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@ARTICLE{Bucher:201273,
      author       = {Bucher, Denis and Guidoni, Leonardo and Carloni, Paolo and
                      Rothlisberger, Ursula},
      title        = {{C}oordination {N}umbers of {K}+ and {N}a+ {I}ons {I}nside
                      the {S}electivity {F}ilter of the {K}cs{A} {P}otassium
                      {C}hannel: {I}nsights from {F}irst {P}rinciples
                      {M}olecular {D}ynamics},
      journal      = {Biophysical journal},
      volume       = {98},
      number       = {10},
      issn         = {0006-3495},
      address      = {New York, NY},
      publisher    = {Rockefeller Univ. Press},
      reportid     = {FZJ-2015-03578},
      pages        = {L47 - L49},
      year         = {2010},
      abstract     = {Quantum mechanics/molecular mechanics (QM/MM)
                      Car-Parrinello simulations were performed to estimate the
                      coordination numbers of K+ and Na+ ions in the selectivity
                      filter of the KcsA channel, and in water. At the DFT/BLYP
                      level, K+ ions were found to display an average coordination
                      number of 6.6 in the filter, and 6.2 in water. Na+ ions
                      displayed an average coordination number of 5.2 in the
                      filter, and 5.0 in water. A comparison was made with the
                      average coordination numbers obtained from using classical
                      molecular dynamics (6.7 for K+ in the filter, 6.6 for K+ in
                      water, 6.0 for Na+ in the filter, and 5.2 for Na+ in water).
                      The observation that different coordination numbers were
                      displayed by the ions in QM/MM simulations and in classical
                      molecular dynamics is relevant to the discussion of
                      selectivity in K-channels.Potassium channels are membrane
                      proteins that can catalyze K+ ions permeation across
                      cellular membranes while simultaneously discriminating the
                      permeation of Na+ ions by several orders of magnitude. To
                      uncover the mechanism of K-channel selectivity in
                      theoretical studies, the KcsA channel has proved to be a
                      particularly useful system, because it is relatively small,
                      and it contains the essential structural elements that are
                      shared by all potassium channels (1). The selectivity of the
                      KcsA channel is believed to originate from the conserved
                      TVGYG signature sequence, which forms a narrow constriction
                      in the tetrameric pore called the selectivity filter (Fig.
                      1). The K+/Na+ selectivity in the KcsA channel was initially
                      proposed to arise from the geometrical arrangement of
                      ligands in the filter (1), the so-called snug-fit
                      hypothesis. However, molecular dynamics (MD) simulations
                      have shown that the selectivity filter is relatively
                      flexible and that Na+ ions are able to interact with the
                      carbonyl ligands that pave the interior of the selectivity
                      filter (2). This leads to the idea that other interactions,
                      such as the repulsion between carbonyl groups, play an
                      important role in the selectivity (3). In addition, the
                      selectivity has been discussed as arising from the favorable
                      arrangement of the carbonyl in the filter, which may promote
                      high coordination numbers, compared to the ion coordination
                      numbers in water (4 and 22).},
      cin          = {GRS / IAS-5},
      ddc          = {570},
      cid          = {I:(DE-Juel1)GRS-20100316 / I:(DE-Juel1)IAS-5-20120330},
      pnm          = {899 - ohne Topic (POF2-899)},
      pid          = {G:(DE-HGF)POF2-899},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000277858400001},
      pubmed       = {pmid:20483308},
      doi          = {10.1016/j.bpj.2010.01.064},
      url          = {https://juser.fz-juelich.de/record/201273},
}