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Title Pressure Induced Structural Changes and Gas Diffusion Pathways in Monomeric Fluorescent Proteins
Publication Date
Degree PhD
Discipline/Department Physics
Degree Level doctoral
University/Publisher Florida International University
Abstract Fluorescent proteins (FPs) are extremely valuable biochemical markers which have found a wide range of applications in cellular and molecular biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for in vivo applications in mammalian cell imaging. Fluorescent proteins consist of a chromophore caged in the beta-barrel protein scaffold. The photophysical properties of an FP is determined by its chromophore structure and its interactions with the protein barrel. Application of hydrostatic pressure on FPs results in the modification of the chromophore environment which allows a systematic study of the role of the protein-chromophore interactions on photophysical properties of FPs. Using Molecular Dynamics (MD) computer simulations, I investigated the pressure induced structural changes in the monomeric variants mCherry, mStrawberry, and Citrine. The results explain the molecular basis for experimentally observed pressure responses among FP variants. It is found that the barrel flexibility, hydrogen bonding interactions and chromophore planarity of the FPs can be correlated to their contrasting photophysical properties at vaious pressures. I also investigated the oxygen diffusion pathways in mOrange and mOrange2 which exhibit marked differences in oxygen sensitivities as well as photostability. Such computational identifications of structural changes and oxygen diffusion pathways are important in guiding mutagenesis efforts to design fluorescent proteins with improved photophysical properties.
Subjects/Keywords fluorescence; chromophore; quenching; parameterization; diffusion pathways; hydrogen bonding; chromophore planarity; Physics
Contributors Prem P. Chapagain; Bernard S. Gerstman; Xuewen Wang; David C. Chatfield
Country of Publication us
Record ID oai:digitalcommons.fiu.edu:etd-1968
Repository fiu
Date Retrieved
Date Indexed 2018-08-10
Created Date 2013-03-28 07:00:00

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