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Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein–DNA Complexes
Journal of Chemical Theory and Computation ( IF 5.5 ) Pub Date : 2018-02-03 00:00:00 , DOI: 10.1021/acs.jctc.7b00954
Masahiro Shimizu 1 , Shoji Takada 1
Affiliation  

While coarse-grained (CG) simulations have widely been used to accelerate structure sampling of large biomolecular complexes, they are unavoidably less accurate and thus the reconstruction of all-atom (AA) structures and the subsequent refinement is desirable. In this study we developed an efficient method to reconstruct AA structures from sampled CG protein–DNA complex models, which attempts to model the protein–DNA interface accurately. First we developed a method to reconstruct atomic details of DNA structures from a three-site per nucleotide CG model, which uses a DNA fragment library. Next, for the protein–DNA interface, we referred to the side chain orientations in the known structure of the target interface when available. The other parts are modeled by existing tools. We confirmed the accuracy of the protocol in various aspects including the structure deviation in the self-reproduction, the base pair reproducibility, atomic contacts at the protein–DNA interface, and feasibility of the posterior AA simulations.

中文翻译:

从粗粒蛋白质-DNA复合物模型重建原子结构

尽管粗粒度(CG)模拟已广泛用于加速大型生物分子复合物的结构采样,但它们不可避免地准确性较低,因此需要重建全原子(AA)结构并进行后续改进。在这项研究中,我们开发了一种从采样的CG蛋白-DNA复杂模型重建AA结构的有效方法,该方法试图精确地建模蛋白质-DNA界面。首先,我们开发了一种从三个位点的每个核苷酸CG模型重建DNA结构原子细节的方法,该模型使用了DNA片段文库。接下来,对于蛋白质-DNA界面,我们在可用的情况下参考目标界面已知结构中的侧链方向。其他部分由现有工具建模。
更新日期:2018-02-03
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