A toolkit and benchmark study for FRET-restrained high-precision structural modeling

Stanislav Kalinin; Thomas Peulen; Simon Sindbert; Paul J. Rothwell; Sylvia Berger; Tobias Restle; Roger S. Goody; Holger Gohlke; Claus A.M. Seidel

doi:10.1038/nmeth.2222

A toolkit and benchmark study for FRET-restrained high-precision structural modeling

Stanislav Kalinin^*, Thomas Peulen, Simon Sindbert, Paul J. Rothwell, Sylvia Berger, Tobias Restle, Roger S. Goody, Holger Gohlke, Claus A.M. Seidel

^*Korrespondierende/r Autor/-in für diese Arbeit

352 Zitate (Scopus)

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.

Originalsprache	Englisch
Zeitschrift	Nature Methods
Jahrgang	9
Ausgabenummer	12
Seiten (von - bis)	1218-1225
Seitenumfang	8
ISSN	1548-7091
DOIs	https://doi.org/10.1038/nmeth.2222
Publikationsstatus	Veröffentlicht - 01.12.2012

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We dedicate this paper to the memory of our brilliant colleague, Robert M. Clegg, a pioneer in the application of FRET in the life sciences and a remarkable human being. We would like to thank E. Schweinberger, O. Kensch and B.M. Wöhrl for assistance with the experiments, E. Haustein for analytical software, H. Sanabria for help with data visualization and A. Scheidig for helpful discussions. We acknowledge financial support from the Volkswagen Foundation (to R.S.G. and C.A.M.S.; grant no. I/74470), Max-Planck Society (to R.S.G.), German Federal Ministry of Education and Research (BMBF) (BioFuture grant no. 0311865) and German Science Foundation within SPP 1258 (grant no. SE 1195/12-2) (to C.A.M.S.) and ‘Fit for Excellence’ initiative of HHU (to H.G.). T.P. thanks the International Helmholtz Research School of Biophysics and Soft Matter (IHRS BioSoft), and S.S. thanks the NRW Research School of Biological Structures in Molecular Medicine and Biotechnology (BioStruct) for scholarships.

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abstract = "We present a comprehensive toolkit for F{\"o}rster 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 {\AA}. 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.",

author = "Stanislav Kalinin and Thomas Peulen and Simon Sindbert and Rothwell, \{Paul J.\} and Sylvia Berger and Tobias Restle and Goody, \{Roger S.\} and Holger Gohlke and Seidel, \{Claus A.M.\}",

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AU - Kalinin, Stanislav

AU - Peulen, Thomas

AU - Sindbert, Simon

AU - Rothwell, Paul J.

AU - Berger, Sylvia

AU - Restle, Tobias

AU - Goody, Roger S.

AU - Gohlke, Holger

AU - Seidel, Claus A.M.

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AB - 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.

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A toolkit and benchmark study for FRET-restrained high-precision structural modeling

Abstract

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