Revealing Biological Mechanisms with Mathematical Modeling and Fluorescence Microscopy

Michael Rust
Harvard University

In order to understand the mechanisms that give rise to biological function, we must move beyond an inventory of the components involved towards a quantitative picture including both how those components interact dynamically and how they are spatially organized within a cell.  I will describe my efforts to obtain this kind of understanding in a model circadian clock system derived from photosynthetic cyanobacteria.    At the core of this clock are three interacting proteins that generate an autonomous ~24 hour rhythm in phosphorylation of one of the components.  Remarkably, this nonlinear oscillator can be reconstituted in a test tube using only purified proteins.  I will show how a simple mathematical model using kinetic parameters constrained by experimental measurements can quantitatively explain both the origin of stable oscillations and the ability of the oscillator to phase shift in response to a stimulus.  I will conclude by discussing fluorescence techniques I developed as a graduate student for tracking the motion of proteins and resolving their structure in cells at length scales below the diffraction limit of light.  A fusion of these optical methods with mathematical modeling and biochemistry will allow us to bring our understanding of this circadian clock and other biological systems out of the test tube and into the complex environment of a living cell.