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Microbial Cell Research Thrusts (continued) 3. Modeling Interactions Goal: Use high-end computing to model gene-gene, gene-protein, and protein-protein interactions as well as the internal biochemistry of the cell.  Challenges: A microbial cell is not simply a "bag of dilute salt water" within which gene products freely diffuse. There is much internal organization due to structural cytoskeletal components, partitioning of gene products in different parts of the cell so that they can efficiently participate in their appropriate pathways, concentration gradients across the volume of the cell, and physical effects caused by the cell membrane and intracellular constituents (in fact, the cell interior is thought to resemble Jello). Very little is known of this internal "milieu" of any microbial cell. Much greater understanding is required so that the results from biochemical, structural, and expression studies can be properly integrated with knowledge of the physical character of the cell's internal environment. All of DOE's capabilities will be needed: imaging the internal components will be a major task pushing the limits of current imaging technologies and new microscopic techniques. Mass spectrometry techniques also will be used to image and identify protein-protein interactions and characterize structures using internal linking compounds. The computational demands will be enormous because the aim is nothing less than to model not only the physical distribution (over time and under different circumstances) of all the gene products but to incorporate into this model the spectrum of gene regulatory, gene-protein, and protein-protein interactions.  published 06/05/00

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