Searching for Structure Files: The crystal structure of HMG-CoA reductase complexed with a statin molecule has been solved. This is the structure you read about in the reading assignment due for this lab. To obtain the crystal structure data file (pdb file), follow these steps:
1. Do a Google search for “pdb” or go directly to the RCSB site
http://www.rcsb.org/pdb/. This data bank contains al of the macromolecule 3-D structure files (pdb files). Pdb files are named in 4 characters (numbers and letters).
• Search for the 1HW9 pdb file. The summary information page for
1HW9 contains a title for the entry, the compound crystal ized, and the species of the source of the protein.
• Click on “Download Files” at the left of the screen. • On this page, choose to download the “PDB text” file. The
“1HW9.pdb” file should now be on your desktop.
Viewing the structure file: Note: This is written for Mac users and needs to be tested and modified for PC users.
1. Do a Google search for “starbiochem” or go directly to:
2. Click the large “Start” icon at the StarBiochem homepage.
3. “StarBiochem.jnlp” icon should appear on your desktop or your download
folder, depending on the browser preferences are set.
4. At the StarBiochem homepage, select “Sample Problem Sets” at the left of
the page. Then select “StarBiochem User Guide” to download the 5 page User Guide.
5. Double-click on “StarBiochem.jnlp” (on your desktop or in your download
6. When the program opens, go to the pul down menu under “File” and select
“Open/Import.” Find the 1HW9.pdb file on your desktop and open this file.
7. When the file opens, al the covalent bonds in the structure are showing.
Use your mouse to rotate, move, and zoom the molecule in the window. Specific directions for different mouse types are in the User Guide, p. 2.
8. The crystal structure is a homotetramer, meaning it contains 4 identical
polypeptide chains labelled A – D. The 1HW9 crystal structure was solved with simvastatin (SIM) and ADP bound in the active sites. The protein is drawn with blue bonds and the bound simvastatin and ADP are drawn with yel ow bonds.
9. Each of the menu bars on the right can be expanded by clicking on the
arrow at the right of the bar. The menu bars are described in the User Guide p. 3-5. First, expand the Structure bar, select the Secondary tab, and check the All Ribbons box to veiw the secondary structure of the protein.
10. Next select the Quaternary tab from the Structure bar. Put a checkmark
in the Chains box to give a different color for al the separate polypeptide chains. Rotate the molecule to see how the four polypeptide chains are bound together to form the homotetramer.
11. Go to the View Controls bar. Check the Draw box under Atoms. The
box for Draw Bonds should also be checked. Move the transparency slide bar to zero for Unselected. This should cause the protein to disappear.
12. Next return to the Structure bar and select the Primary tab. Al the amino
acid residues in the structure are listed here in their three-letter code. Click on Asp 690 to select this amino acid side chain. It should appear in the protein-viewing window. The atoms are colored based on atom type:
Carbon – gray Oxygen – red Nitrogen – blue Phosphorous and Sulfur – yel ow
Note: hydrogens and hydrogen bonds are not shown in this program and are often not shown in crystal structures because they are not very electron-rich. The data used to solve crystal structures are based on electron density in the protein crystal scattering X-rays.
13. Next select the PDB Tree bar. Double-click on the 1HW9 folder then
control-open apple click on SIM_3. (If you just click on the SIM_3 without holding down the control and open apple key, the Asp 690 wil disappear and you wil need to go back and reselect it with a control-open apple click.) If you notice the program working very slowly, quit it and restart it. Load 1HW9 again then start at step 11.
The molecule window should now show the Asp 690 side chain and simvastatin. Rotate these so you can see the two closes oxygen atoms between Asp 690 and Sim_3. It is thought that a hydrogen is shared between these oxygens in a hydrogen bond. This hydrogen bond is important for binding the drug in the enzyme active site, blocking enzyme activity. The glycine side chain (in the mutant enzyme) doesn’t have this bonding ability, so simvistatin is held less tightly in the enzyme and may not even bind at all. For this reason, patients with a Gly 690 do not respond well to simvastatin therapy for lowering their cholesterol levels.
14. This is the end of the tutorial, but you can go back and play with the
transparency bars under View Controls to see the ful protein again. By moving the Unselected bar to 20% instead of zero, you can view a faint structure of the protein in the background. Also, by deselecting the Draw box under Bonds, you are able to view just the secondary structure of the protein.
15. To save a picture file (as a .tiff file) from this program, it is possible to use
the Grab program for Macs or to do a screen capture for PC’s. The Grab program is essential y a screen capture program for Macs. Once Grab is open, select Capture, then Selection to draw a box around part of the screen you would like to capture. Then name and save the file.
Effect of Dietary Thiamin Supplementation on Milk Production by Dairy Cows R. D. Shaver and M. A. Bal ABSTRACT fiber carbohydrate, PEM = polioencephalomalacia, TH = thiamin supplemented diet, TLC = theoretical length We conducted three experiments to determine theeffects of dietary thiamin supplementation on milk pro-duction by dairy cows. In trial 1, 28 Holstein cows were INTRO
Antibiotic susceptibility of extended-spectrum ß-lactamase-producing Enterobacteriaceae Antibiotic Reference Laboratory, Communicable Disease Group, Institute of Environmental Science and Research (ESR), PO Box 50-348, Porirua. Email: ARL@esr.cri.nz Introduction • Extended-spectrum ß-lactamases (ESBLs) confer resistance to all• The plasmids may also carry other resistance genes.