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

Polymers

卷:13

Ramon Crehuet¹  Elvira Guàrdia²  Agustí Emperador² 

[1] CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), Jordi Girona 18-26, 08034 Barcelona, Spain;

[2] Department of Physics, Universitat Politècnica de Catalunya, B4-B5 Campus Nord, Jordi Girona 1-3, 08034 Barcelona, Spain;

关键词: water model;    protein association;    protein–protein interaction;    ubiquitin;    ACTR;    molecular dynamics;   

DOI  :  10.3390/polym13020176

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown