Analysis of Protein-Ligand Binding on the Proteomic Scale

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DESCRIPTION (provided by applicant): Genome- and proteome-based gene expression profiling studies have been widely used over the past decade to characterize biological states and drug action. While such differential gene expression profiling studies can help identify the cellular pathways and physiological processes associated with a biological state or with the biological activity of a therapeutic agent, they often fail to produce a detailed molecular level understanding of the biological state or drug mode-of-action because gene expression levels are not directly tied to protein function. This has limited the number of useful protein biomarkers and therapeutic targets discovered from such studies, and left gaps in our understanding of drug-action. Proposed here is the use of thermodynamic measurements of protein stability to profile the protein-interaction networks associated with different biological states and drug action. Such thermodynamic measurements of protein stability are expected to be more closely related to protein function than are protein expression levels, and thus produce more useful protein biomarkers and therapeutic targets of disease and generate a better understanding of drug action. The proposed work will use a chemical modification- and mass spectrometry-based method, termed SPROX, to make thermodynamic measurements of protein stability on the proteomic scale in several different age-, disease-, and drug-related biological states. The specific aims of this work are: (1) to streamline and improve the data analysis pipeline in proteome-wide SPROX experiments; (2) to characterize the thermodynamic stability of proteins derived from four different cell culture models of breast cancer using the SPROX technique and determine which proteins have altered stabilities in the different cell culture models; (3) to characterize the thermodynamic stability of proteins derived from breast cancer cells grown in the presence and in the absence of tamoxifen using the SPROX technique and determine which proteins have altered stabilities in the presence of tamoxifen; (4) to characterize the thermodynamic stability of mouse proteins derived from a mouse model of aging using the SPROX technique and determine which proteins have altered stabilities as a function of age; and (5) to use the proteins identified in (2)-(4) to characterize the altered protein interaction networks associated with the different age-, disease-, and drug-related biological states in this study.