Modeling Macromolecular Transport through Channels

描述(由申请人提供)：我们建议开发大分子模型，以基本了解带电聚合物分子如何通过蛋白质通道。在直接高速检测单个多核苷酸分子序列和随机检测单个大分子分析物的前景的刺激下，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费解，需要了解聚合物物理，并结合化学特性的描述。我们建议实现在大长度和时间尺度上有效的聚合物物理概念，并结合布朗动力学模拟在较小长度和时间尺度上考虑细节。本提案涉及对以下方面的基本理解：(1)DNA/RNA分子如何在电场作用下通过α-溶血素通道，并计算具有大分子传输的通道的离子电流；(2)离散电导态的起源和蛋白质孔中工程聚合物的构象；(3)RNA转运因子及其通过核孔复合体的粗粒模型的发展。我们独特的理论、模拟和与活跃的实验者合作的结合，将对理解信号转导、DNA/RNA和蛋白质的高速测序、生物战剂的筛选、药物诊断以及疾病及其控制的大分子方面产生直接而深远的影响。

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.