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

密歇根州立大学的Katharine Hunt和Robert Cukier得到了化学理论、模型和计算方法计划的支持，他们开发计算工具来确定在光场中作用于荧光标记蛋白质分子的力，并研究光诱导荧光标记蛋白质构象变化的可能性。注意力集中在大小介于小分子极限和米氏散射极限之间的单个标记分子上，在小分子极限中，偶极梯度力占主导地位，在米氏散射极限中，由于被物体散射的光子动量的变化而产生的力是最重要的。该分析包括标记的蛋白质分子内的极化率的变化以及随着时间的变化，因为荧光基团在光场的响应下被电子激发。利用Cukier小组的CUKMODY程序，将作用在蛋白质分子核上的力的变化纳入分子动力学模拟，以模拟用荧光素标记的溶剂化、发光的亮氨酸拉链蛋白质，并模拟捕捉DNA的改良拉链蛋白质bZIP。理论工作描述了激光作用于生物分子上的力以及光诱导标记有染料分子的蛋白质构象变化的可能性。这项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最新发展。

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.