Images courtesy of Meltec
First came genomics, then proteomics. Next up: functional proteomics, a strategy aimed at understanding the relationships between cellular proteins. One such state-of-the-art technology is MELK, a patented "topological proteomics" approach from Meltec in Magdeburg, Germany.
MELK, or multiepitope-ligand kartographie, combines cell biology and biomathematics to visualize three-dimensional protein networks of intact cells at the cellular and subcellular levels. By observing multiple proteins simultaneously (up to 50 at a time so far) in space, quantity, and time, the technology provides researchers with a bird's-eye view of any cell of interest.
"MELK is not meant to compete with genomics and proteomics tools, but rather add value to those already powerful technologies by addressing the organization of the proteome in cells or tissues," says Ronald Koop, head of biological research at Meltec. Ultimately, this type of contextual data can enhance the drug-discovery process by prioritizing and validating existing drug targets, as well as identifying new ones. Meltec has already used the MELK technology to uncover a protein associated with amyo-trophic lateral sclerosis, commonly known as ALS or Lou Gehrig disease.
Evotec, a European company specializing in the discovery and development of new drugs, is evaluating MELK as a toxicology screen for candidate small-molecule drugs. Timm Jessen, Evotec's chief scientific officer, says this strategy helps to vet candidate drugs based upon how much they disturb the normal protein networks of cells. "This way we don't waste money on developing drugs with significant toxic side effects," he says.
Nonetheless, the technology has limitations. MELK works only on fixed whole cells, precluding real-time imaging of live cells. Furthermore, researchers must know ahead of time the identities of the proteins that comprise the networks of interest. "When assessing toxicology, we have to try our best to choose the right proteins," says Jessen. "There's a bit of guesswork involved."
BLEACHING THE SIGNAL The basic principle behind MELK is similar to that of popular co-localization experiments: Antibodies specific for different proteins are tagged with fluorescent labels and then visualized within the cell under a light microscope. What makes MELK unique is its patented bleaching technology. Following what would be a typical co-localization experiment, the fluorescent signals are bleached out, and a brand new cycle targeted at a different protein begins anew. The process is repeated for each protein of interest, typically 30 at a time. Finally, all the signals are compiled into one panoramic shot of the cell, with a resolution of approximately 100 nm.
To make sense of all the data, Meltec developed a patented set of biomathematical tools. These statistically driven computer programs establish patterns of distribution for proteins within a cell, and compare these patterns from sample to sample. "If you compare a normal cell and a diseased cell, MELK will find subtle changes in the statistical distribution of protein networks," says Koop. "It's up to the biologist to decide which observed changes are worth pursuing further."
ONE CELL AT A TIME Unlike conventional genomics and proteomics techniques such as expression profiling, which average thousands of cells in a single experiment, MELK looks at one cell at a time. Koop explains how this added sensitivity might benefit a cancer researcher. "With genomics and proteomics tools, you can identify a potential cancer-causing protein from a collection of tumor cells. But not all tumor cells are alike. Some might be undergoing apoptosis, while others could be transmitting a major growth signal. Using MELK, it would be possible to correlate your novel protein with one of these subpopulations of tumor cells."
Another advantage to MELK lies in its added third dimension: space. Current proteomic strategies typically measure changes in the quantity of a protein over time; MELK looks at changes in both quantity and location over time. This allows researchers to catch changes in the distribution of a protein (indicating a change in function) that might otherwise go unnoticed. Like other functional proteomics tools, MELK is helping researchers to chart the vast sea of proteins. Says Koop, "We are putting proteins in perspective."