The Study Of The External Effects On The Structure Of Two All-? Proteins By Molecular Dynamics Simulation

Protein,as an important component of organism tissues and organs,plays the crucial role in life activities.In recent years,the researches on proteins are growing vigorously and some significant results have been obtained.However,due to the strict requirements of the conventional experimental methods and sample preparation of the protein,it can not clearly reflect the structural transformation process of protein in the organism.With the rapid development of computer technology,more and more researchers use computer simulation to study protein system.In this paper,the molecular dynamics simulation method is applied to study two all-?proteins including.(1)The temperature effect on the structure of proteins was studied by molecular dynamics simulation.The results showed that with the increasing temperature,the bond energy,including bond-stretching energy,bond-bending energy and bond-torsional energy,is increased.While van der Waals energy are decreased with the increasing temperature.The total potential energy increases due to the increase of electrostatic energy.(2)The dynamic behavior of the wild type(WT)and mutant(D43N)of protein1BBL in an external electric field was studied.It was found that the stability of wild-type and mutant decreased and their structure became more incompact when they were applied to the external electric field.In addition,the flexibility of some fragments in mutant(D43N)is increased.(3)The structural characteristic of proteins immersed in different concentration of salt solution was studied.The conformational transition,radial distribution function and the number of hydrogen bonds of protein 1BBL and protein 2BRD in different types of salt solution were well discussed.The simulation results show that compared with other divalent cationic salt solutions,the addition of Ca²⁺significantly reduces the number of hydrogen bonds in the protein to decrease the stability of the protein.The radial distribution function reveals the distribution rules of cations and carboxylic oxygen in salt solution.The results also concluded that the binding of Na Cl and KCl with the protein is closer than divalent cation salt solution.(4)MD simulations were performed to investigate the effect of Au-nanoparticles on the structural stability and conformational transition of the protein 1BBL.According to the analysis of the energy and structural information,the results show that the van der Waals energy is sharply decreased with the increasing size of the nanoparticles,which as the basic reason for the decrease of the total potential energy.Meanwhile,the radius of gyration of the protein increases,and the structural stability is weakened as the number of hydrogen bonds decreased.Our simulation results also clearly capture the structural transitions of the protein sample from helix to turn or random coil conformation induced by the increasing size of the Au-nanoparticles.