Seattle 12-02 Event

Program: 5:00 to 5:30 Coffee and Conversation 5:30 “Analysis of Macromolecular Complexes by Quantitative Proteomics” Jeffrey Ranish, Institute for Systems Biology 6:00 “Emerging Technologies for the Study of Protein-Protein Interactions” Karin Hughes, Prolinx Incorporated click here to view biographies
Presentation	Abstract
“Analysis of Macromolecular Complexes by Quantitative Proteomics” Jeffrey Ranish, Institute for Systems Biology, jranish@systemsbiology.org	A generic strategy is described for determining the specific composition of macromolecular complexes. It is based on the use of Isotope Coded Affinity Tag (ICAT) reagents and mass spectrometry to compare the relative abundances of tryptic peptides derived from suitable pairs of purified or partially purified protein complexes. In one application, the genuine protein components of a large RNA Polymerase II (Pol II) preinitiation complex (PIC) were distinguished from a background of copurifying proteins by comparing the relative abundances of peptides derived from a control sample and the specific complex that was purified from nuclear extracts by a single-step promoter DNA affinity procedure. In a second application, a potential new component of the transcription machinery is immunopurified and peptides derived from the immunopurified sample and a control sample are used to identify specific copurifying proteins. The results are used to confirm the specific association of the new factor with components of the transcription machinery. The use of quantitative mass spectrometry to guide identification of specific complex components in partially purified samples provides the researcher with powerful new tools for the comprehensive analysis of macromolecular complexes. The technology can also be used to detect quantitative changes in the abundance and composition of protein complexes.
“Emerging Technologies for the Study of Protein-Protein Interactions” Karin Hughes, Prolinx Incorporated, Karin.Hughes@prolinx.com	Studying a "proteome"-or the full complement of proteins in a cell, tissue, organ, system or organism-requires the study of protein-protein interactions. Existing methods for the characterization of proteins and their interactions include 2-D gel electrophoresis, mass spectrometry, and x-ray crystallography. Emerging technologies that hold significant promise for protein interaction analysis are protein microarrays and surface plasmon resonance (SPR). These complementary technologies significantly expand the protein analysis repertoire. This talk will describe the use of these technologies for studying protein-protein interactions.