The Dissolution of Cellulose in Ionic Liquids - A Molecular Dynamics Study

The use of ionic liquids for the dissolution of cellulose promises an alternative method for the thermochemical pretreatment of biomass that may be more efficient and environmentally acceptable than conventional techniques in aqueous solution. Understanding how ionic liquids act on cellulose is essential for improving pretreatment conditions and thus detailed knowledge of the interactions between solute and solvent molecules is necessary. Here, results from the first all-atom molecular dynamics simulation of an entire cellulose microfibril in 1-butyl-3-methylimidazolium chloride (BmimCl) are presented and the interactions and orientations of solvent ions with respect to glucose units on the hydrophobic and hydrophilic surfaces of the fiber are analyzed in detail, shedding light on the initiation stages of cellulose dissolution. Moreover, replica-exchange simulations of a single cellulose chain fully solvated in BmimCl and in water are performed for a total of around 13 μs in order to study the dynamics and thermodynamics of the end state of the dissolution. The results indicate that chloride anions predominantly interact with cellulose hydroxyl groups and disrupt the intrachain O3H’···O5 hydrogen bonds, which are essential for the integrity of cellulose fibers. The cations stack preferentially on the hydrophobic cellulose surface, governed by non-polar interactions with cellulose, which can stabilize detached cellulose chains by compensating the interaction between stacked layers. Moreover, a frequently occurring intercalation of cations on the hydrophilic surface is observed, which by separating cellulose layers can also potentially facilitate the initiation of fiber disintegration. The single-chain simulations indicate that differences in cellulose solvation mechanisms between the two solvents exist. Although global size-related properties of the cellulose chain are comparable in the two solvents, local conformational properties of cellulose differ significantly between the BmimCl and water solutions. In general, the results indicate that solute-solvent interaction energies are more favorable and that the cellulose chain is more flexible in BmimCl than in water. Taken together, the simulations explain how ionic liquids can facilitate cellulose dissolution: the synergistic action of anions and cations helps to initiate fiber deconstruction through specific interactions on the fiber surface and to solvate single cellulose chains through favorable solvent interactions and conformational flexibility

Replica-Exchange Molecular Dynamics Simulations of Cellulose Solvated in Water and in the Ionic Liquid 1‑Butyl-3-Methylimidazolium Chloride

Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H′···O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures

Automated Identification of Flexible Multivalent IDP-Bound Assemblies in Electron Micrographs

The quantitative characterization of compositional and conformational heterogeneity is an outstanding problem in structural biology and a focus of attention in the electron microscopy (EM) community. Here, we report automated analysis for a particular class of multivalent intrinsically disordered proteins (IDPs) bound to hub proteins, which exhibit not only a multiplicity of bound species but also continuous conformational flexibility. Such flexibility currently presents a significant challenge to standard methods of EM analysis, because “class averaging” effectively washes out the heterogeneity of primary interest. Alternatively, manual procedures can be used, but these are time-consuming and bias-prone. In the present work, we study a five-binding site IDP (Nup159) thought to bind in parallel duplex fashion to “hub” LC8 homodimers. We employ negative-stain EM (NSEM) because of its high contrast for single particle analysis and visualization of the small (∼20kDa) LC8 homodimer, although our approach should be applicable whenever there is sufficient contrast and a heterogeneous ensemble of oligomeric particles in EM micrographs. Procedurally, our scoring function identifies IDP-bound LC8 complexes based on chemical restraints imparted by the multivalent IDP scaffold, such as spacing and angles separating bound LC8 dimers. The results show a population distribution of oligomeric species (with 2, 3, 4 and 5 LC8 dimers), which is consistent with manually analyzed data. In addition, the automated procedure identifies several assemblies that were missed by initial manual analysis. Importantly, our automated approach allows for quantitative analysis of the ensemble of conformational states that are sampled by each of these classes, which had been obscured by traditional class averaging methods. The data also reveal the presence of oligomers with more than five LC8 dimers bound, suggesting out-of-register binding to the Nup159 duplex, which is a new finding

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 cholesterol\u2019s 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 headgroup\u2019s 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.Peer reviewed: YesNRC publication: Ye

Continuum Dynamics and Statistical Correction of Compositional Heterogeneity in Multivalent IDP oligomers resolved by Single-Particle EM

Multivalent intrinsically disordered protein (IDP) complexes are prevalent in biology and act in regulation of diverse processes, including transcription, signaling events, and the assembly and disassembly of complex macromolecular architectures. These systems pose significant challenges to structural investigation, due to continuum dynamics imparted by the IDP and compositional heterogeneity resulting from characteristic low-affinity interactions. Here, we developed a modular pipeline for automated single-particle electron microscopy (EM) distribution analysis of common but relatively understudied semi-ordered systems: \u27beads-on-a-string\u27 assemblies, composed of IDPs bound at multivalent sites to the ubiquitous ∼20kDacross-linking hub protein LC8. This approach quantifies conformational geometries and compositional heterogeneity on a single-particle basis, and statistically corrects spurious observations arising from random proximity of bound and unbound LC8. The statistical correction is generically applicable to oligomer characterization and not specific to our pipeline. Following validation, the approach was applied to the nuclear pore IDP Nup159 and the transcription factor ASCIZ. This analysis unveiled significant compositional and conformational diversity in both systems that could not be obtained from ensemble single particle EM class-averaging strategies, and new insights for exploring how these architectural properties might contribute to their physiological roles in supramolecular assembly and transcriptional regulation. We expect that this approach may be adopted to many other intrinsically disordered systems that have evaded traditional methods of structural characterization