Engineering topics
O’Neill, Hugh
Publications and source records attributed to O’Neill, Hugh.
Dynamic entity formed by protein and its hydration water
The interaction between protein and water plays a pivotal role in shaping the structure, dynamics, and function of biomacromolecules. A comprehensive understanding of this intricate interplay necessitates a systematic evaluation of interaction strength and its consequential impact on the dynamics of proteins and water across diverse protein systems. Despite numerous works on understanding the dynamics of water and proteins and the coupling between them, there are still unanswered questions. Here, we combine neutron scattering and isotope labeling to probe the dynamics of proteins and their hydration water in a variety of protein systems. We consider proteins of different structures and varying thermostability as well as proteins within living cells with distinct growth temperatures. Simultaneous characterization of protein and hydration water dynamics across diverse systems was achieved. Moreover, we performed water sorption isothermal measurements on three representative proteins to correlate the observed dynamics with the strength of the interaction energies governing each system. The experimental results underscore that proteins manifesting stronger attractive interactions with water display diffusionlike dynamics with higher flexibility upon hydration, concomitant with a reduced mobility in hydration water. Significantly, our findings suggest that, in fact, it is the interaction between protein and its hydration water that facilitates the transfer of mobility from water to protein, with stronger interactions correlating to greater protein flexibility and slower hydration water diffusion. Published by the American Physical Society 2024
Ectopic Production of 3,4-Dihydroxybenzoate in Planta Affects Cellulose Structure and Organization
Lignocellulosic biomass is a highly sustainable and largely carbon dioxide neutral feedstock for the production of biofuels and advanced biomaterials. Although thermochemical pretreatment is typically used to increase the efficiency of cell wall deconstruction, genetic engineering of the major plant cell wall polymers, especially lignin, has shown promise as an alternative approach to reduce biomass recalcitrance. Poplar trees with reduced lignin content and altered composition were previously developed by overexpressing bacterial 3-dehydroshikimate dehydratase (QsuB) enzyme to divert carbon flux from the shikimate pathway. In this work, three transgenic poplar lines with increasing QsuB expression levels and different lignin contents were studied using small-angle neutron scattering (SANS) and wide-angle X-ray scattering (WAXS). SANS showed that although the cellulose microfibril cross-sectional dimension remained unchanged, the ordered organization of the microfibrils progressively decreased with increased QsuB expression. This was correlated with decreasing total lignin content in the QsuB lines. WAXS showed that the crystallite dimensions of cellulose microfibrils transverse to the growth direction were not affected by the QsuB expression, but the crystallite dimensions parallel to the growth direction were decreased by ~20%. Cellulose crystallinity was also decreased with increased QsuB expression, which could be related to high levels of 3,4-dihydroxybenzoate, the product of QsuB expression, disrupting microfibril crystallization. In addition, the cellulose microfibril orientation angle showed a bimodal distribution at higher QsuB expression levels. Altogether, this study provides new structural insights into the impact of ectopic synthesis of small-molecule metabolites on cellulose organization and structure that can be used for future efforts aimed at reducing biomass recalcitrance.
Synthesis of Perdeuterated Alkyl Amines/Amides with Pt/C as Catalyst under Mild Conditions
A convenient method for the synthesis of perdeuterated alkyl amides/amines is disclosed. Perdeuterated acetyl amides can be achieved by a hydrogen–deuterium (H/D) exchange protocol with Pt/C as a catalyst and D 2 O as a deuterium source under mild conditions. Further, after removal or reduction of the acetyl group, this protocol can provide perdeuterated primary, secondary, and tertiary amines, which are difficult to achieve via other methods.
Simple Scattering: Lipid nanoparticle structural data repository
Lipid nanoparticles (LNPs) are being intensively researched and developed to leverage their ability to safely and effectively deliver therapeutics. To achieve optimal therapeutic delivery, a comprehensive understanding of the relationship between formulation, structure, and efficacy is critical. However, the vast chemical space involved in the production of LNPs and the resulting structural complexity make the structure to function relationship challenging to assess and predict. New components and formulation procedures, which provide new opportunities for the use of LNPs, would be best identified and optimized using high-throughput characterization methods. Recently, a high-throughput workflow, consisting of automated mixing, small-angle X-ray scattering (SAXS), and cellular assays, demonstrated a link between formulation, internal structure, and efficacy for a library of LNPs. As SAXS data can be rapidly collected, the stage is set for the collection of thousands of SAXS profiles from a myriad of LNP formulations. In addition, correlated LNP small-angle neutron scattering (SANS) datasets, where components are systematically deuterated for additional contrast inside, provide complementary structural information. The centralization of SAXS and SANS datasets from LNPs, with appropriate, standardized metadata describing formulation parameters, into a data repository will provide valuable guidance for the formulation of LNPs with desired properties. To this end, we introduce Simple Scattering, an easy-to-use, open data repository for storing and sharing groups of correlated scattering profiles obtained from LNP screening experiments. Here, we discuss the current state of the repository, including limitations and upcoming changes, and our vision towards future usage in developing our collective knowledge base of LNPs.
Deconvoluting Structures of Component Plant Biopolymers Using Deuterium Labeled Brassica oleracea Stems
Several Brassica species are cultivated globally for the production of seed oils as food, lubricants, and increasingly biofuels. The stem and leaf residues of these herbaceous dicotyledonous crops constitute another feedstock for biofuels and other products. Plant cell walls are complex, multipolymeric structures that consist primarily of polysaccharides and lignin. Cellulose chains coalesce to form crystalline microfibrils while the amorphous biopolymers, hemicellulose, and lignin form a network structure and fill the interstitial space. Neutron scattering has been used for the structural study of the assembly and deconstruction of the plant cell walls. However, similar neutron sensitivity of the different amorphous biopolymers has made structural association to individual component biopolymers nontrivial and ambiguous. To improve the association of structural features to specific biopolymer components, partial deuteration of the plant cell wall can be employed to increase the difference in the neutron scattering length density between amorphous carbohydrate and lignin plant polymers. Vegetative stems from partially deuterated Brassica oleracea acephala (kale) plants were obtained commercially, and the plant cell wall structures were studied by contrast-variation small-angle neutron scattering (CV-SANS) and Fourier-transform infrared spectroscopy (FTIR). FTIR results indicated that deuterium substitution for hydrogen in the carbohydrates was higher than that in lignin. By combining CV-SANS and FTIR results, the neutron scattering length density (nSLD) of the polysaccharides and lignin was determined to match nSLD of 65%:35% and 48%:52% D 2 O/H 2 O solvent mixtures, respectively. These nSLD values were higher than the nSLD values of polysaccharides and lignin for H 2 O grown biopolymers. The nSLD increase correlates to replacing about 42.5% of hydrogens present as both C–H and O–H groups in cellulose with deuterium atoms, while only 21% for lignin. In conclusion, this study lays the foundation to use partially deuterated plants to deconvolute structural features of the different component biopolymers, especially cellulose, hemicellulose, and lignin, of the plant cell wall without introducing unintended structural modifications due to the pretreatment extraction processes.
Evidence for Lignin–Carbohydrate Complexes from Studies of Transgenic Switchgrass and a Model Lignin–Pectin Composite
Lignin–carbohydrate complexes (LCCs) form through interactions of lignin with plant cell wall polysaccharides and are thought to be a significant source of biomass recalcitrance. In this work, we investigated LCCs formed between lignin and pectin homogalacturonan (HG). The structural changes in HG deficient transgenic switchgrass (GAUT4-knockdown, GAUT4-KD) after hot water pretreatment were compared to wild-type plants using small-angle neutron scattering (SANS), which showed that there were ~2.2-fold more lignin aggregates in GAUT4-KD biomass compared to the wild type. This demonstrated that decreased pectin resulted in more lignin redistribution and suggested that interactions between lignin and HG restrict lignin mobility in plant cell walls. To better understand the types of interactions between lignin and pectin, a model composite was prepared by polymerizing either protiated or partially deuterated coniferyl alcohol to form a dehydrogenation polymer (DHP) in the presence of HG. Small-angle X-ray scattering (SAXS) showed that the DHP and HG form a highly interconnected network structure that is not observed in a physical mixture of the individual polymers. Contrast matching SANS revealed the structure of DHP and HG in the composite and showed that the HG forms a swollen interconnected polymer network (power-law exponent, P = 1.5) interspersed with DHP particles (radius of gyration, Rg, 264 Å) that are composed of solvent-accessible DHP polymers (P = 2.3). Fourier transform infrared spectroscopy showed a unique ester absorption band in the DHP/HG composites. Solid-state nuclear magnetic resonance (NMR) analysis also supports interactions between DHP and HG. Overall, this study provides new insights into the relationship between primary and secondary cell wall polymers during cell wall synthesis and how LCCs formed between pectin and lignin could represent a previously unrecognized source of biomass recalcitrance. This knowledge may help develop new approaches to modulate cell wall properties to improve biofuel and bioproduct production.