Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing,Computational and Structural Biotechnology Journal

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Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2021-11-18 , DOI: 10.1016/j.csbj.2021.11.014
Punam Rattu ₁ , Flo Glencross ₂ , Sophie L Mader ₃ , Chris-Kriton Skylaris ₁ , Stephen J Matthews ₂ , Sarah L Rouse ₂ , Syma Khalid _{1,

3}

Affiliation

Two proteins of the membrane protein complex, CsgG and CsgF, are studied as proteinaceous nanopores for DNA sequencing. It is highly desirable to control the DNA as it moves through the pores, this requires characterisation of DNA translocation and subsequent optimization of the pores. In order to inform protein engineering to improve the pores, we have conducted a series of molecular dynamics simulations to characterise the mechanical strength and conformational dynamics of CsgG and the CsgG-CsgF complex and how these impact ssDNA, water and ion movement. We find that the barrel of CsgG is more susceptible to damage from external electric fields compared to the protein vestibule. Furthermore, the presence of CsgF within the CsgG-CsgF complex enables the complex to withstand higher electric fields. We find that the eyelet loops of CsgG play a key role in both slowing the translocation rate of DNA and modulating the conductance of the pore. CsgF also impacts the DNA translocation rate, but to a lesser degree than CsgG.

中文翻译：

通过大肠杆菌蛋白 CsgG 和 CsgF 进行单链 DNA 易位的原子水平表征，用于纳米孔测序

研究了膜蛋白复合物中的两种蛋白 CsgG 和 CsgF 作为用于 DNA 测序的蛋白质纳米孔。当 DNA 通过孔隙时，非常需要对其进行控制，这需要对 DNA 易位进行表征并随后对孔隙进行优化。为了为蛋白质工程提供改善孔隙的信息，我们进行了一系列分子动力学模拟，以表征 CsgG 和 CsgG-CsgF 复合物的机械强度和构象动力学，以及它们如何影响 ssDNA、水和离子运动。我们发现，与蛋白质前庭相比，CsgG 的桶更容易受到外部电场的损伤。此外，CsgG-CsgF复合物中CsgF的存在使得该复合物能够承受更高的电场。我们发现 CsgG 的孔眼环在减缓 DNA 易位速率和调节孔电导方面发挥着关键作用。 CsgF 也会影响 DNA 易位率，但程度小于 CsgG。

更新日期：2021-11-18

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