X-ray Crystallography

I've been doing, or attempting to do, a lot of protein crystallography lately.  This is one scientific discipline which is really more of an art than a science.  Growing protein crystals is really a hit or miss proposition in which your protein is exposed to often times hundreds if not thousands of different chemical environments to try to get crystals to grow.  It's usually started with a random matrix screen (purchased from companies that specialize in making screens).  Since I've been doing so much lately I decided to take a bunch and pictures and illustrate a brief overview of the art/science.

Usually crystals are grown in either hanging drop or microbatch trays.  I usually use both - the hanging drop for initial screening and the microbatch for fine tuning.  A microbatch tray can contain 72 different conditions and uses only 6-10 microliters of buffer/enzyme, so it's good for not wasting a lot of material.  Here's a microbatch tray:

Once crystals are obtained, they're incredibly small - usually only .1-.4 millimeters (100-400 micrometers) across.  Needless to say, microscopes are an integral part of the process.

  I took a few pictures of crystals by just putting my camera up against one eyepiece of the microscope:

The crystals have to be plucked out of the solution using a small cryo-loop and from here on out all steps have to happen at liquid nitrogen temperatures.  The crystals are protected from the formation of ice by cryo-protectants such as ethylene glycol.  Here's a picture of a protein crystal mounted on a loop - this crystal was about 300 micrometers across.

Once the crystal is mounted, it's ready for the x-ray beam.  Here's a typical set up: The object on the left is the x-ray beam, the top left is the cryo jet (liquid nitrogen), the right is the beam stop, and the bottom is where the crystal will be mounted.

Here's what it looks like when the crystal is mounted and is in position to be hit by the x-ray beam.

Here's what the whole system looks like - the large flat faced cylinder is the detector where the diffracted x-rays will be measured.

When data is being collected, the detector swings around to be directly next to the crystal and x-ray beam.

I was just screening crystals quickly on the day I took these, so the data collection was only about a minute.  The data you get out looks like this:

Each dot above is a reflection from the diffraction of the x-ray beam by the crystal lattice structure.  It then takes several hours to get a full data set and a lot of computing power to turn dots on a detector into a three dimensional protein structure.  This particular enzyme hasn't been solved yet, so this is where the current story ends.  Hope you learned something new.

  • cellophane
    so, in practical terms, what does this do?
    by cellophane at 06/25/09 7:28AM
  • cellophane
    btw, you have a REALLY nice camera! :)
    by cellophane at 06/25/09 7:28AM
  • danbrown
    This is all about getting the structure of proteins. It really helps figuring out what they do.
    by danbrown at 06/25/09 10:32AM
  • angela
    You are!! :)
    by angela at 10/05/09 6:47PM

My Little Brother Gets Hitched

My family all flew out to California last weekend for my brother's wedding.  Getting there was pretty fun b/c we had to fly through Dallas which had bad storms both time we had to go.  This essentially meant that we had just enough time to get off the plane, use the bathroom, and get back on the next one.  Still, I took a few pics out of the window on our flight from Dallas to L.A.

Once in L.A. we really didn't have much to do until time for the wedding set-up and rehearsal.  I did a pic of my brother wearing his new birthday present from me - it says "This is Why I'm Hot"

We ate lunch at Bubba Gump's one day and my mom wanted to take a picture of me with my feet in the shoes that they have in front of every one of their restaurants - I had to kick off my flip-flops and my feet barely fit inside the large, oversize metal shoes - they look like they belong on my feet, like they're my own shoes.

On Friday we went to help set up for the reception after the wedding that was at ECCU, where my brother works.  It's a really nice building.  All we had to do was decorate the tables and get out the plates, cups, etc.

My wife took some pics at the rehearsal and at the wedding the next day.  I took a few, too, of course.  Considering the huge wedding party (9 bridesmaids and groomsmen plus a junior bridesmaid and flowergirl), everything went really well.  My Granny and Aunt Clelia came out for the wedding, too.  It was a nice wedding - beautiful ceremony and a good time with family.

Me and my Granny and Aunt Clelia:

My dad performed the ceremony - here's a practice shot with Christy, my dad, Jon, me, and Mike (Jon's friend).

The whole wedding party - all 23 of us.

My dad playing the bongos - something he really should not ever do.

The happy couple at the rehearsal dinner.

On the day of the wedding Jac took a bunch of pictures while the photogrophers were taking pics of the groomsmen and bridesmaids outside of the church.  No pictures of the actual wedding ceremony, but I took some of the reception later.  All in all a great day.  Very proud of my little brother.

So, my brother and his new wife are now on their honeymoon for the next two weeks.  My family still had one more day in California after the wedding, so naturally, we went to Disneyland - always a fun day.  I didn't take my good camera with me, so all of the Disney pics were taken on my iPhone, hence the decreased quality.

This shot cracks me up - a regular duck on a tiny street (replica of the park from Mary Poppins).  I just love the juxtaposition and how it makes the duck look giant.

And now for some random pictures from ECCU and Disney fireworks (mostly taken from my hotel).

  • spot
    great pictures! What type of camera do you have?
    by spot at 05/21/09 12:37PM
  • summeraly
    Those are amazing pictures! Looks absolutely beautiful!
    by summeraly at 06/01/09 8:13AM

Still Alive

It's been quite awhile since I've done any of this blogging stuff. That's mostly because I've been real busy writing three different papers and preparing a presentation for a committee meeting. The committee meeting is in the past now, and lets just leave it at that. Two papers have been completed, one for the committee meeting and one that we'll be sending in for publication soon. We'll see how that goes. The third paper is my thesis, which is up to about 40 pages now. Still a long way to go, but my committee wants me to wait until the end of the year now to defend as opposed to this summer, so I've got a bit more time to work on it.

So, work has settled down a bit now that the committee meeting is in the past and life returns to a bit more normal pace. After a long day on Monday I did a short photo walk therapy session around my house. There was a big storm moving out and another on the way so the sky was really cool. I've also been taking a lot of macro pics of the spring flowers, mostly at/around my house. What kinds of things do you like to do after a long day?

  • angela
    Phototherapy! yay!
    by angela at 04/15/09 10:59AM

My First Author Paper - Finally!

I finally got my first First Author publication today.  Our paper on the evolution of the fosfomycin resistance enzymes using DNA Shuffling techniques was accepted today and has already been published online.  I'm pretty excited since this puts me one step closer to graduating, which makes my wife happy.  And all you married guys out there know, life is much better when the wife is happy.  Anyways, just wanted to share that with the two people that might actually read this.

The basic idea here was that we took two genes - one that codes for a good resistance enzyme and one that codes for a terrible resistance enzyme - chopped them up, mixed them together, and reassembled the fragments.  What came out were genes that encoded for much better resistance enzymes despite being 90% identical to the original terrible enzyme.  A 10% change in the DNA led to a substantial change in the ability of these enzymes to provide resistance to the antibiotic.  It's a pretty quick and simple way to try and model the nature of the evolution of this resistance.  And it just got published, so yay.
  • angela
    by angela at 02/05/09 10:17PM
  • jaclynbrown
    You rock. I love what a big geek you are.
    by jaclynbrown at 02/23/09 2:30PM
  • antiisaacholman
    by antiisaacholman at 02/24/09 9:58PM

There's Always More, I Guess

So, there's actually a Part IV of this conversation up now at my brother's blog Sans Approbation. He asks a few more questions and I'll actually get around to answering them soon. Check it out.

Science Rocks.