title: 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 consider as case studies dye-labeled protein-DNA intermediates in Cre site-specific recombination. We carried out MD simulations in both an aqueous solution and glycerol/water mixtures to assess the effects of experimental solvent systems on dye dynamics. Our results unequivocally show that MD simulations capture solvent effects and dye-dye interactions that can dramatically affect energy transfer efficiency. We also show that results from SA models and MD simulations strongly diverge in cases where donor and acceptor fluorophores are in close proximity. Although atomistic simulations are computationally more expensive than SA models, explicit MD studies are likely to give more realistic results in both homogeneous and mixed solvents. Our study underscores the model-dependent nature of FRET analyses, but also provides a starting point to develop more realistic in silico approaches for obtaining experimental ensemble and single-molecule FRET data.
authors.affiliation: Department of Bioengineering, University of Texas at Dallas, Richardson, Texas; Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas.
authors.forename: Massa J
authors.initials: MJ
authors.lastname: Shoura
authors.affiliation: Department of Chemistry, University of Texas at Dallas, Richardson, Texas.
authors.forename: R J K Udayana
authors.initials: RJKU
authors.lastname: Ranatunga
authors.affiliation: Department of Physics and Astronomy, University of Leeds, Leeds, UK.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Harris
authors.affiliation: Department of Chemistry, University of Texas at Dallas, Richardson, Texas.
authors.forename: Steven O
authors.initials: SO
authors.lastname: Nielsen
authors.affiliation: Department of Bioengineering, University of Texas at Dallas, Richardson, Texas; Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas; Department of Physics, University of Texas at Dallas, Richardson, Texas. Electronic address: sdlevene@utdallas.edu.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Levene
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes / Q000737:chemistry*; D019426:Integrases / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D012995:Solubility
chemical_list: D005456:Fluorescent Dyes; D004247:DNA; C045073:Cre recombinase; D019426:Integrases
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