# Molecular Dynamics Simulation Reveal the Structure-Activity Relationships of Kainoid Synthases
## 2 Results and Discussion
### Binding Energy Analysis of Kainoid Synthases  
In the case of solvation energy, RMSD, Rg, distance, Buried SASA, and interaction energy were comprehensively considered to select the complex trajectory in a stable state. The MM-PBSA (Molecular Mechanics-Poisson Boltzmann Surface Area) method was used to calculate the binding-energy-related terms, as shown in the Table 2. From the enthalpy point of view alone, since the water box is a polar environment, the protein cavity is usually a non-polar environment, so the substrate is easy to bind to water, but not easy to bind to enzymes. On account of the fact that substrates cNGG and PKA are easy to dissolve in water, we considered the \(\Delta\)Epol. In the PnDabC-cNGG complex, the electrostatic interaction \(\Delta\)Eele was higher than the van der Waals force interaction energy \(\Delta\)Evdw, the former being 3.1 times the latter. Both \(\Delta\)Eele and \(\Delta\)Evdw were much higher than the hydrophobic interaction \(\Delta\)Enonpol. Therefore, in the composition of the PnDabC-cNGG binding energy, the electrostatic interaction played a major role and the van der Waals force interaction played a minor role, while the hydrophobic interaction played a complementary role. The \(\Delta\)EMMPBSA of PnDabC-cNGG was 74.724 \(\pm\) 6.145 kJ/mol, which was greater than zero. This is because small molecules carry more charges and have larger electrostatic interactions, which makes the polar solvation energy larger, resulting in the final calculated binding energy being greater than zero. The electrostatic interaction \(\Delta\)Eele in the DsKabC-PKA complex was higher than the van der Waals force interaction energy. The former was 3.2 times the latter, and both were much higher than the hydrophobic interaction \(\Delta\)Enonpol. Therefore, in the composition of DsKabC-PKA binding energy, the electrostatic interaction played a major role, the van der Waals force interaction played a secondary role, and the hydrophobic interaction played a supplementary role. The \(\Delta\)EMMPBSA of DsKabC-PKA was 34.465 \(\pm\) 2.689 kJ/mol, which was greater than zero due to polar solvation energy as well. For the GfKabC-PKA complex, the electrostatic interaction \(\Delta\)Eele in the complex was higher than the van der Waals force interaction energy \(\Delta\)Evdw, being three times \(\Delta\)Evdw. Both were much higher than the hydrophobic interaction \(\Delta\)Enonpol. Therefore, \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Complex** & **PnDabC-cNGG** & **DsKabC-PKA** & **GfKabC-PKA** \\ \hline \(\Delta\)Evdw & \(-133.164\pm 6.729\) & \(-71.61\pm 1.427\) & \(-60.76\pm 5.734\) \\ \(\Delta\)Eele & \(-411.14\pm 25.248\) & \(-230.503\pm 3.59\) & \(-186.169\pm 19.89\) \\ \(\Delta\)Epol & \(641.384\pm 24.122\) & \(351.107\pm 4.775\) & \(244.753\pm 21.658\) \\ \(\Delta\)Enonpol & \(-22.355\pm 0.216\) & \(-14.529\pm 0.031\) & \(-13.796\pm 0.807\) \\ \(\Delta\)EMMPBSA & \(74.724\pm 6.145\) & \(34.465\pm 2.689\) & \(-15.972\pm 4.005\) \\ \(-\)TAS & \(82.94\pm 6.966\) & \(32.564\pm 2.885\) & \(53.314\pm 6.549\) \\ \(\Delta\)Gibnd 1  & 157.664 \(\pm\) 4.835 & \(67.029\pm 4.931\) & \(37.342\pm 2.572\) \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Binding energy and its composition in stable state (unit kJ/mol). Figure 16: The relaxation level and electrostatic potential energy of the active pocket of kainoid synthases at the midpoint of the simulation. in the composition of GfKabC-PKA binding energy, the electrostatic interaction played a major role, the van der Waals force interaction played a secondary role, and the hydrophobic interaction played a supplementary role. The \(\Delta\)EMMPBSA of GfKabC-PKA was \(-15.972\pm 4.005\) kJ/mol. \(\Delta\)Epol of GfKabC-PKA was the smallest, which indicates that more easily dissolved in the simulation process of GfKabC-PKA and the water molecule had the greatest influence on the complex system. Enzyme promiscuity is a modern term that is not fully understood at present.