Effect of the Water Model in Simulations of Protein-Protein Recognition and Association.

ABSTRACT: 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.

SUBMITTER: Emperador A 

PROVIDER: S-EPMC7825341 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature