1 / 16

Proteomics

Proteomics. Handout Another on the website - copier not cooperating. Today - overview Thursday - Debora - tools Next week - structural proteomics, protein:protein interactions, subcellular localization Reminder - Exam - March 4. Genome of the week - Enterococcus faecalis.

hoodl
Download Presentation

Proteomics

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. Proteomics • Handout • Another on the website - copier not cooperating. • Today - overview • Thursday - Debora - tools • Next week - structural proteomics, protein:protein interactions, subcellular localization • Reminder - Exam - March 4

  2. Genome of the week - Enterococcus faecalis • E. faecalis - urinary tract infections, bacteremia, endocarditis. • Organism sequenced is vancomycin resistant. • Vancomycin is often last available antibiotic - resistance to this drug often means no other antibiotics will work. • Major cause of nosocomial infections. • Possible transfer of vanomycin resistance genes to more serious pathogens is a major concern.

  3. Genome of the week - Enterococcus faecalis • Over 25% of the E. faecalis genome consists of foreign DNA. • Phages, insertions sequences, transposons. • Likely contributed to the acquistion of resistance to multiple antibiotics. • Over 35 PTS systems • Responsible for transporting sugars into the cell. • Most found in any sequenced genome, likely utilize undigested sugars in the intestine.

  4. Why study proteins? • They are the machines that make cells function. • RNA levels do not always accurately predict protein levels. • Often processes are regulated at the transcriptional level. • Some processes are controlled post-transcriptionally. • Most often proteins are the targets of drugs.

  5. Proteomics -large scale analysis of proteins • Protein levels - Determining the abundance of proteins in a sample. • 2D gel electrophoresis, mass spectrometry, protein microarrays • Interacting proteins - determining which proteins come together to form functional complexes. • Yeast 2-hybrid, affinity purification • Subcellular localization - site of localization can often provide clues to the function of a protein. • GFP tagging, immunofluorescence microscopy. • Protein activity - investigating the biochemical activities of proteins. • Structural genomics - high-throughput analysis of the protein structure

  6. From www.probes.com

  7. Proteins • Primary structure - sequence • Searching databases • Identifying functional domains • Secondary and tertiary structure - 3D folding of proteins. • Proteins have unique 3D structures • Identify functional domains • VAST - online structural tool from NCBI

  8. Western Blot • Determine the presence and level of a protein in a cell lysate. • http://web.mit.edu/esgbio/www/rdna/rdna.html - review of Northern, Western, and Southern blots.

  9. Monitoring protein levels - large scale • 2D gel electrophoresis • Old technology - not as useful for lowly expressed proteins. • Mass spectrometry • Many new techniques for protein detection and quantitation being developed. • Protein microarrays • Many developing technologies

  10. Protein microarrays • Analysis of thousands of proteins at one time. • Many different types • Antibody arrayed - detect many proteins • Proteins arrayed - detect interacting proteins • Proteins arrayed - detect interacting small molecules • Etc.

  11. Templin et al. 2002 Trend in Biotch. Vol 20

  12. Protein:protein interactions

  13. Protein activity arrays

  14. Small molecule arrays

  15. From the Macbeath laboratory website. See for more info the following website: http://cgr.harvard.edu/macbeath/research/protein_microarrays/protein_microarrays.html

  16. Why bother with DNA microarrays? • Protein microarrays are not as robust • DNA is DNA - all features will behave similarly under single hybridization conditions. • Proteins are unique - will behave differently. • Protein microarrays are costly • $500-1000 per antibody • $10 per oligo • Used for different purposes

More Related