Phase behavior of supported lipid bilayers: A systematic study by coarse-grained molecular dynamics simulations.

Solid-supported lipid bilayers are utilized by experimental scientists as models for biological membranes because of their stability. However, compared to free standing bilayers, their close proximity to the substrate may affect their phase behavior. As this is still poorly understood, and few computational studies have been performed on such systems thus far, here we present the results from a systematic study based on molecular dynamics simulations of an implicit-solvent model for solid-supported lipid bilayers with varying lipid-substrate interactions. The attractive interaction between the substrate and the lipid head groups that are closest to the substrate leads to an increased translocation of the lipids from the distal to the proximal bilayer-leaflet. This thereby leads to a transbilayer imbalance of the lipid density, with the lipid density of the proximal leaflet higher than that of the distal leaflet. Consequently, the order parameter of the proximal leaflet is found to be higher than that of the distal leaflet, the higher the strength of lipid interaction is, the stronger the effect. The proximal leaflet exhibits gel and fluid phases with an abrupt melting transition between the two phases. In contrast, below the melting temperature of the proximal leaflet, the distal leaflet is inhomogeneous with coexisting gel and fluid domains. The size of the fluid domains increases with increasing the strength of the lipid interaction. At low temperatures, the inhomogeneity of the distal leaflet is due to its reduced lipid density.

Reads2Type: a web application for rapid microbial taxonomy identification.

BACKGROUND: Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data. RESULTS: Raw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete genomes. Using a dataset of 1003 whole genome sequenced bacteria from various sequencing platforms, Reads2Type was able to identify the species with 99.5 % accuracy and on the minutes time scale. CONCLUSIONS: In comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing files, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html.

Flip-flop of steroids in phospholipid bilayers: effects of the chemical structure on transbilayer diffusion.

The transverse motion of molecules from one leaflet to the other of a lipid bilayer, or flip-flop, represents a putative mechanism for their transmembrane transport and may contribute to the asymmetric distribution of components in biomembranes. However, a clear understanding of this process is still missing. The scarce knowledge derives from the difficulty of experimental determination. Because of its slow rate on the molecular time scale, flip-flop is challenging also for computational techniques. Here, we report a study of the passive transbilayer diffusion of steroids, based on a kinetic model derived from the analysis of their free energy surface, as a function of their position and orientation in the bilayer. An implicit membrane description is used, where the anisotropy and the nonuniformity of the bilayer environment are taken into account in terms of the gradients of density, dielectric permittivity, acyl chain order parameters, and lateral pressure. The flip-flop rates are determined by solving the Master Equation that governs the time evolution of the system, with transition rates between free energy minima evaluated according to the Kramers theory. Considering various steroids (cholesterol, lanosterol, ketosterone, 5-cholestene, 25-hydroxycholesterol, and testosterone), we can discuss how differences in molecular shape and polarity affect the pathway and the rate of flip-flop in a liquid crystalline 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) bilayer, at low steroid concentration. We predict time scales ranging from microseconds to milliseconds, strongly affected by the presence of polar substituents and by their position in the molecular skeleton.

Modelling of proteins in membranes.

This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among others, the following phenomena are discussed: interactions of interfacially adsorbed peptides, pore-forming amphipathic peptides, adsorption of charged proteins onto oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins.

Predictions of phase separation in three-component lipid membranes by the MARTINI force field.

The phase behavior of the coarse-grained MARTINI model for three-component lipid bilayers composed of dipalmytoyl-phosphatidylcholine (DPPC), cholesterol (Chol), and an unsaturated phosphatidylcholine (PC) was systematically investigated by molecular dynamics simulations. The aim of this study is to understand which types of unsaturated PC induce the formation of thermodynamically stable coexisting phases when added to mixtures of DPPC and Chol and to unravel the mechanisms that drive phase separation in such three-component mixtures. Our simulations indicate that the currently used MARTINI force field does not induce such phase separation in mixtures of DPPC, Chol, and unsaturated PCs with a low unsaturation level, such as palmitoyl-oleoyl-phosphatidylcholine (POPC) or dioleoyl-phosphatidylcholine (DOPC). Also, we found that phase separation does occur in mixtures of DPPC, Chol, and polyunsaturated PCs, such as dilinoleyl-phosphatidylcholine (DUPC) and diarachidonoyl-phosphatidylcholine (DAPC). Through systematic tweaking of the interactions between the hydrophobic groups of the PC molecules, we show that the appearance of phase separation in three-component lipid bilayers, as modeled through the MARTINI force field, is primarily due to the interactions between the coarse-grained molecules, i.e., the beads, rather than due to the differences between the conformations of saturated and unsaturated lipid acyl chains, namely entropy driven.

Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins.

Biological membranes are complex and highly cooperative structures. To relate biomembrane structure to their biological function it is often necessary to consider simpler systems. Lipid bilayers composed of one or two lipid species, and with embedded proteins, provide a model system for biological membranes. Here we present a mesoscopic model for lipid bilayers with embedded proteins, which we have studied with the help of the dissipative particle dynamics simulation technique. Because hydrophobic matching is believed to be one of the main physical mechanisms regulating lipid-protein interactions in membranes, we considered proteins of different hydrophobic length (as well as different sizes). We studied the cooperative behavior of the lipid-protein system at mesoscopic time- and lengthscales. In particular, we correlated in a systematic way the protein-induced bilayer perturbation, and the lipid-induced protein tilt, with the hydrophobic mismatch (positive and negative) between the protein hydrophobic length and the pure lipid bilayer hydrophobic thickness. The protein-induced bilayer perturbation was quantified in terms of a coherence length, xi(P), of the lipid bilayer hydrophobic thickness profile around the protein. The dependence on temperature of xi(P), and the protein tilt-angle, were studied above the main-transition temperature of the pure system, i.e., in the fluid phase. We found that xi(P) depends on mismatch, i.e., the higher the mismatch is, the longer xi(P) becomes, at least for positive values of mismatch; a dependence on the protein size appears as well. In the case of large model proteins experiencing extreme mismatch conditions, in the region next to the so-called lipid annulus, there appears an undershooting (or overshooting) region where the bilayer hydrophobic thickness is locally lower (or higher) than in the unperturbed bilayer, depending on whether the protein hydrophobic length is longer (or shorter) than the pure lipid bilayer hydrophobic thickness. Proteins may tilt when embedded in a too-thin bilayer. Our simulation data suggest that, when the embedded protein has a small size, the main mechanism to compensate for a large hydrophobic mismatch is the tilt, whereas large proteins react to negative mismatch by causing an increase of the hydrophobic thickness of the nearby bilayer. Furthermore, for the case of small, peptidelike proteins, we found the same type of functional dependence of the protein tilt-angle on mismatch, as was recently detected by fluorescence spectroscopy measurements.

Characterization of the thermotropic behavior and lateral organization of lipid-peptide mixtures by a combined experimental and theoretical approach: effects of hydrophobic mismatch and role of flanking residues.

A combined experimental and theoretical study was performed on a series of mixtures of dipalmitoylphosphatidylcholine (DPPC) and synthetic peptides to investigate their thermotropic behavior and lateral organization. The experimental study was based on differential scanning calorimetry (DSC) and phosphorous nuclear magnetic resonance ((31)P-NMR) techniques; the theoretical study was based on calculations on a microscopic molecular interaction model, where the lipid-peptide interaction is built on the hydrophobic matching principle. The chosen peptides, WALP and KALP, consist of a hydrophobic stretch, of variable length, of alternating leucine and alanine residues, flanked on both ends with tryptophan and lysine residues, respectively. By systematically varying the peptide hydrophobic length it was thus possible to explore different matching conditions between the peptide's hydrophobic length and the lipid bilayer hydrophobic thickness, and to investigate the potential role of flanking residues. The results show that both the WALP and the KALP peptides tend to favor the liquid-crystalline (or fluid) phase of the system; i.e., they tend to depress the main-transition temperature, T(m), of pure DPPC. However, the detailed effects of both peptides on the lateral phase behavior of the lipid-peptide system are dependent on the peptide length and the type of flanking residues. The results suggest that below T(m), the shortest among the WALP and KALP peptides induce gel-fluid phase separation in the system within an extensive temperature-composition region. The longer the hydrophobic length of the peptides is, the more narrow this region appears to become.

Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis.

The performance of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks in wheat variety classification is further evaluated.1 Two principal issues were studied: (a) the number of varieties that could be classified correctly; and (b) various means of pre-processing mass spectrometric data. The number of wheat varieties tested was increased from 10 to 30. The main pre-processing method investigated was based on Gaussian smoothing of the spectra, but other methods based on normalisation procedures and multiplicative scatter correction of data were also used. With the final method, it was possible to classify 30 wheat varieties with 87% correctly classified mass spectra and a correlation coefficient of 0.90.