% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@ARTICLE{Smolin:20685,
      author       = {Smolin, N. and Biehl, R. and Kneller, G.B. and Richter, D.
                      and Smith, J.C.},
      title        = {{F}unctional domain motions in proteins on the 1 - 100 ns
                      timescale: {C}omparison of neutron spin echo spectroscopy of
                      phosphoglycerate kinase with molecular dynamics simulation},
      journal      = {Biophysical journal},
      volume       = {102},
      issn         = {0006-3495},
      address      = {New York, NY},
      publisher    = {Rockefeller Univ. Press},
      reportid     = {PreJuSER-20685},
      pages        = {1108 - 1117},
      year         = {2012},
      note         = {The research was sponsored by the Laboratory Directed
                      Research and Development Program of Oak Ridge National
                      Laboratory, managed by UT-Battelle, LLC, for the U.S.
                      Department of Energy under contract No. DE-AC05-00OR22725.
                      This research used resources of the National Energy Research
                      Scientific Computing Center, which is supported by the
                      Office of Science of the U.S. Department of Energy under
                      contract No. DE-AC02-05CH11231.},
      abstract     = {Protein function often requires large-scale domain motion.
                      An exciting new development in the experimental
                      characterization of domain motions in proteins is the
                      application of neutron spin-echo spectroscopy (NSE). NSE
                      directly probes coherent (i.e., pair correlated) scattering
                      on the ~1-100 ns timescale. Here, we report on all-atom
                      molecular-dynamics (MD) simulation of a protein,
                      phosphoglycerate kinase, from which we calculate small-angle
                      neutron scattering (SANS) and NSE scattering properties. The
                      simulation-derived and experimental-solution SANS results
                      are in excellent agreement. The contributions of
                      translational and rotational whole-molecule diffusion to the
                      simulation-derived NSE and potential problems in their
                      estimation are examined. Principal component analysis
                      identifies types of domain motion that dominate the internal
                      motion's contribution to the NSE signal, with the largest
                      being classic hinge bending. The associated free-energy
                      profiles are quasiharmonic and the frictional properties
                      correspond to highly overdamped motion. The amplitudes of
                      the motions derived by MD are smaller than those derived
                      from the experimental analysis, and possible reasons for
                      this difference are discussed. The MD results confirm that a
                      significant component of the NSE arises from internal
                      dynamics. They also demonstrate that the combination of NSE
                      with MD is potentially useful for determining the forms,
                      potentials of mean force, and time dependence of functional
                      domain motions in proteins.},
      keywords     = {Diffusion / Molecular Dynamics Simulation / Movement /
                      Neutron Diffraction: methods / Phosphoglycerate Kinase:
                      chemistry / Phosphoglycerate Kinase: metabolism / Protein
                      Structure, Tertiary / Rotation / Saccharomyces cerevisiae:
                      enzymology / Scattering, Small Angle / Time Factors /
                      Phosphoglycerate Kinase (NLM Chemicals) / J (WoSType)},
      cin          = {ICS-1 / JCNS-1},
      ddc          = {570},
      cid          = {I:(DE-Juel1)ICS-1-20110106 / I:(DE-Juel1)JCNS-1-20110106},
      pnm          = {BioSoft: Makromolekulare Systeme und biologische
                      Informationsverarbeitung (FUEK505) / 544 - In-house Research
                      with PNI (POF2-544)},
      pid          = {G:(DE-Juel1)FUEK505 / G:(DE-HGF)POF2-544},
      experiment   = {EXP:(DE-MLZ)KWS2-20140101},
      shelfmark    = {Biophysics},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:22404933},
      pmc          = {pmc:PMC3296038},
      UT           = {WOS:000301280900017},
      doi          = {10.1016/j.bpj.2012.01.002},
      url          = {https://juser.fz-juelich.de/record/20685},
}