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

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) we...

Descripción completa

Detalles Bibliográficos
Autores principales: Liem, Steven Y., Popelier, Paul L. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2019
Materias:
Original Paper
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7406532/
https://www.ncbi.nlm.nih.gov/pubmed/31292786
http://dx.doi.org/10.1007/s00894-019-4095-3
_version_ 1783567443546865664
author Liem, Steven Y.
Popelier, Paul L. A.
author_facet Liem, Steven Y.
Popelier, Paul L. A.
author_sort Liem, Steven Y.
collection PubMed
description 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. [Figure: see text]
format Online
Article
Text
id pubmed-7406532
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Springer Berlin Heidelberg
record_format MEDLINE/PubMed
spelling pubmed-74065322020-08-13 The influence of water potential in simulation: a catabolite activator protein case study Liem, Steven Y. Popelier, Paul L. A. J Mol Model Original Paper 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. [Figure: see text] Springer Berlin Heidelberg 2019-07-10 2019 /pmc/articles/PMC7406532/ /pubmed/31292786 http://dx.doi.org/10.1007/s00894-019-4095-3 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Original Paper
Liem, Steven Y.
Popelier, Paul L. A.
The influence of water potential in simulation: a catabolite activator protein case study
title The influence of water potential in simulation: a catabolite activator protein case study
title_full The influence of water potential in simulation: a catabolite activator protein case study
title_fullStr The influence of water potential in simulation: a catabolite activator protein case study
title_full_unstemmed The influence of water potential in simulation: a catabolite activator protein case study
title_short The influence of water potential in simulation: a catabolite activator protein case study
title_sort influence of water potential in simulation: a catabolite activator protein case study
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7406532/
https://www.ncbi.nlm.nih.gov/pubmed/31292786
http://dx.doi.org/10.1007/s00894-019-4095-3
work_keys_str_mv AT liemsteveny theinfluenceofwaterpotentialinsimulationacataboliteactivatorproteincasestudy
AT popelierpaulla theinfluenceofwaterpotentialinsimulationacataboliteactivatorproteincasestudy
AT liemsteveny influenceofwaterpotentialinsimulationacataboliteactivatorproteincasestudy
AT popelierpaulla influenceofwaterpotentialinsimulationacataboliteactivatorproteincasestudy

Ejemplares similares