title: Modest influence of FRET chromophores on the properties of unfolded proteins.
abstract: Single-molecule Förster resonance energy transfer (FRET) experiments are often used to study the properties of unfolded and intrinsically disordered proteins. Because of their large extinction coefficients and quantum yields, synthetic heteroaromatic chromophores covalently linked to the protein are often used as donor and acceptor fluorophores. A key issue in the interpretation of such experiments is the extent to which the properties of the unfolded chain may be affected by the presence of these chromophores. In this article, we investigate this question using all-atom explicit solvent replica exchange molecular dynamics simulations of three different unfolded or intrinsically disordered proteins. We find that the secondary structure and long-range contacts are largely the same in the presence or absence of the fluorophores, and that the dimensions of the chain with and without chromophores are similar. This suggests that, at least in the cases studied, extrinsic fluorophores have little effect on the structural properties of unfolded or disordered proteins. We also find that the critical FRET orientational factor κ(2), has an average value and equilibrium distribution very close to that expected for isotropic orientations, which supports one of the assumptions frequently made when interpreting FRET efficiency in terms of distances.
authors.affiliation: Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania.
authors.forename: Gül H
authors.initials: GH
authors.lastname: Zerze
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Best
authors.affiliation: Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania. Electronic address: jeetain@lehigh.edu.
authors.forename: Jeetain
authors.initials: J
authors.lastname: Mittal
mesh_terms: D031541:Fluorescence Resonance Energy Transfer; D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D012997:Solvents / Q000737:chemistry
chemical_list: D064267:Intrinsically Disordered Proteins; D012997:Solvents