Colin A. Smith; Alison L. O'Neil; Candice M. Etson
Protein design and computational molecular dynamics simulations have been a newly developed field. The mini Fluorescence Activating Protein, or the mFAP protein, is a de novo designed protein created by the Baker lab at the University of Washington. The structure consists of 115 amino acids that construct a β-barrel with a docked DFHBI ligand bound at the top of the protein. β -barrel proteins provide a good environment to enclose a ligand and rigidify the molecule within the protein cavity. With the increase in the ligand planarity/rigidity, an increase in fluorescence can be observed. Since many mFAP sequences have been previously identified and constructed, the primary goal of the project was to relate the variations in the observed relative brightness data of each protein to the planarity of the DFHBI molecule. Two variants, mFAP-A and mFAP-G, were studied and mFAP-A was hypothesized to be the brighter molecule. A brighter DFHBI molecule involves limited deviation from planarity of the imidazole and the phenyl dihedral angles. Upon excitation of the DFHBI molecule from the ground state to the excited state, the molecule can either fluoresce back to the ground state or become isomerized in the excited state and then quenched in the ground state. Rosetta homology structure modelling generated the starting mFAP structures to be used in molecular dynamics simulations. Ground state and excited state simulations for mFAP-A and mFAP-G showed that mFAP-G remained planar more frequently in the ground state and remained planar for a longer time in the excited state. Quantum yield values also validated that mFAP-G was brighter, which did not support the original hypothesis that stated mFAP-A should be the brighter mutant.
Poon, Ivy, "Simulations of Isomerization/Quenching in De Novo Designed Mini Fluorescent Proteins" (2019). Masters Theses. 232.
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