What is Del working on in Oz? (part 1)

Well, here it is friends and family, my first blog entry. And it will be about science! Continue to read if you dare…

The task of my post-doctoral fellowship is to design biocatalysts using combined computational modeling and directed evolution. I have other projects here as well, but this is the job I was hired to do. This is all well and interesting since a. I have never done this before, and b. this has only been done successfully a handful of times…ever. So it will be challenging and when I succeed you can all say “Good job Del!” or when I fail you can say “It’s okay Del you did your best, anyway it was a really hard problem!” and behind my back you can whisper “Dumbass went all the way to Australia to tackle an impossible problem and he couldn’t pull it off…how lame!” Now you may be asking what he hell “to design biocatalysts using combined computational modeling and directed evolution “ even means. It is for those of you asking this question that I’m writing this post. I’ll try to answer the most obvious questions over two blog posts:

1. What is a biocatalyst?
2. Why do I want to design them?
3. What is computer modeling?
4. What is directed evolution?

Okay let’s get started. Question 1: What is a biocatalyst? Well, it is an enzyme. Enzymes are a type of molecule that performs chemical reactions in your body. These reactions include breaking down your food, passing signals around your body, making your blood clot, making your toenails grow, and a whole mess of other things. You need enzymes because the chemical reactions your body needs to survive don’t happen at the right speed for them to be useful. For example you eat glucose (sugar) and you get energy to do your tasks. Your body oxidizes glucose to carbon dioxide, which you breath out, and in the process you get some energy, which is used to keep you alive and healthy. Your body uses enzymes to do this. You can oxidize glucose to carbon dioxide without the aid of enzymes. Just get some sugar and leave it exposed to air. Wait for it… nothing happens? Well using oxygen to oxidize sugar happens very slowly. We need to add something to speed things up. Well, what if we burn the sugar? That works, but most of the energy goes away as heat and we can’t use it for anything. This is the same problem your body faces. You need to extract the heat from burning glucose and use that to do other jobs. Enzymes make this possible: they act as catalysts for your body’s chemical reactions.

How do they do it you may ask? Well before I answer that question I’m going to give you all a basic biology lesson about what an enzyme is made of and inevitably what you are made of. The answer for the most part is protein. Enzymes are made of protein, or rather enzymes are proteins. Though not all proteins are enzymes. Proteins are the basic mechanical building blocks of nearly all life (this could be debated for viruses but we won’t talk about that now). Also, they perform nearly all tasks that are involved with maintaining life.

So what does a protein look like? For starters they are very small. Only the biggest proteins can just barely be seen with the most powerful microscopes. More specifically they range in sizes from say 1 nanometer to 10 nanometers. But they can join together to make structures that are much bigger (these are the ones that can be barely resolved by the most powerful microscopes). By the way, one nanometer is 1 billionth of a meter. So if you can take the smallest mark on your ruler (1 millimeter) and divide it into a million equal parts, they will each be 1 nanometer in size. So proteins are really tiny. How do we see them then? Well it turns out that the reason we can’t see them is that the light we use to see is actually larger than the protein (the wavelength of visible light is longer than the dimensions of the protein). So we need a very special camera that takes pictures with much smaller (shorter wavelength) light: x-rays. To see a protein we need the high energy x-rays that come off of particles whipping around almost as fast as the speed of light in big rings called particle accelerators. My boss is an expert in using these high-energy xrays and some very special cameras and computer programs to figure out what proteins look like. Here are some pictures of smaller proteins compared against Rhinovirus AKA “The Common Cold” (whose coat is made of protein).

This picture was cropped from a great poster available at the RCSB (http://www.rcsb.org). Click to zoom in so you can read the names if you're interested.

Now, the next question is how does your body make proteins? This is actually one of the fundamental concepts of biology. So fundamental in fact that they give it a really stupid name: “The Central Dogma of Molecular Biology”. I will explain the central dogma using a factory as an example.

In the boss’s office (nucleus of the cell) there are sets of blueprints (your DNA) on how to make all of the different things a factory can make (your proteins). The blueprints don’t ever leave the boss’s office, so we need to make copies so the assembly line can go to work. So we make a photocopy (the process of transcription) of the blueprint and this photocopy (mRNA) is what the assembly line will use. Now the photocopy is read by the assembly line (the process of translation) and the end product is made (protein). The assembly line is actually a big (well big compared to proteins) device called the ribosome. Below is a picture of this process (DNA and mRNA and final protein not drawn to scale sorry!).

When the ribosome makes a protein, it assembles it from basic building blocks called amino acids. These amino acids are attached end to end like differently colored beads on a string and your DNA determines the order in which they are attached. But this string of beads needs to fold up to make a functional protein. This magical act of self-assembly is called protein folding (and is what I studied under Vijay Pande while at Stanford University). This YouTube video shows a computer simulation of a protein folding (this is from work done by a number of talented lab-mates of mine and published in http://pubs.acs.org/doi/abs/10.1021/ja9090353). Note that this movie uses a different representation of the protein than the previous pictures. The arrows and coils are meant to show what shape the "string" is in while the balls and sticks are meant to show what shape the "beads" are in.

So, let’s summarize. We know that enzymes are proteins that do chemical reactions in such a way as to make them useful to our body. We also know that proteins are assembled from amino acids like beads on a string according to instructions written into our DNA. We know that these proteins are very small, but can do all sorts of tasks in your cells (some of them actually even look like larger real world objects such as scissors, salad tongs, camera lenses, etc). And we know that these proteins fold up into the correct shape in order to do their job (imagine how cool it would be if you could just attach all of the parts of a car end to end and then have them magically fold up into a functioning automobile…just goes to show what crazy and amazing things happen on the scale of really small things like the cells in your body!)

Well that was question 1. I’ll answer the other 3 (the answers will not be so long!) in the next blog post. Hope to see you then!