1 / 22

PC1 β -lactamase

PC1 β -lactamase. Protein Data Bank. The PDB is a resource which compiles essential information about many proteins. Go to the PDB website at www.pdb.org. PC1 – β - lactamase. We’ll be investigating β -lactamase. Type PC1 into the search box. More than one result is produced…

morrillr
Download Presentation

PC1 β -lactamase

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. PC1 β-lactamase

  2. Protein Data Bank • The PDB is a resource which compiles essential information about many proteins. • Go to the PDB website at www.pdb.org.

  3. PC1 – β-lactamase • We’ll be investigating β-lactamase. Type PC1 into the search box. • More than one result is produced… • How should we choose the one we want to look at? • What does the information given about each mean? • How do you know? • Which one do you think we should choose?

  4. 3blm • Click on 3blm • Underneath the image of the structure, click on ProteinWorkshop. • Ribbon vs. Atom view • Color changes • Label changes

  5. Our preferred view • Ribbons • Colored by compound • No water molecules visible (for now)

  6. 1°, 2° Structure • Divide into pairs. Each group will investigate the following portions of the enzyme. • Residues 31-100 • Residues 101-170 • Residues 171-240 • Residues 241-290 • First make your residues visible as atoms and molecules (visibility tool) As you go, use your amino acid reference translate each residue’s 3 letter abbreviation into it’s 1 letter abbreviation. Type this your 1 letter list into a Powerpoint slide and email it to me. We’ll combine this information in the next slide. • Use the labeling tool to label your segment by residue. • Prepare to show and tell and to describe the geometry of your segment

  7. 1° structure • Residues 31-100 • Residues 101-170 • Residues 171-240 • Residues 241-290

  8. 2° structure

  9. 2° structure

  10. 2° structure

  11. 2° structure

  12. Hydropathicity • Describes the hydrophillicness / hydrophobicness of a protein. • Two ways: • Change coloring in Protein Workshop • Input your sequence into a Kyte-Doolittle converter (http://www.vivo.colostate.edu/molkit/hydropathy/index.html) • Do both of these and be prepared to describe your segment’s 2° structure in terms of the result.

  13. Hydropathicity

  14. Hydropathicity

  15. 3° structure • Let’s try to group the types of tertiary indicators found in your segments • α-helices • β-sheets • Turns • Folds –

  16. 3° structure

  17. 4° structure • With your partner, go back to the pdb mainpage for 3blm and try to determine the 4° structure. • Look to see if there are any ligands. Think about what a ligand would be and would mean in this context. • Prepare to justify your conclusions to your classmates.

  18. 4° structure

  19. Remember what β-lactams are supposed to do…

  20. What about water in the β-lactams senario? It is this reaction which β-lactamases catalyze!

  21. So what now? • You’re the drug researcher trying to develop a effective β-lactam… • What considerations should you investigate regarding β-lactamases? • What traits of the β-lactams? • What traits of the β-lactamases? • Which are more easily studied?

  22. References • Buckwell, S. C.; Page, M. I.; Longridge, J. L., Hydrolysis of 6-alkyl penicillins catalyzed by b-lactamase I from Bacillus cereus and by hydroxide ion. Journal of the Chemical Society, Perkin Transactions 2: Physical Organic Chemistry (1972-1999) 1988, (10), 1809-13. • Herzberg, O., Refined crystal structure of beta- lactamase from Staphylococcus aureus PC1 at 2.0 A resolution. J Mol Biol 1991, 217, (4), 701-19. 3. www.pdb.org 4. Protein Workshop Viewer accessed via www.pdb.org

More Related