IRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.

ABSTRACT: The HIV-1 transactivation response RNA element (TAR), which is essential to the lifecycle of the virus, has been suggested, based on NMR and hydrodynamic measurements, to undergo substantial, collective, structural dynamics that are important for its function. To deal with the significant coupling between overall diffusional rotation and internal motion expected to exist in TAR, here we utilize an isotropic reorientational eigenmode dynamics analysis of simulated molecular trajectories to obtain a detailed description of TAR dynamics and an accurately quantified pattern of dynamical correlations. The analysis demonstrates the inseparability of internal and overall motional modes, confirms the existence and reveals the nature of collective domain dynamics, and additionally reveals that the

SUBMITTER: Musselman C 

PROVIDER: S-EPMC1896250 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature