Founded in the spring of 1999, the Harvard Institute of Proteomics (HIP) at Harvard Medical School aims to provide tools to determine the function of every protein encoded by the human genome and appropriate model and disease organisms. To this end, HIP scientists are building collections of genes from humans and organisms including Saccharomyces cerevisiae, Vibrio cholerae, Yersinia pestis, Pseudomonas aeruginosa and Bacillus anthracis, as well as some mouse and viral genes. In addition, a number of projects are focused on specific groups of medically relevant genes.

The Breast Cancer 1000 Project has developed a repository of clones for 1,000 genes that contribute to the onset of breast cancer, a subset of which have already been tested in functional assays to identify cDNAs that induce cancer-like phenotypes. Another project aims to clone the entire range of human kinases. The expression clones generated at HIP, along with the technology to use them, will be made available to all researchers.

Joshua LaBaer (pictured), co-founder and director of the institute, says his group has developed methods for the high-throughput purification of proteins expressed in Escherichia coli and downstream processes to determine their functions or properties. “In one project, we are purifying all the proteins produced by the organism Francisella tularensis, the parasite that causes tularaemia,” says LaBaer. The organism's proteome consists of about 1,600 proteins, all of which have been expressed in E. coli and purified. The purified proteins are then used in high-throughput functional screens “to find proteins that produce an immune response”. A similar study focuses on the genome of the bacterium V. cholerae, which can cause cholera in humans. Such studies are not only yielding important drug targets but laying the groundwork for studies targeting the much more complex human proteome.

LaBaer says that two bottlenecks affecting the purification of proteins from Y. pestis, the plague bacterium, are the “the ability to express large or hydrophobic proteins in bacteria, and avoiding the inclusion-body problem.” Partly for this reason the institute is now moving towards the development of protein arrays, with proteins being synthesized on the array rather than spotted on them. In their protocol, plasmid DNA is spotted on the array and genes are then transcribed and translated in a cell-free system. The resulting proteins, hundreds of them per chip, are immobilized in situ and can be used to test for protein–protein interactions and other functional assays. Although the technology is not yet ready for primetime, LaBaer says they are having success with it. The development of these types of arrays may alleviate the need to produce and purify proteins from E. coli, as scientists will be able to conduct functional studies directly on the arrays.

L.B.