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Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

Kyungreem HanRichard M VenableAnne-Marie BryantChristopher J LegacyRong ShenHui LiBenoı T RouxArne GerickeRichard W Pastor
Published in: The journal of physical chemistry. B (2018)
All-atom molecular dynamics simulations combined with graph-theoretic analysis reveal that clustering of monomethyl phosphate dianion (MMP2-) is strongly influenced by the types and combinations of cations in the aqueous solution. Although Ca2+ promotes the formation of stable and large MMP2- clusters, K+ alone does not. Nonetheless, clusters are larger and their link lifetimes are longer in mixtures of K+ and Ca2+. This "synergistic" effect depends sensitively on the Lennard-Jones interaction parameters between Ca2+ and the phosphorus oxygen and correlates with the hydration of the clusters. The pronounced MMP2- clustering effect of Ca2+ in the presence of K+ is confirmed by Fourier transform infrared spectroscopy. The characterization of the cation-dependent clustering of MMP2- provides a starting point for understanding cation-dependent clustering of phosphoinositides in cell membranes.
Keyphrases
  • single cell
  • ionic liquid
  • rna seq
  • molecular dynamics simulations
  • cell migration
  • aqueous solution
  • protein kinase
  • convolutional neural network
  • gene expression
  • machine learning
  • risk assessment