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.