1. Improving the Performance of MM/PBSA in Protein–Protein Interactions via the Screening Electrostatic Energy
- Author
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Yue-Wen Yin, Hong-ming Ding, Yan-Jing Sheng, and Yu-qiang Ma
- Subjects
Work (thermodynamics) ,Materials science ,010304 chemical physics ,Binding free energy ,Force field (physics) ,Adipates ,General Chemical Engineering ,Electric potential energy ,Static Electricity ,Binding energy ,Thermodynamics ,Succinates ,General Chemistry ,Interaction energy ,Dielectric ,Molecular Dynamics Simulation ,Library and Information Sciences ,01 natural sciences ,0104 chemical sciences ,Computer Science Applications ,Protein–protein interaction ,010404 medicinal & biomolecular chemistry ,0103 physical sciences ,Protein Binding - Abstract
Accurate calculation of protein-protein binding free energy is of great importance in biological and medical science, yet it remains a hugely challenging problem. In this work, we develop a new strategy in which a screened electrostatic energy (i.e., adding an exponential damping factor to the Coulombic interaction energy) is used within the framework of the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Our results show that the Pearson correlation coefficient in the modified MM/PBSA is over 0.70, which is much better than that in the standard MM/PBSA, especially in the Amber14SB force field. In particular, the performance of the standard MM/PBSA is very poor in a system where the proteins carry like charges. Moreover, we also calculated the mean absolute error (MAE) between the calculated and experimental ΔG values and found that the MAE in the modified MM/PBSA was indeed much smaller than that in the standard MM/PBSA. Furthermore, the effect of the dielectric constant of the proteins and the salt conditions on the results was also investigated. The present study highlights the potential power of the modified MM/PBSA for accurately predicting the binding energy in highly charged biosystems.
- Published
- 2021