|In this work we report molecular dynamics simulation at room temperature of three proteins (1CRN Crambin, 1ENG engrailed Homeodomain and 1VII Villain Headpiece) in water using the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. Many body polarization effects are a key element of this force field, which uses permanent atomic multipoles through quadrupole and induced dipole. |
We show that water molecules located in protein clefts present longer residence times than those in the bulk, indicating that a distinct dynamics of hydrogen bonds take place inside the protein layer. Structural and dynamics properties of water about specific protein groups were analyzed using selected distribution and self correlation functions. Numerical estimates of dipole moment fluctuations and averages were also performed, showing consistent correlations for each hydrated structure. This response of water when subjected to heterogeneous environments accents the relevance of using polarizable force fields in biomolecular simulations.
PHYS Poster Session - Water Mediated Interactions
7:30 PM-10:00 PM, Wednesday, August 20, 2008 Pennsylvania Convention Center -- Hall C, Poster