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.
| Original language | English |
|---|---|
| Pages (from-to) | 399-408 |
| Number of pages | 10 |
| Journal | Journal of Chemical Information and Modeling |
| Volume | 59 |
| Issue number | 1 |
| DOIs | |
| State | Published - 28 Jan 2019 |
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Assessing the Performance of the Nonbonded Mg2+ 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 journal › Article
TY - JOUR
T1 - Assessing the Performance of the Nonbonded Mg2+ Models in a Two-Metal-Dependent Ribonuclease
AU - Zuo, Zhicheng
AU - Liu, Jin
PY - 2019/1/28
Y1 - 2019/1/28
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85059486112&partnerID=8YFLogxK
U2 - 10.1021/acs.jcim.8b00627
DO - 10.1021/acs.jcim.8b00627
M3 - Article
C2 - 30521334
AN - SCOPUS:85059486112
VL - 59
SP - 399
EP - 408
JO - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
SN - 1549-9596
IS - 1
ER -