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@ARTICLE{Gushchin:202109,
      author       = {Gushchin, Ivan and Gordeliy, Valentin and Grudinin, Sergei},
      title        = {{T}wo {D}istinct {S}tates of the {HAMP} {D}omain from
                      {S}ensory {R}hodopsin {T}ransducer {O}bserved in {U}nbiased
                      {M}olecular {D}ynamics {S}imulations},
      journal      = {PLoS one},
      volume       = {8},
      number       = {7},
      issn         = {1932-6203},
      address      = {Lawrence, Kan.},
      publisher    = {PLoS},
      reportid     = {FZJ-2015-04398},
      pages        = {e66917 -},
      year         = {2013},
      abstract     = {HAMP domain is a ubiquitous module of bacterial and
                      archaeal two-component signaling systems. Considerable
                      progress has been made recently in studies of its structure
                      and conformational changes. However, the mechanism of signal
                      transduction through the HAMP domain is not clear. It
                      remains a question whether all the HAMPs have the same
                      mechanism of action and what are the differences between the
                      domains from different protein families. Here, we present
                      the results of unbiased molecular dynamics simulations of
                      the HAMP domain from the archaeal phototaxis signal
                      transducer NpHtrII. Two distinct conformational states of
                      the HAMP domain are observed, that differ in relative
                      position of the helices AS1 and AS2. The longitudinal shift
                      is roughly equal to a half of an α-helix turn, although
                      sometimes it reaches one full turn. The states are closely
                      related to the position of bulky hydrophobic aminoacids at
                      the HAMP domain core. The observed features are in good
                      agreement with recent experimental results and allow us to
                      propose that the states detected in the simulations are the
                      resting state and the signaling state of the NpHtrII HAMP
                      domain. To the best of our knowledge, this is the first
                      observation of the same HAMP domain in different
                      conformations. The simulations also underline the difference
                      between AMBER ff99-SB-ILDN and CHARMM22-CMAP forcefields, as
                      the former favors the resting state and the latter favors
                      the signaling state.},
      cin          = {ICS-6},
      ddc          = {500},
      cid          = {I:(DE-Juel1)ICS-6-20110106},
      pnm          = {452 - Structural Biology (POF2-452)},
      pid          = {G:(DE-HGF)POF2-452},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000321341000022},
      doi          = {10.1371/journal.pone.0066917},
      url          = {https://juser.fz-juelich.de/record/202109},
}