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PC1 lactamase

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The PDB is a resource which compiles essential information about many proteins. ... We'll be investigating -lactamase. Type PC1 into the search box. ... – PowerPoint PPT presentation

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Title: PC1 lactamase


1
PC1 ß-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 ß-lactamase
  • Well be investigating ß-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 residues 3
    letter abbreviation into its 1 letter
    abbreviation. Type this your 1 letter list into
    a Powerpoint slide and email it to me. Well
    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/hy
    dropathy/index.html)
  • Do both of these and be prepared to describe your
    segments 2 structure in terms of the result.

13
Hydropathicity
14
Hydropathicity
15
3 structure
  • Lets try to group the types of tertiary
    indicators found in your segments
  • a-helices
  • ß-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 ß-lactams are supposed to do
20
What about water in the ß-lactams senario?
  • It is this reaction which ß-lactamases catalyze!

21
So what now?
  • Youre the drug researcher trying to develop a
    effective ß-lactam
  • What considerations should you investigate
    regarding ß-lactamases?
  • What traits of the ß-lactams?
  • What traits of the ß-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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