Study On The Dynamics Of Proteins With The Effect Of Electric Field And Electrolyte Solution

Proteins,which has the functions of nutrient storage,contractile activity,defense,identification,catalysis,transportation and regulation in organisms,are the main undertakers of life activities in the organism.In recent years,the researches on proteins have been well investigated and some significant results have been obtained.Because of the strict requirements in preparing protein samples and hardly representation of the protein in vivo by conventional experimental methods,it is urgent to improve the current methods in studying the proteins.With the development of computer technology and large-scale parallel computing,more and more scientists start studying the scientific problems about protein system by computer simulations.It becomes the third way to discover the real world besides experimental and theoretical methods.In this thesis,the background and research status about proteins in a complex environment are briefly introduced.The theoretical basis and the procedure of molecular dynamics simulation are explained.The software and representations or parameters are declared.Then,the dynamic behaviors of proteins in the external electric field or electrolyte solutions are well investigated by the molecular dynamics simulations.The main contents of this thesis are listed as follows:(1)The effect of the external electric field on the structural transition of the protein is studied by molecular dynamics simulations.The results show that the values of root mean square deviation and radius of gyration sharply increase with simulation time when the electric field is high enough.The characteristic time,which the structural parameters reach the plateau,decreases with increasing external electric field strength.The dipole moment along the direction of electric field increases with the strength of it,indicating the orientation of the charged residues in the protein.The number of intramolecular hydrogen bonds is inversely proportional to the radius of gyration of the protein.It indicates the positive effect on stabilization of the protein.The secondary structural analysis by Stride algorithm show that ? sheet is easily to unfold than ? helix with the applying the electric field.(2)The effect of the electrolyte solutions on the potential energy and structural properties of the protein is studied by molecular dynamics simulations.The results show that the bonded-potential energy is hardly influenced by external electrolyte solutions.VDW energy slightly increases but the electrostatic potential energy sharply decreases with the concentration of the electrolyte solution.The concentration and the valence number of ions both affect the protein system.In a certain concentration of the electrolyte solution(0.3 mol/L),the radius of gyration of the protein has the minimum value,which indicate the looser structure with low stability.With the increase of concentration and the valence number of ions of the electrolyte solution,? helix trends to unwinding.But the electrolyte solution with the medium concentration promotes the formation of ? sheet.