Evaluation on performance of MM/PBSA in nucleic acid-protein systems

doi:10.1088/1674-1056/ac3a5c

中国物理B ›› 2022, Vol. 31 ›› Issue (4): 48701-048701.doi: 10.1088/1674-1056/ac3a5c

Evaluation on performance of MM/PBSA in nucleic acid-protein systems

Yuan-Qiang Chen(陈远强)¹, Yan-Jing Sheng(盛艳静)¹, Hong-Ming Ding(丁泓铭)^1,†, and Yu-Qiang Ma(马余强)^2,‡

1 Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China;
2 National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China

收稿日期:2021-10-11 修回日期:2021-11-11 接受日期:2021-11-17 出版日期:2022-03-16 发布日期:2022-03-16
通讯作者: Hong-Ming Ding, Yu-Qiang Ma E-mail:dinghm@suda.edu.cn;myqiang@nju.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11874045 and 11774147).

Evaluation on performance of MM/PBSA in nucleic acid-protein systems

Yuan-Qiang Chen(陈远强)¹, Yan-Jing Sheng(盛艳静)¹, Hong-Ming Ding(丁泓铭)^1,†, and Yu-Qiang Ma(马余强)^2,‡

1 Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China;
2 National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China

Received:2021-10-11 Revised:2021-11-11 Accepted:2021-11-17 Online:2022-03-16 Published:2022-03-16
Contact: Hong-Ming Ding, Yu-Qiang Ma E-mail:dinghm@suda.edu.cn;myqiang@nju.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11874045 and 11774147).

1. 2022-048701-SI.pdf(686KB)

摘要/Abstract

摘要： The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method has been widely used in predicting the binding affinity among ligands, proteins, and nucleic acids. However, the accuracy of the predicted binding energy by the standard MM/PBSA is not always good, especially in highly charged systems. In this work, we take the protein-nucleic acid complexes as an example, and showed that the use of screening electrostatic energy (instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA. In particular, the Pearson correlation coefficient of dataset II in the modified MM/PBSA (i.e., screening MM/PBSA) is about 0.52, much better than that (< 0.33) in the standard MM/PBSA. Further, we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA. The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.

关键词: molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA), screening electrostatic interaction, protein, nucleic acid, molecular dynamics simulation

Abstract: The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method has been widely used in predicting the binding affinity among ligands, proteins, and nucleic acids. However, the accuracy of the predicted binding energy by the standard MM/PBSA is not always good, especially in highly charged systems. In this work, we take the protein-nucleic acid complexes as an example, and showed that the use of screening electrostatic energy (instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA. In particular, the Pearson correlation coefficient of dataset II in the modified MM/PBSA (i.e., screening MM/PBSA) is about 0.52, much better than that (< 0.33) in the standard MM/PBSA. Further, we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA. The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.

Key words: molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA), screening electrostatic interaction, protein, nucleic acid, molecular dynamics simulation

中图分类号: (Proteins)

87.14.E-

87.14.G- (Nucleic acids) 87.15.A- (Theory, modeling, and computer simulation) 87.15.kj (Protein-polynucleotide interactions)

Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强). Evaluation on performance of MM/PBSA in nucleic acid-protein systems[J]. 中国物理B, 2022, 31(4): 48701-048701.

Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强). Evaluation on performance of MM/PBSA in nucleic acid-protein systems[J]. Chin. Phys. B, 2022, 31(4): 48701-048701.

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Evaluation on performance of MM/PBSA in nucleic acid-protein systems

Evaluation on performance of MM/PBSA in nucleic acid-protein systems

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