Modeling Macromolecular Transport through Protein Channels and Nanopores

通过蛋白质通道和纳米孔模拟大分子运输

• 批准号: 7619016
• 负责人: MURUGAPPAN MUTHUKUMAR
• 金额: $ 26.08万
• 依托单位: UNIVERSITY OF MASSACHUSETTS AMHERST
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-06-06 至 2010-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7619016
• 关键词: Accounting; Address; Behavior; Biological; Biological Phenomena; Biological Warfare; Cells; Charge; Chemicals; Collaborations; Complex; Confined Spaces; Crowding; DNA; DNA Sequence; Data; Detection; Development; Diagnostic; Disease; Electrophysiology (science); Entropy; Environment; Enzymes; Event; Experimental Designs; Figs - dietary; Genes; Genome; Goals; Grant; Head; Hemolysin; In Vitro; Injection of therapeutic agent; Laboratories; Length; Life; Membrane; Modeling; Molecular; Molecular Conformation; Monitor; Movement; Nuclear Pore Complex; Nucleotides; Outcome; Pharmacologic Substance; Physics; Pilum; Polymers; Polynucleotides; Procedures; Process; Protein translocation; Proteins; Protocols documentation; Reporting; Research; Research Personnel; Role; Screening procedure; Signal Transduction; Single-Stranded DNA; Site; Specificity; Speed; Statistical Mechanics; Structure; Technology; Time; Virus; War; Work; analog; base; detector; electric field; feeding; in vivo; insight; nanopore; programs; research study; simulation; single molecule; solid state; success; theories

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 and solid-state nanopores. Such a molecular understanding is crucial for probing the fundamental process of polymer translocation and for a successful development of high-speed detection of DNA sequences. Stimulated by the need to sequence enormous number of genomes immediately and inexpensively, very exciting single-molecule electrophysiology experiments have recently been reported. Although couched in the technology of sequencing, these experiments are the in vitro analogs of the more complex biological translocation processes. Even under such simpler conditions, the results of these experiments are very puzzling and require an understanding of polymer physics, in combination with 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) effects of secondary structures on the mechanism of movement of single stranded DNA/RNA through alpha-hemolysin pores and on the ionic current signatures, (2) enzyme-modulated DNA translocation through pores to optimize the speed of the polymer in the pore to enable simultaneous interrogation at a single-base level, and (3) conformations of dsDNA inside solid-state nanopores to enable a steady movement required for sequencing strategies and to understand the electrodynamical behavior of semiflexible dsDNA molecules under spatial constraints. Our unique combination of theory, simulations, and collaborations with active experimentalists, will have a direct and profound impact on understanding of polymer translocation, high-speed sequencing of DNA/RNA and proteins, signal transduction, screening of biological warfare agents, pharmaceutical diagnostics, and macromolecular aspects of diseases and their control.

描述（由申请人提供）：我们建议开发基本分子理解带电聚合物分子如何通过蛋白质通道和固态纳米孔移动所需的大分子建模。这样的分子理解是至关重要的探测聚合物易位的基本过程，并成功地开发高速检测的DNA序列。由于需要立即和廉价地测序大量的基因组，最近报道了非常令人兴奋的单分子电生理学实验。虽然这些实验是以测序技术为载体，但它们是更复杂的生物易位过程的体外模拟。即使在如此简单的条件下，这些实验的结果也非常令人困惑，需要对聚合物物理学的理解，并结合化学特性。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。本发明提出了对以下的基本理解：（1）二级结构对单链DNA/RNA通过α-溶血素孔的运动机制和对离子电流特征的影响，（2）酶调节的DNA通过孔的移位以优化孔中聚合物的速度，从而能够在单碱基水平上同时询问，以及（3）固态纳米孔内dsDNA的构象，以实现测序策略所需的稳定运动，并理解半柔性dsDNA分子在空间约束下的电动力学行为。我们独特的理论，模拟和与活跃的实验学家合作的结合，将对理解聚合物易位，DNA/RNA和蛋白质的高速测序，信号转导，生物战剂的筛选，药物诊断和疾病及其控制的大分子方面产生直接和深远的影响。