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.

Bibliographical metadata

Original languageEnglish
JournalJournal of molecular modeling
Publication statusAccepted/In press - 13 Jun 2019