School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA.
Soft Matter. 2021 Apr 7;17(13):3586-3593. doi: 10.1039/d0sm01639j. Epub 2021 Jan 5.
The emerging field of hybrid DNA-protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with the versatility of protein interactions. However, the design and computational study of these hybrid structures is difficult due to the system sizes involved. To aid in the design and in silico analysis process, we introduce here a coarse-grained DNA/RNA-protein model that extends the oxDNA/oxRNA models of DNA/RNA with a coarse-grained model of proteins based on an anisotropic network model representation. Fully equipped with analysis scripts and visualization, our model aims to facilitate hybrid nanomaterial design towards eventual experimental realization, as well as enabling study of biological complexes. We further demonstrate its usage by simulating DNA-protein nanocage, DNA wrapped around histones, and a nascent RNA in polymerase.
新兴的杂交 DNA-蛋白质纳米技术领域带来了许多新的材料的可能性，这些材料将 DNA 纳米技术的可寻址性与蛋白质相互作用的多功能性结合在一起。然而，由于所涉及的系统规模，这些混合结构的设计和计算研究是困难的。为了辅助设计和计算机分析过程，我们在这里引入了一个粗粒化的 DNA/RNA-蛋白质模型，该模型通过基于各向异性网络模型表示的蛋白质粗粒化模型扩展了 DNA/RNA 的 oxDNA/oxRNA 模型。我们的模型配备了分析脚本和可视化功能，旨在促进杂交纳米材料的设计，以最终实现实验，同时也能够研究生物复合物。我们通过模拟 DNA-蛋白质纳米笼、DNA 包裹组蛋白和聚合酶中的新生 RNA，进一步展示了它的用途。
