Proteomics/Protein Chips/Applications

Applications:

Applications
Protein chips are a powerful resource which offers high-throughput methodology approaching that of DNA microarrays thus narrowing the gap between genomics and proteomics.

Protein chip experiments, like the field of proteomics itself, can be divided into two types of questions.
 * 1) Qualitative - What is it? What does it do?  Does it interact with anything?
 * 2) Quantitative - How much is there?

Protein chip applications are numerous and span the entire field. They include:
 * Probing a tissue extract for disease markers
 * Investigating protein-protein, protein-nucleic acid, and protein-drug interactions
 * Determining the amount of a protein in a particular sample
 * Identifying antibodies in a particular sample

Some specific examples of protein chip applications are:
 * Looking for hepatitis B antibodies in a human blood sample
 * Identifying biomarkers for ovarian cancer
 * Diagnosing SARS

Example Application
Zhu, H. et al. (2001) utilized protein chips in an effort to study the yeast proteome.1 Protein chips offer a high throughput method of analyzing such data. However, hurtles had to be cleared in order to over express the proteins from the proteome.

Zhu, H. et al. utilized high copy expression vectors and recombinant technology to clone 5800 ORFs from the yeast genome, which translates into approximately 80% of the yeast proteome. The expressed proteins were printed to the protein chips using a microarrayer and two varieties of protein chip surfaces: aldehyde-treated and nickel coated. Although both treatments were successful, the nickel coated chip was superior to the aldehyde-treated chip.

The group then checked the reproducibility of their protein spotting attempts. They found that more than 93% of the proteins were surely attached to the chip, and, in repeating the experiment, found that more than 95% of the proteins were correctly reproduced.

The main goal, or application if you will, of this experiment was to determine protein function. In order to do this, the proteins on the chips were tested for protein-protein and protein-lipid interactions.

The group provides a good example of how the results were interpreted. They probed the proteins on the chip for calmodulin binding functionality and observed both known and novel calmodulin binding proteins. Calmodulin is a calcium binding proteins that is highly conserved and is involved in many cellular processes. Through the analysis of the sequences of these proteins, Zhu, H. et al. were able to develop consensus sequences that identify motifs that should be associated with calmodulin binding.

Limitations of the study include confounding through indirect protein interactions and the possible absence of some post-translational modifications.

The effects of this study were to elucidate the potential of protein chips for observing protein - protein, protein - lipid, and protein - drug interactions within an eukaryotic cell's proteome. The paper for this study can be found here and a website containing supplemental materials can be found here.

Resources
1.Zhu, H. et al. "Global Analysis of Protein Activities Using Proteome Chips." Science 293.5537 (2001): 2101-2105. | View the paper.