3.5 Molecular Dynamics Simulation
We performed molecular dynamics simulations of target proteins and three candidates up to 100ns long. The results showed that the complex formed by combining the three ligands with the target protein was stable, which further indicated that the three ligands could be candidates for the target protein. We calculated the energy changes in the 100ns process (figure 19), analyzed the energy changes in the complex during the simulation process, and concluded that the ligand target protein interaction was in an appropriate state. For the complexes of NLPR3 protein and its three candidates, the total energy of the whole simulation was about -2115,000 ~ -2100,000 kJ/mol.
Root mean square deviation (RMSD) was also calculated to study the binding stability of the target protein to the receptor. As can be seen from figure 20 (a), RMSD values of the three ligands and target protein complexes all increased around 0~15ns, and then tended to stabilize, with a very stable curve. The RMSD variation of 2007_22057 with target protein complex was larger than that of the other two ligands. From this result, it can be concluded that during the period of 0~15ns, ligand binds to target protein, leading to significant changes in RMSD value, after which RMSD value tends to be stable, indicating that the complex has good stability. The RMSD change curve of the protein (FIG. 20 (b)) is similar to the RMSD change curve of the complex, while the RMSD change curve of the ligand (FIG. 20 (c)) is different from the other two change curves, possibly because the RMSD value of the ligand is lower, contributing less to the RMSD value of the complex.
Protein compactness changes can be expressed by calculating Gyrate. The gyrate value measures the distance of the atom relative to each center of mass. The smaller the value, the smaller the rotation change, indicating that during the simulation process, the denser the complex. In general, the rate of rotation tends to decline. It can be seen from figure 21 (a) that the three ligands and target proteins were in the simulation process, and the gyrate of the proteins was stable after 20ns, while the gyrate was not significantly changed during the whole simulation process, indicating that the stability of the complex was good. Moreover, the gyrate of the protein showed a decreasing trend after 80ns, indicating that the structure was tightened. It can be seen from figure 21 (b) that the gyrate of the three ligands in the simulation process is more complicated than that of the protein, but the value is smaller, which has little influence on the whole.
By calculating MSD, we can judge the changes between the initial state and the final state of the protein and ligand, which can show the movement trend of each ligand or protein. The lower the MSD value, the higher the stability of the complex. On the contrary, the higher the MSD value, the lower the stability of the complex. And the rise of MSD values show that ligand has a tendency to escape, as can be seen from the figure 22 (a), in the process of the whole simulation, the combination of three ligand and protein MSD values continue to rise, explain three ligands are there is a certain trend of escape, and (b) in figure 22, three ligands in simulation of the final stages of MSD values decreased shows three ligands have stable trend.
Through SASA analysis, we can understand the hydrophobicity and surface state of proteins. As can be seen from figure 23 (a), the SAS value of proteins tends to be stable after the first decline. It can be seen from figure 23 (b) that the SASA values of all ligands are very stable in the simulation process. This can further determine the stability of the complex.
Through RMSF analysis, we can detect the fluctuation of each residue and understand the changes of key residues during simulation. The average structure of a protein is an average set of atomic coordinates. From figure 24, we can see the RMSF value of each protein residue during the simulation of the three ligands and proteins. The higher the RMSF value, the greater the variation of the residue during simulation.
The average structure of the three ligands and proteins in the simulation process was superimposed with the corresponding final state structure (FIG. 25) to observe whether the two structures were similar, so as to determine the stability of the complex bound to the target protein. Our RMSD values were 1.341, 0.952, and 1.388, respectively. This indicates that the three ligand - target protein binding complexes have good stability in the simulated final state.
Finally, the initial and final states of ligand and target proteins in the simulation process are shown in figure 26. The ligand stays in the same pocket of the target protein throughout the simulation.