Toward the rational design of fluorescent proteins : elucidating the photodynamics of the GFP chromophore in various environments
Abstract/Contents
- Abstract
- The green fluorescent protein (GFP) has revolutionized the fields of chemistry and biology. Due to their ability to highlight protein dynamics in living organisms, GFP and GFP-like proteins have emerged as ubiquitous tools in biological imaging. The versatility of GFP has inspired a rainbow-like palette of fluorescent reporters; however, the creation of novel GFP variants is often imprecise and inefficient. Using molecular dynamics simulations, I unravel the intricate steric and electronic factors responsible for the performance of these fluorescent proteins. Across many systems (i.e., gas phase, water, and GFP/Dronpa2 scaffolds), I study the photodynamics of the GFP chromophore. Changes to the chromophore's intrinsic properties (e.g. fluorescence propensity, photoisomerization quantum yield, etc.) are monitored as the molecule occupies various condensed phase systems. Applying this knowledge, I have developed a computational workflow that can (1) generate structures for tens of thousands of GFP mutants and (2) characterize these mutants using steric and electronic features. This structural data is coupled with machine learning models to identify important interactions within the system and inspire the creation of novel GFP reporters.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2022; ©2022 |
| Publication date | 2022; 2022 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Jones, Chey Marcel |
|---|---|
| Degree supervisor | Martinez, Todd J. (Todd Joseph), 1968- |
| Thesis advisor | Martinez, Todd J. (Todd Joseph), 1968- |
| Thesis advisor | Boxer, Steven G. (Steven George), 1947- |
| Thesis advisor | Markland, Thomas E |
| Degree committee member | Boxer, Steven G. (Steven George), 1947- |
| Degree committee member | Markland, Thomas E |
| Associated with | Stanford University, Department of Chemistry |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Chey Marcel Jones. |
|---|---|
| Note | Submitted to the Department of Chemistry. |
| Thesis | Thesis Ph.D. Stanford University 2022. |
| Location | https://purl.stanford.edu/gy709ry9024 |
Access conditions
- Copyright
- © 2022 by Chey Marcel Jones
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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