Effect of the water model in simulations of protein–protein recognition and association
PublisherMultidisciplinary Digital Publishing Institute (MDPI)
Rights accessOpen Access
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.
CitationEmperador, A.; Crehuet Simon, R.; Guardia, E. Effect of the water model in simulations of protein–protein recognition and association. "Polymers", 6 Gener 2021, vol. 13, núm. 176, p. 1-9.