Micholas Dean Smith

Force-Field Induced Bias in the Structure of Aβ21–30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields

In this work we examine the dynamics of an intrinsically disordered protein fragment of the amyloid β, the Aβ21-30, under seven commonly used molecular dynamics force fields (OPLS-AA, CHARMM27-CMAP, AMBER99, AMBER99SB, AMBER99SB-ILDN, AMBER03, and GROMOS53A6), and three water models (TIP3P, TIP4P, and SPC/E). We find that the tested force fields and water models have little effect on the measures of radii of gyration and solvent accessible surface area (SASA); however, secondary structure measures and intrapeptide hydrogen-bonding are significantly modified, with AMBER (99, 99SB, 99SB-ILDN, and 03) and CHARMM22/27 force-fields readily increasing helical content and the variety of intrapeptide hydrogen bonds. On the basis of a comparison between the population of helical and β structures found in experiments, our data suggest that force fields that suppress the formation of helical structure might be a better choice to model the Aβ21-30 peptide.

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.

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.

Effect of ionic aqueous environments on the structure and dynamics of the Aβ(21-30) fragment: a molecular-dynamics study.

The amyloid β-protein (Aβ) has been implicated in the pathogenesis of Alzheimers disease. The role of the structure and dynamics of the central Aβ21-30 decapeptide region of the full-length Aβ is considered crucial in the aggregation pathway of Aβ. Here we report results of isobaric-isothermal (NPT) all-atom explicit water molecular dynamics simulations of the monomeric form of the wild-type Aβ21-30 fragment in aqueous salt environments formed by neurobiologically important group IA (NaCl, KCl) and group IIA (CaCl2, MgCl2) salts. Our simulations reveal the existence of salt-specific changes to secondary structure propensities, lifetimes, hydrogen bonding, salt-bridge formation, and decapeptide-ion contacts of this decapeptide. These results suggest that aqueous environments with the CaCl2 salt, and to a much lesser extent the MgCl2 salt, have profound effects by increasing random coil structure propensities and lifetimes and diminishing intrapeptide hydrogen bonding. These effects are rationalized in terms of direct cation-decapeptide contacts and changes to the hydration-shell water molecules. On the other side of the spectrum, environments with the NaCl and KCl salts have little influence on the decapeptides secondary structure despite increasing hydrogen bonding, salt-bridge formation, and lifetime of turn structures. The observed enhancement of open structures by group IIA may be of importance in the folding and aggregation pathway of the full-length Aβ.

Changes to the structure and dynamics in mutations of Aβ(21-30) caused by ions in solution.

The structure and dynamics of the 21-30 fragment of the amyloid β-protein (Aβ(21-30)) and its Dutch [Glu22Gln], Arctic [Glu22Gly], and Iowa [Asp23Asn] isoforms are of considerable importance, as their folding may play an important role in the pathogenesis of sporadic and familial forms of Alzheimers disease and cerebral amyloid angiopathy. A full understanding of this pathologic folding in in vivo environments is still elusive. Here we examine the interactions and effects of two neurobiologically relevant salts (CaCl2 and KCl) on the structure and dynamics of Aβ(21-30) decapeptide monomers containing the Dutch, Arctic, and Iowa charge-modifying point mutations using isobaric-isothermal (NPT) explicit water all-atom molecular-dynamics simulations. Measurements of secondary structure populations, intrapeptide hydrogen bonding, salt bridging, secondary structure lifetimes, cation-residue contacts, water-peptide hydrogen bonding, and hydration-shell water residence times reveal a variety of ion and mutation-dependent modifications to the decapeptides structure and dynamics. In general, Ca(2+) has the effect of increasing coil-state populations and lifetimes, modifying the behavior of the decapeptides hydration shell and diminishing intrapeptide hydrogen bonding, while K(+) is found to diminish coil populations and lifetimes and, for the case of the Iowa mutant, dramatically increase the decapeptides propensity for β secondary structures. Mutation-dependent effects highlight the different roles of the Glu22 and Asp23 residues in either solvating or enhancing turn structures, respectively. Taken together, our results provide insights into the differential roles of different ionic species as well as specific effects on the Glu22 and Asp23 residues of Aβ(21-30) mediated by ion-decapeptide interactions and the solvent, which could be important interaction mechanisms relevant to the peptides behavior in both in vitro and in vivo environments.

Impact of hydration and temperature history on the structure and dynamics of lignin

The full utilization of plant biomass for the production of energy and novel materials often involves high temperature treatment. Examples include melt spinning of lignin for manufacturing low-cost carbon fiber and the relocalization of lignin to increase the accessibility of cellulose for production of biofuels. These temperature-induced effects arise from poorly understood changes in lignin flexibility. Here, we combine molecular dynamics simulations with neutron scattering and dielectric spectroscopy experiments to probe the dependence of lignin dynamics on hydration and thermal history. We find a dynamical and structural hysteresis: at a given temperature, the lignin molecules are more expanded and their dynamics faster when the lignin is cooled than when heated. The structural hysteresis is more pronounced for dry lignin. The difference in dynamics, however, follows a different trend, it is found to be more significant at high temperatures and high hydration levels. The simulations also reveal syringyl units to be more dynamic than guiacyl. The results provide an atomic-detailed description of lignin dynamics, important for understanding lignin role in plant cell wall mechanics and for rationally improving lignin processing. The lignin glass transition, at which the polymer softens, is lower when lignin is cooled than when heated; therefore extending the cooling phase of processing and shortening the heating phase may offer ways to lower processing costs.

The Stability of a β-Hairpin Is Altered by Surface–Water Interactions under Confinement

Understanding protein folding and stability in in vivo confined environments is a challenging problem from both experimental and computational points of views. Despite recent insights, an appreciation and complete understanding of how the solvent influences the structure and stability of proteins under complex confined environments is still lacking. Here, using all-atom molecular dynamics simulations in explicit solvent, we report the effects of confinement on the lifetime of a metastable β-hairpin structure in the Aβ(21-30) decapeptide. Our results show that the values of these lifetimes depend on the nature of the confining surface, where smooth and rough hydrophobic confining walls have solvent-mediated stabilizing and destabilizing effects, respectively. The source of the destabilization found inside atomically rough confining walls lies in surface-peptide interactions that break the β-hairpin in this peptide, whereas smooth confining walls stabilize it by forming well-ordered layers of water that keep the decapeptide solvated in the inner part of the pore and away from the surface. In addition, we show that the size of the confining pore can tune the value of the lifetimes where pore sizes comparable to the size of the decapeptide have the largest effects.

Cellulose-hemicellulose interactions at elevated temperatures increase cellulose recalcitrance to biological conversion

It has been previously shown that cellulose-lignin droplets’ strong interactions, resulting from lignin coalescence and redisposition on cellulose surface during thermochemical pretreatments, increase cellulose recalcitrance to biological conversion, especially at commercially viable low enzyme loadings. However, information on the impact of cellulose–hemicellulose interactions on cellulose recalcitrance following relevant pretreatment conditions are scarce. Here, to investigate the effects of plausible hemicellulose precipitation and re-association with cellulose on cellulose conversion, different pretreatments were applied to pure Avicel® PH101 cellulose alone and Avicel mixed with model hemicellulose compounds followed by enzymatic hydrolysis of resulting solids at both low and high enzyme loadings. Solids produced by pretreatment of Avicel mixed with hemicelluloses (AMH) were found to contain about 2 to 14.6% of exogenous, precipitated hemicelluloses and showed a remarkably much lower digestibility (up to 60%) than their respective controls. However, the exogenous hemicellulosic residues that associated with Avicel following high temperature pretreatments resulted in greater losses in cellulose conversion than those formed at low temperatures, suggesting that temperature plays a strong role in the strength of cellulose–hemicellulose association. Molecular dynamics simulations of hemicellulosic xylan and cellulose were found to further support this temperature effect as the xylan–cellulose interactions were found to substantially increase at elevated temperatures. Furthermore, exogenous, precipitated hemicelluloses in pretreated AMH solids resulted in a larger drop in cellulose conversion than the delignified lignocellulosic biomass containing comparably much higher natural hemicellulose amounts. Increased cellulase loadings or supplementation of cellulase with xylanases enhanced cellulose conversion for most pretreated AMH solids; however, this approach was less effective for solids containing mannan polysaccharides, suggesting stronger association of cellulose with (hetero) mannans or lack of enzymes in the mixture required to hydrolyze such polysaccharides.

Temperature-dependent phase behaviour of tetrahydrofuran-water alters solubilization of xylan to improve co-production of furfurals from lignocellulosic biomass

Xylan is an important polysaccharide found in the hemicellulose fraction of lignocellulosic biomass that can be hydrolysed to xylose and further dehydrated to the furfural, an important renewable platform fuel precursor. Here, pairing molecular simulation and experimental evidence, we reveal how the unique temperature-dependent phase behaviour of water–tetrahydrofuran (THF) co-solvent can delay xylan solubilization to synergistically improve catalytic co-processing of biomass to furfural and 5-HMF. Our results indicate, based on polymer correlations between polymer conformational behaviour and solvent quality, that both co-solvent and aqueous environments serve as ‘good’ solvents for xylan. Interestingly, the simulations also revealed that unlike other cell-wall components (i.e., lignin and cellulose), the make-up of the solvation shell of xylan in THF–water is dependent on the temperature-phase behaviour. At temperatures between 333 K and 418 K, THF and water become immiscible, and THF is evacuated from the solvation shell of xylan, while above and below this temperature range, THF and water are both present in the polysaccharides solvation shell. This suggested that the solubilization of xylan in THF–water may be similar to aqueous-only solutions at temperatures between 333 K and 418 K and different outside this range. Experimental reactions on beachwood xylan corroborate this hypothesis by demonstrating 2-fold reduction of xylan solubilization in THF–water within a miscible temperature regime (445 K) and unchanged solubilization within an immiscible regime (400 K). Translating this phase-dependent behaviour to processing of maple wood chips, we demonstrate how the weaker xylan solvation in THF–water under miscible conditions can delay furfural production from xylan, allowing 5-HMF production from cellulose to “catch-up” such that their high yield production from biomass can be synergized in a single pot reaction.