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<p>Magnesium is an essential element involved in diverse life activities. The strong polarization and significant charge transfer effects pose challenges to the traditional fixed charge force fields. Here we establish the ABEEM/MM magnesium force field for proteins and aqueous solutions. The interaction potentials of magnesium with water and proteins are treated as the ABEEM/MM bonded model (ABEEM-BM) in the Morse potential function form. Based on quantum mechanical (QM) results, the related parameters are optimized and determined. The charge distributions of model molecules from ABEEM-BM and the ABEEM/MM nonbonded model (ABEEM-NBM) agree well with the QM results. The potential energy surfaces (PESs) for bond stretching and angle bending between magnesium and ligands by ABEEM-BM have a good consistency with those from QM. Molecular dynamics (MD) simulations of 40 aqueous magnesium protein segments are carried out using ABEEM-BM, ABEEM-NBM, OPLS-AA, AMBER99, and CHARMM22 force fields. The root mean square deviations (RMSDs) for bond length and angle by ABEEM-BM are 0.088 Å and 5.99°, respectively, which are smaller than those from the others. MD simulations of aqueous magnesium solutions are carried out using ABEEM-BM and ABEEM-NBM. The radial and angular distribution functions from ABEEM-BM reproduce the best structural properties, and the rate constant is 4.7 × 10<sup>5</sup> s<sup>− 1</sup>. Moreover, the dynamic changing picture of charge transfer and the coordination number (CN) during water exchange processes is presented by ABEEM model. The overall performance of ABEEM models is evidently better than those from fixed charge force fields.</p> Graphical Abstract <p></p>

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ABEEM/MM Magnesium Force Field for Proteins and Aqueous Solutions

  • 期刊论文

  • 发表日期：

    2025年8月14日

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  • Jing Zhang,
  • Linan Lu,
  • Runqiang Yu,
  • Linlin Liu,
  • Lei Wang,
  • Cui Liu,
  • Lidong Gong,
  • Zhongzhi Yang

摘要

Magnesium is an essential element involved in diverse life activities. The strong polarization and significant charge transfer effects pose challenges to the traditional fixed charge force fields. Here we establish the ABEEM/MM magnesium force field for proteins and aqueous solutions. The interaction potentials of magnesium with water and proteins are treated as the ABEEM/MM bonded model (ABEEM-BM) in the Morse potential function form. Based on quantum mechanical (QM) results, the related parameters are optimized and determined. The charge distributions of model molecules from ABEEM-BM and the ABEEM/MM nonbonded model (ABEEM-NBM) agree well with the QM results. The potential energy surfaces (PESs) for bond stretching and angle bending between magnesium and ligands by ABEEM-BM have a good consistency with those from QM. Molecular dynamics (MD) simulations of 40 aqueous magnesium protein segments are carried out using ABEEM-BM, ABEEM-NBM, OPLS-AA, AMBER99, and CHARMM22 force fields. The root mean square deviations (RMSDs) for bond length and angle by ABEEM-BM are 0.088 Å and 5.99°, respectively, which are smaller than those from the others. MD simulations of aqueous magnesium solutions are carried out using ABEEM-BM and ABEEM-NBM. The radial and angular distribution functions from ABEEM-BM reproduce the best structural properties, and the rate constant is 4.7 × 105 s− 1. Moreover, the dynamic changing picture of charge transfer and the coordination number (CN) during water exchange processes is presented by ABEEM model. The overall performance of ABEEM models is evidently better than those from fixed charge force fields.

Graphical Abstract