Biology subjects

Domene, C.

Publications and source records attributed to Domene, C..

3 recordsLinked to original sources

bioRxiv2025

Role of Water Models in Simulations of Ion Conduction in Potassium Channels

Potassium channels exhibit high selectivity and conductance, yet the atomic details of ion permeation, particularly the involvement of water molecules, remain debated. Two main conduction mechanisms have been proposed: the hard knock-on, in which ions traverse the selectivity filter in direct contact, and the soft knock-on, which involves co-permeation of water molecules. Using microsecond molecular dynamics simulations with the OPC water model, the AMBER19SB protein force field, and the 12-6-4 Sengupta et al. ion model, we observed that both hard and soft knock-on mechanisms are accessible and, notably, can reversibly transition in the MthK and KcsA channels across all simulated membrane potentials. These reversible transitions contrast with previous observations using the TIP3P water model, where water entry either disrupted conduction or was expelled, favoring exclusive hard knock-on events. Our results suggest that the choice of the water model, force field, and ion parameters significantly influences the observed conduction mechanism. Importantly, the coexistence of hard and soft knock-on in these simulations provides a potential reconciliation between structural data supporting hard knock-on and streaming potential measurements demonstrating water co-permeation. These findings reintroduce soft knock-on as a viable conduction mechanism and highlight the critical role of simulation parameters in reproducing potassium channel permeation behavior.

biophysics↗

bioRxiv2024

Building predictive Markov State Models of ion channel permeation from Molecular Dynamics

Molecular dynamics (MD) simulation of biological processes has always been a very challenging task due to the long timescales of the processes involved and the challenges associated with handling the large amount of output data. Markov State Models (MSMs) have been recently introduced as a powerful tool in this area of research, as they provide a mechanistically comprehensible synthesis of the large amount of MD data and, at the same time, can be used to estimate experimental properties of biological processes. Of the many studies on protein simulation and the MSM-assisted approach, only a few have addressed ion channel permeation and, more importantly, none of these have tried to build a model capable to predict the currents passing through the channels, which are ultimately crucial for comparing simulations with experimental results. Herein, we propose a method for building an MSM of ion channel permeation that correctly evaluates the current flowing through the channel. This was done by including in the model the definition of a flux matrix carrying information on the charge moving across the channel, suitably built to be used in conjunction with the transition matrix to predict the ion current. The proposed method is also able to drastically reduce the number of states so to obtain an MSM simple enough to be easily understood. Finally, we applied the method to the KcsA channel, obtaining a four-state MSM capable of accurately reproducing the single channel ion current from microseconds MD trajectories.

biophysics↗

bioRxiv2022

Redox regulation of Kv7 channels through EF3 hand of calmodulin

Neuronal KV7 channels, important regulators of cell excitability, are among the most sensitive proteins to reactive oxygen species. The S2S3 linker of the voltage sensor was reported as a site mediating redox modulation of the channels. Recent structural insights reveal potential interactions between this linker and the Ca2+-binding loop of the third EF-hand of calmodulin (CaM), which embraces an antiparallel fork formed by the C-terminal helices A and B. We found that precluding Ca2+ binding to the EF3 hand, but not to EF1, EF2 or EF4 hands, abolishes oxidation-induced enhancement of Kv7.4 currents. Monitoring FRET between helices A and B tagged with fluorescent proteins, we observed that S2S3 peptides cause a reversal of the signal in the presence of Ca2+, but have no effect in the absence of this cation or if the peptide is oxidized. The capacity of loading EF3 with Ca2+ is essential for this reversal of the FRET signal, whereas the consequences of obliterating Ca2+ binding to EF1, EF2 or EF4 are negligible. Furthermore, we show that EF3 is necessary and sufficient to translate Ca2+ signals to reorient the AB fork. Our data is consistent with the proposal that oxidation of cysteine residues in the S2S3 loop relieves Kv7 channels from a constitutive inhibition imposed by interactions between the EF3 hand of CaM which is necessary and sufficient for this signaling. SignificanceOxidation-dependent enhancement of the KV7/M-channels plays a cytoprotective role in neurons. Here, we show that calmodulin (CaM), the main protein that conveys information from transient intracellular Ca2+ oscillations, plays a critical role in oxidative signal transduction. The prevailing view is that the main role of the EF-hands is to respond to Ca2+ and that the two EF-hands of CaM in each lobe act in coordination during signaling. We find that EF3 by itself is sufficient and necessary for the oxidative response of Kv7 channel complex and for gating the Calcium Responsive Domain of Kv7 channels. In addition, the direction of EF3-dependent signaling can be reversed by protein-protein interactions with solvent exposed regions outside the target binding groove between EF-hands.

cell biology↗