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Dissertation
Minimalist models for the pre-unfolding oscillations and photo-switching properties of single GFP-like molecules
Doctor of Philosophy (Ph.D.), Drexel University
Jun 2012
DOI:
https://doi.org/10.17918/etd-3846
Abstract
Green fluorescent proteins (GFP) and GFP-like proteins have become one of the most important tools for imaging of biological processes in live cells. They exhibit photo-switching properties, which include photo-activation/deactivation and color switching. Single GFP-mut2 molecule immobilized in silica gels exhibits interesting oscillatory behaviors, right before it unfolds in the presence of denaturants. These oscillations are attributed to the switching between a neutral and an anionic chemical state of the chromophore. The associated off-time distribution of green fluorescence also changes from an exponential curve of the native state to a near-Gaussian distribution caused by the unfolding process. To understand the nature of this oscillatory behavior as well as other photo-switching properties of GFP-like molecules, we have carried out a theoretical study of these proteins using stochastic dynamics. Two stochastic methods are employed: one is analytical and the other is numerical, solving a set of rate equations based on the Gillespie algorithm. Aiming at constructing a minimalist model for the oscillatory behaviors we have examined a three-state, a four-state, as well as a six-state model for such processes. Within physically reasonable ranges of the transition rates, a three-state model cannot explain observed effects of GFP-mut2 and a four-state model is sufficient in generating off-time distributions peaking near the observed values. However, for the same set of rates, the intensities of the fluorescent emissions do not agree with the observed values. The six-state model does give results in reasonable agreement with the experiment data for GFP-mut2. A sensitivity analysis is also carried out to determine the effects of transition rates on the fluorescent intensities. The methods can also be applied to other photo-switching GFP-like fluorescent proteins, which we demonstrate with the example of Dronpa.
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Details
- Title
- Minimalist models for the pre-unfolding oscillations and photo-switching properties of single GFP-like molecules
- Creators
- Hanbing Lin - DU
- Contributors
- Jian-Min Yuan (Advisor) - Drexel University (1970-)
- Awarding Institution
- Drexel University
- Degree Awarded
- Doctor of Philosophy (Ph.D.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Resource Type
- Dissertation
- Language
- English
- Academic Unit
- College of Arts and Sciences; Physics; Drexel University
- Other Identifier
- 3846; 991014632410804721