RUI: Investigation of the structure and dynamics of type IV pilus filaments using all-atom and coarse-grained molecular dynamics

该项目将使用先进的计算方法来更好地理解蛋白质丝的生物力学特性，其应用范围从生物纳米技术到细胞运动和细菌感染。细菌和古细菌可以通过从细胞膜上伸出的长长的“粘性”细丝附着在表面上，这种细丝被称为IV型菌毛（T4P）。这些细丝是由一种叫做毛蛋白的蛋白质的数千个副本组成的，它们非常坚固，同时也非常灵活。例如，单个细菌的T4P纤维可以支撑细菌体重的10,000倍，T4P可以拉伸到其原始长度的三倍而不会断裂。该项目将使用一种被称为分子动力学模拟的计算方法来研究T4P细丝的结构和动力学。使用这种计算方法，模拟力将应用于T4P细丝，以探测它们对拉伸的反应，这将允许识别为T4P提供强大强度的相互作用。从这项工作中获得的关于T4P的见解将为生物纳米技术的应用提供信息，T4P在细菌粘附和运动中的作用，并将扩展我们对蛋白质细丝的一般知识。此外，该项目将在生物、物理、化学和计算机科学的交叉领域为本科生提供重要的培训。它还将开发计算学习模块，并将其纳入本科科学课程，以培养学生在所有科学领域日益重要的计算方法。本项目采用计算/理论为主导的方法：(1)利用全原子分子动力学模拟，在全原子分辨率水平上研究淋病奈瑟菌、脑膜炎奈瑟菌和铜绿假单胞菌三种生物的T4P细丝的动力学；(2)建立粗粒度模型，研究T4P细丝的结构特性，包括T4P在外部作用力下发生的结构转变。这种全面的、多尺度的计算方法将提供对T4P在与T4P功能相关的多个长度和时间尺度上的强度和动力学的见解，并且重要的是将弥合目前在T4P细丝的生物力学实验和理论理解之间存在的知识差距。具体来说，全原子模拟将用于表征T4P结构的非均质性，并确定在T4P在外力作用下表现出的多晶转变的初始阶段，pilin亚基之间维持T4P结构完整性的最重要的相互作用。外部力量将应用于T4P使用操纵分子动力学协议。此外，全原子和粗粒度模拟将结合使用，以确定重要的T4P长丝性能，如杨氏模量、持久长度和扭转刚度。最后，粗粒度的T4P细丝受力模拟将允许开发T4P细丝完全力过渡状态的第一个模型，为细丝在分子尺度上如何改变形状提供前所未有的分子尺度见解。本项目开发的粗粒度T4P模型将作为从原子尺度到细胞生物学尺度的桥梁的起始模型。该项目将为T4P生物力学提供新的见解，有助于对T4P在原核生物中的作用的基本理解，并提高对螺旋生物聚合物可塑性的理解。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project will use advanced computational approaches to better understand the biomechanical properties of a protein filament that has applications ranging from bionanotechnology to cell motion and bacterial infection. Bacteria and archaea can adhere to surfaces using long, "sticky" filaments that protrude from their cell membranes called type IV pili (T4P). These filaments, which are made of thousands of copies of a protein called pilin, are incredibly strong, yet simultaneously extremely flexible. For example, a single bacterial T4P filament can support up to 10,000 times a bacterium's body weight, and T4P can be stretched to three times their original length without breaking. This project will use a computational approach known as molecular dynamics simulation to investigate the structure and dynamics of T4P filaments. Using this computational approach, simulated forces will be applied to T4P filaments to probe how they respond to being stretched, which will allow the identification of interactions that provide T4P with their great strength. The insights about T4P that will result from this work will inform applications in bionanotechnology, the role that T4P play in bacterial adhesion and motion, and will expand our general knowledge about protein filaments. Furthermore, this project will provide significant training to undergraduate students in a highly cross-disciplinary area of research at the interface of biology, physics, chemistry, and computer science. It will also develop computational learning modules and incorporate them into the undergraduate science curriculum to train students in the computational methods that are increasingly important in all scientific fields.This project uses a computation/theory-led approach to: (1) investigate the dynamics of T4P filaments from three organisms, N. gonorrhoeae, N. meningitidis, and P. aeruginosa, at the all-atom level of resolution using all-atom molecular dynamics simulation, and (2) develop coarse-grained models to study the structural properties of T4P filaments, including the structural transition that occurs for T4P under external force. This comprehensive, multi scale computational approach will provide insights into the strength and dynamics of T4P across multiple length and time scales relevant to T4P function, and importantly will bridge the gap in knowledge that currently exists between the experimental and theoretical understanding of the biomechanics of T4P filaments. Specifically, all-atom simulations will be used to characterize T4P structural heterogeneity and to identify the most important interactions between pilin subunits for maintaining T4P structural integrity in the initial stages of the polymorphic transition that T4P exhibit under the application of external force. External forces will be applied to T4P using steered molecular dynamics protocols. Additionally, all-atom and coarse-grained simulations will be used in combination to determine important T4P filament properties such as the Young's modulus, persistence length, and torsional rigidity. Finally, coarse-grained simulations of T4P filaments under force will allow for the development of the first model of the fully force-transitioned state of a T4P filament, providing unprecedented molecular-scale insights into how the filament changes shape at the molecular scale. The coarse-grained T4P model developed in this project will act as a starting model for bridging from the atomistic scale to the scale of cellular biology. This project will provide novel insights into T4P biomechanics, aid in the fundamental understanding of the role of T4P in prokaryotes, and improve understanding of the plasticity of helical biopolymers.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.