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@ARTICLE{Reinartz:888467,
      author       = {Reinartz, Ines and Weiel, Marie and Schug, Alexander},
      title        = {{FRET} {D}yes {S}ignificantly {A}ffect {SAXS} {I}ntensities
                      of {P}roteins},
      journal      = {Israel journal of chemistry},
      volume       = {60},
      number       = {7},
      issn         = {1869-5868},
      address      = {Weinheim},
      publisher    = {Wiley-VCH},
      reportid     = {FZJ-2020-04935},
      pages        = {725 - 734},
      year         = {2020},
      abstract     = {Structural analyses in biophysics aim at revealing a
                      relationship between a molecule's dynamic structure and its
                      physiological function. Förster resonance energy transfer
                      (FRET) and small‐angle X‐ray scattering (SAXS) are
                      complementary experimental approaches to this. Their
                      concomitant application in combined studies has recently
                      opened a lively debate on how to interpret FRET measurements
                      in the light of SAXS data with the popular example of the
                      radius of gyration, commonly derived from both FRET and
                      SAXS. There still is a lack of understanding in how to
                      mutually relate and interpret quantities equally obtained
                      from FRET or SAXS, and to what extent FRET dyes affect SAXS
                      intensities in combined applications. In the present work,
                      we examine the interplay of FRET and SAXS from a
                      computational simulation perspective. Molecular simulations
                      are a valuable complement to experimental approaches and
                      supply instructive information on dynamics. As FRET depends
                      not only on the mutual separation but also on the relative
                      orientations, the dynamics, and therefore also the shapes of
                      the dyes, we utilize a novel method for simulating
                      FRET‐dye‐labeled proteins to investigate these aspects
                      in atomic detail. We perform structure‐based simulations
                      of four different proteins with and without dyes in both
                      folded and unfolded conformations. In‐silico derived radii
                      of gyration are different with and without dyes and depend
                      on the chosen dye pair. The dyes apparently influence the
                      dynamics of unfolded systems. We find that FRET dyes
                      attached to a protein have a significant impact on
                      theoretical SAXS intensities calculated from simulated
                      structures, especially for small proteins. Radii of gyration
                      from FRET and SAXS deviate systematically, which points to
                      further underlying mechanisms beyond prevalent explanation
                      approaches.},
      cin          = {JSC / NIC},
      ddc          = {540},
      cid          = {I:(DE-Juel1)JSC-20090406 / I:(DE-Juel1)NIC-20090406},
      pnm          = {511 - Computational Science and Mathematical Methods
                      (POF3-511) / Forschergruppe Schug $(hkf6_20200501)$},
      pid          = {G:(DE-HGF)POF3-511 / $G:(DE-Juel1)hkf6_20200501$},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000550773000008},
      doi          = {10.1002/ijch.202000007},
      url          = {https://juser.fz-juelich.de/record/888467},
}