Figure 1.
Examples that illustrate recent applications of DFTB3/MM and CG (BMW-MARTINI) models where the proper description of water proved essential: (a) the proton storage site in bacteriorhodopsin involves a proton delocalized between amino acid side chains that are solvated by active site water;65−67 (b) proton transfers in cytochrome c oxidase proceed through water wire and a neutral glutamate near a hydrophobic cavity;69,75 (c) catalytic specificity and promiscuity in alkaline phosphatase are modulated in part by solvent molecules accessible to the active site;70,71 (d) capturing the distinct phase behaviors of cationic peptide/lipid mixtures with coarse-grained simulations relies on a careful treatment of electrostatics and water.74