Effect of the Water Model in Simulations of Protein–Protein Recognition and Association

We study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the abs...

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Detalles Bibliográficos
Autores principales: Emperador, Agustí, Crehuet, Ramon, Guàrdia, Elvira
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825341/
https://www.ncbi.nlm.nih.gov/pubmed/33419008
http://dx.doi.org/10.3390/polym13020176
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author Emperador, Agustí
Crehuet, Ramon
Guàrdia, Elvira
author_facet Emperador, Agustí
Crehuet, Ramon
Guàrdia, Elvira
author_sort Emperador, Agustí
collection PubMed
description We study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the absence of dissociation events. We also find that TIP4P/2005 is the only water model that reproduces the fast association/dissociation dynamics of ubiquitin and best identifies its binding surface. Our results show the critical role of the water model in the description of protein–protein interactions and binding.
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spelling pubmed-78253412021-01-24 Effect of the Water Model in Simulations of Protein–Protein Recognition and Association Emperador, Agustí Crehuet, Ramon Guàrdia, Elvira Polymers (Basel) Article We study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the absence of dissociation events. We also find that TIP4P/2005 is the only water model that reproduces the fast association/dissociation dynamics of ubiquitin and best identifies its binding surface. Our results show the critical role of the water model in the description of protein–protein interactions and binding. MDPI 2021-01-06 /pmc/articles/PMC7825341/ /pubmed/33419008 http://dx.doi.org/10.3390/polym13020176 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Emperador, Agustí
Crehuet, Ramon
Guàrdia, Elvira
Effect of the Water Model in Simulations of Protein–Protein Recognition and Association
title Effect of the Water Model in Simulations of Protein–Protein Recognition and Association
title_full Effect of the Water Model in Simulations of Protein–Protein Recognition and Association
title_fullStr Effect of the Water Model in Simulations of Protein–Protein Recognition and Association
title_full_unstemmed Effect of the Water Model in Simulations of Protein–Protein Recognition and Association
title_short Effect of the Water Model in Simulations of Protein–Protein Recognition and Association
title_sort effect of the water model in simulations of protein–protein recognition and association
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825341/
https://www.ncbi.nlm.nih.gov/pubmed/33419008
http://dx.doi.org/10.3390/polym13020176
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