Soft Matter and Biosystems, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.
Department of Chemistry, The College of New Jersey, Ewing, NJ, USA.
Methods Mol Biol. 2022;2340:357-378. doi: 10.1007/978-1-0716-1546-1_16.
The nanomechanical characterization of several biological fibrils that are the result of protein aggregation via molecular dynamics simulation is nowadays feasible, and together with atomic force microscopy experiments has widened our understanding of the forces in the regime of pN-nN and system sizes of about hundreds of nanometers. Several methodologies have been developed to achieve this target, and they range from the atomistic representation via molecular force fields to coarse-grained strategies that provide comparable results with experiments in a systematic way. In this chapter, we discuss several methodologies for the calculation of mechanical parameters, such as the elastic constants of relevant biological systems. They are presented together with details about parameterization and current limitations. Then, we discuss some of the applications of such methodologies for the description of bacterial filament and β-amyloid systems. Finally, the latest lines of development are discussed.
通过分子动力学模拟对几种生物纤维进行纳米力学特性研究现在已经成为可能，这与原子力显微镜实验一起，拓宽了我们对 pN-nN 范围内的力以及大约数百纳米系统尺寸的理解。已经开发出了几种实现这一目标的方法，从通过分子力场的原子表示法到粗粒化策略，这些方法以系统的方式提供了与实验相比可比较的结果。在本章中，我们讨论了几种计算机械参数的方法，例如相关生物系统的弹性常数。同时还介绍了参数化和当前限制的细节。然后，我们讨论了这些方法在描述细菌丝和β-淀粉样蛋白系统中的一些应用。最后，讨论了最新的发展方向。
