Microarrays can be used to monitor gene expression

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Microarrays can be used to monitor gene expression
http//videocast.nih.gov/ram/proteomics030502.ram
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From Structural Genomics to Proteomics
Finding out what our proteins do
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Devising a computational modeling system
to look at protein active sites

• The inadequacies of structure-function
• relationships
• Where do water molecules stick?
• Crystal structures of protein complexes
• (in concert with structural genomic
  studies)
• Moonlighting proteins
• (in concert with functional genomic
  studies)

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The fickle nature of enzymes
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Using a proteome to understand physiology
www.expasy.ch
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Protein identification methods
Edman degradation
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Mass spectroscopy offers immense precision
and sensitivity
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and versatility
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Utility of Protein Chips

• High-throughput assays for
• Biochemical activities
• Protein interactions

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Human proteome turning to bio-panning
Produce a antibody reporter for each gene product
First step Clone each gene and express gene
product using Gateway technology Second step
Make high affinity anti-sera Third step Screen
protein chip Although steps one and two appear
cost prohibitive, it is actually step three that
has required the most time and research.
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Surface chemistry is the biggest obstacle

• Some solutions
• Microfabricated polyacrylamide gel pads
• Aldehyde-containing silane coating (amino
  reactive)
• Nickel-coated slides

• For the human proteome Currently use a 20-step
  reaction to
• provide a covalent capture surface which reduces
  non-specific
• binding and holds 70 fmole of peptide for four
  days

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Other high throughput ways of looking at proteins

• Protein chips
• Protein Quantitation measuring
  antibody-antigen
• genome-www.stanford.edu/proteinarrays/proteinarray
  s.pdf
• http//bioinfo.mbb.yale.edu/e-print/protchip-natge
  n/text.pdf
• Drug discovery - Microarrays of receptor targets
• or immobilized receptors
• http//www.clontech.com/whatsnew/announcements/AbA
  rray.shtml
• Two-hybrid system
• http//cmmg.biosci.wayne.edu/finlab/YTHnetworks.ht
  ml
• Phage and yeast display
• http//www.niddk.nih.gov/fund/other/genoproteo/w
  ang.pdf
• http//www.invitrogen.com80/Content/Tech-Online/m
  olecular_biology/manuals_pps/pyd1_man.pdf
• http//web.mit.edu/cheme/kdw-lab/presentations/Yea
  st_display_FAQs.pdf