Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study.

ABSTRACT: In Förster resonance energy transfer (FRET) experiments, extracting accurate structural information about macromolecules depends on knowing the positions and orientations of donor and acceptor fluorophores. Several approaches have been employed to reduce uncertainties in quantitative FRET distance measurements. Fluorophore-position distributions can be estimated by surface accessibility (SA) calculations, which compute the region of space explored by the fluorophore within a static macromolecular structure. However, SA models generally do not take fluorophore shape, dye transition-moment orientation, or dye-specific chemical interactions into account. We present a detailed molecular-dynamics (MD) treatment of fluorophore dynamics for an ATTO donor/acceptor dye pair and specifically conside

SUBMITTER: Shoura MJ 

PROVIDER: S-EPMC4129480 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature