E. Lindahl

Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization

The paper investigates how cardiolipin interacts with membrane proteins to stabilize them, using a model protein and simulations to identify key factors.

Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface

This study uses molecular dynamics simulations and Markov state modeling to predict an open state of GABAA receptors, showing chloride ion conductance and desensitization mechanisms.

Vestibular modulation by stimulant derivatives in a pentameric ligand-gated ion channel

This study investigates how psychostimulant derivatives modulate the prokaryotic pentameric ligand-gated ion channel sTeLIC through a vestibular pocket, revealing a structure-function mechanism for allosteric potentiation.

An Allosteric Cholesterol Site in Glycine Receptors Characterized Through Molecular Simulations

The paper uses molecular simulations to identify state-dependent cholesterol interactions at an allosteric site in glycine receptors, linking lipid binding to receptor function and pharmaceutical relevance.

Divergent mechanisms of steroid inhibition in the human {rho}1 GABA(A) receptor

The paper characterizes the inhibitory mechanisms of two neuroactive steroids at the human {rho}1 GABAA receptor using cryo-EM, electrophysiology, and molecular dynamics simulations.

Symmetry-adapted Markov state models of closing, opening, and desensitizing in α7 nicotinic acetylcholine receptors

This study uses symmetry-adapted Markov state modeling to analyze conformational transitions in α7 nAChRs, revealing lipid modulation effects and asymmetric transition pathways between functional states.

Constant-pH molecular dynamics simulations of closed and open states of a proton-gated ion channel

This paper uses constant-pH molecular dynamics simulations to study pH-mediated conformational changes in the GLIC ion channel, identifying pH-sensitive residues and state-dependent pKa shifts.

Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor

The paper identifies a stimulant derivative binding in a cryptic vestibular pocket of the 5-HT3A receptor using computational and experimental methods.

Structure and dynamics of differential ligand binding in the human {rho}-type GABA(A) receptor

This study presents cryo-EM structures of the human ρ1 GABAAR under different conditions, revealing structural mechanisms of gating and modulation with implications for pharmaceutical design.

Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids

The paper develops a more sensitive nicotine biosensor, iNicSnFR12, capable of detecting nicotine in diluted biofluids at clinically relevant concentrations.

Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM

The paper identifies lipid binding sites in the GLIC ion channel using cryo-EM and simulations, revealing state-dependent interactions in both closed and open conformations.

Automated simulation-based membrane-protein refinement into cryo-EM data

This paper introduces an automated method using density-guided molecular dynamics simulations to refine membrane-protein models into cryo-EM maps, showing improved model quality and pixel-size correction.

Gentle and fast all-atom model refinement to cryo-EM densities via Bayes' approach

The paper introduces a Bayesian refinement method for cryo-EM density maps, improving structure modeling by balancing fit and stereochemistry with a new potential and adaptive force scaling.

Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel

This study characterizes the structural dynamics of the calcium-sensitive channel DeCLIC using cryo-EM, SANS, and MD simulations, revealing conformational flexibility in the NTD and calcium binding site.

Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators

This study characterizes the functional states of the α7 nicotinic acetylcholine receptor using computational methods, revealing state-dependent interactions with lipids and ligands.

Predictions of Skin Permeability Using Molecular Dynamics Simulation from Two-Dimensional Sampling of Spatial and Alchemical Perturbation Reaction Coordinates

The paper introduces a molecular dynamics simulation method using two-dimensional reaction coordinates to predict skin permeability and demonstrates its accuracy with ex vivo/in vitro data.

Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium

This study investigates the SARS-CoV-2 E protein's effects on membrane curvature and intracellular calcium, using experimental and computational methods.

Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering

This study uses small-angle neutron scattering to examine conformational changes in the bacterial ion channel GLIC under resting and activating conditions, finding no evidence for divergent mechanisms.

A cationic lipid site at the outward transmembrane face of a pentameric ligand-gated ion channel

This study identifies a cationic lipid binding site on the outward face of the ELIC pLGIC, supported by simulations and mutagenesis, with implications for lipid modulation and drug design.

Markov state models of proton- and gate-dependent activation in a pentameric ligand-gated ion channel

The paper constructs Markov state models of GLIC channel gating using enhanced sampling and functional recordings, revealing protonation and mutation effects on conformational transitions and symmetrization.

Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations

The paper reports cryo-EM structures and simulations of GLIC under different pH conditions, revealing conformational changes and electrostatic remodeling during proton-induced gating.

A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics

The paper identifies a blueprint for high affinity SARS-CoV-2 Mpro inhibitors by analyzing protein dynamics and redefining druggability through virtual screening and pharmacophore modeling.

Characterization of the dynamic resting state of a pentameric ligand-gated ion channel by cryo-electron microscopy and simulations

The paper uses cryo-EM and simulations to characterize the resting and activating states of GLIC, revealing structural changes and energy landscape dynamics.

Bacterial protein domains with a novel Ig-like fold bind human CEACAM receptors

This study identifies a novel Ig-like fold in bacterial adhesins that binds human CEACAM receptors, suggesting a broad mechanism for bacterial pathogenesis.

Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA

The paper determines the cryo-EM structure of the PolD-PCNA complex from Pyrococcus abyssi, revealing the molecular basis for increased processivity through PCNA interaction.

RELION-3: new tools for automated high-resolution cryo-EM structure determination

RELION-3 introduces new tools for automated high-resolution cryo-EM structure determination, improving resolution through enhanced processing methods and hardware flexibility.

Molecular basis for voltage sensitivity in membrane proteins

The paper introduces a computational method to predict voltage-sensing elements in membrane proteins by analyzing their response to membrane potential changes, identifying residues and ions involved in voltage sensitivity.

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

The paper introduces a new cryo-EM single-particle analysis tool called multi-body refinement to model flexible macromolecular complexes and generate reconstructions and motion movies.