Research and development activities directed toward commercial production of cellulosic ethanol have created the opportunity to dramatically increase the transformation of lignin to value-added products. Here, we highlight recent advances in this lignin valorization effort. Discovery of genetic variants in native populations of bioenergy crops and direct manipulation of biosynthesis pathways have produced lignin feedstocks with favorable properties for recovery and downstream conversion. Advances in analytical chemistry and computational modeling detail the structure of the modified lignin and direct bioengineering strategies for future targeted properties. Refinement of biomass pretreatment technologies has further facilitated lignin recovery, and this coupled with genetic engineering will enable new uses for this biopolymer, including low-cost carbon fibers, engineered plastics and thermoplastic elastomers, polymeric foams, fungible fuels, and commodity chemicals.

The crystal and molecular structure together with the hydrogen-bonding system in cellulose Ibeta has been determined using synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from tunicin. These samples diffracted both synchrotron X-rays and neutrons to better than 1A resolution (>300 unique reflections; P2(1)). The X-ray data were used to determine the C and O atom positions. The resulting structure consisted of two parallel chains having slightly different conformations and organized in sheets packed in a "parallel-up" fashion, with all hydroxymethyl groups adopting the tg conformation. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The hydrogen atoms involved in the intramolecular O3...O5 hydrogen bonds have well-defined positions, whereas those corresponding to O2 and O6 covered a wider volume, indicative of multiple geometry with partial occupation. The observation of this disorder substantiates a recent infrared analysis and indicates that, despite their high crystallinity, crystals of cellulose Ibeta have an inherent disorganization of the intermolecular H-bond network that maintains the cellulose chains in sheets.

Neutron crystallography is a newly blossoming field of structural biology. As described in the historical account given by Benno Schoenborn in this issue, its origins can be traced back to the Cambridge MRC tearoom in 1965 when it was discussed as the only plausible experimental method for directly determining the location of H atoms in proteins. Knowing the location of H atoms can provide information on the protonation states of amino-acid residues and ligands, the identity of solvent molecules, and the nature of bonds involving hydrogen. Neutron crystallography can also be used to identify H atoms that are exchanged with their isotope deuterium (deuteration) and the extent of this replacement, thus providing a tool for identifying isotopically labeled features, for studying solvent accessibility and macromolecular dynamics, and for identifying minimal protein folding domains. This unique information, which is often difficult or impossible to obtain using X-ray crystallography, is important for understanding protein function and enzyme mechanism. However, it wasn't until 1968 that neutron crystallography was first used to study a protein at the nuclear reactor run by Brookhaven National Laboratory. With limited equipment and a relatively low flux beam, it took several months to collect a 2 Å data set from the 17 kDa transport protein myoglobin using a crystal that was several tens of mm 3 in volume.Over the years since that beginning, growth has been relatively slow mainly because there have been a limited number of available instruments and their fluxes have been relatively weak compared with X-ray beams, therefore requiring larger crystal sizes. However, the uniqueness of the type of information that can be provided by neutrons, and its complementarity to the information provided by X-rays, has given neutrons a small but important role in biology in the past. Recently, the prospects for this field have changed dramatically and there has been great increase in the application of neutrons in biology. This can be related to improvements in beamline instrumentation, neutron sources, data collection and sample preparation methods, and new approaches to and computational tools for structure determination. These advances are pushing practicable sample sizes down to fractions of a mm 3 , data collection times down to a few days or even hours, and are allowing increasingly complex biological systems to be studied. Growth is bound to continue with the current construction of new and more powerful spallation neutron sources throughout the world and continued improvements to existing facilities. During this period of growth several new opportunities and also challenges have arisen. The recent International Conference on Neutrons in Biology reported in this issue was a rare opportunity for the neutron macromolecular crystallography community to come together to discuss these issues and to develop a common vision for the future development of the field.One of the most immediate challenges discussed was an inconsistency in ...

The crystal and molecular structure, together with the hydrogen-bonding system in cellulose I(alpha), has been determined using atomic-resolution synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall of the freshwater alga Glaucocystis nostochinearum. The X-ray data were used to determine the C and O atom positions. The resulting structure is a one-chain triclinic unit cell with all glucosyl linkages and hydroxymethyl groups (tg) identical. However, adjacent sugar rings alternate in conformation giving the chain a cellobiosyl repeat. The chains organize in sheets packed in a "parallel-up" fashion. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The differences between the structure and hydrogen-bonding reported here for cellulose I(alpha) and previously for cellulose I(beta) provide potential explanations for the solid-state conversion of I(alpha) --> I(beta) and for the occurrence of two crystal phases in naturally occurring cellulose.

The COVID-19 disease caused by the SARS-CoV-2 coronavirus has become a pandemic health crisis. An attractive target for antiviral inhibitors is the main protease 3CL Mpro due to its essential role in processing the polyproteins translated from viral RNA. Here we report the room temperature X-ray structure of unliganded SARS-CoV-2 3CL Mpro, revealing the ligand-free structure of the active site and the conformation of the catalytic site cavity at near-physiological temperature. Comparison with previously reported low-temperature ligand-free and inhibitor-bound structures suggest that the room temperature structure may provide more relevant information at physiological temperatures for aiding in molecular docking studies.

A revised crystal structure for mercerized cellulose based on high-resolution synchrotron X-ray data collected from ramie fibers is reported (space group P2(1), a = 8.10(3) A, b = 9.03(3) A, c = 10.31(5) A, gamma = 117.10(5) degrees; 751 reflections in 304 composite spots; theta < 21.11 degrees; lambda = 0.7208 A; LALS refinement with d > 1.5 A, R' ' = 0.16; SHELX97 refinement with d > 1 A, R = 0.21). As with regenerated cellulose the crystal structure consists of antiparallel chains with different conformations but with the hydroxymethyl groups of both chains near the gt position. However, the conformation of the hydroxymethyl group of the center chain in the structure reported here differs significantly from the conformation in regenerated cellulose. This may be related to a large observed difference in the amount of hydroxymethyl group disorder: approximately 30% for regenerated cellulose and approximately 10% for mercerized cellulose.

The crystal and molecular structure and hydrogen bonding system in cellulose II have been revised using new neutron diffraction data extending to 1.2 Å resolution collected from two highly crystalline fiber samples of mercerized flax. Mercerization was achieved in NaOH/H2O for one sample and in NaOD/D2O for the other, corresponding to the labile hydroxymethyl moieties being hydrogenated and deuterated, respectively. Fourier difference maps were calculated in which neutron difference amplitudes were combined with phases calculated from two revised X-ray models of cellulose II, A and B‘. The revised phasing models were determined by refinement against the X-ray data set of Kolpak and Blackwell, using the LALS methodology. Both models A and B‘ have two antiparallel chains organized in a P21 space group and unit cell parameters:  a = 8.01 Å, b = 9.04 Å, c = 10.36 Å, and γ = 117.1°. Model A has equivalent backbone conformations for both chains but different conformations for the hydroxymethyl moieties:  gt for the origin chain and tg for the center chain. Model B‘, based on the recent crystal structures of cellotetraose, − has different conformations for the two chains but nearly equivalent conformations for the hydroxymethyl moieties. On the basis of the X-ray data alone, model A and model B‘ could not be differentiated. From the neutron Fourier difference maps, possible labile hydrogen atom positions were identified for each model and refined using LALS. We were able to eliminate model A in favor of model B‘. The hydrogen-bonding scheme identified for model B‘ is significantly different from previous proposals based on the crystal structures of cellotetraose, − MD simulations of cellulose II, and any potential hydrogen-bonding network in the structure of cellulose II determined in earlier X-ray fiber diffraction studies. , The exact localization of the labile hydrogen atoms involved in this bonding, together with their donor and acceptor characteristics, is presented and discussed. This study provides, for the first time, the coordinates of all of the atoms in cellulose II.

Conversion of lignocellulose to biofuels is partly inefficient due to the deleterious impact of cellulose crystallinity on enzymatic saccharification. We demonstrate how the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils. We provide a molecular-scale explanation of these phenomena through molecular dynamics (MD) simulations and enzymatic assays. Ammonia transformed the naturally occurring crystalline allomorph I(β) to III(I), which led to a decrease in the number of cellulose intrasheet hydrogen bonds and an increase in the number of intersheet hydrogen bonds. This rearrangement of the hydrogen bond network within cellulose III(I), which increased the number of solvent-exposed glucan chain hydrogen bonds with water by ~50%, was accompanied by enhanced saccharification rates by up to 5-fold (closest to amorphous cellulose) and 60-70% lower maximum surface-bound cellulase capacity. The enhancement in apparent cellulase activity was attributed to the "amorphous-like" nature of the cellulose III(I) fibril surface that facilitated easier glucan chain extraction. Unrestricted substrate accessibility to active-site clefts of certain endocellulase families further accelerated deconstruction of cellulose III(I). Structural and dynamical features of cellulose III(I), revealed by MD simulations, gave additional insights into the role of cellulose crystal structure on fibril surface hydration that influences interfacial enzyme binding. Subtle alterations within the cellulose hydrogen bond network provide an attractive way to enhance its deconstruction and offer unique insight into the nature of cellulose recalcitrance. This approach can lead to unconventional pathways for development of novel pretreatments and engineered cellulases for cost-effective biofuels production.