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@ARTICLE{NavarroRetamal:901866,
      author       = {Navarro-Retamal, Carlos and Schott, Stephan and Gohlke,
                      Holger and Dreyer, Ingo},
      title        = {{C}omputational {A}nalyses of the {A}t{TPC}1 ({A}rabidopsis
                      {T}wo-{P}ore {C}hannel 1) {P}ermeation {P}athway},
      journal      = {International journal of molecular sciences},
      volume       = {22},
      number       = {19},
      issn         = {1422-0067},
      address      = {Basel},
      publisher    = {Molecular Diversity Preservation International},
      reportid     = {FZJ-2021-03874},
      pages        = {10345 -},
      year         = {2021},
      abstract     = {Two Pore Channels (TPCs) are cation-selective voltage- and
                      ligand-gated ion channels in membranes of intracellular
                      organelles of eukaryotic cells. In plants, the TPC1 subtype
                      forms the slowly activating vacuolar (SV) channel, the most
                      dominant ion channel in the vacuolar membrane. Controversial
                      reports about the permeability properties of plant SV
                      channels fueled speculations about the physiological roles
                      of this channel type. TPC1 is thought to have high Ca2+
                      permeability, a conclusion derived from relative
                      permeability analyses using the Goldman–Hodgkin–Katz
                      (GHK) equation. Here, we investigated in computational
                      analyses the properties of the permeation pathway of TPC1
                      from Arabidopsis thaliana. Using the crystal structure of
                      AtTPC1, protein modeling, molecular dynamics (MD)
                      simulations, and free energy calculations, we identified a
                      free energy minimum for Ca2+, but not for K+, at the luminal
                      side next to the selectivity filter. Residues D269 and E637
                      coordinate in particular Ca2+ as demonstrated in in silico
                      mutagenesis experiments. Such a Ca2+-specific coordination
                      site in the pore explains contradicting data for the
                      relative Ca2+/K+ permeability and strongly suggests that the
                      Ca2+ permeability of SV channels is largely overestimated
                      from relative permeability analyses. This conclusion was
                      further supported by in silico electrophysiological studies
                      showing a remarkable permeation of K+ but not Ca2+ through
                      the open channel.},
      cin          = {JSC / NIC / IBI-7 / IBG-4},
      ddc          = {540},
      cid          = {I:(DE-Juel1)JSC-20090406 / I:(DE-Juel1)NIC-20090406 /
                      I:(DE-Juel1)IBI-7-20200312 / I:(DE-Juel1)IBG-4-20200403},
      pnm          = {2171 - Biological and environmental resources for
                      sustainable use (POF4-217) / 2172 - Utilization of renewable
                      carbon and energy sources and engineering of ecosystem
                      functions (POF4-217) / 5111 - Domain-Specific Simulation
                      Data Life Cycle Labs (SDLs) and Research Groups (POF4-511) /
                      Forschergruppe Gohlke $(hkf7_20200501)$ / DFG project
                      267205415 - SFB 1208: Identität und Dynamik von
                      Membransystemen - von Molekülen bis zu zellulären
                      Funktionen},
      pid          = {G:(DE-HGF)POF4-2171 / G:(DE-HGF)POF4-2172 /
                      G:(DE-HGF)POF4-5111 / $G:(DE-Juel1)hkf7_20200501$ /
                      G:(GEPRIS)267205415},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {34638686},
      UT           = {WOS:000708182600001},
      doi          = {10.3390/ijms221910345},
      url          = {https://juser.fz-juelich.de/record/901866},
}