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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 four 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. Graphical abstract Catabolite activator protein.

SUBMITTER: Liem SY

PROVIDER: S-EPMC7406532 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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The influence of water potential in simulation: a catabolite activator protein case study.

Liem Steven Y SY Popelier Paul L A PLA

Journal of molecular modeling 20190710 8

We present a rare comparison of structures of the same protein but generated by different potentials. We used four 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 str ...[more]

PMID: 31292786

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