Biology subjects

de Groot, B.

Publications and source records attributed to de Groot, B..

4 recordsLinked to original sources

bioRxiv2026

A chemical perturbation scan on a K2P channel modulator pocket identifies affinity hotspots

Ion permeation in the two-pore-domain K+ (K2P) channel TREK1 is gated largely at the selectivity filter (SF), by a C-type-like inactivation mechanism involving distortions of the SF structure; and by a carbonyl flip, which disrupts K+ coordination. Both are prevented by a small-molecule activator bound adjacent to the SF, in a site termed the modulator pocket; yet which pocket regions carry the binding signal, and whether they couple to gating, is unclear. We use 46 chemical substitutions on the activator ML335, evaluated by non-equilibrium alchemical free-energy calculations, as an affinity perturbation scan on the lower- and upper pocket. The response is strongly asymmetric: Lower-ring substitutions impair binding, which we trace to a {pi}-{pi} stacking network connecting the M3, P2, P1 helices, and the SF. Conversely, upper-ring substitutions are tolerated and reshape contacts with the Cap-P1 and SF2-M4 loops; and with the upper SF. The identified affinity hotspots overlap with residues independently implicated in TREK gating by external cues such as pH, temperature, pressure, and cytosolic-sensor transduction, suggesting that high-affinity pocket sites might also shape the gating landscape.

biophysics↗

bioRxiv2026

Sodium Ions Regulate GPCR Activation by Remodeling Allosteric Coupling Networks and Hydration Patterns

Sodium ions (Na+) are key modulators of G-protein coupled receptor (GPCR) function, yet their mechanistic role remains incompletely understood. Here, we reveal a novel mode of Na+-mediated inactivation in the dopamine D2 receptor (DRD2), where Na+ reshapes long-range allosteric coupling networks and disrupts a continuous internal water column essential for activation. Using extensive molecular dynamics simulations and alchemical free energy calculations, we show that Na+ induces inactive-like residue interactions in the active state and triggers the formation of a distinct hydration gap. We also identify previously unreported Na+ binding sites and quantify their impact on the active-inactive state equilibrium by thermodynamic scanning. These findings provide mechanistic insights into Na+-driven allosteric regulation of GPCRs and highlight new opportunities for drug design targeting ion-sensitive receptor states. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/714850v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@db861forg.highwire.dtl.DTLVardef@42722dorg.highwire.dtl.DTLVardef@561bc7org.highwire.dtl.DTLVardef@139c9e4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Charge Scaling in Potassium Channel Simulations: Conductance, Ion Occupancy, Voltage Response, and Selectivity

Potassium (K+) channels are widely distributed in many types of organisms. They combine high efficiency ([~]100 pS) and K+/Na+ selectivity by a conserved selectivity filter (SF). Molecular Dynamics (MD) simulations can provide detailed, atomistic mechanisms of this sophisticated ion permeation. However, currently there are clear inconsistencies between computational predictions and experimental results. Firstly, the ion occupancy of the SF in simulations is lower than expected ([~]2.5 in MD compared to [~]4 in X-ray crystallography). Secondly, in many reported MD simulations of K+ channels, K+ conductance is typically an order of magnitude lower than experimental values. This discrepancy is in part because the force fields used in MD simulations of potassium channels do not account for polarization. One of the proposed solutions is the Electronic Continuum Correction (ECC), a force field modification that scales down formal charges, to introduce the polarization in a mean-field way. When the ECC is used in conjunction with the Charmm36m force field, the simulated K+ conductance increases 13-fold. Following the analysis of ion occupancy states using Hamiltonian Replica Exchange (HRE) simulations, we propose a new parameter set for Amber14sb, that also leads to a similar increase in conductance. These two force fields are then used to compute, for the first time, the full current-voltage (I-V) curves from MD simulations, approaching quantitative agreement with experiments at all voltages. In general, the ECC-enabled simulations are in excellent agreement with experiment, in terms of ion occupancy, conductance, current-voltage response, and K+/Na+ selectivity. Significance StatementPotassium (K+) channels are essential membrane proteins that facilitate the selective conduction of K+ ions while excluding Na+ ions. Incorporation of electronic polarization effects through the Electronic Continuum Correction (ECC) method enables molecular dynamics simulations to reproduce rapid K+ permeation under physiological voltage conditions. In this study, we demonstrate that employing ECC approximated polarization in molecular dynamics simulations allows for the prediction of multiple channel properties: conductance, ion occupancy, voltage response, and selectivity, with unprecedented accuracy. Furthermore, our simulations provide atomistic insights into the asymmetrical current-voltage (I-V) relationship observed in the MthK channel.

biophysics↗

bioRxiv2023

Bayesian Maximum Entropy Ensemble Refinement

The principle of maximum entropy provides a canonical way to include measurement results into a thermodynamic ensemble. Observable features of a thermodynamic system, which are measured as averages over an ensemble are included into the partition function by using Lagrange multipliers. Applying this principle to the systems energy leads to the well-known exponential form of the Boltzmann probability density. Here, we present a Bayesian approach to the estimation of maximum entropy parameters from nuclear Overhauser effect measurements in order to achieve a refined ensemble in molecular dynamics simulations. To achieve this goal, we leverage advances in the treatment of doubly intractable Bayesian inference problems by adaptive Markov Chain Monte Carlo methods. We illustrate the properties and viability of our method for alanine dipeptide as a simple model system and trp-cage as an example for a more complex peptide.

bioinformatics↗