lec9 note - -1-LECTURE 9. 13 Sept 2010 (P. J....

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Unformatted text preview: -1-LECTURE 9. 13 Sept 2010 (P. J. Hollenbeck)BIOL 231PROTEIN STRUCTURE & FUNCTION, STRUCTURAL BASIS OF PROTEIN-LIGAND BINDINGRead: Chap 4: pp. 140-60; study panel 4-2DVD: study 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 3Eand 4Estructure(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 deposittheir data at a central, publicly available site, the Protein Data Bank or PDB. The datais 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 thePDB for over 65,000 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 andmanipulate protein structure files. Although more powerful software packages areavailable for research use, this on-line resource is very instructive, and you should useit to repeat the exercises that we do in lecture on your own. For one of the homeworkproblems assigned for today you will also use the features of the site. On the PDBhome 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 thespecific entry “101m” (it’s on the 14 page of results) and click the thumbnail image next tothit. (Hint: search the id# instead). This will display a results page with a cartoon structure onthe right, and a toggle labeled “Biological Molecule” above it. Click the arrowhead to the leftof “Biological Molecule” to reveal the label “Asymmetric Unit.” Now go to the menu belowthe cartoon structure, click on “Other Viewers,” select “WebMol Viewer” and wait a momentwhile 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 byholding the left button and dragging on the image. Pick out some R-groups near the proteinsurface and try to identify them – acidic, basic or large residues are easiest. If you put thecursor directly over a residue, at the top of the grey control strip at right, the single letterabbrev and residue number are displayed. * Use the top right pull-down menu to choose “MainCh,” which hides the R-groups andshows 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-2-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. ” button from the right-hand set of menus....
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This note was uploaded on 09/18/2011 for the course BIOLOGY 231 taught by Professor Petethollenbeck during the Fall '10 term at Purdue University.

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lec9 note - -1-LECTURE 9. 13 Sept 2010 (P. J....

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