title: Molecular Dynamic Indicators of the Photoswitching Properties of Green Fluorescent Proteins.
abstract: Reversibly photoswitchable fluorescent proteins (RSFPs) are highly useful probes for a range of applications including diffraction-unlimited fluorescence microscopy. It was previously shown that reversible photoswitching not only involves cis-trans isomerization and protonation-deprotonation of the chromophore but also results in a marked difference in β-barrel flexibility. In this work, we performed flexibility profiling and functional mode analysis (FMA) using molecular dynamics calculations to study how the flexibility of the RSFP β-barrel influences the photoswitching properties of several fluorescent proteins. We also used Partial Least-Squared (PLS) FMA to detect promising mutation sites for the modulation of photoswitching properties of RSFPs. Our results show that the flexibility of RSFP does depend on its state with a systematically higher flexibility in the dark state compared to the bright state. In particular our method highlights the importance of Val157 in Dronpa, which upon mutation yields a striking difference in the collective motions of the two mutants. Overall, we show that PLS-FMA yields information, complementary to static structures, that can guide the rational design of fluorescent proteins.
authors: Quantum Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven , Celestijnenenlaan 200F, 3001 Heverlee, Belgium.
authors: Daryna
authors: D
authors: Smyrnova
authors: Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven , Celestijnenenlaan 200F, 3001 Heverlee, Belgium.
authors: Benjamien
authors: B
authors: Moeyaert
authors: Quantum Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven , Celestijnenenlaan 200F, 3001 Heverlee, Belgium.
authors: Servaas
authors: S
authors: Michielssens
authors: Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven , Celestijnenenlaan 200F, 3001 Heverlee, Belgium.
authors: Johan
authors: J
authors: Hofkens
authors: Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven , Celestijnenenlaan 200F, 3001 Heverlee, Belgium.
authors: Peter
authors: P
authors: Dedecker
authors: Quantum Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven , Celestijnenenlaan 200F, 3001 Heverlee, Belgium.
authors: Arnout
authors: A
authors: Ceulemans
mesh_terms: D003624:Darkness; D049452:Green Fluorescent Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008027:Light; D056004:Molecular Dynamics Simulation; D009068:Movement; D017354:Point Mutation; D017433:Protein Structure, Secondary
chemical_list: D049452:Green Fluorescent Proteins