Manipulating the Proteome

Harvard University (Medical School), Boston MA

Investigators

Abstract

The completion of the genome projects provides the compelling opportunity to exploit the new information to elucidate the function of all proteins. This is a daunting task given the large number of predicted protein species. Compared with the study of gene expression and gene sequence, the high-throughput (HT) study of proteins is still in its infancy-the full-length coding sequences of most genes are just now becoming available, proteins exhibit a more complex chemistry than nucleic acids, and few HT protein methods exist. There does exist a large armamentarium of powerful tools of the study of proteins on an individual basis Tools exist to measure the sub-cellular location of a protein, the partners with which it interactions, the modification that affect its function, and its biochemical activity, to name a few. An important next step will be to adapt these methods to the HT setting. The execution of all of these methods begins with the same common steps: capture of the coding region, transfer to an expression vector, expression and possibly purification of the protein, and finally functional analysis. A number of bottlenecks currently prevent HT functional analysis of proteins. These include the need of large collections of "expression-ready" coding regions, the need for HT methods for expressing proteins in eukaryotic cells, and the need for HT methods for protein production and purification. Our Center wishes to address these needs and revolutionize HT protein study by exploiting the availability of new gene collections, new cloning strategy, and new bioinformatics and automation technologies. Central to our approach is the availability of FLEX repository, which currently has over 8000 full-length cloned coding regions in a format that allows the simultaneous transfer of thousands of genes into any expression vector overnight. This will allow us to take large subsets of genes and readily move them into a wide variety of expression vectors to develop new HT assay platforms for proteins. Our Center will focus on the next steps of high throughput analysis. Our goal will be to prepare the methodology and approaches that will allow workers to utilize the proteome for biological for biological studies. Our Center comprises five organization units which address: 1) Retroviral gene introduction and cell-based assay platforms, 2) Cell-free protein expression systems, 3) Eukaryotic expression systems, 4) High-throughput protein purification, and 5) Cell-free assay platforms. We are also supported by an Engineering Core and a Bioinformatics Core, which work directly with each of the Units. The focus of this Center is to develop a toolkit of technologies that will enable the genome-scale study of protein function.