A coarse-grained representation of DNA immersed in an external protein force-field
A coarse-grained representation of DNA immersed in an external protein force-field
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沉浸在外部蛋白质力场中的 DNA 的粗粒度表示
DOI：
10.1016/j.bpj.2021.11.1669
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发表时间：
2022
影响因子：
3.4
通讯作者：
Bores C
中科院分区：
文献类型：
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作者：
Bores C
我们提出了一个多尺度的方法，旨在研究DNA沉浸在由蛋白质产生的外场。我们的模型捕捉不同层次的细节耦合oxDNA粗粒度模型与刚性蛋白质的变量表示，覆盖范围从粗粒度到全原子。核酸和蛋白质之间的交叉相互作用是通过Lennard-Jones势加上德拜相互作用来定义的，德拜相互作用解释了盐对DNA静电的隐含影响。我们已经使用了大肠杆菌的大肠杆菌素E7的核酸酶结构域作为一个案例研究的参数化和测试模型。我们还使用LAMMPS分子动力学引擎研究了模型在不同系统中的并行性能。许多计算复杂性仍然具有挑战性的DNA-蛋白质复合物可以从这种方法中受益。
We present a multi-scale approach aiming at studying DNA immersed in the external field generated by a protein. Our model captures different levels of detail by coupling oxDNA coarse-grained model with a variable representation of a rigid protein-covering the range from coarse grained to full atomistic. The cross-interactions between the nucleic acids and the protein are defined via a Lennard-Jones potential plus Debye interactions that account for the implicit effect of salt on DNA electrostatics. We have used the nuclease domain of colicin E7 from Escherichia coli as a case study for parameterizing and testing the model. We have also studied the parallel performance of the model in different systems using the LAMMPS molecular dynamics engine. Many DNA-protein complexes whose computational complexity remains challenging may benefit from this approach.