Assessing the Performance of the Nonbonded Mg 2+ Models in a Two-Metal-Dependent Ribonuclease

Zhicheng Zuo, Jin Liu

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Magnesium ions (Mg 2+ ), abundant in living cells, are essential for biomolecular structure, dynamics, and function. The biological importance of Mg 2+ has motivated continuous development and improvement of various Mg 2+ models for molecular dynamics (MD) simulations during the last decades. There are four types of nonbonded Mg 2+ 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 Mg 2+ 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 Mg 2+ -containing biomolecular systems.

Original languageEnglish
Pages (from-to)399-408
Number of pages10
JournalJournal of Chemical Information and Modeling
Volume59
Issue number1
DOIs
StatePublished - 28 Jan 2019

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Ribonucleases
Metals
performance
Lennard-Jones potential
Molecular dynamics
Ribonuclease H
simulation
Computer simulation
RNA
Magnesium
Metal ions
DNA
Cells
Ions
interaction

Cite this

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abstract = "Magnesium ions (Mg 2+ ), abundant in living cells, are essential for biomolecular structure, dynamics, and function. The biological importance of Mg 2+ has motivated continuous development and improvement of various Mg 2+ models for molecular dynamics (MD) simulations during the last decades. There are four types of nonbonded Mg 2+ 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 Mg 2+ 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 Mg 2+ -containing biomolecular systems.",
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Assessing the Performance of the Nonbonded Mg 2+ Models in a Two-Metal-Dependent Ribonuclease . / Zuo, Zhicheng; Liu, Jin.

In: Journal of Chemical Information and Modeling, Vol. 59, No. 1, 28.01.2019, p. 399-408.

Research output: Contribution to journalArticle

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