Acceptable protein and solvent behavior in primary hydration shell simulations of hen lysozyme.
The "primary hydration shell" method in molecular dynamics simulations uses a two- to three-layer thick shell of explicitly represented water molecules as the solvent around the protein of interest. We show that despite its simplicity, this computationally cheap model is capable of predicting acceptable water and protein behavior using the CHARMM22/CMAP potential function. For protein dynamics, comparisons are made with Lipari-Szabo order parameters. These have been derived from NMR relaxation parameters for pico-nano second motions of the NH groups in the main-chain and NH(2) groups in Asn/Gln side chains in hen lysozyme. It is also shown that an even simpler, and therefore faster, water-shell model leads to results in similarly good agreement with experiments, and also compared with simulations using a full box of water with periodic boundary conditions or with an implicit solvation model. Thus, the primary hydration shell method should be useful in making larger systems accessible to extensive simulations.
Hamaneh
Mehdi Bagheri
MB
Buck
Matthias
M
D000465:Algorithms; D016477:Artifacts; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009113:Muramidase / Q000737:chemistry* / Q000648:ultrastructure*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D012997:Solvents; D014867:Water; C421864:hen egg lysozyme; D009113:Muramidase