Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway
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 repo...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-09-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/22/19/10345 |
| _version_ | 1797516345480314880 |
|---|---|
| author | Carlos Navarro-Retamal Stephan Schott-Verdugo Holger Gohlke Ingo Dreyer |
| author_facet | Carlos Navarro-Retamal Stephan Schott-Verdugo Holger Gohlke Ingo Dreyer |
| author_sort | Carlos Navarro-Retamal |
| collection | DOAJ |
| description | 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 Ca<sup>2+</sup> 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 <i>Arabidopsis thaliana</i>. Using the crystal structure of AtTPC1, protein modeling, molecular dynamics (MD) simulations, and free energy calculations, we identified a free energy minimum for Ca<sup>2+</sup>, but not for K<sup>+</sup>, at the luminal side next to the selectivity filter. Residues D269 and E637 coordinate in particular Ca<sup>2+</sup> as demonstrated in in silico mutagenesis experiments. Such a Ca<sup>2+</sup>-specific coordination site in the pore explains contradicting data for the relative Ca<sup>2+</sup>/K<sup>+</sup> permeability and strongly suggests that the Ca<sup>2+</sup> 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<sup>+</sup> but not Ca<sup>2+</sup> through the open channel. |
| first_indexed | 2024-03-10T06:59:56Z |
| format | Article |
| id | doaj.art-7fc284d36ec2473e83c8789233fa8b41 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T06:59:56Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-7fc284d36ec2473e83c8789233fa8b412023-11-22T16:08:11ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-09-0122191034510.3390/ijms221910345Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation PathwayCarlos Navarro-Retamal0Stephan Schott-Verdugo1Holger Gohlke2Ingo Dreyer3Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Campus Talca, Universidad de Talca, Talca 346000, ChileJohn von Neumann Institute for Computing (NIC), Forschungszentrum Jülich GmbH, 52425 Jülich, GermanyJohn von Neumann Institute for Computing (NIC), Forschungszentrum Jülich GmbH, 52425 Jülich, GermanyCentro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Campus Talca, Universidad de Talca, Talca 346000, ChileTwo 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 Ca<sup>2+</sup> 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 <i>Arabidopsis thaliana</i>. Using the crystal structure of AtTPC1, protein modeling, molecular dynamics (MD) simulations, and free energy calculations, we identified a free energy minimum for Ca<sup>2+</sup>, but not for K<sup>+</sup>, at the luminal side next to the selectivity filter. Residues D269 and E637 coordinate in particular Ca<sup>2+</sup> as demonstrated in in silico mutagenesis experiments. Such a Ca<sup>2+</sup>-specific coordination site in the pore explains contradicting data for the relative Ca<sup>2+</sup>/K<sup>+</sup> permeability and strongly suggests that the Ca<sup>2+</sup> 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<sup>+</sup> but not Ca<sup>2+</sup> through the open channel.https://www.mdpi.com/1422-0067/22/19/10345TPC1SV channelpermeabilitymolecular dynamics simulationin silico electrophysiology |
| spellingShingle | Carlos Navarro-Retamal Stephan Schott-Verdugo Holger Gohlke Ingo Dreyer Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway International Journal of Molecular Sciences TPC1 SV channel permeability molecular dynamics simulation in silico electrophysiology |
| title | Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway |
| title_full | Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway |
| title_fullStr | Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway |
| title_full_unstemmed | Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway |
| title_short | Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway |
| title_sort | computational analyses of the attpc1 arabidopsis two pore channel 1 permeation pathway |
| topic | TPC1 SV channel permeability molecular dynamics simulation in silico electrophysiology |
| url | https://www.mdpi.com/1422-0067/22/19/10345 |
| work_keys_str_mv | AT carlosnavarroretamal computationalanalysesoftheattpc1arabidopsistwoporechannel1permeationpathway AT stephanschottverdugo computationalanalysesoftheattpc1arabidopsistwoporechannel1permeationpathway AT holgergohlke computationalanalysesoftheattpc1arabidopsistwoporechannel1permeationpathway AT ingodreyer computationalanalysesoftheattpc1arabidopsistwoporechannel1permeationpathway |