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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Bibliographic Details
Published inPolymers Vol. 13; no. 2; p. 176
Main Authors Emperador, Agustí, Crehuet, Ramon, Guàrdia, Elvira
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 06.01.2021
MDPI
Subjects
ACTR
Binding
Fluid dynamics
Interfaces
molecular dynamics
Physical simulation
protein association
Proteins
protein–protein interaction
Simulation
ubiquitin
water model
protein association
protein–protein interaction
water model
molecular dynamics
ACTR
ubiquitin
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Summary: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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ISSN:2073-4360
2073-4360
DOI:10.3390/polym13020176