论文标题
杂化纳米技术的粗粒核酸蛋白模型
Coarse-Grained Nucleic Acid-Protein Model for Hybrid Nanotechnology
论文作者
论文摘要
杂化DNA-蛋白质纳米技术的新兴领域带来了许多新型材料的潜力，这些材料结合了DNA纳米技术与蛋白质相互作用的多功能性。但是，由于涉及的系统大小，这些混合结构的设计和计算研究很困难。为了帮助设计和计算机分析过程中，我们在这里介绍了一个粗粒的DNA/RNA蛋白模型，该模型将基于各向异性网络模型表示的蛋白质的粗粒蛋白模型扩展了DNA/RNA的oxDNA/OXRNA模型。我们的模型完全配备了分析脚本和可视化，旨在促进混合纳米材料设计，以实现实验实现，并促进对生物复合物的研究。我们通过模拟DNA-蛋白纳米层，包裹组蛋白的DNA和聚合酶中的新生RNA来进一步证明其用法。
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 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.
