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• W2903876351 abstract "Magnesium ions (Mg2+), abundant in living cells, are essential for biomolecular structure, dynamics, and function. The biological importance of Mg2+ has motivated continuous development and improvement of various Mg2+ models for molecular dynamics (MD) simulations during the last decades. There are four types of nonbonded Mg2+ models: the point charge models based on a 12–6 or 12–6–4 type Lennard-Jones (LJ) potential, and the multisite models based on a 12–6 or 12–6–4 LJ potential. Here, we systematically assessed the performance of these four types of nonbonded Mg2+ models (21 models in total) in terms of maintaining a challenging intermediate state configuration captured in the structure of a prototypical two-metal-ion RNase H complex with an RNA/DNA hybrid. Our data demonstrate that the 12–6–4 multisite models, which account for charge-induced dipole interactions, perform the best in reproducing all the unique coordination modes in this intermediate state and maintaining the correct carboxylate denticity. Our benchmark work provides a useful guideline for MD simulations and structural refinement of Mg2+-containing biomolecular systems." @default.
• W2903876351 created "2018-12-22" @default.
• W2903876351 creator A5073165804 @default.
• W2903876351 creator A5081800735 @default.
• W2903876351 date "2018-12-06" @default.
• W2903876351 modified "2023-09-27" @default.
• W2903876351 title "Assessing the Performance of the Nonbonded Mg²⁺ Models in a Two-Metal-Dependent Ribonuclease" @default.
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• W2903876351 doi "https://doi.org/10.1021/acs.jcim.8b00627" @default.
• W2903876351 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/30521334" @default.
• W2903876351 hasPublicationYear "2018" @default.
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