date: 2023-03-20T07:56:08Z
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pdf:docinfo:title: Comparison of Empirical Zn2+ Models in Protein?DNA Complexes
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Keywords: zinc ions; protein?DNA complex; molecular dynamics simulations
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subject: Zinc ions are the second most abundant ions found in humans. Their role in proteins can be merely structural but also catalytic, owing to their transition metal character. Modelling their geometric?coordination versatility by empirical force fields is, thus, a challenging task. In this work, we evaluated three popular models, specifically designed to represent zinc ions with regard to their capability of preserving structural integrity. To this end, we performed molecular dynamics simulations of two zinc-containing protein?DNA complexes, which differed in their zinc coordination, i.e., four cysteines or two cysteines and two histidines. The most flexible non-bonded 12-6-4 Lennard?Jones-type model shows a preference for six-fold coordination of the Zn2+-ions in contradiction to the crystal structure. The cationic dummy atom model favours tetrahedral geometry, whereas the bonded extended zinc AMBER force field model, by construction, best preserves the initial geometry of a regular or slightly distorted tetrahedron. Our data renders the extended zinc AMBER force field the best model for structural zinc ions in a given geometry. In more complicated cases, though, more flexible models may be advantageous.
dc:creator: Senta Volkenandt and Petra Imhof
dcterms:created: 2023-03-20T07:51:31Z
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dcterms:modified: 2023-03-20T07:56:08Z
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title: Comparison of Empirical Zn2+ Models in Protein?DNA Complexes
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pdf:docinfo:keywords: zinc ions; protein?DNA complex; molecular dynamics simulations
pdf:docinfo:modified: 2023-03-20T07:56:08Z
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dc:title: Comparison of Empirical Zn2+ Models in Protein?DNA Complexes
modified: 2023-03-20T07:56:08Z
cp:subject: Zinc ions are the second most abundant ions found in humans. Their role in proteins can be merely structural but also catalytic, owing to their transition metal character. Modelling their geometric?coordination versatility by empirical force fields is, thus, a challenging task. In this work, we evaluated three popular models, specifically designed to represent zinc ions with regard to their capability of preserving structural integrity. To this end, we performed molecular dynamics simulations of two zinc-containing protein?DNA complexes, which differed in their zinc coordination, i.e., four cysteines or two cysteines and two histidines. The most flexible non-bonded 12-6-4 Lennard?Jones-type model shows a preference for six-fold coordination of the Zn2+-ions in contradiction to the crystal structure. The cationic dummy atom model favours tetrahedral geometry, whereas the bonded extended zinc AMBER force field model, by construction, best preserves the initial geometry of a regular or slightly distorted tetrahedron. Our data renders the extended zinc AMBER force field the best model for structural zinc ions in a given geometry. In more complicated cases, though, more flexible models may be advantageous.
pdf:docinfo:subject: Zinc ions are the second most abundant ions found in humans. Their role in proteins can be merely structural but also catalytic, owing to their transition metal character. Modelling their geometric?coordination versatility by empirical force fields is, thus, a challenging task. In this work, we evaluated three popular models, specifically designed to represent zinc ions with regard to their capability of preserving structural integrity. To this end, we performed molecular dynamics simulations of two zinc-containing protein?DNA complexes, which differed in their zinc coordination, i.e., four cysteines or two cysteines and two histidines. The most flexible non-bonded 12-6-4 Lennard?Jones-type model shows a preference for six-fold coordination of the Zn2+-ions in contradiction to the crystal structure. The cationic dummy atom model favours tetrahedral geometry, whereas the bonded extended zinc AMBER force field model, by construction, best preserves the initial geometry of a regular or slightly distorted tetrahedron. Our data renders the extended zinc AMBER force field the best model for structural zinc ions in a given geometry. In more complicated cases, though, more flexible models may be advantageous.
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pdf:docinfo:creator: Senta Volkenandt and Petra Imhof
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creator: Senta Volkenandt and Petra Imhof
meta:author: Senta Volkenandt and Petra Imhof
dc:subject: zinc ions; protein?DNA complex; molecular dynamics simulations
meta:creation-date: 2023-03-20T07:51:31Z
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meta:keyword: zinc ions; protein?DNA complex; molecular dynamics simulations
Author: Senta Volkenandt and Petra Imhof
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