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Nano-domains in ionic liquids (IL) that involve cations with long attached alkyl chains are characterized by analyzing their structural and energetic features. Nitrate anions that are paired with guanidinium-based cations, to which alkyl chains of increasing length from butyl to decyl are attached, are simulated with molecular dynamics simulations. All simulations utilize our previously developed...
Human DNA polymerase β (pol β) fills gaps in DNA as part of base excision DNA repair. Due to its small size it is a convenient model enzyme for other DNA polymerases. Its active site contains two Mg 2+ ions, of which one binds an incoming dNTP and one catalyzes its condensation with the DNA primer strand. Simulating such binuclear metalloenzymes accurately but computationally efficiently is...
The GTPase Ras p21 is a crucial switch in cellular signal transduction. Fourier transform infrared (FTIR) spectra of the substrate guanosine triphosphate (GTP) show remarkable changes when it binds to the enzyme. The reduced band widths indicate that the flexible GTP molecule is guided by the protein into a preferred conformation. The delocalized phosphate vibrations of unbound GTP become localized...
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