Dynamics of non-covalent interactions during the P-O bond cleavage reaction by ribonuclease A.

In this work, an atomistic-scale investigation of the phosphodiester P-O bond cleavage reaction by the enzyme ribonuclease A was carried out using computer simulation techniques. It is shown that during the reaction the network of non-covalent interactions in the active center of the ribonuclease changes significantly, while the role of these non-covalent interactions is different: coordination of the corresponding groups, electron density transfer, and ligand holding in the active center. It is shown that the process of proton transfer from Asp121 to His119 is the first stage of this reaction; at the same time, the hydrogen bond between the phosphate ligand and the imino group of Arg39 is broken, which, although keeping the ligand in the active center, does not allow the ligand to orient itself more conveniently for subsequent proton transfers.

Distribution of zwitter-ionic tryptophan between the micelles of 1-dodecyl-3-methyl imidazolium and aqueous medium from molecular dynamic simulation.

Ionic liquids that form micelles have great potential as drug carriers and separating agents for bioactive substances. For such applications, a key issue is the distribution of the target substance between the micelle and its environment. We perform MD simulations to study solubilization of zwitter-ionic tryptophan in micelles of 1-dodecyl-3-methylimidazolium bromide.

Structural Properties of Span 80/Tween 80 Reverse Micelles by Molecular Dynamics Simulations.

The sorbitan monooleate (Span 80)/poly(oxyethylene) sorbitan monooleate (Tween 80) reverse micelles (RMs) in the water-in- n-decane microemulsion were studied using the molecular dynamics simulation. The coexistence of the large RMs with the hydrodynamic radii R ∼ 10-20 nm and small RMs with R ∼ 1-2 nm was previously specified for this system. Models of both surfactants and decane were based on the united-atom approach to allow us to describe the structural properties of the small RMs.