Tuesday, May 24, 2011

What I do all day

I often get asked what it is I do, and I often fumble the question. Despite the fact that I have an English major under my belt in addition to all of the science training, it is hard for me to tell a story about the science that I do without getting people lost in the jargon. (David is much better at this than I am.) For scientists, talking about our jobs is like playing a game of Taboo - many of the words are (and should be) disallowed, because they won't allow people outside of science to fully understand. However, I have had some really great results in lab recently, so I thought I would try to talk about what it is I am working on so I can share my great results with all of you.

And so...a little background. (There will be pictures later, so feel free to skip to the bottom of the page.)

As a biochemist, I am interested in studying proteins. If you think of a cell as a giant city, proteins are all of the people inside of the city going to work every day. Each protein is made of up of the same types of building blocks, but how these building blocks come together to make each unique protein are a big part of what dictates what job a protein will perform in the cell (just as we all have traits and talents enabling us to do whatever it is that we do). My thesis project at Penn was spent learning about how proteins are built to do the jobs that they do. I studied the building blocks of proteins and applied that knowledge towards using those blocks to engineer new, designed (non-natural) proteins to perform specific, existing functions. At Cornell, I wanted to take my studies in a slightly different direction. Instead of studying the individual building blocks and how to put them together myself, I now want to know what natural proteins look like once they are fully assembled. What is their structure? And how does the way the protein is structured contribute to its ability to perform its job? And so...how do we get information about the structure of proteins? There are many different techniques to do this, but the technique my laboratory uses is called x-ray crystallography. So what does that mean exactly?

Did you all ever have these kits as a child? Or perhaps you ate these? (I know I had an obsession with these rocks of sugary goodness for a stretch of time in elementary school.) Just as salt and sugar molecules can form crystals, so can protein molecules. Crystals are advantageous to study because they are ordered (what allows them to form). This basically means that when a crystal of protein forms, it is many protein molecules coming together in one solid, with each protein having its building blocks in the exact same arrangement. To relate this back to people, this would be the equivalent of having multiple copies of me in a room (that room would be LOUD) in the exact same position without moving! If one of my copies blinked, or scratched her head, the "Sarah crystal" would crack and the whole room would become disordered. This is what makes protein crystallography so difficult - proteins, like people (me in particular) are dynamic, which means their building blocks are always moving into slightly different positions. They aren't designed to "stay put" in one conformation (position) and most of the time, their jobs actually depend on them being dynamic. Finding a condition for them to crystallize and "stay put" is bit of scientific voodoo and a lot of luck, though there are sets of conditions that have been demonstrated to be better than others for crystallizing proteins. (As there are for salts and sugars, which is why there are kits and recipes for the examples above.)

And so, for the past year, it has been my goal to crystallize a specific protein (that has a specific job that I find cool and exciting) and determine its structure. No one has ever determined the structure of this protein before, so it would be a big advancement to my field to know how the arrangement of this protein's building blocks contribute to why and how it functions. The great result I would like to share with all of you is that after a VERY frustrating year, I have finally made progress!

Above is a photo of my protein crystals, clustered together. (Sorry, the image is not great, because I am still learning how to use the camera attached to our microscope.) These crystals are not ideal because they grew together rather than separately, but I was able to break them apart without damaging them (luck rather than skill). These crystals are 100 microns big, which translates to being 0.1 mm, or 0.003 inches. Working with them is challenging for me because I have to use a microscope just to see them, and when I am looking through the microscope, I cannot watch what my hands are doing at the same time. These crystals are made of many copies of just a small part of my entire protein. Some proteins are very large assemblies of building blocks (mine is), and it can be easier to isolate and study the structure of many small pieces individually rather than going for the whole thing all at once. (Imagine studying just the arm of a Mr. Potato Head doll, and then the nose, and then the leg, and so forth, and then using what you learned to put together the whole toy.) Obtaining my protein (and its pieces) was not an easy task, and I spent almost my entire first year working on just that part.

Once I obtained protein crystals, I needed to do an experiment to help me determine how all of its building blocks are arranged (structure). We mount the crystal and expose it to a beam (narrow stream) of x-rays (electromagnetic radiation, just like the x-rays used in medicine, but much more focused). Just like getting an x-ray of your arm produces a 2-D image of your "structure," we get a 2-D image of our protein structure too.

My 2-D image looks like the picture above, and this is called a diffraction pattern. Basically, the x-rays bounce off the surface of the crystal (this is called diffraction) onto a detector. The pattern above is the read-out of all of the diffraction spots (each dot) that occurred from the crystal at a single angle. We then change the angle of the beam by 1 degree and measure this pattern again, and do this for all 360 angles (or one full rotation). The further the spots are spread out from the center of the beam (the cross in the white spot in the center of the image), the more data we have, and the more detailed our structure can be. We can combine the 2-D diffraction data collected at all 360 angles into one data set, and then mathematically convert that into 3-D coordinates (to over-simplify it a bit). This is the stage that I am at right now. I will eventually use what we know about other protein structures and the known 3-D coordinates for each type of building block to build up the 3-D structure of my protein.

Cornell has one of six facilities in the United States to collect high resolution x-ray diffraction data (called synchrotrons), and it is called CHESS - Cornell High Energy Synchrotron Source. Working at CHESS is like what I imagine it would be like to work on a submarine. There are so many switches and lights and monitors! I keep waiting to push the button that shuts the whole place down by mistake, but so far, I have not caused any major disasters while collecting data. Also, there are many safety protocols in place to ensure that none of us get exposed to massive amounts of x-rays while we are collecting data, and many of them involve loud alarms that sound until doors and switches are locked securely. It is amazing how difficult it is to turn a key and close a door when a giant alarm is sounding all around you! I still get stressed out just from the noise.

This lighted sign tells us that everything is running and we are able to collect data.

And so, that is a bit about what I have been up to over the past few weeks! Hopefully some of this made some sense. I will post what my protein structure looks like once it is solved.

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