Barmak Mostofian

Mechanical Properties of Nanoscopic Lipid Domains

The lipid raft hypothesis presents insights into how the cell membrane organizes proteins and lipids to accomplish its many vital functions. Yet basic questions remain about the physical mechanisms that lead to the formation, stability, and size of lipid rafts. As a result, much interest has been generated in the study of systems that contain similar lateral heterogeneities, or domains. In the current work we present an experimental approach that is capable of isolating the bending moduli of lipid domains. This is accomplished using neutron scattering and its unique sensitivity to the isotopes of hydrogen. Combining contrast matching approaches with inelastic neutron scattering, we isolate the bending modulus of ∼13 nm diameter domains residing in 60 nm unilamellar vesicles, whose lipid composition mimics the mammalian plasma membrane outer leaflet. Importantly, the bending modulus of the nanoscopic domains differs from the modulus of the continuous phase surrounding them. From additional structural measurements and all-atom simulations, we also determine that nanoscopic domains are in-register across the bilayer leaflets. Taken together, these results inform a number of theoretical models of domain/raft formation and highlight the fact that mismatches in bending modulus must be accounted for when explaining the emergence of lateral heterogeneities in lipid systems and biological membranes.

Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution

Ionic liquids dissolve cellulose in a more efficient and environmentally acceptable way than conventional methods in aqueous solution. An understanding of how ionic liquids act on cellulose is essential for improving pretreatment conditions and thus detailed knowledge of the interactions between the cations, anions and cellulose is necessary. Here, to explore ionic liquid effects, we perform all-atom molecular dynamics simulations of a cellulose microfibril in 1-butyl-3-methylimidazolium chloride and analyze site–site interactions and cation orientations at the solute–solvent interface. The results indicate that Cl− anions predominantly interact with cellulose surface hydroxyl groups but with differences between chains of neighboring cellulose layers, referred to as center and origin chains; Cl− binds to C3-hydroxyls on the origin chains but to C2- and C6-hydroxyls on the center chains, thus resulting in a distinct pattern along glucan chains of the hydrophilic fiber surfaces. In particular, Cl− binding disrupts intrachain O3H–O5 hydrogen bonds on the origin chains but not those on the center chains. In contrast, Bmim+ cations stack preferentially on the hydrophobic cellulose surface, governed by non-polar interactions with cellulose. Complementary to the polar interactions between Cl− and cellulose, the stacking interaction between solvent cation rings and cellulose pyranose rings can compensate the interaction between stacked cellulose layers, thus stabilizing detached cellulose chains. Moreover, a frequently occurring intercalation of Bmim+ on the hydrophilic surface is observed, which by separating cellulose layers can also potentially facilitate the initiation of fiber disintegration. The results provide a molecular description why ionic liquids are ideal cellulose solvents, the concerted action of anions and cations on the hydrophobic and hydrophilic surfaces being key to the efficient dissolution of the amphiphilic carbohydrate.

Interactions between Ether Phospholipids and Cholesterol As Determined by Scattering and Molecular Dynamics Simulations

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterols molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroups phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

Cosolvent pretreatment in cellulosic biofuel production: effect of tetrahydrofuran-water on lignin structure and dynamics

The deconstruction of cellulose is an essential step in the production of ethanol from lignocellulosic biomass. However, the presence of lignin hinders this process. Recently, a novel cosolvent based biomass pretreatment method called CELF (Cosolvent Enhanced Lignocellulosic Fractionation) which employs tetrahydrofuran (THF) in a single phase mixture with water, was found to be highly effective at solubilizing and extracting lignin from lignocellulosic biomass and achieving high yields of fermentable sugars. Here, using all-atom molecular-dynamics simulation, we find that THF preferentially solvates lignin, and in doing so, shifts the equilibrium configurational distribution of the biopolymer from a crumpled globule to coil, independent of temperature. Whereas pure water is a bad solvent for lignin, the THF : water cosolvent acts as a “theta” solvent, in which solvent : lignin and lignin : lignin interactions are approximately equivalent in strength. Under these conditions, polymers do not aggregate, thus providing a mechanism for the observed lignin solubilization that facilitates unfettered access of celluloytic enzymes to cellulose.

Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications.

Pretreatment facilitates more complete deconstruction of plant biomass to enable more economic production of lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative to aqueous-only methods by enhancing lignin removal to allow unfettered access to cellulose. However, there is a limited mechanistic understanding of the interactions between the co-solvents and cellulose that impedes further improvement of such pretreatment methods. Recently, tetrahydrofuran (THF) has been identified as a highly effective co-solvent for the pretreatment and fractionation of biomass. To elucidate the mechanism of the THF-water interactions with cellulose, we pair simulation and experimental data demonstrating that enhanced solubilization of cellulose can be achieved by the THF-water co-solvent system at equivolume mixtures and moderate temperatures (≤445 K). The simulations show that THF and water spontaneously phase separate on the local surface of a cellulose fiber, owing to hydrogen bonding of water molecules with the hydrophilic cellulose faces and stacking of THF molecules on the hydrophobic faces. Furthermore, a single fully solvated cellulose chain is shown to be preferentially bound by water molecules in the THF-water mixture. In light of these findings, co-solvent reactions were performed on microcrystalline cellulose and maple wood to show that THF significantly enhanced cellulose deconstruction and lignocellulose solubilization at simulation conditions, enabling a highly versatile and efficient biomass pretreatment and fractionation method.

The solvation structures of cellulose microfibrils in ionic liquids

The use of ionic liquids for non-derivatized cellulose dissolution promises an alternative method for the thermochemical pretreatment of biomass that may be more efficient and environmentally acceptable than more conventional techniques in aqueous solution. Here, we performed equilibrium MD simulations of a cellulose microfibril in the ionic liquid 1-butyl-3-methylimidazolium chloride (BmimCl) and compared the solute structure and the solute-solvent interactions at the interface with those from corresponding simulations in water. The results indicate a higher occurrence of solvent-exposed orientations of cellulose surface hydroxymethyl groups in BmimCl than in water. Moreover, spatial and radial distribution functions indicate that hydrophilic surfaces are a preferred site of interaction between cellulose and the ionic liquid. In particular, hydroxymethyl groups on the hydrophilic fiber surface adopt a different conformation from their counterparts oriented towards the fiber’s core. Furthermore, the glucose units with these solvent-oriented hydroxymethyls are surrounded by the heterocyclic organic cation in a preferred parallel orientation, suggesting a direct and distinct interaction scheme between cellulose and BmimCl.

Molecular Driving Forces behind the Tetrahydrofuran–Water Miscibility Gap

The tetrahydrofuran-water binary system exhibits an unusual closed-loop miscibility gap (transitions from a miscible regime to an immiscible regime back to another miscible regime as the temperature increases). Here, using all-atom molecular dynamics simulations, we probe the structural and dynamical behavior of the binary system in the temperature regime of this gap at four different mass ratios, and we compare the behavior of bulk water and tetrahydrofuran. The changes in structure and dynamics observed in the simulations indicate that the temperature region associated with the miscibility gap is distinctive. Within the miscibility-gap temperature region, the self-diffusion of water is significantly altered and the second virial coefficients (pair-interaction strengths) show parabolic-like behavior. Overall, the results suggest that the gap is the result of differing trends with temperature of minor structural changes, which produces interaction virials with parabolic temperature dependence near the miscibility gap.

Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane

Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. We advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model included as Supporting Information to this Letter and at ( http://cmb.ornl.gov/members/cheng ). The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.