title: A toolkit and benchmark study for FRET-restrained high-precision structural modeling.
abstract: We present a comprehensive toolkit for Förster resonance energy transfer (FRET)-restrained modeling of biomolecules and their complexes for quantitative applications in structural biology. A dramatic improvement in the precision of FRET-derived structures is achieved by explicitly considering spatial distributions of dye positions, which greatly reduces uncertainties due to flexible dye linkers. The precision and confidence levels of the models are calculated by rigorous error estimation. The accuracy of this approach is demonstrated by docking a DNA primer-template to HIV-1 reverse transcriptase. The derived model agrees with the known X-ray structure with an r.m.s. deviation of 0.5 Å. Furthermore, we introduce FRET-guided 'screening' of a large structural ensemble created by molecular dynamics simulations. We used this hybrid approach to determine the formerly unknown configuration of the flexible single-strand template overhang.
authors.affiliation: Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität (HHU), Düsseldorf, Germany. stanislav.kalinin@uni-duesseldorf.de
authors.forename: Stanislav
authors.initials: S
authors.lastname: Kalinin
authors.forename: Thomas
authors.initials: T
authors.lastname: Peulen
authors.forename: Simon
authors.initials: S
authors.lastname: Sindbert
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Rothwell
authors.forename: Sylvia
authors.initials: S
authors.lastname: Berger
authors.forename: Tobias
authors.initials: T
authors.lastname: Restle
authors.forename: Roger S
authors.initials: RS
authors.lastname: Goody
authors.forename: Holger
authors.initials: H
authors.lastname: Gohlke
authors.forename: Claus A M
authors.initials: CA
authors.lastname: Seidel
mesh_terms: D017931:DNA Primers / Q000737:chemistry; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D054303:HIV Reverse Transcriptase / Q000737:chemistry*; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation
chemical_list: D017931:DNA Primers; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase