August 15, 2013
As the summer winds to a close, it seems that my project has wrapped up very nicely and there is little left to do. After spending several weeks on mass spectrometry analysis and collecting data, we made some graphs for various amino acid residues showing the amount of modified protein versus the amount unmodified. We compared the results of the protein in its hexamer form versus in its shell form so as to understand more about how these shells are constructed.
I then used this information to color code the pdb (protein data base) file of the shell protein, providing a much clearer visualization of the modifications caused by irradiation. It is very useful to have the crystal structure of the hexamer, even if it does not necessarily look the same when not crystallized. While the results do not provide conclusive evidence about function as related to the structure, it is a step forward in understanding how carboxysomes are formed and has been passed on to the scientists who originally purified the protein. I will be returning for a meeting with them in early September, which I’m sure will be very informative.
For now I’m assisting with an experiment involving other proteins on a different beamline, which has more to do with learning about the technique of protein footprinting. It’s been very exciting to work with a method that is new and developing, and especially to have used it in a way that has never been tested before: in vivo. Unfortunately, though we have the cell samples that we irradiated, they have not been run through the mass spectrometer yet, so I’ll just have to hear about those results later. Luckily, since the lab is so close to home, I’ll be able to keep up with goings on for some time to come. It’s been a fantastic opportunity to work here and I hope I’ll be lucky to have similar experiences in the future.
July 25, 2013
Setting up the beamline for their experiments.
I write this sitting at a spacious L-shaped desk in a sunny office overlooking the Berkeley hills, from which I can just barely see to the other side of the bay. This, by some stroke of luck that sent an administrator to another department, is now “mine.” As it’s been a while since I last posted, I’ll try to make this as comprehensive as possible.
It was really in my first couple of weeks here that we really jumped into performing experiments. This was serendipitous, not intentional, as beam time is precious and scheduled far in advance. Thus, we had to make sure all of the protein samples and equipment were ready by a certain day, and then had to make sure all the experiments were run in the allotted time. The basic setup of our beamline was this: we separated the protein solutions into batches according to how long they would be irradiated for, and one by one, we ran them through tiny glass capillaries hooked up to a pump with only a tiny bit of the capillary exposed to the beam. The flow rate determined how long the sample was exposed for. Here’s what the pump looked like:
Working at the synchrotron was exciting because, as I explained before, it’s like a museum with all the research posters on display, not to mention the equipment for some of the beamlines looks really cool in an intensely complicated way (think lots of metal chambers with what look like portholes and wires going everywhere). The only downside of the one we were using is that since it is not used for only one kind of experiment so there was a lot of waiting around for the technician to tinker with it and get it perfectly aligned. In the end though, we got it up and running and got all of our samples through
The lab where Jenny is working.
Since that finished, it’s been data analysis data analysis data analysis. Our collaborators at JBEI ran the mass spec for us, so using that data and the program MassHunter, we’ve been identifying the modifications that were made to the proteins by irradiation. Essentially, whether or not certain changes happened to certain residues tells us about the structure of the protein in its hexamer form versus in its shell form. Again, this is a protein that forms carboxysome shells, which contain carbon sequestering enzymes.
Tomorrow I’m attending a talk by Cheryl Kerfeld, an expert on carboxysomes, which should be interesting and helpful as far as understanding the big picture. For now I’m learning how to assess a large amount of data on a lot of little details and enjoying the view.
July 6, 2013
Concerning the location
Though it wouldn’t seem that having a placement in Berkeley is particularly exciting (considering that other internships are in India, Ghana, and other exciting places), I was actually elated upon receiving my acceptance letter because at the time I was studying abroad and rather burnt out on travelling. Besides which, as an incoming senior, I’m being forced to think about my post-graduation plans and opportunities in the bay area are abundant and more easily explored from the comfort of the Berkeley Hills. A national lab is an exciting place to work – the place is rich with history, given that the ALS is the former site of Ernest Lawrence’s cyclotron. In fact, I would say it is the most exciting building to work in because with access to the synchrotron, one can circumambulate the outer hallway and read about a large variety of research projects that range from crystallography to materials science. Also, have you seen the view from LBNL?
Concerning the people
Some preliminary internet research of my supervisor, Corie Ralston told me that she spends most of her time running crystallography beamlines at the ALS and writes science fiction in her spare time, and therefore was guaranteed to be awesome. She has lived up to, and actually surpassed, this expectation and I feel incredibly lucky to be working with someone so friendly and knowledgeable. Not only has she been great at explaining the uses of the beamline and the goals of protein footprinting, I’ve also had some great conversations with her about women in STEM fields and living in the Berkeley Student Cooperative.
The person I see most often is Sayan Gupta, a biophysicist who actually performs the protein footprinting experiments. He is great to work with and has been helping me a lot with data analysis and running the beamline experiments. The other week we drove down to JBEI and I got to see the fancy mass spectrometry machines they have there.
Concerning the research
The best blanket term for what I’ve been doing here is “protein footprinting.” Essentially we’ve been using hard X-rays to modify proteins and by examining these modifications we learn more about their structures. The really exciting thing is that we just ran an experiment in vivo and hopefully if we get some useable data it will be the first time this has been done. Running these experiments on cells is useful because crystallized proteins aren’t necessarily in the same form that they take in biological systems. By keeping them in the cell, or even just in solution, we learn more about how they actually look and function. The relevance to climate research comes in with a protein called “shell,” which forms carboxysomes (microcompartments containing enzymes involved in carbon fixation). Last week we had “beam time” and shot some lasers at it so we’ll soon have some data to be interpreted once JBEI sends us the mass spectrometry results!