There's a whole lot of simulating going on

Another biological ‘water wire’ is reported by Guillaume Lamoureux at U. Penn. and colleagues [Biophys. J. doi:10.1529/biophysj.106.102756]. They have simulated that ammonium transporter AmtB of E. coli, which has a hydrophobic channel that is thought to pass ammonia but to exclude water and charged species. The simulations, however, show that water can get inside and form a three-molecule chain. How this affects the permeation of ammonia (and exclusion of ammonium) isn’t yet clear, but it appears that the mechanisms proposed so far may run into problems.

Ulf Ryde at Lund and colleagues have simulated water in the active-site cavities of four human cytochromes: P450, 2A6, 2C8 and 3A4 [Rydberg et al., J. Phys. Chem. B, doi:10.1021/jp070390c]. In contrast to the crystal structures, they find that all the cavities are filled with water. That in 2A6 is small and contains only two waters, but the others have big cavities with around 40-60 water molecules – a volume of 1500-2100 angstroms. In these big cavities, water is rapidly exchanged with the environment through three to six channels. Those in 2A6 remain bound there, although quite mobile.

L-alanine acts rather like a surfactant in a water droplet, according to the density-functional MD simulations of Ivan Degtyarenko at Helsinki University of Technology and colleagues [J. Phys. Chem. B 111, 4227; 2007]. The amino acid moves to the droplet surface with its methyl group exposed, and the primary hydration shell of (on average seven) ordered and rather rigid water molecules forms around the carboxylate and ammonium groups.

More on the hydration of urea comes from Hinonori Kokubo and Montgomery Pettitt [J. Phys. Chem. B doi:10.1021/jp067659x]. They suggest that, to put it crudely, urea passes almost unnoticed in water – certainly, there’s no evidence of it acting as a structure-breaker. Another nail in the coffin for this hoary old idea.