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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…

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PC1 β -lactamase

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  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

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