Protein microarray

A protein microarray, sometimes referred to as a protein binding microarray, provides a multiplex approach to identify protein-protein interactions, to identify the substrates of protein kinases, or to identify the targets of biologically active small molecules. The array is a piece of glass on which different molecules of protein have been affixed at separate locations in an ordered manner thus forming a microscopic array. The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.

Related microarray technologies also include DNA microarrays, cellular microarrays, antibody microarrays, tissue microarrays and chemical compound microarrays.

Applications

Protein microarrays (also biochip, proteinchip) are measurement devices used in biomedical applications to determine the presence and/or amount (referred to as quantitation) of proteins in biological samples, e.g. blood. They have the potential to be an important tool for proteomics research. Usually a multitude of different capture agents, most frequently monoclonal antibodies, are deposited on a chip surface (glass or silicon) in a miniature array. This format is often also referred to as a microarray (a more general term for chip based biological measurement devices).

Types of chips

There are several types of protein chips, the most common being glass slide chips and nano-well arrays.

Production of protein arrays

The proteins can be externally synthesised, purified and attached to the array. Alternatively they can be synthesised in-situ and directly attached to the array.

The proteins can be synthesised through biosynthesis, cell-free DNA expression or chemical synthesis. In-situ synthesis is possible with the latter two. With cell-free DNA expression, proteins are attached to the support right after their production. Peptides chemically procured by solid phase peptide synthesis are already attached to the support. Selective deprotection is carried out through lithographic methods or by the so-called SPOT-synthesis.

Artifacts to avoid

• 1) To avoid variability in results, use a very efficient lysis buffer and maintain consistent sample processing conditions;
• 2) Many antibodies don't work well as capture reagents, even if they do work well in western blotting and other denaturing conditions. Some antibodies often bind poorly to intact proteins in a cell extract;
• 3) Different proteins like different solution conditions, so if you do not see binding it doesn't mean that there is no binding between the two partners in physiological conditions;
• 4) Adjust the solute conditions to avoid non-specific association: change salt concentration, pH, add 1% alignate;
• 5) on the array's surface the conjugated protein should be in the right conformation (i.e., folded, NOT denatured), anchored by the same amino acid (in the same orientation), and be kept away from the surface by a linker to avoid steric hindrance.

Types of capture molecules

Capture molecules used are most commonly antibodies; however, antigens are used in applications where antibodies are detected in serum. More recently there has been a push towards other types of capture molecules which are more similar in their nature such as peptides or aptamers. Antibodies have several problems including the fact that there are not antibodies for most proteins and also problems with specificity in some commercial antibody preparations. Nevertheless, antibodies still represent the most well-characterized and effective protein capture agent for microarrays. Recently, nucleic acids, receptors, enzymes, and proteins have been spotted onto chips and used as capture molecules. This allows a vast variety of experiments to be conducted on protein-protein interactions, and all other protein binding substrates.

Detection methods

Although protein microarrays may use similar detection methods as DNA Microarrays, a problem is that protein concentrations in a biological sample may be many orders of magnitude different from that for mRNAs. Therefore, protein chip detection methods must have a much larger range of detection.

The preferred method of detection currently is fluorescence detection. Fluorescent detection is safe, sensitive, and can have a high resolution. The fluorescent detection method is compatible with standard microarray scanners, however some minor alterations to software may need to be made. Other common detection methods include colorimetric, chemiluminescent and label free Surface Plasmon Resonance.

See also

• Antibody microarray
• Cellular microarray
• Chemical compound microarray
• DNA microarray
• Tissue microarray
• MicroArray and Gene Expression (MAGE)

References

• Gavin MacBeath and Stuart L. Schreiber (8 September 2000) "Printing Proteins as Microarrays for High-Throughput Function Determination". Science 289 (5485), 1760–1763
• Richard B. Jones, Andrew Gordus, Jordan A. Krall, and Gavin MacBeath (12 January 2006) "A quantitative protein interaction network for the ErbB receptors using protein microarrays". Nature 439, 168–174. This gives an example of the applied use of protein microarrays.
• Daniel S. Chen, Mark M. Davis MM (2006) Molecular and functional analysis using live cell microarrays. Curr Opin Chem Biol 10:28–34

External links

• High density functional protein arrays
• Custom peptides and proteins microarrays
• 'Self Assembly Nature's Way to Do It' Freeview Video of a Royal Institution Discourse by Kuniaki Nagayama, Toyko University supplied by the Vega Science Trust.
• Principles of Protein Microarrays; Mark Schena
• Antigen Microarrays for Serodiagnosis of Infectious Diseases
• Biomarker Discovery using Protein Arrays
• Feature article about protein microarrays from the December 1, 2007 issue of Analytical Chemistry
• Assays with Protein Arrays