Computers

  2010 JUN 17 - (VerticalNews.com) -- "The hysteresis observed frequently in the adsorption isotherm of gas in porous material is currently subject to intense research. The nature of the hysteresis itself and in particular recent observations on the uptake dynamics inside the hysteresis loop are described as poorly understood puzzles even in recent literature (Wallacher, D.; Kunzer, N.; Kovalev, D.; Knorr, N.; Knorr, K. Phys. Rev. Lett. 2004, 92, 195704-1; Valiullin, R.; Naumov, S.; Galvosas, P.; Karger, J.; Woo, H.-J.; Porcheron, F.; Monson, P. Nature 2006, 443, 965-968)," scientists in Leipzig, Germany report ...read more

  2010 MAY 6 - (VerticalNews.com) -- According to a study from the United States, "Developing accurate models of water for use in computer simulations is important for the study of many chemical and biological systems, including lipid bilayer self-assembly. The large temporal and spatial scales needed to study such self-assembly have led to the development and application of coarse-grained models for the lipid lipid, lipid solvent, and solvent solvent interactions. ...read more

  2010 MAY 6 - (VerticalNews.com) -- "We have carried out a DFT computational investigation of the catalytic mechanism of caspases, using a model system obtained from the crystallographic structure of caspase-7. In particular, we have considered the activation of the catalytic dyad (His-144 and Cys-186) and the breaking of the substrate peptide bond," scientists in Bologna, Italy report.

  "We have suggested a novel mechanism for the catalytic activation, which is rather different from that usually proposed for other cysteine proteases. Following our hypothesis the activation mechanism consists of three distinct kinetic steps leading to the protonation of the catalytic His-144 and the deprotonation of Cys-186, which is activated as a nucleophile. This mechanism corresponds to a rather complex multiple proton transfer where the substrate aspartate and one water molecule act as proton shuttles. The role played by the aspartate group explains the high specificity of caspases toward substrates containing the aspartate residue that behaves as a cofactor. Apart from acting as proton shuttles and ''assisting'' almost all proton transfers, the two water molecules included in our model form a complex network of hydrogen bonds that involve enzyme and substrate and stabilize the charges developing on the substrate during of the reaction. We have demonstrated the existence of an alternative reaction channel leading directly from the initial complex to the peptide bond cleavage in a single kinetic step," wrote G.P. Miscione and colleagues, University of Bologna ...read more