Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors

Minniberger, Sonja; Abdolvand, Saeid; Braunbeck, Sebastian; Sun, Han; Plested, Andrew J.R.

doi:10.1016/j.jmb.2023.167970

Cited by 5 publications

(13 citation statements)

References 63 publications

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“…To independently assess the accuracy of the predictions obtained using the recently developed force field for the calcium ions, we obtained experimental structural information on the AMPAR selectivity filter in the presence of Ca 2+ . We used the prokaryotic NaK channel as scaffold for crystallization, as in our previous study of monovalent cations . Specifically, we determined the crystal structures of a construct that replaces DGNF in the SF of NaK with C-DI from AMPAR, in the presence of either Rb + and Ca 2+ (resolution: 2.75 Å, PDB ID: 8AYQ, Figure B) or Rb + and Ba 2+ (resolution: 2.10 Å, PDB ID: 8AYP, Figure S4).…”

Section: Resultsmentioning

confidence: 99%

“…Protein expression and purification were performed as previously described . The hexahistidine tag was removed by incubation with trypsin (1:250 molar ratio) for 1 h at room temperature.…”

Section: Methodsmentioning

confidence: 99%

“…This is consistent with previous X-ray analysis of a NaK C-DI mutant with monovalent cations only. 48 In contrast, the Ca 2+ density is observed at three distinct sites (Figure 5B): (i) S 5 : directly below the SF formed by the T63 side chain; (ii) S v : in the vestibule, stabilized by the C66 backbone; (iii) S 0 : at the upper mouth of the SF bonded to the D67 side chain.…”

Section: Calcium Permeation Mechanism In Ampa Receptorsmentioning

confidence: 95%

“…We used the prokaryotic NaK channel as scaffold for crystallization, as in our previous study of monovalent cations. 48 Specifically, we determined the crystal structures of a construct that replaces DGNF in the SF of NaK with C-DI from AMPAR, in the presence of either Rb + and Ca 2+ (resolution: 2.75 Å, PDB ID: 8AYQ, Figure 5B) or Rb + and Ba 2+ (resolution: 2.10 Å, PDB ID: 8AYP, Figure S4). The X-ray structures revealed distinct ion binding profiles for monovalent and divalent cations within and around the SF (Figure 5B).…”

Section: Calcium Permeation Mechanism In Ampa Receptorsmentioning

confidence: 99%

“…Figure 5. (A) Relative one-dimensional ion occupancy in the SF of NaK C-DI derived from Ca 2+ MD simulations (orange), performed with the multisite Ca 2+ model compatible with CHARMM (this work) and K + MD simulations (cyan), with CHARMM 48. The origin is set to the hydroxy group of T63.…”

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confidence: 99%

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Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel

Schackert

Biedermann

Abdolvand

et al. 2023

J. Chem. Inf. Model.

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The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are neurotransmitter-activated cation channels ubiquitously expressed in vertebrate brains. The regulation of calcium flux through the channel pore by RNA-editing is linked to synaptic plasticity while excessive calcium influx poses a risk for neurodegeneration. Unfortunately, the molecular mechanisms underlying this key process are mostly unknown. Here, we investigated calcium conduction in calcium-permeable AMPAR using Molecular Dynamics (MD) simulations with recently introduced multisite force-field parameters for Ca 2+ . Our calculations are consistent with experiment and explain the distinct calcium permeability in different RNA-edited forms of GluA2. For one of the identified metal binding sites, multiscale Quantum Mechanics/Molecular Mechanics (QM/ MM) simulations further validated the results from MD and revealed small but reproducible charge transfer between the metal ion and its first solvation shell. In addition, the ion occupancy derived from MD simulations independently reproduced the Ca 2+ binding profile in an X-ray structure of an NaK channel mimicking the AMPAR selectivity filter. This integrated study comprising X-ray crystallography, multisite MD, and multiscale QM/MM simulations provides unprecedented insights into Ca 2+ permeation mechanisms in AMPARs, and paves the way for studying other biological processes in which Ca 2+ plays a pivotal role.

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Section: Resultsmentioning

confidence: 99%

“…Protein expression and purification were performed as previously described . The hexahistidine tag was removed by incubation with trypsin (1:250 molar ratio) for 1 h at room temperature.…”

Section: Methodsmentioning

confidence: 99%

Section: Calcium Permeation Mechanism In Ampa Receptorsmentioning

confidence: 95%

Section: Calcium Permeation Mechanism In Ampa Receptorsmentioning

confidence: 99%

mentioning

confidence: 99%

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