Effect of the Water Model in Simulations of Protein-Protein Recognition and Association
POLYMERS(2021)
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.
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关键词
water model,protein association,protein–,protein interaction,ubiquitin,ACTR,molecular dynamics
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