Imidazolium-Based Lipid Analogues and Their Interaction with Phosphatidylcholine Membranes.

4,5-Dialkylated imidazolium lipid salts are a new class of lipid analogues showing distinct biological activities. The potential effects of the imidazolium lipids on artificial lipid membranes and the corresponding membrane interactions was analyzed. Therefore, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) was employed to create an established lipid monolayer model and a bilayer membrane.

Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane.

Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 μs molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid membrane model that reflects its native lipid composition. We describe in detail the setup of the protein complex and the many natural cofactors and characterize their mobility.

P3HT:DiPBI bulk heterojunction solar cells: morphology and electronic structure probed by multiscale simulation and UV/vis spectroscopy.

Coarse grained molecular dynamics simulations are performed for a mixture of poly(3-hexylthiophene) (P3HT) and diperylene bisimide (DiPBI). The effect of different annealing and cooling protocols on the morphology is investigated and the resulting domain structures are analyzed. In particular, π-stacked clusters of DiPBI molecules are observed whose size decreases with increasing temperature.

Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent.

Coarse-grained (CG) models allow simulation of larger systems for longer times by decreasing the number of degrees of freedom compared with all-atom models. Here we introduce an implicit-solvent version of the popular CG Martini model, nicknamed "Dry" Martini. To account for the omitted solvent degrees of freedom, the nonbonded interaction matrix underlying the Martini force field was reparametrized.

Structure of P3HT crystals, thin films, and solutions by UV/Vis spectral analysis.

Optical absorption spectra of poly(3-hexylthiophene) (P3HT) are calculated in solution, spin-coated thin films, and the bulk crystal using a multiscale simulation approach. The structure of the amorphous thin film is obtained from coarse grained molecular dynamics (MD) simulations and subsequent back-mapping onto an atomistic force field representation. The absorption spectra are computed using TDDFT by statistically averaging over an ensemble of molecules taken from the MD simulations.

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex.

Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we describe the derivation of molecular mechanics parameters for the cofactors associated with the function of the photosystem II core complex: plastoquinone, plastoquinol, heme b, chlorophyll A, pheophytin, and β-carotene.

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide.

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width.

Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations.

The thylakoid membrane is mainly composed of non-common lipids, so called galactolipids. Despite the importance of these lipids for the function of the photosynthetic reaction centers, the molecular organization of these membranes is largely unexplored. Here we use multiscale molecular dynamics simulations to characterize the thylakoid membrane of both cyanobacteria and higher plants.

The power of coarse graining in biomolecular simulations.

Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity.

Phytochemicals perturb membranes and promiscuously alter protein function.

A wide variety of phytochemicals are consumed for their perceived health benefits. Many of these phytochemicals have been found to alter numerous cell functions, but the mechanisms underlying their biological activity tend to be poorly understood. Phenolic phytochemicals are particularly promiscuous modifiers of membrane protein function, suggesting that some of their actions may be due to a common, membrane bilayer-mediated mechanism.

Simulation of polyethylene glycol and calcium-mediated membrane fusion.

We report on the mechanism of membrane fusion mediated by polyethylene glycol (PEG) and Ca(2+) by means of a coarse-grained molecular dynamics simulation approach. Our data provide a detailed view on the role of cations and polymer in modulating the interaction between negatively charged apposed membranes. The PEG chains cause a reduction of the inter-lamellar distance and cause an increase in concentration of divalent cations.

Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model.

We calculate the Gaussian curvature modulus kappa of a systematically coarse-grained (CG) one-component lipid membrane by applying the method recently proposed by Hu et al. [Biophys. J.

Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors.

We present results from coarse grain molecular dynamics simulations of mixed model membranes consisting of saturated and unsaturated lipids together with cholesterol, in which lipid-anchored membrane proteins are embedded. The membrane proteins studied are the peripherally bound H-Ras, N-Ras, and Hedgehog, and the transmembrane peptides WALP and LAT. We provide a molecular view on how the presence and nature of these lipid anchors affects partitioning of the proteins between liquid-ordered and liquid-disordered domains.

Improved Parameters for the Martini Coarse-Grained Protein Force Field.

The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough.

Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields.

The interactions between amino acid side chains govern protein secondary, tertiary, and quaternary structure formation. For molecular modeling approaches to be able to realistically describe these phenomena, the underlying force fields have to represent these interactions as accurately as possible. Here, we compare the side chain-side chain interactions for a number of commonly used force fields, namely the all-atom OPLS, the united-atom GROMOS, and the coarse-grain MARTINI force field.

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form.

Cholesterol in bilayers with PUFA chains: doping with DMPC or POPC results in sterol reorientation and membrane-domain formation.

Using neutron diffraction Harroun et al. [(2006) Biochemistry 45, 1227-1233; (2008) Biochemistry 47, 7090-7096] carried out studies that unequivocally demonstrated cholesterol preferentially sequestering in the middle of bilayers (i.e.