Doctoral Program in Biology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
J Chem Inf Model. 2024 Oct 14;64(19):7184-7188. doi: 10.1021/acs.jcim.4c01467. Epub 2024 Oct 3.
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).
了解细胞环境对蛋白质构象的影响对于阐明活细胞内蛋白质的功能至关重要。在使用分子动力学（MD）模拟的研究中，碳纳米管和疏水笼已被广泛用于模拟核糖体隧道和伴侣等特定大型生物分子内部的细胞环境。然而，最近的研究表明，这些均匀的疏水模型可能无法充分捕捉每个生物分子内部的环境影响。基于这些事实，有必要生成具有对应于目标生物分子内成分的变化化学性质的球形和圆柱形模型。我们开发了一种生物分子环境模拟模型生成器（BEMM-GEN），它可以生成具有用户指定化学性质的球形和圆柱形模型，并允许将任意蛋白质构象集成到生成的模型中。BEMM-GEN 提供模型和蛋白质复合物结构，以及用于 MD 模拟的相应参数文件（AMBER 和 GROMACS），用户可以根据生成的输入文件立即运行他们的 MD 模拟。BEMM-GEN 可以通过 Python 包管理器（pip install BEMM-gen）自由下载和安装。源代码文件和操作用户手册可在 GitHub（https://github.com/y4suda/BEMM-GEN）上获得。
