Stochastic Modeling of Protein Interactions in the ER

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DESCRIPTION (provided by applicant): The majority of cellular functions are mediated by protein-protein interactions. Control of these interactions Is achieved directly from specificity of protein activity and indirectly though selective interactions with partner co-factors. Traditionally quantitative data on transient interactions comes from an in vitro assay where the interactions of partner proteins are isolated from other cellular factors. When extrapolating these numbers to in vivo conditions it is usually assumed that the protein milieu is homogenous. Yet it is clear that the dynamic nature of these interactions creates suborganellar pools of proteins. The dynamic effect of complex heterogeneous environments on cellular function has not been adequately quantitated, where local concentrations of protein partners will be different from their overall concentration in the cell. This research proposal focuses on the effects of these localized environments on the action of the cellis protein folding organelle, the endoplasmic reticulum (ER). Utilizing a combination of emerging quantitative fluorescent microscopy techniques, mathematical modeling and yeast genetics, the proposed research will quantitatively determine the role of the protein-protein interactions of BiP, the resident ER hsp70 chaperone, on its localization and function. Improperly folded proteins and the failure of proteins to traverse the early step of secretion is linked to diabetes, cystic fibrosis, and several neurological diseases. This proposal integrates biological scientists with engineers to develop a fundamental understanding of cellular networks and create a methodology to explain deficiencies in secretion. In addition, this research will provide insight to specific cellular functions important for the secretory process that have been difficult to address by traditional biochemical methods.