A Typical Workflow to Simulate Cytoskeletal Systems

Summary

This protocol demonstrates how to use Cytosim, an Open Source cytoskeleton simulation, to investigate the behavior of a network of filaments connected by molecular motors and passive crosslinkers. A generic workflow with step-by-step instructions is followed to vary the number of crosslinkers and plot the resulting network contractility.

Abstract

Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modeling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and the interactions between these elements. Thus, computer simulations can be used to investigate the collective behavior of the system precisely, in a way that is complementary to experiments. Cytosim is an Open Source cytoskeleton simulation suite designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It also offers the possibility to simulate passive crosslinkers, diffusible crosslinkers, nucleators, cutters, and discrete versions of the motors that only step on unoccupied lattice sites on a filament. Other objects complement the filaments by offering spherical or more complicated geometry that can be used to represent chromosomes, the nucleus, or vesicles in the cell.

Cytosim offers simple command-line tools for running a simulation and displaying its results, which are versatile and do not require programming skills. In this workflow, step-by-step instructions are given to i) install the necessary environment on a new computer, ii) configure Cytosim to simulate the contraction of a 2D actomyosin network, and iii) produce a visual representation of the system. Next, the system is probed by systematically varying a key parameter: the number of crosslinkers. Finally, the visual representation of the system is complemented by the numerical quantification of contractility to view, in a graph, how contractility depends on the composition of the system. Overall, these different steps constitute a typical workflow that can be applied with few modifications to tackle many other problems in the cytoskeletal field.

Introduction

The cytoskeleton consists of filaments within the cell and associated molecules such as molecular motors, which often constitute a dynamic meshwork with remarkable mechanical properties. The cytoskeleton exists in various configurations in different cell types across nearly all life forms. Its correct functioning is essential for fundamental cellular processes such as division, motility, and polarization. It also governs cell-to-cell mechanical interactions, thereby influencing the morphogenesis of tissues and organisms. The cytoskeleton underlies several functions and manifests itself in many biological processes. For example, the contraction of muscles is linked to ....

Protocol

NOTE: The protocol consists of these steps: platform preparation for Windows 10, MacOS, and Linux; the installation of Cytosim; configuration of the simulation and test run and the graphical display; multiple runs, varying a parameter: the number of crosslinkers in the network; generating a graph to view how contractility is affected by the number of crosslinkers; parallel runs; and random sampling. All text following a ">" are commands that are to be entered verbatim in the terminal window. The ">.......

Discussion

The method outlined in this article relies on three small and independent Python programs, which were used in diverse ways throughout the described protocol. The first script preconfig is a versatile tool that can replace the need for writing custom Python scripts²⁷. It is used to generate multiple configuration files from a single template file, specifying which parameter should be varied and how it should be varied. To vary multiple parameters, one can simply add more code snippets into.......

Materials

Name	Company	Catalog Number	Comments
A personal computer			MacOS, Windows 10 or Linux
config.cym.tpl			template configuration file; https://gitlab.com/f-nedelec/cytosim.git
jove.cym			Cytosim configuration file
make_page.py			Python script; https://github.com/nedelec/make_page.py
preconfig			Python script; https://github.com/nedelec/preconfig
scan.py			Python script; https://github.com/nedelec/scan.py