Homology Modeling And Molecular Docking Of Helicobacter Pylori GyrB Protein

Helicobacter pylori(HP)infection can cause a series of stomach lesions,even induce gastric cancer.Interaction between Fic-1 protein with Fic domain and GyrB domain in DNA helicase.GyrB is an indispensable constituent protein in the process of biological genetic information replication and transduction.However,the specific mode between Fic-1 protein and GyrB is not yet clear,there is no Helicobacter pylori DNA helicase GyrB protein three-dimensional structure in PDB database.Therefore,in this paper,the homology modeling of Helicobacter pylori DNA helicase GyrB was carried out by computer simulation and the molecular docking with Fic-1protein to explore the specific interaction.After careful screening,the crystal structure of Streptococcus pneumoniae,the crystal structure of Escherichia coli DNA helicase,the crystal structure of GyrB ATPase region of Mycobacterium tuberculosis and the crystal structure of Staphylococcus aureus DNA helicase were determined as templates to construct Helicobacter pylori DNA gyrase GyrB crystal structure by using homology modeling method,after repeated optimization and energy minimization,through the Ramachandran plot and Verify3 D structural rationality analysis,continuous screening.Subsequently,the GyrB crystal structure was obtained by homology modeling.The structure is evaluated by Ramachandran plot,with 95.1% of the residues in allowed region and4.9% of the residues in impermissible region,and none of the residues in impermissible region were not critical Residues;84.99% of the residues had a Verify3 D score > 0.2,and less than 10%amino acid residues have a Verify3 D score <0.Therefoer,it is a reasonable conformation for molecular docking.In order to explore the specific interaction between GyrB and Fic-1,the optimal structural model of Helicobacter pylori DNA helicase GyrB and Fic-1 protein were molecular docking experiments to explore the specific interaction.After docking,the analysis of the optimal docking model revealed that the key residues in the GyrB model were:Tyr-708,Leu-711,Asn-715,Pro-716,Leu-748,Pro-756,Arg-757,Arg-758 and Ala-759;the key residues in the Fic-1werePhe-246,Asn-247,Leu-249,Met-258,Asn-315,Cys-316,Leu-319,Ser-320,Met-423,Arg-424,Gly-426,Phe-427 and Pro-428.The interaction between Fic-1 and GyrB is hydrophobic,hydrogen-bonding and cation-? interaction.The interaction between the two residues determines the stability of the Fic-1/GyrB complex.The above studies show that the interaction between Helicobacter pylori DNA helicase GyrB and Fic-1 provides a powerful theoretical basis for the design of effective drugs that blockHelicobacter pylori infection at the molecular level.