Ion selectivity in protein binding sites is of great significance to biological functions.Although additive force fields have been successfully applied to various protein-related studies,it is difficult to well captur...Ion selectivity in protein binding sites is of great significance to biological functions.Although additive force fields have been successfully applied to various protein-related studies,it is difficult to well capture the subtle metal-protein interaction for the prediction of ion selectivity,due to the remarkable polarization and charge transfer effect between the metals and the surrounding residues.Quantum mechanics-based methods are well-suited for dealing with these systems,but they are too costly to apply in a direct manner.In this work,the reference-potential method(RPM)was used to measure the selectivity for calcium and magnesium cations in the binding pocket of parvalbumin B protein by calculating the free energy change associated with this substitution reaction at an ab initio quantum mechanics/molecular mechanics(QM/MM)level.The alchemical transformations were performed at the molecular mechanics level,and the relative binding free energy was then corrected to the QM/MM level via thermodynamic perturbation.In this way,the free energy change at the QM/MM level for the substitution reaction was obtained without running the QM/MM simulations,thus remarkably enhancing the efficiency.In the reweighting process,we found that the selection of the QM region greatly affects the accuracy of the QM/MM method.In particular,the charge transfer effect on the free energy change of a reaction cannot be neglected.展开更多
基金supported by the Ministry of Science and Technology of China(No.2016YFA0501700)the National Natural Science Foundation of China(No.22073030)supported by the Supercomputer Center of East China Normal University(ECNU Public Platform for Innovation No.001)。
文摘Ion selectivity in protein binding sites is of great significance to biological functions.Although additive force fields have been successfully applied to various protein-related studies,it is difficult to well capture the subtle metal-protein interaction for the prediction of ion selectivity,due to the remarkable polarization and charge transfer effect between the metals and the surrounding residues.Quantum mechanics-based methods are well-suited for dealing with these systems,but they are too costly to apply in a direct manner.In this work,the reference-potential method(RPM)was used to measure the selectivity for calcium and magnesium cations in the binding pocket of parvalbumin B protein by calculating the free energy change associated with this substitution reaction at an ab initio quantum mechanics/molecular mechanics(QM/MM)level.The alchemical transformations were performed at the molecular mechanics level,and the relative binding free energy was then corrected to the QM/MM level via thermodynamic perturbation.In this way,the free energy change at the QM/MM level for the substitution reaction was obtained without running the QM/MM simulations,thus remarkably enhancing the efficiency.In the reweighting process,we found that the selection of the QM region greatly affects the accuracy of the QM/MM method.In particular,the charge transfer effect on the free energy change of a reaction cannot be neglected.
