Molecular Dynamics Study Of Catalase Exerted By External Electric Field

Catalase(CAT)is a kind of terminal oxidoreductase with great significance in nature.Typical catalases usually consist of four identical subunits,each of which has about 460 amino acid residues.CAT can specifically and efficiently catalyze the decomposition of hydrogen peroxide into oxygen and water.Based on this principle,CAT is widely used in the field of electrochemical hydrogen peroxide biosensor to detect hydrogen peroxide content.To date,the relevant properties of CAT under the electric field in the detection process are not fully understood.Therefore,the study explores the properties of CAT under a certain electric field by means of molecular dynamics simulation.On this basis,in order to better maintain the stability of the CAT enzyme electrode of biosensor and prolong its service life,in the mean time,ensuring that the CAT enzyme protein structure does not affect the folding assembly and function of the amino acid structure,the mutant CAT system was constructed by further modifying seven amino acid residues on the outer surface of each subunit of CAT,which reduces the charge amount.The properties of the mutant CAT system was studied in terms of microscopic scale through molecular dynamics simulation.In addition,preliminary modeling and molecular dynamics simulation of graphene were carried out in this thesis,which provided a theoretical reference for further understanding of the adsorption mechanism between the catalase-graphene electrode and the adsorption performance of the biosensor.In this study,the crystal structure of catalase derived from Enterococcus faecalis organisms and expressed in Bacillus subtilis was obtained from the PDB protein database.After pretreatment,the initial CAT system and the modified mutant CAT system model were constructed and applied.Molecular dynamics simulation of CAT system and mutant CAT system were carried out by GROMACS software under certain intensity of electric field.The simulation results of CAT and mutant CAT system under electric field were as follows: The total energy,potential energy and kinetic energy remained basically unchanged.The energy of LJ(SR),angle and proper dihedral angle fluctuated slightly,RMSD,RMSF,and radius of gyration Rg all had a small upward trend,while the atomic versus distance volatility was large,The forms and quantities of alpha-helix and beta-fold in enzymatic proteins changed slightly,The number of internal hydrogen bonds remained unchanged between the enzyme proteins,while the number of hydrogen bonds fluctuated slightly between the enzyme protein with the surrounding solvent water molecules.Compared with CAT system,the moving distance of the center of mass in the mutant CAT simulation system was significantly smaller in the direction of electric field,and the overall results of the above-mentioned levels changed more smoothly and steadily.In conclusion,under the electric field,the three-dimensional structure of the whole enzyme protein remained basically balanced and stable.Compared with the CAT simulation system,the energy term,the stability of the backbone atoms and the internal structure of the enzyme protein,the movement of amino acid residues,the shape and volume of the molecular structure of the enzyme protein in different directions,and the secondary structure of the mutant CAT simulation system were less affected by the electric field,and the whole system was more stable and gentle.It provides a theoretical reference for further improvement and application of catalase electrode.