Biology subjects

Sandberg, J. W.

Publications and source records attributed to Sandberg, J. W..

3 recordsLinked to original sources

bioRxiv2025

Structural mechanism of lipid modulation of pentameric ligand-gated ion channel activity

Pentameric ligand-gated ion channels (pLGICs) are sensitive to the lipid environment. However, the structural mechanism of how specific lipids support the agonist response of any pLGIC is poorly understood. Using the model pLGIC, ELIC (Erwinia ligand-gated ion channel), we find that phosphatidylethanolamine (PE) or cardiolipin (CL) are sufficient to support activation of a non-desensitizing mutant called ELIC5. Cryo-EM structures of unliganded and agonist-bound ELIC5 in the absence of PE or CL show increased structural heterogeneity and destabilization of the resting and open-channel states. Importantly, the unliganded structure of ELIC5 in a phosphatidylcholine (PC)-only environment shows variability that resembles agonist-induced changes. The structures also reveal a CL binding site at an outer leaflet M3-M4 site. Together with functional measurements in asymmetric liposomes and coarse-grained molecular dynamics simulations, the data indicate that CL supports ELIC activity by binding to this M3-M4 site thereby stabilizing an agonist-responsive resting state of the channel.

biophysics↗

bioRxiv2025

SARS-CoV E protein couples asymmetric leaflet thickness and curvature deformations

The Envelope protein (E protein) of SARS-CoVs 1 and 2 has been implicated in the viral budding process and maintaining the spherical shape of the virus, but direct evidence linking the protein to long-range membrane deformation is still lacking. Computational predictions from molecular simulation have offered conflicting results, some showing long-range E-induced membrane curvature and others showing only local deformations. In the present study, we determine the mechanism driving these deformations by modulating the degree of hydrophobic mismatch between protein and membrane. We observe that certain barostat and restraint settings, common in coarse-grained MD simulations, can prevent equilibration of the membrane area. Our results indicate that the E protein does not induce long-range curvature, but does exhibit severe local deformations that are exacerbated by hydrophobic mismatch. These deformations occur in conjunction with local leaflet thickness asymmetry, suggesting asymmetry and curvature couple to reduce the free energy cost of a deformed membrane. HighlightsO_LIE protein pentamers from SARS-CoV-1 and SARS-CoV-2 do not induce long-range curvature in membranes when simulated in isolation. C_LIO_LIPrevious findings documenting long-range membrane deformation may reflect the use of restraint and barostat settings that trap the membrane in a compressed state. C_LIO_LIE proteins induce large, asymmetric membrane deformations local to the protein, but these deformations do not propagate into the bulk. C_LIO_LIMembrane leaflet thickness asymmetry may be non-negligible around proteins that are not cylindrical. C_LIO_LIMembrane leaflet thickness asymmetry and mean curvature couple to alleviate free energy cost of deformation. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/649534v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@196eec7org.highwire.dtl.DTLVardef@168b3borg.highwire.dtl.DTLVardef@eef5corg.highwire.dtl.DTLVardef@848526_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Computing absolute binding affinities by Streamlined Alchemical Free Energy Perturbation

Free Energy Perturbation (FEP) is a powerful but challenging computational technique for estimating differences in free energy between two or more states. This document is intended both as a tutorial and as an adaptable protocol for computing free energies of binding using free energy perturbations in NAMD. We present the Streamlined Alchemical Free Energy Perturbation (SAFEP) framework. SAFEP shifts the computational frame of reference from the ligand to the binding site itself. This both simplifies the thermodynamic cycle and makes the approach more broadly applicable to superficial sites and other less common geometries. As a practical example, we give instructions for calculating the absolute binding free energy of phenol to lysozyme. We assume familiarity with standard procedures for setting up, running, and analyzing molecular dynamics simulations using NAMD and VMD. While simulation times will vary, the human tasks should take no more than 3 to 4 hours for a reader without previous training in free energy calculations or experience with the VMD Colvars Dashboard. Sample data are provided for all key calculations both for comparison and readers convenience.

biophysics↗