Paper Citing NAMD - Abstract
Sgourakis, Nikolaos G.; Garcia, Angel E.
The Membrane Complex between Transducin and Dark-State Rhodopsin Exhibits Large-Amplitude Interface Dynamics on the Sub-Microsecond Timescale: Insights from All-Atom MD Simulations
JOURNAL OF MOLECULAR BIOLOGY, 398:161-173, APR 23 2010
Rhodopsin, the prototype class A G-protein-coupled receptor, is a very important model system for all seven-transmembrane domain proteins. Characterization of the interactions between rhodopsin and transducin, its intracellular G-protein counterpart, and the fluctuations in these interactions due to thermal motions is required for an understanding of early events in the mechanism of signal transduction. In this study, we used all-atom molecular dynamics simulations of a transmembrane protein complex between rhodopsin and the heterotrimeric transducin (G alpha beta gamma) in an all-atom DOPC (1,2-dioleoylsn-glycero-3-phosphocholine) membrane-water environment. Based on the analysis of a microsecond-timescale simulation trajectory, we characterized the dynamics of the system and its effects in the structural features of the protein subunits. Our simulations describe a highly dynamic interaction interface where the system is alternating between distinct domain orientations at the 10- to 100-ns timescale that can be further classified into interaction modes involving contacts between distinct structural features on the protein subunits. We related our results with experimental measurements from a variety of studies and high-resolution models of activated rhodopsin. Monitoring key structural features that are involved in the activation process along our simulation trajectory indicates the presence of extensive dynamics in the dark-adapted state, including a motion of Y223 from helix 3 toward the "ionic-lock" interactions of the conserved FRY motif. The dynamic picture shown here is consistent with a framework in which the dark-state fluctuations sample conformations consistent with the activated state. These results provide an atomic-level description of the dynamics of the full complex and further suggest novel mutagenesis experiments that can be used to investigate the stability and dynamics of this model membrane protein receptor system. (C) 2010 Published by Elsevier Ltd.
