Exploring Interaction Mechanisms Between EBOV VP35 And Inhibitor,Carbon Nanotube And DsRNA By Molecular Dynamics Simulation

Ebola viruses(EBOVs)cause an acute and serious illness which is often fatal if untreated,and there is no effective vaccine and drug until now.Multifunctional VP35 is critical for viral replication,RNA silencing suppression and nucleocapsid formation,and it is considered as a future target for the molecular biology technique.Herein,we studied the binding models and interaction mechanisms of the pyrrole-based compounds(GAO 17),single-walled carbon nanotube(SWCNT)and dsRNA binding to the VP35 ?D of Ebola virus by molecular dynamics simulation method.(1)Exploring the binding models and interaction mechanisms of GAO 17 binding to the VP35 IID by molecular dynamics simulation methodThe first basic patch(FBP)of VP35 IID could combine with the nuclear protein of EBOVs,which plays an important role in the transcription and replication of EBOVs.In the present work,the binding of GAO 17 to wild-type(WT),single(K248A,K251A,and I295A)and double(K248A/I295A)mutant VP35 were investigated by all-atom molecular dynamic(MD)simulations and Molecular Mechanics Generalized Born surface area(MM/GBSA)energy calculation.The calculated results indicate that the binding with GA017 makes the binding pocket more stable and reduces the space of the binding pocket.Moreover,the electrostatic interactions(?Eeie)and VDW energy(?Evdw)provide the major forces for affinity binding,and single mutation I295A and double mutation K248A/I295A have great influence on the conformation of the VP35 binding pocket.Interestingly,the residues R300-G301-D302 of I295Aform a new helix and the sheet formed by the residues V294-I295-H296-I297 disappears in the double mutation K248A/I295A as compared with WT.Moreover,the binding free energy calculations show that I295 A and K248A/I295A mutations decrease of absolute binding free energies while K248A and K251A mutations increase absolute binding free energy.Our calculated results are in good agreement with the experimental results that K248A/I295A double mutant results in near-complete loss of compound binding.The obtained information will be useful for design effective inhibitors for treating Ebola virus.(2)Exploring the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 IID FBP of EBOVs by docking and molecular dynamics simulation.Carbon nanotubes,which have a lot of excellent characterizations,gained tremendous attention as a versatile nanomaterial with abundant application.Carbon nanotubes have also demonstrated immense potentials in the areas of drug deliver and drug design.First,docking method was used to investigate the binding model of different size SWCNT,and then 22 conformation were selected to study deeply by MD simulation.Meanwhile the mutant systems(K248A,I295A and K248A/I295A)also were studied by MD simulation and MM/GBSA energy calculation to investigate the effect of residue mutation to the binding.The docking results and MD simulation indicate that longer and bigger SWCNTs have a great effect to the VP35 IID conformation,for example,the SWCNT directly destroyed the secondary structure of VP35 IID in the VS7-a system,and the binding of SWCNT make the a helix formed by 305-309 keep away from the a helix formed by 238-252,all of these prove a longer and bigger SWCNT make the conformation of VP35 ?D unstable.The binding energy calculation indicate that limit increase the length of SWCNT have a positive effect to the binding,but a bigger diameter do not have a significant effect to the binding energy.The key residues mutation have a little effect of the binding free energy between VP35 and SWCNT,although all the three mutant systems have a little decrease.Moreover,the VDW provides the major forces for affinity binding in all the four systems.The results could be an important reference to the toxicity studies and inhibitor design of SWCNT.(3)Exploring the micromechanism of VP35 ?D CBP interaction and recognition dsRNA by molecular dynamics simulation.CBP of VP35 ?D can antagonize host double-stranded RNA(dsRNA)sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends.Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain(IID)abrogates its dsRNA-binding activity,and impairs VP35-mediated interferon(IFN)antagonism.Herein the detailed binding mechanism between dsRNA and WT,single mutant,and double mutant were investigated by all-atom molecular dynamics(MD)simulation and binding energy calculation.R312A/R322Adouble mutations results in a completely different binding site and orientation upon the structure analyses.The calculated binding free energy results reveal that R312A,R322A,and K339A single mutations decrease the binding free energies by 17.82,13.18,and 13.68 kcal/mol,respectively.The binding energy decomposition indicates that the strong binding affinity of the key residues are mainly due to the contributions of electrostatic interactions in the gas phase,where come from the positively charged side chain and the negatively charged dsRNA backbone.R312A,R322A,and K339A single mutations have no significant effect on VP35 IID conformation,but the mutations influence the contributions of electrostatic interactions in the gas phase.The calculated results reveal that end-cap residues which mainly contribute VDW interactions can recognize and capture dsRNA blunt ends,and the central basic residues(R312,R322,and K339)which mainly contribute favorable electrostatic interactions with dsRNA backbone can fix dsRNA binding site and orientation.