A generic model for lipid monolayers, bilayers, and membranes

We describe a simple coarse-grained model which is suited to study lipid layers and their phase transitions. Lipids are modeled by short semiflexible chains of beads with a solvophilic head and a solvophobic tail component. They are forced to self-assemble into bilayers by a computationally cheap `phantom solvent' environment. The model reproduces the most important phases and phase transitions of monolayers and bilayers. Technical issues such as Monte Carlo parallelization schemes are briefly discussed.Comment: 4 pages, 4 figures conference paper for the CCP 2006 (Gyeongju, Korea

Coarse-grained simulation of transmembrane peptides in the gel phase

We use Dissipative Particle Dynamics simulations, combined with parallel tempering and umbrella sampling, to investigate the potential of mean force between model transmembrane peptides in the various phases of a lipid bilayer, including the low-temperature gel phase. The observed oscillations in the effective interaction between peptides are consistent with the different structures of the surrounding lipid phases

Fluctuation-Induced Interactions between Rods on a Membrane

We consider the interaction between two rods embedded in a fluctuating surface. The modification of fluctuations by the rods leads to an attractive long-range interaction between them. We consider fluctuations governed by either surface tension (films) or bending rigidity (membranes). In both cases the interaction falls off with the separation of the rods as $1/R^4$. The orientational part of the interaction is proportional to $\cos^2\left[ \theta_1+\theta_2 \right]$ in the former case, and to $\cos^2\left[ 2\left(\theta_1+\theta_2\right) \right]$ in the latter, where $\theta_1$ and $\theta_2$ are angles between the rods and the line joining them. These interactions are somewhat reminiscent of dipolar forces and will tend to align collections of such rods into chains.Comment: REVTEX, 14 pages, with 2 Postscript figure

Proton Wires in an Electric Field: the Impact of Grotthuss Mechanism on Charge Translocation

We present the results of the modeling of proton translocation in finite H-bonded chains in the framework of two-stage proton transport model. We explore the influence of reorientation motion of protons, as well as the effect of electric field and proton correlations on system dynamics. An increase of the reorientation energy results in the transition of proton charge from the surrounding to the inner water molecules in the chain. Proton migration along the chain in an external electric field has a step-like character, proceeding with the occurrence of electric field threshold-type effects and drastic redistribution of proton charge. Electric field applied to correlated chains induces first a formation of ordered dipole structures for lower field strength, and than, with a further field strength increase, a stabilization of states with Bjerrum D-defects. We analyze the main factors responsible for the formation/annihilation of Bjerrum defects showing the strong influence of the complex interplay between reorientation energy, electric field and temperature in the dynamics of proton wire.Comment: 28 pages, 9 figure

Defect formation of lytic peptides in lipid membranes and their influence on the thermodynamic properties of the pore environment

We present an experimental study of the pore formation processes of small amphipathic peptides in model phosphocholine lipid membranes. We used atomic force microscopy to characterize the spatial organization and structure of alamethicin- and melittin- induced defects in lipid bilayer membranes and the influence of the peptide on local membrane properties. Alamethicin induced holes in gel DPPC membranes were directly visualized at different peptide concentrations. We found that the thermodynamic state of lipids in gel membranes can be influenced by the presence of alamethicin such that nanoscopic domains of fluid lipids form close to the peptide pores, and that the elastic constants of the membrane are altered in their vicinity. Melittin-induced holes were visualized in DPPC and DLPC membranes at room temperature in order to study the influence of the membrane state on the peptide induced hole formation. Also differential scanning calorimetry was used to investigate the effect of alamethicin on the lipid membrane phase behavior.Comment: 11 pages, 7 figures, 1 tabl

Effect of Lipid Characteristics on the Structure of Transmembrane Proteins

AbstractThe activity of embedded proteins is known to vary with lipid characteristics. Indeed, it has been shown that some cell-membrane proteins cannot function unless certain non-bilayer-forming lipids (i.e., nonzero spontaneous curvature) are present. In this paper we show that membranes exert a line tension on transmembrane proteins. The line tension, on the order of 1–100kT/protein, varies with the lipid properties and the protein configuration. Thus, membranes composed of different lipids favor different protein conformations. Model predictions are in excellent agreement with the data of Keller et al. (Biophys. J. 1993, 65:23–27) regarding the conductance of alamethicin channels

Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers

We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: Direct interactions, lipid-induced depletion interactions, lipid bridging, lipid packing, and a smooth long-range contribution. The mechanisms leading to "hydrophobic mismatch" interactions are critically analyzed.Comment: 16 pages, 8 figures, accepted for publication in Biophysical Journa

Identification of additional homologues of subunits VII and VIII of the ubiquinol-cytochrome <i>c</i> oxidoreductase enables definition of consensus sequences

AbstractThe Candida utilis QCR7 gene encoding subunit VII of the ubiquinol-cytochrome c oxidoreductase was isolated by functional complementation of the Saccharomyces cerevisiae subunit VII-null mutant. Several other subunit VII homologues as well as homologues for subunit VIII were identified by screening the GenBank database. Some of these homologues for subunit VII could only be identified as such using a consensus sequence that was derived from the multiple sequence alignment. Definition of the consensus should facilitate further analysis of structure/function relationships in this protein

Toy amphiphiles on the computer: What can we learn from generic models?

Generic coarse-grained models are designed such that they are (i) simple and (ii) computationally efficient. They do not aim at representing particular materials, but classes of materials, hence they can offer insight into universal properties of these classes. Here we review generic models for amphiphilic molecules and discuss applications in studies of self-assembling nanostructures and the local structure of bilayer membranes, i.e. their phases and their interactions with nanosized inclusions. Special attention is given to the comparison of simulations with elastic continuum models, which are, in some sense, generic models on a higher coarse-graining level. In many cases, it is possible to bridge quantitatively between generic particle models and continuum models, hence multiscale modeling works on principle. On the other side, generic simulations can help to interpret experiments by providing information that is not accessible otherwise.Comment: Invited feature article, to appear in Macromolecular Rapid Communication