The Influence of Water Potential in Simulation: a Catabolite Activator Protein Case Study

Yun Liem; Paul Popelier

doi:10.1007/s00894-019-4095-3

The Influence of Water Potential in Simulation: a Catabolite Activator Protein Case Study

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Abstract

We present a rare comparison of structures of the same protein but generated by different potentials. We used 4 popular water potentials (SPC, TIP3P, TIP4P, TIP5P) in conjunction with the equally popular ff99SB. However, the ff12SB protein potential was used with TI3P only. Simulations (60 ns) were run on the catabolite activator protein (CAP), which is a textbook case of allosteric interaction. Overall, all potentials generated largely similar structures but failed to reproduce a crucial structural feature determined by NMR experiment. This example shows the need to develop next-generation potentials.

Original language	English
Journal	Journal of molecular modeling
Early online date	10 Jul 2019
DOIs	https://doi.org/10.1007/s00894-019-4095-3
Publication status	Published - 2019

Keywords

SPC
TIP3P
TIP4P
TIP5P
ff12SB
ff99SB
Force Field
Protein
Molecular Dynamics

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title = "The Influence of Water Potential in Simulation: a Catabolite Activator Protein Case Study",

abstract = "We present a rare comparison of structures of the same protein but generated by different potentials. We used 4 popular water potentials (SPC, TIP3P, TIP4P, TIP5P) in conjunction with the equally popular ff99SB. However, the ff12SB protein potential was used with TI3P only. Simulations (60 ns) were run on the catabolite activator protein (CAP), which is a textbook case of allosteric interaction. Overall, all potentials generated largely similar structures but failed to reproduce a crucial structural feature determined by NMR experiment. This example shows the need to develop next-generation potentials. ",

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AU - Liem, Yun

AU - Popelier, Paul

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AB - We present a rare comparison of structures of the same protein but generated by different potentials. We used 4 popular water potentials (SPC, TIP3P, TIP4P, TIP5P) in conjunction with the equally popular ff99SB. However, the ff12SB protein potential was used with TI3P only. Simulations (60 ns) were run on the catabolite activator protein (CAP), which is a textbook case of allosteric interaction. Overall, all potentials generated largely similar structures but failed to reproduce a crucial structural feature determined by NMR experiment. This example shows the need to develop next-generation potentials.

KW - SPC

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KW - TIP4P

KW - TIP5P

KW - ff12SB

KW - ff99SB

KW - Force Field

KW - Protein

KW - Molecular Dynamics

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SN - 1610-2940

JO - Journal of molecular modeling

JF - Journal of molecular modeling

ER -

The Influence of Water Potential in Simulation: a Catabolite Activator Protein Case Study

Abstract

Keywords

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