title: Three-dimensional molecular modeling with single molecule FRET.
abstract: Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes.
authors.affiliation: The Howard Hughes Medical Institute, Stanford University, CA 94305, USA. brunger@stanford.edu
authors.forename: Axel T
authors.initials: AT
authors.lastname: Brunger
authors.forename: Pavel
authors.initials: P
authors.lastname: Strop
authors.forename: Marija
authors.initials: M
authors.lastname: Vrljic
authors.forename: Steven
authors.initials: S
authors.lastname: Chu
authors.forename: Keith R
authors.initials: KR
authors.lastname: Weninger
mesh_terms: D003198:Computer Simulation; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D005456:Fluorescent Dyes / Q000737:chemistry; D007091:Image Processing, Computer-Assisted; D046911:Macromolecular Substances / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation
chemical_list: D005456:Fluorescent Dyes; D046911:Macromolecular Substances