BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation

Abstract

Understanding the influence of the cellular environment on protein conformations is crucial for elucidating protein functions within living cells. In studies using molecular dynamics (MD) simulation, carbon nanotubes and hydrophobic cages have been widely used to emulate the cellular environment inside specific large biomolecules such as ribosome tunnels and chaperones. However, recent studies suggest that these uniform hydrophobic models may not adequately capture the environmental effects inside each biomolecule. Based on these facts, it is necessary to generate spherical and cylindrical models with varied chemical properties corresponding to the components within target biomolecules. We developed a biomolecular environment-mimicking model generator (BEMM-GEN) that generates spherical and cylindrical models with user-specified chemical properties and allows the integration of arbitrary protein conformations into the generated models. BEMM-GEN provides model and protein complex structures, along with the corresponding parameter files for MD simulation (AMBER and GROMACS), and users immediately run their MD simulation based on the generated input files. BEMM-GEN can be freely downloaded and installed via a Python package manager (pip install BEMM-gen). The source code files and a user manual for operation are provided on GitHub (https://github.com/y4suda/BEMM-GEN).