Document Detail


A toolkit and benchmark study for FRET-restrained high-precision structural modeling.
MedLine Citation:
PMID:  23142871     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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:
Stanislav Kalinin; Thomas Peulen; Simon Sindbert; Paul J Rothwell; Sylvia Berger; Tobias Restle; Roger S Goody; Holger Gohlke; Claus A M Seidel
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-11-11
Journal Detail:
Title:  Nature methods     Volume:  -     ISSN:  1548-7105     ISO Abbreviation:  Nat. Methods     Publication Date:  2012 Nov 
Date Detail:
Created Date:  2012-11-12     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101215604     Medline TA:  Nat Methods     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität (HHU), Düsseldorf, Germany.
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