2010 Annual Report 1a.Objectives (from AD-416) The ultimate goal of this project is to identify proteins of interest in certain diseases chosen for study by Prosetta and ARS, and any locations of protein-protein and protein-ligand binding relevant to the mechanisms of those diseases, for use inter alia in understanding a mechanism of action (MOA) between the protein and a particular ligand to develop new diagnostics, therapeutics, and prophylactics. 1b.Approach (from AD-416) Prosetta will provide ARS with putative protein targets that Prosetta will purify using a variety of affinity techniques; the proteins may include various modifications and cross-links. Final purification will be done by SDS-PAGE gels that will be stained with coomassie blue. The proteins of interest will be cut from the gels are then processed to yield a set of peptides, which be analyzed by mass spectrometry to identify the sequences and structural features of the proteins. Further analysis will be performed to reveal the location of any modifications or crosslinks. Documents Trust with Prosetta Bioconformatics, Inc. Log 38879. 3.Progress Report This report documents research conducted under a Trust Agreement between ARS and PROSETTA BIOCONFORMATICS, INC. Additional details for the research can be found in the report for the parent project 5325-32000-008-00D, DETECTION OF TRANSMISSIBLE SPONGIFORM ENCEPHALOPATHY AGENTS IN LIVESTOCK, WILDLIFE, AGRICULTURAL PRODUCTS, AND THE ENVIRONMENT. In the first year of the collaboration we identified several new proteins not previously known to interact inside living cells. This information helps us understand normal and abnormal processes in which proteins are involved in disease states such as scrapie. Prosetta has chosen to extend the Agreement through December 2010 and provide funding for another year of work.