The influence of water potential in simulation: a catabolite activator protein case study
Steven Y Liem1,2, Paul L A Popelier3,4
1Manchester Institute of Biotechnology (MIB), University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain.
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.
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