The plant cell wall biopolymers lignin, cellulose and hemicellulose are potential renewable sources of clean biofuels and high-value chemicals. However, the complex 3D structure of lignocellulosic ...biomass is recalcitrant to deconstruction. Major efforts to overcome this recalcitrance have involved pretreating biomass before catalytic processing. This Perspective describes recent work aimed at elucidating the molecular-level physical phenomena that drive biomass assembly. These are at play in commonly employed aqueous-based and thermochemical pretreatments. Several key processes have been found to be driven by biomass solvation thermodynamics, an understanding of which therefore facilitates the rational improvement of methods aimed at the complete solubilization and fractionation of the major biomass components.This Perspective describes the physical molecular driving forces that stabilize native lignocellulosic plant biomass structures and govern thermochemical biomass pretreatments. Understanding these driving forces can help us to design efficient methods for deconstructing biomass into biofuels and other bioproducts.
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. ...Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
Low‐molecular‐weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The ...binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc=15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self‐aggregate even at high pretreatment temperatures.
Lignin conforms! Understanding the shape and conformations of low‐molecular weight lignin at pretreatment temperatures is important because the lignin shape strongly influences undesirable lignin binding to cellulose, which represents a major obstacle in the conversion of biomass to biofuels. Based on molecular dynamics simulations of lignin polymers, it is found that lignin in water adopts more spherical conformations with increasing degree of polymerization.
The interaction of xylan, an abundant plant polysaccharide, with cellulose microfibrils is essential for secondary cell wall strength. A deeper understanding of these interactions is crucial both to ...improve our understanding of plant cell wall architecture and to design alternate strategies to overcome cellulose recalcitrance for the production of biofuels and sustainable biomaterials. Naturally occurring acetate or glucuronic acid substitutions on xylan have been shown to influence xylan-cellulose interactions. Here, we use unrestrained molecular dynamics simulations to determine the interactions with the (110) hydrophilic face of cellulose fibers of four different xylans. In the absence of cellulose, all xylans, independent of the substitution pattern, adopt a highly flexible threefold helical screw conformation. However, when xylan is spatially close to a cellulose surface 1,2 linked acetyl xylans (2AcX) adopt rigid twofold helical screw conformations. The 2AcX conformations are primarily stabilized by interactions between the acetylated oxygen and the glycosidic linkage with C-O6 of cellulose. In contrast, the glycosidic oxygens and acetyl decorations for 1,3 linked acetyl groups (3AcX) are oriented away from the cellulose surface and the 3AcX xylans maintain threefold helical screw conformations on the cellulose surface. Our results show that evenly spaced chemical functionalization (with acetyl groups) and the position of substitution (1,2) on xylan backbone play key roles in tuning the xylan-cellulose interactions to stabilize the twofold helical screw conformations of xylan on the cellulose surface. A comparison with previous experimental findings further suggests that 1,2 substitutions induce twofold helical screw conformations of xylan on the cellulose surface irrespective of the chemical nature of the substituent, while 1,3 substitutions primarily bind lignin in threefold helical screw conformations rather than cellulose in plant cell walls.
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical ...to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.
Interactions of water with cellulose are of both fundamental and technological importance. Here, we characterize the properties of water associated with cellulose using deuterium labeling, neutron ...scattering and molecular dynamics simulation. Quasi-elastic neutron scattering provided quantitative details about the dynamical relaxation processes that occur and was supported by structural characterization using small-angle neutron scattering and X-ray diffraction. We can unambiguously detect two populations of water associated with cellulose. The first is "non-freezing bound" water that gradually becomes mobile with increasing temperature and can be related to surface water. The second population is consistent with confined water that abruptly becomes mobile at ~260 K, and can be attributed to water that accumulates in the narrow spaces between the microfibrils. Quantitative analysis of the QENS data showed that, at 250 K, the water diffusion coefficient was 0.85 ± 0.04 × 10
m
sec
and increased to 1.77 ± 0.09 × 10
m
sec
at 265 K. MD simulations are in excellent agreement with the experiments and support the interpretation that water associated with cellulose exists in two dynamical populations. Our results provide clarity to previous work investigating the states of bound water and provide a new approach for probing water interactions with lignocellulose materials.
Lignocellulosic biomass, a potentially important renewable organic source of energy and chemical feedstock, resists degradation to glucose in industrial hydrolysis processes and thus requires ...expensive thermochemical pretreatments. Understanding the mechanism of biomass breakdown during these pretreatments will lead to more efficient use of biomass. By combining multiple probes of structure, sensitive to different length scales, with molecular dynamics simulations, we reveal two fundamental processes responsible for the morphological changes in biomass during steam explosion pretreatment: cellulose dehydration and lignin-hemicellulose phase separation. We further show that the basic driving forces are the same in other leading thermochemical pretreatments, such as dilute acid pretreatment and ammonia fiber expansion.
Histone tails play an important role in gene transcription and expression. We present here a systematic computational study of the role of histone tails in the nucleosome, using replica exchange ...molecular dynamics simulations with an implicit solvent model and different well-established force fields. We performed simulations for all four histone tails, H4, H3, H2A, and H2B, isolated and with inclusion of the nucleosome. The results confirm predictions of previous theoretical studies for the secondary structure of the isolated tails but show a strong dependence on the force field used. In the presence of the entire nucleosome for all force fields, the secondary structure of the histone tails is destabilized. Specific contacts are found between charged lysine and arginine residues and DNA phosphate groups and other binding sites in the minor and major DNA grooves. Using cluster analysis, we found a single dominant configuration of binding to DNA for the H4 and H2A histone tails, whereas H3 and H2B show multiple binding configurations with an equal probability. The leading stabilizing contribution for those binding configurations is the attractive interaction between the positively charged lysine and arginine residues and the negatively charged phosphate groups, and thus the resulting charge neutralization. Finally, we present results of molecular dynamics simulations in explicit solvent to confirm our conclusions. Results from both implicit and explicit solvent models show that large portions of the histone tails are not bound to DNA, supporting the complex role of these tails in gene transcription and expression and making them possible candidates for binding sites of transcription factors, enzymes, and other proteins.
A cellulose synthesis complex with a "rosette" shape is responsible for synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte ...algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. This work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. The conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. This study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.
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