All-atom Molecular Dynamics Studies Of The Protein-protein Interactions Of Ebolavirus

An epidemic of Ebola virus(EBOV)disease causes considerable morbidity and mortality in West Africa.EBOV genome consists of seven viral genes—VP24,VP30,VP35,nucleoprotein(NP),the matrix protein(VP40),the RNA-dependent RNA polymerase(L),as well as the glycoprotein(GP).Ebola nucleocapsid was influenced by three viral proteins which were NP,VP35 and VP24.In this work,we focus on the binding mechanisms of EBOV NP-VP35,NP-VP35 mutants and VP24-KPNA5 using molecular dynamic simulation method.(1)Exploring the binding modes of Ebola viruses nucleoprotein and VP35 by all-atom molecular simulation and computational alanine scanning analysisIn this work,molecular dynamic(MD)simulations were performed to investigate the interaction between free NP N-terminal(NPNTD)and NPNTD in complex with VP35 peptide(NPNTD-VP35).Molecular Mechanics Generalized Born Surface Area(MM-GB/SA)energy calculation was carried out after simulation.Energy analyses revealed that electrostatic interaction and van der Waals(VDW)interaction in the gas phase provide driving forces for binding affinity,especially electrostatic interaction.Moreover,decomposition of binding free energy,hydrogen bonds analysis and computational alanine scanning results suggested that NPNTD residues R240,K248 and R260 as well as VP35 residues E24,E31 and R37 played crucial roles in the binding mode.This research may reveal the detailed binding mechanisms between NPNTD and VP35,and provide insight into designing pharmacological interventions against EBOV.(2)A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide mutantsConformational analysis of the systems demonstrate that combination with VP35 may lead to the conformational transition of NPNTD from "open" to "closed" state.According to the analyses of binding free energies and their decomposition,VP35 residue R37 plays crucial role in wild type(WT)as well as mutant systems.Mutations of 129 and L33 to aspartate as well as M34 to proline affect binding affinity mainly through influencing electrostatic interaction.In addition,mutations mainly affect ?-hairpin and loop regions,among which,M34P may has the greatest influence to the binding,and VP35 residue R37 plays the most cruical role in the binding.The obtained results show that EBOV VP24 binding to KPNA5 will rigidify their binding-face,and both proteins will be compacted during binding.According to the analyses of binding free energies of WT and the eight mutant systems,MUT3 makes the most effectively contributions to the interaction,additionally MUT4,R398A and double mutant have the second effectively influence.It is exhibited that VP24 residues R137 and T138 will be the potential targets for EBOV VP24 inhibitors,and KPNA5 residues R396,8398,R480 will be the potential targets to prevent KPNA5 binding to VP24,which will ultimately block the anti-IFN signaling.Our investigations provide theoretical data to understand the binding modes of EBOV proteins.The precise binding mechanisms of the complex may shed light on the development of potential novel inhibitors against EBOV infection.