Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing.
Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing.
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DOI：
10.1016/j.csbj.2021.11.014
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发表时间：
2021
影响因子：
6
通讯作者：
Khalid S
中科院分区：
文献类型：
--
作者：
Rattu P;Glencross F;Mader SL;Skylaris CK;Matthews SJ;Rouse SL;Khalid S
大肠杆菌膜蛋白复合物的两种蛋白质CsgG和CsgF被研究为用于DNA测序的蛋白质纳米孔。非常希望在DNA移动通过孔时控制DNA，这需要表征DNA易位和随后的孔优化。为了告知蛋白质工程以改善孔，我们进行了一系列分子动力学模拟，以确定CsgG和CsgG-CsgF复合物的机械强度和构象动力学以及这些如何影响ssDNA，水和离子运动。我们发现，桶CsgG是更容易受到损害，从外部电场相比，蛋白前庭。此外，CsgG-CsgF复合物中CsgF的存在使得复合物能够承受更高的电场。我们发现，CsgG的β-环在减缓DNA的易位速率和调节孔的电导方面起着关键作用。CsgF也影响DNA易位率，但程度低于CsgG。
Two proteins of the Escherichia coli 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.
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影响因子：
3.7
作者：
Jo S;Kim T;Im W
通讯作者：
Im W
DOI：
10.1073/pnas.1411942111
发表时间：
2014-12-16
影响因子：
11.1
作者：
Cao, Baohua;Zhao, Yan;Huang, Yihua
通讯作者：
Huang, Yihua
影响因子：
3.4
作者：
Aksimentiev, A;Schulten, K
通讯作者：
Schulten, K
影响因子：
64.8
作者：
Goyal, Parveen;Krasteva, Petya V.;Van Genven, Nani;Gubellini, Francesca;Van den Broeck, Imke;Troupiotis-Tsailaki, Anastassia;Jonckheere, Wim;Pehau-Arnaudet, Gerard;Pinkner, Jerome S.;Chapman, Matthew R.;Hultgren, Scott J.;Howorka, Stefan;Fronzes, Remi;Remaut, Han
通讯作者：
Remaut, Han
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML