Conformational flexibility and binding interactions of the G protein ?? heterodimer.

ABSTRACT: Previous NMR experiments on unbound G protein ?? heterodimer suggested that particular residues in the binding interface are mobile on the nanosecond timescale. In this work we performed nanosecond-timescale molecular dynamics simulations to investigate conformational changes and dynamics of G?? in the presence of several binding partners: a high-affinity peptide (SIGK), phosducin, and the GDP-bound ? subunit. In these simulations, the high mobility of G?W99 was reduced by SIGK, and it appeared that a tyrosine might stabilize G?W99 by hydrophobic or aromatic stacking interactions in addition to hydrogen bonds. Simulations of the phosducin-G?? complex showed that the mobility of G?W99 was restricted, consistent with inferences from NMR. However, large-scale conformational changes of G?? due to binding, which were hypothesized in the NMR study, were not observed in the simulations, most likely due to their short (nanosecond) duration. A pocket consisting of hydrophobic amino acids on G? appears to restrict G?W99 mobility in the crystal structure of the G???? heterotrimer. The simulation trajectories are consistent with this idea. However, local conformational changes of residues G?W63, G?W211, G?W297, G?W332, and G?W339 were detected during the MD simulations. As expected, the magnitude of atomic fluctuations observed in simulations was greater for ? than for the ?? subunits, suggesting that ? has greater flexibility. These observations support the notion that to maintain the high mobility of G?W99 observed by solution NMR requires that the G?-? interface must open up on time scale longer than can be observed in nanosecond scale simulations.

SUBMITTER: Park MS 

PROVIDER: S-EPMC3974715 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature