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

密歇根州立大学的Katharine Hunt和Robert Cukier获得了化学理论，模型和计算方法计划的奖项，以开发计算工具，用于确定在光场中作用于荧光标记蛋白质分子的力，并检查光诱导荧光标记蛋白质构象变化的可能性。 注意力集中在单个的，标记的分子之间的小分子限制，其中偶极梯度力占主导地位，和米氏散射限制，其中的力量，由于在由对象散射的光子动量的变化是最重要的大小制度的中间。 分析包括标记的蛋白质分子内的极化率的变化和极化率随时间的变化，因为荧光团响应于光场而被电子激发。 作用在蛋白质分子中的核上的力的变化将被并入使用Cukier组的CUKMODY代码的分子动力学模拟中，以模拟用荧光素标记的溶剂化的照明亮氨酸拉链蛋白，并模拟修饰的拉链蛋白bZIP，该理论工作描述了激光场中作用于生物分子的力以及光-诱导染料分子标记的蛋白质构象的变化。 本研究涉及生物分子光子学、单分子光谱学和基于荧光标记的生物分子分析的当前发展。

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.