Biology subjects

Biedermann, J.

Publications and source records attributed to Biedermann, J..

4 recordsLinked to original sources

bioRxiv2024

Atomistic Mechanism of Cation Permeation and Pore Voltage Sensitivity in Cyclic Nucleotide-Gated CNGA1 Ion Channel

Mammalian cyclic nucleotide-gated (CNG) ion channels play a fundamental role in signal transduction within the visual and olfactory sensory cells, converting external stimuli into electrical signals. Here, using large-scale atomistic molecular dynamics (MD) simulations under transmembrane voltages, we uncover the atomistic mechanism of monovalent cation permeation in the homotetrameric CNGA1 channel, involving hydrated cations in the selectivity filter. We propose that hydration fluctuations in the central gate region, driven by pore flexibility, are the underlying mechanism for excess single-channel conductance noise and characteristic single-channel flickering. Furthermore, we suggest an atomistic mechanism for intrinsic voltage sensitivity in the channel pore, mediated by allosteric coupling between the selectivity filter and the central cavity gate. Our study provides atomistic insights into non-selective cation permeation and voltage sensitivity of the CNGA1 channel pore that could not be resolved by static structural analysis alone.

biophysics↗

bioRxiv2024

Atomistic Mechanisms of Calcium Permeation Modulated by Q/R Editing and Selectivity Filter Mutations in GluA2 AMPA Receptors

GluA2 is a key subunit of AMPA receptor ion channels that is abundantly expressed in the vertebrate brain. Post-transcriptional Q/R editing of GluA2 renders AMPARs nearly impermeable to calcium ions, which is crucial for their normal function. Although previous studies have characterized conductivity and selectivity differences between edited and unedited GluA2 variants and heteromeric receptors incorporating GluA2, the atomistic mechanism remains largely unknown. In this study, we investigate ion permeation in the context of multiple Ca2+ binding sites along the pore predicted from MD simulations, considering both mutations and co-permeating monovalent ions. Patch clamp electrophysiology recordings confirmed a binding site at the intracellular mouth of the selectivity filter that confers selectivity for calcium over monovalent ions. A patient mutation at the same site has been previously shown to cause neurodevelopmental abnormalities. Furthermore, MD simulations of GluA2 with different arginine copy number at the Q/R site show that Ca2+ conduction is blocked in the presence of two arginines, whereas K+ is only blocked by four arginines, in explaining the results from decades of electrophysiological work. Finally, MD simulations revealed that Ca2+ reduces K+ conduction by preferentially occupying the intracellular SF binding site, whereas Na+ does not. This result is consistent with electrophysiological results from the D590 mutants, and suggests that divalent binding in the selectivity filter is a major determinant of AMPAR conductance.

biophysics↗

bioRxiv2023

From head to tail - Atomistic mechanism of long-range coupling from the cytosolic sensor domain to the selectivity filter in TREK K2P channels

The two-pore domain potassium (K2P) channels TREK-1 and TREK-2 link neuronal excitability to a variety of stimuli including mechanical force, lipids, temperature and phosphorylation. This regulation involves the C-terminus as a polymodal stimulus sensor and the selectivity filter (SF) as channel gate. Using crystallographic up- and down-state structures of TREK-2 as a template for full atomistic molecular dynamics simulations, we reveal that the SF in down-state undergoes inactivation via conformational changes at the S1 ion coordination site, while the up-state structure maintains a stable and conductive SF. This provides an atomistic understanding of the low channel activity previously assigned to the down state, but not evident from the crystal structure. Furthermore, by using (de-)phosphorylation mimics and chemically attaching lipid tethers to the proximal C-terminus (pCt), we confirm the hypothesis that moving the pCt towards the membrane induces the up-state. We also uncover two gating pathways by which movement of the pCt controls the stability (i.e. conductivity) of the filter gate. Together, these findings provide atomistic insights into the SF gating mechanism and the physiological regulation of TREK channels by phosphorylation.

biophysics↗

bioRxiv2020

Non-selective cation permeation in an AMPA-type glutamate receptor

Fast excitatory synaptic transmission in the central nervous system relies on the AMPA-type glutamate receptor (AMPAR). This receptor incorporates a non-selective cation channel which is opened by the binding of glutamate. Although the open pore structure has recently became available from cryo-electron microscopy (Cryo-EM), the molecular mechanisms governing cation permeability in AMPA receptors are not understood. Here, we combined microsecond molecular dynamics (MD) simulations on a putative open state structure of GluA2 with electrophysiology on cloned channels to elucidate ion permeation mechanisms. Na+, K+ and Cs+ permeated at physiological rates, consistent with a structure that represents a true open state. A single major ion binding site for Na+ and K+ in the pore represents the simplest selectivity filter (SF) structure for any tetrameric cation channel of known structure. The minimal SF comprised only Q586 and Q587, and other residues on the cytoplasmic side formed a cone- shaped void that lacked major interactions with ions. We observed Cl- invasion of the upper pore, explaining anion permeation in the edited form of GluA2. A permissive architecture of the SF accommodated different alkali metals in distinct solvation states to allow rapid, non-selective cation permeation, and co-permeation by water. Simulations suggested Cs+ uses two equally populated ion binding sites in the filter and we confirmed with electrophysiology of GluA2 that Cs+ is more permeant than Na+, consistent with serial binding sites preferentially driving selectivity. Significance StatementAMPA-type glutamate receptors (AMPARs) are key actors in neurotransmission, making the final step in a relay of excitability from one brain cell to another. The receptor contains an integral ion channel, which, when opened by neurotransmitter binding, permits sodium and other cations to cross the cell membrane. We investigated permeation of sodium, potassium and caesium in an AMPAR at the atomistic level using a computational molecular dynamics approach on a structure with the ion channel pore in a presumably open state. We determined that the region selecting between cations is the simplest of any channel of this type. Distinct from ion channels that select single ion species, cations are never fully dehydrated and have only one major ion binding site in the filter. Simulations suggested two similar binding sites for caesium, and studies of AMPARs in mammalian cell membranes showed that this makes caesium more permeant than sodium.

biophysics↗