Modeling Macromolecular Transport through Channels

描述（由申请人提供）：我们建议开发所需的大分子建模，以便对带电聚合物分子如何通过蛋白质通道进行基本的分子理解。在单聚核苷酸分子序列的直接高速检测和单大分子分析物的随机感测的前景的刺激下，最近报道了非常令人兴奋的单分子电生理学实验。这些实验的结果非常令人困惑，需要对聚合物物理学的理解，并结合化学特性的描述。我们建议实施聚合物物理概念有效的大长度和时间尺度，结合布朗动力学模拟占在较小的长度和时间尺度的细节。本提案解决了对以下的基本理解：（1）DNA/RNA分子如何在电场下移动通过α-溶血素通道，以及计算具有大分子运输的通道的离子电流，（2）离散电导状态的起源和工程化到蛋白质孔中的聚合物系链的构象，（3）RNA转运因子及其通过核孔复合体转运的粗粒模型的建立。我们独特的理论，模拟和与活跃的实验学家合作的结合，将对信号转导，DNA/RNA和蛋白质的高速测序，生物战剂的筛选，药物诊断和疾病及其控制的大分子方面的理解产生直接和深远的影响。

DESCRIPTION (provided by applicant): We propose to develop the macromolecular modeling needed for a fundamental molecular understanding of how electrically charged polymer molecules move through protein channels. Stimulated by prospects of direct high-speed detection of sequences in single polynucleotide molecules, and of stochastic sensing of single macromolecular analytes, very exciting single-molecule electrophysiology experiments have recently been reported. The results of these experiments are very puzzling and require an understanding of polymer physics, in combination with descriptions of chemical specificities. We propose to implement polymer physics concepts valid at large length and time scales, in conjunction with Brownian Dynamics simulations accounting for details at smaller length and time scales. The present proposal addresses a fundamental understanding of (1) how DNA/RNA molecules move through alpha-hemolysin channels under an electric field and computation of ionic current of channels with macromolecular transport, (2) origin of discrete conductance states and conformations of polymer tethers engineered into protein pores, and (3) development of coarse-grained models for RNA-carrying transport factors and their transport through nuclear pore complexes. Our unique combination of theory, simulations, and collaborations with active experimentalists, will have a direct and profound impact on understanding of signal transduction, high-speed sequencing of DNA/RNA and proteins, screening of biological warfare agents, pharmaceutical diagnostics, and macromolecular aspects of diseases and their control.