So, I’m a biochemistry student, and I’m currently working on my master’s thesis. Now, I’m not the typical student, so I don’t appreciate that type casting. I’m old, I’m miserable, and I’m not trying to get into heaven anymore. I don’t spend weekends plastered off my ass and I have never seen an episode of Jersey Shore, The O.C. or whatever the hell else kids are watching these days. What I have seen, sort of, is this:
Mammalian Epoxide Hydrolase. That miserable little bastard.
Thank you Protein Data Bank. You can visit the Protein Data Bank too; I left you a link in the margins of the page. I’ll wait; I know it could take a while. If you’re not scientifically minded, start by typing in a common protein name. I’d go with albumin or lipase or something simple. Go ahead try it; then come back. I’ll be here.
Back so soon? I think I put too much faith in you people. I didn’t put that link there for my health, you know. Just try it once, that’s all I ask. Anyhoo, I’m writing my thesis on how to make epoxide hydrolase in the lab and how to tell if it’s working or not. Here’s the problem: I don’t know if it’s working. So far I have not been able to develop a single test to see if it’s working. Now, I have nothing to write about. No successful thesis began with the words, “After working in the lab for two years, I can say with a fair amount of accuracy that I am an abject failure in figuring out if the damn thing works.”
Although, to be fair, there’s ways to say that without actually admitting what an abject failure I actually am. However, I’d really rather not go into that. Now, I know what you’re thinking, because it only makes sense at this point. You’re thinking, “Well, how do you even know it’s in that test tube? I mean, it’s not like you can actually see it in there, and if it’s not doing anything, it just stands to reason…”
You’re right. No, no, you’re absolutely right. So I did some SDS-PAGE gels. The pretty blue line appears if your protein is in there. Here’s my gel. I’ve had better. Yeah, all that crap you see on forensics files is the scientists telling the interns and undergrads to run that shit until they see something absolutely perfect. I’m not so lucky. I don’t have any undergrads.
It’s there, but the damn thing won’t work.
I tried an alphabet soup of tests to see if I could get it to work – it won’t work.
I tried re-folding dialysis – it won’t work.
I tried changing pH, temperature, buffer and co-factors – it won’t work.
I tried begging it – it won’t work.
I tried crying about it – it won’t work.
I tried bribing it – it won’t work.
Remember that big scene where Indiana Jones runs from the big rolling ball in the temple? It looked like this, only it didn’t involve a giant LEGO ball and wasn’t totally fake.
The whole time I watched the original I kept thinking, “Why doesn’t he just lay flat and let the ball pass over him on those ramps?” Seriously. Why didn’t he just do that? Was it the panic of the moment? The rush of adrenaline? Or maybe it was Spielberg telling him that if he didn’t play along he wouldn’t work in that town again. I don’t know. All I know is that the giant ball is coming, but unlike the movies, I don’t have anywhere to duck.
I also don’t have much to say. Maybe I could just try to bullshit my way through this, or write something like, “I like ponies,” and I could squeak by on mental disability. I fear I may not be so lucky. (Although those that know me also know that there’s some merit to the mental disability argument.) There’s a cruel irony to all of this. Here, you want to have nightmares tonight? Look at this:
Schrodinger Wave Equation for Hydrogen. Be afraid, be very afraid.
I’ve had to solve this for at least two dimensions on a one-electron molecule. Yes, it’s just as confusing and diabolical as it sounds. However, once you see the actual proof, the results are not hard to replicate. You see, that nasty piece of business there is actually a road map to success.
The damn enzyme is not. It still doesn’t work. There’s no road map, and those that have published are annoyingly silent on how exactly they managed to get their assays to work. I’m open for suggestions. If not, I think I may have to resort to haiku:
Enzyme does not work
Beating head against a wall
Thesis still eludes
Cut me some slack, it’s a work in progress.
Tags: epoxide hydrolase, Indiana Jones, laboratory, protein data bank, research, Scientific, SDS PAGE