Theory and simulation of dye-labeled protein molecules in optical fields

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Katharine Hunt and Robert Cukier of Michigan State University are supported by an award from the Chemical Theory, Models and Computational Methods program to develop computational tools for determining the forces acting on a fluorescently labeled protein molecule in an optical field and to examine the possibility of light-induced changes in the conformations of fluorescently labeled proteins. Attention focuses on single, labeled molecules in the size regime intermediate between the small-molecule limit, where dipole-gradient forces predominate, and the Mie scattering limit, where the forces due to changes in the momenta of photons scattered by the object are most important. The analysis includes variations in the polarizability within the labeled protein molecule and variations in the polarizability with time, as the fluorophore is electronically excited in response to the optical field. Changes in the forces acting on the nuclei in the protein molecule are to be incorporated into the molecular dynamics simulations using the Cukier group's CUKMODY code, to model a solvated, illuminated leucine zipper protein that is labeled with fluorescein and to model a modified zipper protein bZIP, which traps DNA.The theoretical work characterizes the forces acting on biomolecules in laser fields and the possibility of light-induced changes in the conformations of proteins labeled with dye molecules. This research is related to current developments in biomolecular photonics, single-molecule spectroscopy, and the analysis of biomolecules based on fluorescent labeling.