Molecular Dynamics Simulation On Conformational Rearrangement Of A Broad Neutralizing Antibody To Adaptively Fit The Receptor Binding Site Of H5N1 Influenza Virus

Influenza virus with its strong mutation ability and wide global transmission ability,can cause human respiratory diseases and even cause death,which seriously threaten people's health and cause serious disease burden,the problem has become a major global public health problem.Among them,the avian influenza H5 and H7 subtypes are highly susceptible to pandemic epidemics due to their high pathogenicity,especially the H5N1 and H7N9 influenza viruses have gradually become one of the most threatening infectious diseases for humans.The high variability of the recognized epitopes of different types of influenza viruses has caused great difficulties in the design of vaccines and drugs against influenza viruses.Therefore,it is urgent to further explore the process of influenza viruses being recognized and bound by antibodies in vivo,laying a foundation for the prevention and treatment of anti-influenza virusesThe head of the hemagglutinin protein of the influenza virus is the major recognition region of the neutralizing antibody and thus can also be involved in mediating the binding of virus to host cells.The receptor-binding region of the head of hemagglutinin protein appears as a groove structure,which is specifically recognized by the host sialic acid receptor during infected,and its recognition site is conserved,which can used as a potential target for designing anti-influenza drugs.Although a variety of therapeutic compounds against influenza viruses targeting hemagglutinin have been developed in recent years,their practical effects have been limited.The binding process between influenza virus and antibody needs to be further explored to provide a theoretical basis for drug and vaccine development.With the development of computer technology,structural biology and bioinformatics,the biomacromolecular simulation and drug devvelopment by computer-aided has become more and more popular.Compared with experimental methods,molecular dynamics simulation of protein recognition process has the advantages of observing the effects of molecular disturbance,dynamically observing the recognition process,and understanding the protein allostery process,etc.,and has become an important means of exploring the protein recognition process.This study is based on the crystal structure of fragment antigen binding(Fab)region of the wide-spectrum neutralizing antibody 13D4 against H5N1 and 13D4 Fab:hemagglutinin(HA,VN1194 strains)complex,which determined by our laboratory.The crystal structure of the complex was analyzed by bioinformatics software such as Discovery Studio,and the important role of the 13D4 antibody heavy chain complementarity determining region3(HCDR3)in the binding process was elucidated.Through the structural alignment between the free 13D4 Fab and the complex,we found that 13D4 antibody HCDR3 undergoes allosteric transformation in the binding state and penetrates into the binding domain of HA protein,and fully interacts with HA protein,so as to better fit the groove structure of HA protein head.The simple alignment and superposition between the free 13D4 Fab and the complex structure shows that there is a collision between the free 13D4 Fab and the HA protein.Based on the above exploration of the structure,we used three different molecular dynamics simulation methods to simulate the recognition and allosteric phenomenon of 13D4 antibody and HA protein.The analysis of the simulation results shows that the simulation of conventional dynamics and steer dynamics simulation based on the model is not ideal.After considering the collision phenomena in the model and the steer dynamics simulation make the HCDR3 close to HA too fast,we attempts to improve the simulation method,and proposed a new molecular dynamics simulation strategy for the recognition of allosteric proteins.Based on the model's multiple dynamics simulations,the recognition mechanism of 13D4 antibody and HA protein was further explained,which laid a theoretical foundation and provided data support for the design of targeted influenza virus peptide and vaccine design.Dynamic simulation based on this strategy can more accurately simulate the recognition process of free antibody and antigen epitope,provide a structural basis for further explaining the recognition mechanism of 13D4 antibody and HA protein,in order to design a targeted influenza virus peptide and particle vaccine,which laying a theoretical foundation and providing data support for the design targeted influenza virus peptides and particle vaccines.In summary,based on the crystal structure of 13D4 Fab and 13D4:HA complex,this study used bioinformatics software to analyze antigen-antibody interactions,revealing the important role of 13D4 antibody HCDR3 in the process of HA protein recognition.The molecular dynamics methods was used to simulate the allosteric fit phenomenon of 13D4 antibody HCDR3 in the recognition process of binding region with receptor,and the mechanism of action of 13D4 antibody was elucidated at the atomic level.According to the structural characteristics of 13D4:HA,different dynamics simulation methods were adopted,and manual stepwise molecular dynamics method based on step by step was established,which provided a theoretical basis for further exploring the neutralization epitopes and neutralization mechanism of influenza virus.At the same time,it provides new ideas for the preventions of specical virus based on receptor binding sites and the design of therapeutic peptides and drugs for influenza.