Department of Physics, University of Colorado Boulder, Boulder, USA.
Eur Phys J E Soft Matter. 2021 Aug 18;44(8):105. doi: 10.1140/epje/s10189-021-00097-8.
Interaction of cytoskeletal filaments, motor proteins, and crosslinking proteins drives important cellular processes such as cell division and cell movement. Cytoskeletal networks also exhibit nonequilibrium self-assembly in reconstituted systems. An emerging problem in cytoskeletal modeling and simulation is spatiotemporal alteration of the dynamics of filaments, motors, and associated proteins. This can occur due to motor crowding, obstacles along the filament, motor interactions and direction switching, and changes, defects, or heterogeneity in the filament binding lattice. How such spatiotemporally varying cytoskeletal filaments and motor interactions affect their collective properties is not fully understood. We developed the Cytoskeleton Lattice-based Kinetic Simulator (CyLaKS) to investigate such problems. The simulation model builds on previous work by incorporating motor mechanochemistry into a simulation with many interacting motors and/or associated proteins on a discretized lattice. CyLaKS also includes detailed balance in binding kinetics, movement, and lattice heterogeneity. The simulation framework is flexible and extensible for future modeling work and is available on GitHub for others to freely use or build upon. Here we illustrate the use of CyLaKS to study long-range motor interactions, microtubule lattice heterogeneity, motion of a heterodimeric motor, and how changing crosslinker number affects filament separation.
细胞骨架丝、马达蛋白和交联蛋白的相互作用驱动着细胞分裂和细胞运动等重要的细胞过程。细胞骨架网络在重组系统中也表现出非平衡的自组装。细胞骨架建模和模拟中的一个新兴问题是丝、马达和相关蛋白的动力学的时空变化。这种情况可能是由于马达拥挤、丝上的障碍物、马达相互作用和方向转换以及丝结合晶格的变化、缺陷或异质性引起的。这种时空变化的细胞骨架丝和马达相互作用如何影响它们的集体性质还不完全清楚。我们开发了基于细胞骨架晶格的动力学模拟器（CyLaKS）来研究这些问题。该模拟模型基于之前的工作，将马达的机械化学纳入到一个具有许多相互作用的马达和/或相关蛋白的离散晶格上的模拟中。CyLaKS 还包括结合动力学、运动和晶格异质性的详细平衡。该模拟框架具有灵活性和可扩展性，可供未来的建模工作使用，并在 GitHub 上免费提供给其他人使用或构建。在这里，我们举例说明了 CyLaKS 如何用于研究长程马达相互作用、微管晶格异质性、异二聚体马达的运动以及改变交联蛋白数量如何影响丝的分离。
