Paper Citing NAMD - Abstract
Jardon-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J.
Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin
BIOPHYSICAL JOURNAL, 99:2200-2207, OCT 6 2010
The light-induced isomerization of the retinal from 11-cis to all-trans triggers changes in the conformation of visual rhodopsins that lead to the formation of the activated state, which is ready to interact with the G protein. To begin to understand how changes in the structure and dynamics of the retinal are transmitted to the protein, we performed molecular dynamics simulations of squid rhodopsin with 11-cis and all-trans retinal, and with two different force fields for describing the retinal molecule. The results indicate that structural rearrangements in the binding pocket, albeit small, propagate toward the cytoplasmic side of the protein, and affect the dynamics of internal water molecules. The sensitivity of the active-site interactions on the retinal force-field parameters highlights the coupling between the retinal molecule and its immediate protein environment.
