SDSU STRUCTURAL BIOLOGY PROGRAM


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10/30/08

Great meeting this week! We built upon last week's introduction to x-ray diffraction by discussing the correlation between the unique set of three integer numbers known as the "Miller index" that distinguishes each x-ray reflection spot and the structure of the macromolecule in the crystal unit cell. Besides acting like an "address" to help us keep track of the many reflections recorded during a diffraction experiment, the Miller index relates to a set of parallel planes that cut the unit cell an integer number of times along each of its three axes. As the number of cuts increases, the spacing between the planes decreases and this distance is the source of the "resolution" term as defined for crystallography. As the plane spacing decreases, the angle of the diffracted x-ray increases explaining why high resolution (low interplanar spacing) reflections are found on that outside of a diffraction image while low resolution (high interplanar spacing) spots occupy space near the center of the diffraction pattern. Check out the slides from this week's meeting and view a new homework assignment here.

Assignment
  • Go to: Kevin Cowtan’s excellent "Book of Fourier" site: http://www.ysbl.york.ac.uk/~cowtan/fourier/fourier.html
  • Start experimenting with Phases!

    To view an animated gif of diffraction data collected from an insulin crystal, click here!


    10/23/08

    This week we were introduced the most basic physics of crystallography by learning what is happening as x-rays are diffracted by a crystal. Dr. Huxford lead an enlightening discussion that introduced concepts like the continuous scattering of x-rays by an object, how interference of x-rays through three dimensional arrays gives rise to diffraction at discreet points in space, and how a convolution of these two principles creates a diffraction image. We were introduced to real versus reciprocal space and the Ewald sphere construction for explaining when conditions are appropriate for generating a specific reflection intensity. This week's presentation slides and homework assignment can be viewed here.

    Assignment
  • Go to: Kevin Cowtan’s excellent tutorial on structure factors: http://www.ysbl.york.ac.uk/~cowtan/sfapplet/sfintro.html
  • Click on “Miller Indices” and begin interactively working through the tutorial


    10/16/08

    Thanks to all of you who skipped a painfully boring last presidential debate to attend our latest SBP meeting! If you were unable to attend, you missed Dr. Huxford's presentation on macromolecular crystals and how to grow them. You also missed out on some nice door prizes (thanks James Caldwell for the door prizes!). Check out a copy of the presentation slides here. Next week's topic: Collecting x-ray diffraction data. See you there!

    Assignment
  • Go to: http://phillips-lab.biochem.wisc.edu/tools.html
  • Download the XRayView program and play with it


    10/09/08

    It was such a good meeting this week that we nearly ran out of Kudos bars! Dr. Huxford lead the discussion on the first challenge to a successful molecular structure determination by x-ray crystallography: deriving a source of material for study. That's right. In order to solve the structure of a biological macromolecule you are going to need a lot of it! We talked about how recombinant DNA technology and cell culture make possible the large scale expression of extremely rare or even artificially engineered proteins and how modern purification methods allow for their isolation and concentration. If you missed this meeting you can see a copy of the presentation slides here.

    Assignment
  • Find the web site of Hampton Research and spend 15 minutes browsing it. I bet you will learn something you didn’t know about next week’s topic: growing single crystals of macromolecules.


    10/02/08

    Thanks for another great SBP meeting! This week Dr. Huxford lead the group in a discussion of the seven "hurdles" that must be cleared on the way to a successful macromolecular structure determination by x-ray crystallography. The point of the talk was to impress upon researchers the practical nature of the x-ray experiment. We really do want to grow crystals of some biomolecule, blast them with x-rays, and accurately measure the diffracted rays. With few exceptions (the phase problem being a noteworthy one) the process is about as simple (or complicated, depending on your point of view) as it sounds. Download his presentation and a new homework assignment here.

    Assignment
  • Google "Novagen" and look up information on the pET vector system for recombinant protein expression in E. coli bacteria (TB055.pdf). Download yourself a copy. (You probably don't need to print it.) Learn some clever tricks for getting bacteria to express eukaryotic proteins.


    9/25/08

    Another good meeting on September 24! Thanks to all who attended. We discussed our experiences with downloading macromolecular models from the Protein Data Bank and viewing them on different software platforms. Dr. Huxford lead a discussion on why structural biology is such a valuable tool by sharing some case studies and encouraged students to get into the research literature with a new assignment. You can download his presentation slides here.

    Assignment
  • Go to the National center for Biotechnology Information website (http://www.ncbi.nlm.nih.gov)
  • Search the PubMed database for a paper by Dr. Patricia A. Jennings in the journal Proceedings of the National Academy of Sciences USA from 2007
  • Download the paper
  • Read it
  • Start asking yourself: how did they do it?

    You can now directly download Jenning's paper here.


    9/18/08

    Thanks to all who attended our inaugural meeting this past Wednesday! We had a good time eating pizza and thinking about the structural approach to experimental biology. Please join us next Wednesday at 7:00 p.m. in GMCS 305.

    If you missed the meeting this week or you would like a review then you can read Dr. Huxford's presentation and get this week's assignment here.

    Assignment
  • Go to the website of the Protein Data Bank (http://www.rcsb.org)
  • Look up the file for catalytic subunit of cAMP - dependent protein kinase (PKAc) -- code 1ATP
  • Download the coordinate (.pdb) file
  • Open it in a text viewer and read it (just kidding) look at its format
  • Extra credit, download a viewer (Rasmol, SwissPDBViewer, Pymol) and display the protein structure

    For those who attended, find help with your assignment right here.