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

Standard

The Influence of Water Potential in Simulation: a Catabolite Activator Protein Case Study. / Liem, Yun; Popelier, Paul.

In: Journal of molecular modeling, 2019.

Research output: Contribution to journalArticlepeer-review

Harvard

APA

Vancouver

Author

Bibtex

@article{5e660339da1c42f6a6b6bc81ee23ce6e,
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. ",
keywords = "SPC, TIP3P, TIP4P, TIP5P, ff12SB, ff99SB, Force Field, Protein, Molecular Dynamics",
author = "Yun Liem and Paul Popelier",
year = "2019",
doi = "10.1007/s00894-019-4095-3",
language = "English",
journal = "Journal of molecular modeling",
issn = "1610-2940",
publisher = "Springer Nature",

}

RIS

TY - JOUR

T1 - The Influence of Water Potential in Simulation: a Catabolite Activator Protein Case Study

AU - Liem, Yun

AU - Popelier, Paul

PY - 2019

Y1 - 2019

N2 - 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.

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

KW - TIP3P

KW - TIP4P

KW - TIP5P

KW - ff12SB

KW - ff99SB

KW - Force Field

KW - Protein

KW - Molecular Dynamics

U2 - 10.1007/s00894-019-4095-3

DO - 10.1007/s00894-019-4095-3

M3 - Article

JO - Journal of molecular modeling

JF - Journal of molecular modeling

SN - 1610-2940

ER -