title: Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus.
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.
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China.
authors.forename: Yan-Jun
authors.initials: YJ
authors.lastname: Zhang
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China.
authors.forename: Jing-Na
authors.initials: JN
authors.lastname: Ding
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhong
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China.|Department of Physics, Linyi University, Shandong, 276000, People's Republic of China.
authors.forename: Chang-Ping
authors.initials: CP
authors.lastname: Sun
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China. jghan@ustc.edu.cn.
authors.forename: Ju-Guang
authors.initials: JG
authors.lastname: Han
mesh_terms: D056004:Molecular Dynamics Simulation; D009154:Mutation; D037742:Nanotubes, Carbon; D011485:Protein Binding; D011487:Protein Conformation; D013816:Thermodynamics; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D037742:Nanotubes, Carbon; C080980:VP35 protein, filovirus; D054334:Viral Regulatory and Accessory Proteins
keywords: EBOVs; MD simulations; MM/GBSA; SWCNT; VP35