecule.  In solution they'll be floating independently of each other and it's very rare that they would actually come together in exactly the right relative orientation for say, a bond to be made between them.  In a designed enzyme, you would design a binding site for one molecule, a binding site for the other molecule, and they would be held in exactly the right orientation so that the bond could form between them.

Chris -   You made that sound very simple, but I'm sure it's not.

David -   Well it's not.  There are basically two problems.  First of all, we are making a bit of a hypothesis about how you might speed up the reaction.  I mean, in the case I just gave you, it seems quite intuitive that if you brought these molecules together and held them in the right relative orientation, you would speed the reaction.  But that's not always true.  And the second difficulty is, we may want to be able to create binding sites that hold the two molecules in the right orientation relative to each other, but achieving that is a tall order that really requires mastery of the rules of protein folding .  We'd like to design an amino acid sequence so that the protein folds up in such a way as to create these two binding sites.  So both of them are challenging problems.

Chris -   Now you mentioned amino acids.  Nature endows us with a clutch of these things that we use biologically.  I mean, most proteins that you will find in my body should have one of the 20 commonly used amino acids in them.  Presumably if you can bespoke make proteins though, you're not constrained in the same way nature is, so you could do kinds of exciting reactions.

David -   Yeah, exactly.  So we are now trying to create designed proteins using more than just nature's 20 amino acids.

Chris -   What sorts of functions could you do with that?

David -   One thing one might be able to do is bind metals that aren't normally bound to naturally occurring  proteins, like ruthenium, that could have uses in, say, light capture.  You could incorporate potent chemical functionalities that aren't found in nature to carry out more complex reactions.

Chris -   So you can basically do chemistry that nature can't if you understand first of all how nature has come up with the structures that it does.  What about doing things beyond just enzymes though, because proteins do all kinds of things, they don't just catalyse reactions?

David -   Proteins do many different kinds of things.  Another thing that they do is they bind tightly to other proteins and to targets - so, for example, the way that viruses and bacteria get into your body.  They have proteins on their surface that recognise protein receptors on your cells and this is sort of the first step in entry into your body.  So, molecular recognition is important function carried out by proteins and this is something that we're actively working on.  We've recently designed very small proteins that prevent the flu virus from infecting cells, and we're now engaged in making small protein inhibitors for the entry of many different types of pathogens into cells.

Chris -   In other words, by understanding the structures that the microorganisms themselves use to latch onto a target cell and then penetrate, if you understand what the virus or the bacterium is doing, you can produce a complementary protein or molecule which will interrupt that process because it binds to it better than a cell would.

David - That's exactly right.

Chris -   So how far are we away from being able to come up with some kind of generic recipe book where someone would say, "Right.  I have got a certain structure or certain target for - whatever microorganism that's the flavour of the month - I want to interrupt the infectivity of that."  Can you do that yet?

David -   Well, that's exactly what we're working on and our goal is exactly as you described, to create a sort of general process, a rapid process where given a new pathogen, you could point to a region on its surface and say, "Block this," and a couple of weeks later, you'd be able to block it.  I could say we're also trying to engage the general public in these efforts because we have an online video game called 'fold it' in which the public can get involved in both the enzyme design and inhibitor design.  And in fact, in recent months 'fold it' players have been making very exciting contributions in both areas.

Chris -   How long does it take you to come up with a bespoke molecule that could block flu the way you've described?

David -   It took us about a year and a half.

Chris -   And that's involving millions of computer hours around the world.

David -   Yes.

Chris -   So this is not a trivial problem to solve.

David -   No, not at all.  But we're at the beginning and we're hoping that as we learn more about how to do this, we'll be able to do it more quickly.


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