Back to Search
Start Over
Improving the Performance of MM/PBSA in Protein–Protein Interactions via the Screening Electrostatic Energy
- Source :
- Journal of Chemical Information and Modeling. 61:2454-2462
- Publication Year :
- 2021
- Publisher :
- American Chemical Society (ACS), 2021.
-
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.
- 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
Subjects
Details
- ISSN :
- 1549960X and 15499596
- Volume :
- 61
- Database :
- OpenAIRE
- Journal :
- Journal of Chemical Information and Modeling
- Accession number :
- edsair.doi.dedup.....66c47dbfcf404050c12bf8082d4b97ab