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Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus

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Abstract

VP35 of Ebola viruses (EBOVs) is an attractive potential target because of its multifunction. All-atom molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculations are performed to investigate the single-walled carbon nanotube (SWCNT) as an inhibitor in wild-type (WT) VP35 as well as in three primary mutants (K248A, I295A, and K248A/I295A) through docking the SWCNT in the first basic patch (FBP) of VP35. The SWCNTs of all the four systems effectively bind to the FBP. Interestingly, the sites and orientations of the SWCNT binding to the I295A mutant and K248A/I295A double mutants change significantly to accommodate the variation of the VP35 conformation. Moreover, the VDW can provide the major forces for affinity binding in all four systems.

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Acknowledgements

This work is supported by the National Natural Science Foundation of China (11179035), the Yong teacher training Program of the Shanghai Education committee (A1-5701-15-011-49) as well as Physical electronics disciplines (NO: 12XKJC01).

Author Contributions

Yan-Jun Zhang, designed research, performed research, contributed analytic tools, analyzed data, and wrote the paper.

Jing-Na Ding partly analyzed data.

Hui Zhong partly analyzed data.

Chang-Ping Sun partly analyzed data.

Ju-Guang Han modified the paper.

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Authors and Affiliations

  1. National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People’s Republic of China

    Yan-Jun Zhang, Jing-Na Ding, Hui Zhong, Chang-Ping Sun & Ju-Guang Han

  2. Department of Physics, Linyi University, Shandong, 276000, People’s Republic of China

    Chang-Ping Sun

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  1. Yan-Jun Zhang
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Correspondence to Ju-Guang Han.

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Zhang, YJ., Ding, JN., Zhong, H. et al. Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus. J Biol Phys 43, 149–165 (2017). https://doi.org/10.1007/s10867-016-9440-5

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  • DOI: https://doi.org/10.1007/s10867-016-9440-5

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