Magainin versus Melittin

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Last Updated: Wednesday, 21 August 2013 11:44

Max L Berkowitz and Kolattukudy Santo. The Difference between Magainin-2 and Melittin Assemblies in Phosphatidylcholine Bilayers: Results from Coarse-Grained Simulations. J. Phys. Chem. B, 2012. Just Accepted Manuscript, DOI: 10.1021/jp212018f

We performed coarse-grained computer simulations using MARTINI force field to study the difference in the self assembly and possible pore creation in DPPC phospholipid membranes by two different antimicrobial peptides: magainin-2 and melittin. Simulations showed that magainin-2 peptides create large sized disordered toroidal pores that allow easy water permeation across them. Melittin assemblies contain peptides in U-shaped conformations that, although creating holes in membranes, block effectively the passage of water. These observed structures are consistent with the dye efflux experiments performed on vesicles exposed to solutions containing antimicrobial peptides.

Raft & Amphiphiles

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Last Updated: Wednesday, 21 August 2013 11:44

Hari S. Muddana, Homer H. Chiang, Peter J. Butler. Tuning Membrane Phase Separation Using Nonlipid Amphiphiles. Biophys J, 2012, 102:489-497

Lipid phase separation may be a mechanism by which lipids participate in sorting membrane proteins and facilitate membrane-mediated biochemical signaling in cells. To provide new tools for membrane lipid phase manipulation that avoid direct effects on protein activity and lipid composition, we studied phase separation in binary and ternary lipid mixtures under the influence of three nonlipid amphiphiles, vitamin E (VE), Triton-X (TX)-100, and benzyl alcohol (BA). Mechanisms of additive-induced phase separation were elucidated using coarse-grained molecular dynamics simulations of these additives in a liquid bilayer made from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-diundecanoyl-sn-glycero-phosphocholine (DUPC). From simulations, the additive's partitioning preference, changes in membrane thickness, and alterations in lipid order were quantified. Simulations showed that VE favored the DPPC phase but partitioned predominantly to the domain boundaries and lowered the tendency for domain formation, and therefore acted as a linactant. This simulated behavior was consistent with experimental observations in which VE promoted lipid mixing and dispersed domains in both gel/liquid and liquid-ordered/liquid-disordered systems. From simulation, BA partitioned predominantly to the DUPC phase, decreased lipid order there, and thinned the membrane. These actions explain why, experimentally, BA promoted phase separation in both binary and ternary lipid mixtures. In contrast, TX, a popular detergent used to isolate raft membranes in cells, exhibited equal preference for both phases, as demonstrated by simulations, but nonetheless, was a strong domain promoter in all lipid mixtures. Further analysis showed that TX increased membrane thickness of the DPPC phase to a greater extent than the DUPC phase and thus increased hydrophobic mismatch, which may explain experimental observation of phase separation in the presence of TX. In summary, these nonlipid amphiphiles provide new tools to tune domain formation in model vesicle systems and could provide the means to form or disperse membrane lipid domains in cells, in addition to the well-known methods involving cholesterol enrichment and sequestration.

Amino-acid dimerization

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Last Updated: Wednesday, 21 August 2013 11:17

D.H. de Jong, X. Periole, S.J. Marrink. Dimerization of amino acid side chains: lessons from the comparison of different forcefields. JCTC, in press, 2012

 

The interactions between amino acid side chains govern protein secondary, tertiary as well as quaternary structure formation. For molecular modeling approaches to be able to realisti- cally describe these phenomena, the underlying forcefields have to represent these interactions as accurately as possible. Here we compare the side chain-side chain interactions for a number of commonly used forcefields, namely the all-atom OPLS, the united-atom GROMOS, and the coarse-grained MARTINI forcefield. We do so by calculation of the dimerization free energies between selected pairs of side chains. To mimic both polar and non-polar environments, the simulations are performed in water, n-octanol, and decane. In general, good correlations are found between all three forcefields, with deviations of the order of 1 kT in aqueous solvent. In apolar solvent, however, significantly larger differences are found, especially for charged amino acid pairs between the OPLS and GROMOS forcefields, and for polar interactions in the MARTINI forcefield in comparison to the higher resolution models. We also tested the per- formance of knowledge based potentials with respect to the various forcefields, showing good correlation in aqueous solvent with an exception of aromatic residues for which the interaction strength is underestimated in the knowledge based potentials.

Fusion peptides

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Last Updated: Wednesday, 21 August 2013 11:24

M. Fuhrmans, S.J. Marrink. Molecular view of the role of fusion peptides in promoting positive membrane curvature. JACS, 134:1543–1552,  2012. abstract Fusion peptides are moderately hydrophobic segments of viral and nonviral membrane fusion proteins that enable these proteins to fuse two closely apposed biological membranes. In vitro assays furthermore show that even isolated fusion peptides alone can support membrane fusion in model systems. In addition, the fusion peptides have a distinct effect on the phase diagram of lipid mixtures. Here, we present molecular dynamics simulations investigating the effect of a particular fusion peptide, the influenza hemagglutinin fusion peptide and some of its mutants, on the lipid phase diagram. We detect a systematic shift toward phases with more positive mean curvature in the presence of the peptides, as well as an occurrence of bicontinuous cubic phases, which indicates a stabilization of Gaussian curvature. The wild-type fusion peptide has a stronger effect on the phase behavior as compared to the mutants, which we relate to its boomerang shape. Our results point to a different role of fusion peptides than hitherto assumed, the stabilization of pores rather than stalks along the fusion pathway.

Bolalipid membranes

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Last Updated: Wednesday, 21 August 2013 11:21

M. Bulacu, X. Periole, S.J. Marrink. In-silico design of robust bolalipid membranes, Biomacromol., in press, 2011. DOI:10.1021/bm201454j

The robustness of microorganisms used in industrial fermentations is essential for the efficiency and yield of the production process. A viable tool to increase the robustness is through engineering of the cell membrane and especially by incorporating lipids from species that survive under harsh conditions. Bolalipids are tetraether lipids found in Archaea bacteria, conferring stability to these bacteria by spanning across the cytoplasmic membrane. Here we report on in silico experiments to characterize and design optimal bolalipid membranes in terms of robustness. We use coarse-grained molecular dynamics simulations to study the structure, dynamics, and stability of membranes composed of model bolalipids, consisting of two dipalmitoylphosphatidylcholine (DPPC) lipids covalently linked together at either one or both tail ends. We find that bolalipid membranes differ substantially from a normal lipid membrane, with an increase in thickness and tail order, an increase in the gel-to-liquid crystalline phase transition temperature, and a decrease in diffusivity of the lipids. By changing the flexibility of the linker between the lipid tails, we furthermore show how the membrane properties can be controlled. A stiffer linker increases the ratio between spanning and looping conformations, rendering the membrane more rigid. Our study may help in designing artificial membranes, with tunable properties, able to function under extreme conditions. As an example, we show that incorporation of bolalipids makes the membrane more tolerant toward butanol.

 

Bacterial chemoreceptors

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Last Updated: Wednesday, 21 August 2013 11:21

Hall BA, Armitage JP, Sansom MSP (2011) Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling. PLoS Comput Biol 7(10): e1002204. doi:10.1371/journal.pcbi.1002204

Transmembrane α-helices play a key role in many receptors, transmitting a signal from one side to the other of the lipid bilayer membrane. Bacterial chemoreceptors are one of the best studied such systems, with a wealth of biophysical and mutational data indicating a key role for the TM2 helix in signalling. In particular, aromatic (Trp and Tyr) and basic (Arg) residues help to lock α-helices into a membrane. Mutants in TM2 of E. coli Tar and related chemoreceptors involving these residues implicate changes in helix location and/or orientation in signalling. We have investigated the detailed structural basis of this via high throughput coarse-grained molecular dynamics (CG-MD) of Tar TM2 and its mutants in lipid bilayers. We focus on the position (shift) and orientation (tilt, rotation) of TM2 relative to the bilayer and how these are perturbed in mutants relative to the wildtype. The simulations reveal a clear correlation between small (ca. 1.5 Å) shift in position of TM2 along the bilayer normal and downstream changes in signalling activity. Weaker correlations are seen with helix tilt, and little/none between signalling and helix twist. This analysis of relatively subtle changes was only possible because the high throughput simulation method allowed us to run large (n = 100) ensembles for substantial numbers of different helix sequences, amounting to ca. 2000 simulations in total. Overall, this analysis supports a swinging-piston model of transmembrane signalling by Tar and related chemoreceptors.