Structures and topologies for raft simulations

<p>The tar file contains all initial structures, the topologies, the simulation parameters, and the force field parameters for all simulations reported in the paper "Hydrophobic compounds reshape membrane domains", to be published on PLoS Computational Biology</p

Rhodopsin Forms a Dimer with Cytoplasmic Helix 8 Contacts in Native Membranes

G protein-coupled receptors form dimers and higher-order oligomers in membranes, but the precise mode of receptor–receptor interaction remains unknown. To probe the intradimeric proximity of helix 8 (H8), we conducted chemical cross-linking of endogenous cysteines in rhodopsin in disk membranes. We identified a Cys316–Cys316 cross-link using partial proteolysis and liquid chromatography with mass spectrometry. These results show that a symmetric dimer interface mediated by H1 and H8 contacts is present in native membranes

Overview and statistics of the MD simulations.

<p>The percentage of lipids in the contacting monolayers which, during the simulation, tilt by more than >85° or splay by more than >170° is indicated. The standard error of the average is obtained from the standard deviation between all five simulations. The simulation length and formation of pores is also indicated.</p

Simultaneous pore formation and fusion activity of BPC194.

<p>A: The normalized concentration of dextran inside the liposomes, C_av, (filled circles) and the normalized intensity of membrane-associated DiD per liposome (empty squares) at different P/L ratios. B: Confocal images of the lipid vesicles in the DiD and dextran detection channel at three different P/L ratios; α, P/L = 0; β, P/L = 0.1; and γ, P/L = 0.3. C: Positive-FRET upon peptide addition. The emission of Rhodamine increases due to vesicle fusion. Inset: Controls done with the ‘inactive’ linear analog of BPC194, that is, BPC193 at the same peptide concentrations. D: Negative-FRET upon peptide addition. The emission of NBD increases due to a decrease in FRET efficiency as a result of vesicle fusion. E. Quantification of fusion at different P/L ratios and at two different lipid compositions, 125 µM (full circles) and 250 µM (empty squares). D. Representative cryo-TEM micrographs of DOPG vesicles without peptide (control) and with BPC194 or the linear analog BPC193.</p

Molecular view of the sequence of events of the leaky fusogenic action of cyclic peptides.

<p>A. Initial simulation setup with peptides placed between two bilayers. B. Bridging of proximal leaflets of the two bilayers by BPC194. C. Lipid bulging caused by the action of peptides associated with the bilayers. D. Pre-stalk intermediate accompanied by disordered toroidal pore. E. Close-up of the bridging peptides. F. Close-up of the stalk-pore complex. G–J. Splaying of a lipid during the course of a simulation. The peptides are depicted in pink, the phosphorous atoms in yellow and green respectively and the lipid chains in grey. The water is not shown for clarity. In panel F, the water molecules within the pore in one of the bilayers are shown in blue. The other pore cannot be seen in the zoom-in but is visible in panel D.</p