Molecular Dynamics Simulations On The Stability Of Hepatitis B Core Virus-like Particles

VLPs(virus-like particles)is one of the research hotspots in the field of biological pharmaceutical engineering.However,VLPs may undergo cracking,aggregation or precipitation as the change of temperature,pH value and other factors during production,storage and transportation,which severely limits the industrialization of VLPs vaccine The binding affinity between protein subunits in VLPs can be simulated by molecular simulations and the binding free energies can be calculated by Molecular Mechanism-Poisson Boltzmann Solvent Accessible surface area(MM-PBSA)method,thus laying a theoretical foundation for the investigation of the stability of VLPs.However,currently,the empirical values of dielectric constants are usually used in the method,resulting in underestimation of the effects of protein molecular structures and the solvent environment.Hepatitis B core virus-like particles HBc-VLPs(hepatitis B core antigen virus-like particles)are widely used as vaccine vectors due to their good stability and easy modification,but the dominant mechanisms affecting the stability of VLPs is still unclear.In this work,the stability of protein complexes with different structures in HBc-VLP was studied by molecular dynamics simulation.The dielectric properties of the protein subunits were calculated statistically according to the macromolecular crowding environment and solvent properties,and then the binding free energies were calculated to obtain the stability of the protein complex structure.The main research contents of this work are as follows:(1)The protein complex of dimer,pentamer,hexamer and a large complex formed by one pentamer and two hexamers were studied by molecular dynamics with emphasis on the investigation of dielectric properties.Instead of the popular practice of using the empirical values of the dielectric constant,this work proposes to study the dynamics of the molecular dipole moments of the protein subunits and further obtain the dielectric constants based on Frohlich-Kirkwood model.The results suggest that the dielectric constant of the protein subunit is affected by the solvent properties and the self-assembly structure of the protein subunit in different complex structures,which would further affect the solvation electrostatic energy.(2)With the dielectric constants of protein subunits calculated,the binding free energy between protein subunits in the corresponding complex structures of HBc-VLP was calculated by MM-PBSA method,and the order of affinity between protein subunits is dimer>pentamer>hexamer.However,the hexamer in the large complex is more stable than the pentameter,and the dimer formed at the interface between the pentameter and the hexamer is the most stable.For all the simulated systems,the van der Waals energy and the non-polar solvation energy promote the stability of each complex,while the electrostatic energy and polar solvation energy will weaken the affinity between the protein subunits.The free energy of binding between subunits obtained by using the empirical value of protein dielectric constant does not consider the charge distribution and electrostatic effect of protein molecules in the local environment,so the accuracy of the obtained free energy of binding is not high.(3)The electric dipole moment generated by the high concentration of ions will change the dielectric properties of the solvent,which in turn will change the dielectric constant of the protein and the calculated value of the binding free energy.The addition of 1.5 mol/L NaCl to the large complex system would enhance the affinity between protein subunits in the pentameter,while the stability of other complexes is slightly weakened.Therefore,the influence of salt ions on the affinity between subunits of the VLPs system needs to be specifically analyzed according to the ion concentration and the aggregation form of protein subunits.