Amidst talk of biomarker signatures and proteomics, it’s easy to forget that all proteins share the same chemical skeleton. What you learned in Biochemistry 101 still holds true: all proteins consist of amino acid strands (that’s where the similarities end). As it turns out, it’s the differences, and their consequences, that matter. But researchers facing the daunting task of studying millions of proteins need not fret. Multiplexing technologies, such as protein microarrays, can help. With a wide range of options, companies are offering the wherewithal to advance our understanding of how living systems operate.
The significance of proteins was recognized as early as 1838, when Swede chemist Jöns Jakob Berzelius instituted the name for a group of organic substances that all shared empirical formulas. Derived from the Greek word “prota,” meaning “of primary importance,” proteins hold center stage in solving the puzzle of molecular and cell physiology. Chemical sequencing, assays, blots, and chromatography made up most of the protein research during the 20th century. With the rise of DNA microarrays at the close of that era, the development of protein microarrays gained traction. Today, they are becoming part of the standard protocol in the research lab, while edging their way into clinical diagnostics.
The need for speed is certainly playing a big part in the popularity of protein microarrays. Perhaps equally important is the current view that proteins don’t act alone; they are part of an intricate system of interactions. Thus, “multiplexed measurement is logical for biological discovery with proteins because they constitutively function within networks, pathways, complexes, and families,” according to a review published in the April 2006 issue of Nature Reviews Drug Discovery1. “The activity of an individual protein is dependent not only on its abundance, but also on the effects of interacting, modifying, antagonistic and synergistic proteins.” For example, the amount of just one cytokine can’t tell you nearly as much about a physiological process as the “integration of results from multiplexed measurement of component cytokines in a network,” according to the paper.
Protein microarrays come in many flavors. Among the most popular are those that involve antibodies. You can purchase arrays that feature antibodies spotted on to various solid substrates, such as glass slides, gels, nylon membranes, microplates, and beads. Incubated with tagged proteins, the bound antibodies will give off a detectable signal. Since specific antibodies occupy a particular known position on the array, you can determine the type of proteins that are found in your sample. Or, you can add un-tagged proteins, and then perform a sandwich immunoassay procedure to detect the bound antibodies. Alternatively, the antigens are arrayed and incubated with antibodies or other ligands, such as small molecules.
Several companies are trying to improve sensitivity for the many proteins that play significant roles but are expressed in minute amounts. Some companies have designed protocols to include signal amplification, such as strepavidin for biotin-tagged proteins. You may also want to look into the surface coating of the array. Fluorescent tags can sometimes get trapped in matrices, like three-dimensional surfaces, producing background noise that can obscure small signals. Or, you could try using newer probes, such as gold particles, quantum dots, nanoparticles, or probes detected via chemiluminescence or colorimetry.
The products below are great examples of what you’ll find on the market. Take a look and write the next chapter in protein knowledge.
1 SF Kingsmore, “Multiplexed protein measurement: technologies and applications of protein and antibody arrays,” Nature Reviews Drug Discovery 5:310-321, April 2006
