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lecture09 - LECTURE 9 14 Sept 2009(P J Hollenbeck BIOL 231...

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LECTURE 9. 14 Sept 2009 (P. J. Hollenbeck) BIOL 231 PROTEIN STRUCTURE & FUNCTION, STRUCTURAL BASIS OF PROTEIN-LIGAND BINDING Read: Chap 4: pp. 140-60; study panel 4-2 DVD: study 3 animations – 4.3; 4.9 (Lysozyme); 4.13 (MHC protein I) Problem assignment: 26-28; exam I ‘06, #2; exam I ‘07, #6, 7; ECB Q4-21; pdb web site <be sure to download the page of extra figures that accompany this lecture> I. 3-D Analysis of 3 E and 4 E structure (A) the Protein Data Bank http://www.pdb.org/pdb/home/home.do (1) Researchers who have determined the atomic structure of a protein now deposit their data at a central, publicly available site, the Protein Data Bank or PDB. The data is in the form of a file that contains the 3-D coordinates of all of the atoms except H (study animation 4.3 on your DVD). At present there is structural information in the PDB for almost 60,000 proteins from hundreds of species, with more added every day. (2) The PDB web site has viewing software, WebMol, that can be used to view and manipulate protein structure files. Although more powerful software packages are available for research use, this on-line resource is very instructive, and you should use it to repeat the exercises that we do in lecture on your own. For one of the homework problems assigned for today you will also use the features of the site. On the PDB home page there is a tutorial if you want a self-paced introduction to the features. (B) Features of two proteins (1) myoglobin (id# = 101m) *From the home page, search the database by name: “sperm whale myoglobin” and find the specific entry “101m” (it’s on the 13 page of results) and click the thumbnail image next to th it. (Hint: search the id# instead). This will display a results page with a cartoon structure on the right, and a toggle labeled “Biological Molecule” above it. Click the arrowhead to the left of “Biological Molecule” to reveal the label “Asymmetric Unit.” Now go to the menu below the cartoon structure, click on “Other Viewers,” select “WebMol Viewer ” and wait a moment while it loads the structure. In the WebMol window all atoms will be shown (except H) represented initially in a stick format. C is green; O = red; N = blue; S = yellow. *Zoom in and out by holding the right mouse button and dragging. Rotate myoglobin by holding the left button and dragging on the image. Pick out some R-groups near the protein surface and try to identify them; acidic, basic or large residues are easiest. If you put the cursor directly over a residue, at the top of the grey control strip at right, the single letter abbrev and residue number are displayed. * Use the top right pull-down menu to choose “ MainCh ,” which hides the R-groups and shows only the atoms of the backbone (the “main chain”). With a bit of deft mouse dragging, you can find one end of myoglobin (the N- or C-terminus) and follow the chain to the other -1-
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end. But you can make it easier than that using another feature of the viewer: click the Trace ” button from the right-hand set of menus. This will cause the protein to be built up residue by residue, from N-terminus to C-terminus, before your eyes.
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