Integrative Modeling of Cell Adhesion Processes.

Within a multicellular organism, countless individual cells dynamically organize and rearrange themselves according to a host of extra-cellular signals. To witness the workings of such a complex autonomous machine is amazing; to try to fix it when something goes wrong is baffling. In an attempt to understand how cells regulate the adhesion and migration processes that give rise to such sophisticated spatial organization mechanisms, this dissertation integrates information at multiple length and time scales to investigate the functionality of cell adhesion systems. The resulting body of work is interesting not only for its implications for understanding cell adhesion and migration, but for the approach taken. To understand how cells regulate their adhesion patterns, this work necessarily gathers and incorporates information from the scale of individual proteins to physiological responses to trauma. To gain understanding of how integrins are organized in space, interactions of transmembrane adhesion receptors (integrins) with its extra-cellular ligand are studied via fluorescence microscopy and image analysis. The resulting quantitative description of integrin distribution in space, or integrin clustering, is used to postulate probability models for integrin cluster properties such as size and shape. These probability models, and their application to understanding how cells respond to different concentrations of extra-cellular ligand, provide valuable insight into cellular regulation of integrin clustering. A model for how integrins cluster is postulated and analyzed by computational simulation. The results of the model simulation are used to suggest that integrin clustering may be facilitated by a positive feedback loop that operates between integrin binding and integrin functional regulation. Additionally, this feedback loop is capable of amplifying a relatively small pulse in the activation state of a certain protein into an integrin cluster. These model predictions indicate that the proposed integrin clustering mechanism creates a means by which cells can control integrin clustering through spatial regulation of protein activation states. In order to investigate integrin clustering behavior on a larger scale, a coarse-grained model for integrin clustering was developed and scaled up to represent integrin clustering within a protrusive region of a spreading or migrating cell. This model was used to investigate the means by which integrin properties or extra-cellular ligand properties may regulate integrin clustering. These results are then used to postulate how cell adhesion and migration may be controlled by manipulating the mechanisms that guide integrin clustering. On the scale of an entire cell, the organization of integrins provides distributed control volumes inside of which numerous spatially-regulated intracellular reactions occur. To investigate the influence of integrin spatial organization on these intracellular reactions, a spatial model of an entire cell was created, wherein an intracellular protein, focal adhesion kinase (FAK), is modeled with respect to its recruitment by and activation in integrin clusters. Using reaction rate constants estimated based on experimental data, the model is used to understand how FAK sequestration into integrin clusters affects its dynamic activation and spatial distribution. To understand how cell adhesion processes affect events on the physiological level, a control-system approach was taken to understanding how platelets and proteins in the bloodstream work together to halt blood loss following blood vessel injury, a process termed hemostasis. An organizational framework based on...