Water-mediated interactions influence the binding of thapsigargin to sarco/endoplasmic reticulum calcium adenosinetriphosphatase.

A crystal structure suggests four water molecules are present in the binding cavity of thapsigargin in sarco/endoplasmic reticulum calcium ATPase (SERCA). Computational chemistry indicates that three of these water molecules mediate an extensive hydrogen-bonding network between thapsigargin and the backbone of SERCA. The orientation of the thapsigargin molecule in SERCA is crucially dependent on these interactions.

Molecular docking with ligand attached water molecules.

A novel approach to incorporate water molecules in protein-ligand docking is proposed. In this method, the water molecules display the same flexibility during the docking simulation as the ligand. The method solvates the ligand with the maximum number of water molecules, and these are then retained or displaced depending on energy contributions during the docking simulation.

On the origin of the stereoselectivity in organocatalysed reactions with trimethylsilyl-protected diarylprolinol.

The origin of the enantioselectivity in the TMS-protected (TMS=trimethylsilyl) prolinol-catalysed alpha-heteroatom functionalisation of aldehydes has been investigated by using density functional theory calculations. Eight different reaction paths have been considered which are based on four different conformers of the TMS-protected prolinol-enamine intermediate. Optimisation of the enamine structures gave two intermediates with nearly the same energy.

Cofactor activation and substrate binding in pyruvate decarboxylase. Insights into the reaction mechanism from molecular dynamics simulations.

We have performed long-term molecular dynamics simulations of pyruvate decarboxylase from Zymomonas mobilis. Nine structures were modeled to investigate mechanistic questions related to binding of the cofactor, thiamin diphosphate (ThDP), and the substrate in the active site. The simulations reveal that the proposed three ThDP-tautomers all can bind in the active site and indicate that the equilibrium is shifted toward 4'-aminopyrimidine ThDP in the absence of substrate.

The first catalytic highly enantioselective alkylation of ketimines--a novel approach to optically active quaternary alpha-amino acids.

A series of novel ketimines with intrinsic protecting group anchoring was synthesized and allowed to react with various silylketene acetals in the presence of 5-10 mol % of a chiral Zn(OTf)(2)-(R,R)-Ph-pybox-aqua complex. The corresponding optically active quaternary alpha-amino acid derivatives were obtained in high yields and with enantioselectivities ranging from 34 % up to 95 % ee. The catalyst was studied by (1)H NMR spectroscopy and X-ray crystallography, and a dynamic equilibrium of two species was identified in solution.