Water residence times around copper plastocyanin: a molecular dynamics simulation approach

Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose

“…In order to have sufficient data to calculate the SISF for water in the shells close to lysozyme and trehalose molecules we now consider water oxygen atoms located ≤ 4 Å and ≤ 6 Å from every trehalose or lysozyme atom (see also Refs. 48 or 49). We compare the results obtained from the system containing trehalose and lysozyme, Lyz-Tr(aq) with the ones obtained from the system containing lysozyme only, Lyz(aq).…”

Multinuclear Relaxation Dispersion Studies of Protein Hydration

“…5.3 known that the dynamic perturbation is essentially confined to water molecules in direct contact with the surface (Woessner, 1980;Carlström and Halle, 1988;Volke et al, 1994). That this is the case also for proteins is suggested by molecular dynamics simulations (Brunne et al, 1993;Garcia and Stiller, 1993;Lounnas and Pettitt, 1994;Abseher et al, 1996;Rocchi et al, 1997;Kovacs et al, 1997). It is therefore reasonable to estimate for a monolayer, e.g., using the solvent-accessible surface area of the protein (as computed from crystallographic data) and a molecular area of 15 per water molecule.…”

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

“…We defined those water molecules within 3.5 Å from any of the groove atoms as part of the hydration shell immediately surrounding the DNA, while those beyond 10 Å are defined as bulk water. Since the water molecules can migrate from one solvation shell to another, a dynamic checking of the location of the water molecules is essential during the analysis [85,86]. We characterized the temperature dependent dynamical behavior of the above-defined water species by following the velocity autocorrelation, diffusion, residence time, and the lifetime.…”