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Open AccessArticle

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

1
Department of Physics, Universitat Politècnica de Catalunya, B4-B5 Campus Nord, Jordi Girona 1-3, 08034 Barcelona, Spain
2
CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), Jordi Girona 18-26, 08034 Barcelona, Spain
*
Author to whom correspondence should be addressed.
Polymers 2021, 13(2), 176; https://doi.org/10.3390/polym13020176
Received: 3 December 2020 / Revised: 24 December 2020 / Accepted: 29 December 2020 / Published: 6 January 2021
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. View Full-Text
Keywords: water model; protein association; protein–protein interaction; ubiquitin; ACTR; molecular dynamics water model; protein association; protein–protein interaction; ubiquitin; ACTR; molecular dynamics
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MDPI and ACS Style

Emperador, A.; Crehuet, R.; Guàrdia, E. Effect of the Water Model in Simulations of Protein–Protein Recognition and Association. Polymers 2021, 13, 176.

AMA Style

Emperador A, Crehuet R, Guàrdia E. Effect of the Water Model in Simulations of Protein–Protein Recognition and Association. Polymers. 2021; 13(2):176.

Chicago/Turabian Style

Emperador, Agustí; Crehuet, Ramon; Guàrdia, Elvira. 2021. "Effect of the Water Model in Simulations of Protein–Protein Recognition and Association" Polymers 13, no. 2: 176.

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