I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[15832, 21741]
Abstract: Supramolecular structure and properties of deep eutectic solvents (DESs) are known to be highly affected by the addition of water, and their use as solvents for poorly water-soluble macromolecules is being actively investigated. We report the first experimental investigation of protein crystallization in DESs. Different hydrophilic and hydrophobic eutectic mixtures, hydrated at different levels, have been screened as crystallization media. DESs were added to the solution containing the precipitant and the buffer required to crystallize three test proteins, and we observed that the volume ratio between DES and the corresponding solution is a key parameter for the crystallization process. Successful crystallization was achieved for the hen-egg white lysozyme when using choline chloride:urea, choline chloride:glycerol, and choline chloride:glutamic acid eutectic mixtures at a 1:2 molar ratio. High-resolution X-ray diffraction experiments disclosed the possibility to study the intriguing supramolecular network of the molecular complexes formed between protein and DES in the presence of water molecules. Individual DES components have been found to systematically occupy specific protein sites populated by solvent-exposed aromatic residues. Weak interactions between DES components, possibly mediated by water molecules, which resulted in being frozen in the ordered solvent surrounding the protein units in the crystal lattice, were reconstructed at atomic resolution. DESs were found to have a negligible effect on the protein conformation and its flexibility in the solid state. On the other hand, DESs greatly reduced solvent evaporation from the crystallization drop, thereby increasing the dissolution time of the protein crystals. Finally, DESs were found to serve as local modulators of the ordered solvent, and this resulted in a significant change of the protein solubility. In addition, we found that protein crystallization was sped up by tuning DES hydration. This enables the employment of these environmentally responsible solvents to improve biotechnological processes at the industrial level.
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Jun 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19951]
Open Access
Abstract: Background: Nowadays there is a strong trend towards a circular economy using lignocellulosic biowaste for the production of biofuels and other bio-based products. The use of enzymes at several stages of the production process (e.g., saccharification) can offer a sustainable route due to avoidance of harsh chemicals and high temperatures. For novel enzyme discovery, physically linked gene clusters targeting carbohydrate degradation in bacteria, polysaccharide utilization loci (PULs), are recognized ‘treasure troves’ in the era of exponentially growing numbers of sequenced genomes. Results: We determined the biochemical properties and structure of a protein of unknown function (PUF) encoded within PULs of metagenomes from beaver droppings and moose rumen enriched on poplar hydrolysate. The corresponding novel bifunctional carbohydrate esterase (CE), now named BD-FAE, displayed feruloyl esterase (FAE) and acetyl esterase activity on simple, synthetic substrates. Whereas acetyl xylan esterase (AcXE) activity was detected on acetylated glucuronoxylan from birchwood, only FAE activity was observed on acetylated and feruloylated xylooligosaccharides from corn fiber. The genomic contexts of 200 homologs of BD-FAE revealed that the 33 closest homologs appear in PULs likely involved in xylan breakdown, while the more distant homologs were found either in alginate-targeting PULs or else outside PUL contexts. Although the BD-FAE structure adopts a typical α/β-hydrolase fold with a catalytic triad (Ser-Asp-His), it is distinct from other biochemically characterized CEs. Conclusions: The bifunctional CE, BD-FAE, represents a new candidate for biomass processing given its capacity to remove ferulic acid and acetic acid from natural corn and birchwood xylan substrates, respectively. Its detailed biochemical characterization and solved crystal structure add to the toolbox of enzymes for biomass valorization as well as structural information to inform the classification of new CEs.
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May 2021
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[20820]
Open Access
Abstract: Alternative and sustainable waste sources are receiving increasing attention as they can be used to produce biofuels with a low carbon footprint. Waste fish oil is one such example and can be considered an abundant and sustainable waste source to produce biodiesel. Ultimately this could lead to fishing communities having their own "off-grid" source of fuel for boats and vehicles. At the industrial level biodiesel is currently produced by homogeneous catalysis because of the high catalyst activity and selectivity. In contrast, heterogeneous catalysis offers several advantages such as improved reusability, reduced waste and lower processing costs. Here we investigate the phase evolution of two heterogeneous catalysts, CaO and a Ca3Al2O6:CaO ('C3A:CaO') composite, under in-situ conditions for biodiesel production from fish oil. A new reactor was designed to monitor the evolution of the crystalline catalyst during the reaction using synchrotron powder X-ray diffraction (PXRD). The amount of calcium diglyceroxide (CaDG) began to increase rapidly after approximately 30 minutes, for both catalysts. This rapid increase in CaDG could be linked to ex-situ NMR studies which showed that the conversion of fish oil to biodiesel rapidly increased after 30 minutes. The key to the difference in activity of the two catalysts appears to be that the Ca3Al2O6:CaO composite maintains a high rate of calcium diglyceroxide formation for longer than CaO, although the initial formation rates and reaction kinetics are similar. Overall this specialised in-situ set-up has been shown to be suitable to monitor the phase evolution of heterogeneous crystalline catalysts during the triglycerides transesterification reaction, offering the opportunity to correlate the crystalline phases to activity, deactivation and stability.
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May 2021
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Abstract: Catalytic hydrodeoxygenation (HDO) provides a promising route for upgrading biomass-derived fatty acids to alkanes, which are potential biofuels (e.g. jet fuel (C8–C16) and diesel (C12–C22)) that could reduce our reliance on unsustainable fossil fuels. Currently, catalytic HDO, conducted over catalysts such as molybdenum disulfide, necessitates harsh operating conditions (>300 °C) which is both environmentally and economically unsustainable and promotes unwanted side reactions, e.g. cracking, which compromises product selectivity. Accordingly, the development of novel catalysts, which enable efficient and sustainable HDO, under milder operating conditions, and their translation from lab bench to large-scale production are highly desired. This review discusses the recent development of heterogeneous catalysts for HDO (including reaction pathways, mechanisms, and side reactions) and explores design strategies for the development of new multifunctional catalysts with potential to enable future development of HDO processes under mild conditions. In particular, we consider the sequential cascade transformation of fatty acids into fatty alcohols (via hydrodeoxygenation) and then hydrocarbons (via dehydration and hydrogenation), which requires the coupling of different but complementary catalytic sites, as an attractive alternative mild HDO strategy.
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Mar 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[13467]
Open Access
Abstract: Arms race co-evolution drives rapid adaptive changes in pathogens and in the immune systems of their hosts. Plant intracellular NLR immune receptors detect effectors delivered by pathogens to promote susceptibility, activating an immune response that halts colonization. As a consequence, pathogen effectors evolve to escape immune recognition and are highly variable. In turn, NLR receptors are one of the most diverse protein families in plants, and this variability underpins differential recognition of effector variants. The molecular mechanisms underlying natural variation in effector recognition by NLRs are starting to be elucidated. The rice NLR pair Pik-1/Pik-2 recognizes AVR-Pik effectors from the blast fungus Magnaporthe oryzae, triggering immune responses that limit rice blast infection. Allelic variation in a heavy metal associated (HMA) domain integrated in the receptor Pik-1 confers differential binding to AVR-Pik variants, determining resistance specificity. Previous mechanistic studies uncovered how a Pik allele, Pikm, has extended recognition to effector variants through a specialized HMA/AVR-Pik binding interface. Here, we reveal the mechanistic basis of extended recognition specificity conferred by another Pik allele, Pikh. A single residue in Pikh-HMA increases binding to AVR-Pik variants, leading to an extended effector response in planta. The crystal structure of Pikh-HMA in complex with an AVR-Pik variant confirmed that Pikh and Pikm use a similar molecular mechanism to extend their pathogen recognition profile. This study shows how different NLR receptor alleles functionally converge to extend recognition specificity to pathogen effectors.
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Mar 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[20618]
Open Access
Abstract: Bimetallic nanoparticle catalysts have attracted considerable attention due to their unique chemical and physical properties. The ability of metal‐reducing bacteria to produce highly catalytically active monometallic nanoparticles is well known; however, the properties and catalytic activity of bimetallic nanoparticles synthesized with these organisms is not well understood. Here, we report the one‐pot biosynthesis of Pd/Ag (bio‐Pd/Ag) and Pd/Au (bio‐Pd/Au) nanoparticles using the metal‐reducing bacterium, Shewanella oneidensis, under mild conditions. Energy dispersive X‐ray analyses performed using scanning transmission electron microscopy (STEM) revealed the presence of both metals (Pd/Ag or Pd/Au) in the biosynthesized nanoparticles. X‐ray absorption near‐edge spectroscopy (XANES) suggested a significant contribution from Pd(0) and Pd(II) in both bio‐Pd/Ag and bio‐Pd/Au, with Ag and Au existing predominately as their metallic forms. Extended X‐ray absorption fine‐structure spectroscopy (EXAFS) supported the presence of multiple Pd species in bio‐Pd/Ag and bio‐Pd/Au, as inferred from Pd–Pd, Pd–O and Pd–S shells. Both bio‐Pd/Ag and bio‐Pd/Au demonstrated greatly enhanced catalytic activity towards Suzuki–Miyaura cross‐coupling compared to a monometallic Pd catalyst, with bio‐Pd/Ag significantly outperforming the others. The catalysts were very versatile, tolerating a wide range of substituents. This work demonstrates a green synthesis method for novel bimetallic nanoparticles that display significantly enhanced catalytic activity compared to their monometallic counterparts.
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Mar 2021
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[14739, 20229]
Open Access
Abstract: Prokaryotic laccases are emergent biocatalysts. However, they have not been broadly found and characterized in bacterial organisms, especially in lactic acid bacteria. Recently, a prokaryotic laccase from the lactic acid bacterium Pediococcus acidilactici 5930, which can degrade biogenic amines, was discovered. Thus, our study aimed to shed light on laccases from lactic acid bacteria focusing on two Pediococcus laccases, P. acidilactici 5930 and Pediococcus pentosaceus 4816, which have provided valuable information on their biochemical activities on redox mediators and biogenic amines. Both laccases are able to oxidize canonical substrates as ABTS, ferrocyanide and 2,6‐DMP, and non‐conventional substrates as biogenic amines. With ABTS as a substrate, they prefer an acidic environment and show sigmoidal kinetic activity, and are rather thermostable. Moreover, this study has provided the first structural view of two lactic acid bacteria laccases, revealing new structural features not seen before in other well‐studied laccases, but which seem characteristic for this group of bacteria. We believe that understanding the role of laccases in lactic acid bacteria will have an impact on their biotechnological applications and provide a framework for the development of engineered lactic acid bacteria with enhanced properties.
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Feb 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[12633]
Abstract: We report an engineered panel of ene-reductases (ERs) from Thermus scotoductus SA-01 (TsER) that combines control over facial selectivity in the reduction of electron deficient Cdouble bondC double bonds with thermostability (up to 70 °C), organic solvent tolerance (up to 40 % v/v) and a broad substrate scope (23 compounds, three new to literature). Substrate acceptance and facial selectivity of 3-methylcyclohexenone was rationalized by crystallisation of TsER C25D/I67T and in silico docking. The TsER variant panel shows excellent enantiomeric excess (ee) and yields during bi-phasic preparative scale synthesis, with isolated yield of up to 93 % for 2R,5S-dihydrocarvone (3.6 g). Turnover frequencies (TOF) of approximately 40 000 h−1 were achieved, which are comparable to rates in hetero- and homogeneous metal catalysed hydrogenations. Preliminary batch reactions also demonstrated the reusability of the reaction system by consecutively removing the organic phase (n-pentane) for product removal and replacing with fresh substrate. Four consecutive batches yielded ca. 27 g L−1 R-levodione from a 45 mL aqueous reaction, containing less than 17 mg (10 μM) enzyme and the reaction only stopping because of acidification. The TsER variant panel provides a robust, highly active and stereocomplementary base for further exploitation as a tool in preparative organic synthesis.
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Feb 2021
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B23-Circular Dichroism
I24-Microfocus Macromolecular Crystallography
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Juan F.
Bada Juarez
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Peter J.
Judge
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Suliman
Adam
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Danny
Axford
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Javier
Vinals
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James
Birch
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Tristan O. C.
Kwan
,
Kin Kuan
Hoi
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Hsin-Yung
Yen
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Anthony
Vial
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Pierre-Emmanuel
Milhiet
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Carol V.
Robinson
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Igor
Schapiro
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Isabel
Moraes
,
Anthony
Watts
Diamond Proposal Number(s):
[19152, 11386, 15222]
Open Access
Abstract: Many transmembrane receptors have a desensitized state, in which they are unable to respond to external stimuli. The family of microbial rhodopsin proteins includes one such group of receptors, whose inactive or dark-adapted (DA) state is established in the prolonged absence of light. Here, we present high-resolution crystal structures of the ground (light-adapted) and DA states of Archaerhodopsin-3 (AR3), solved to 1.1 Å and 1.3 Å resolution respectively. We observe significant differences between the two states in the dynamics of water molecules that are coupled via H-bonds to the retinal Schiff Base. Supporting QM/MM calculations reveal how the DA state permits a thermodynamic equilibrium between retinal isomers to be established, and how this same change is prevented in the ground state in the absence of light. We suggest that the different arrangement of internal water networks in AR3 is responsible for the faster photocycle kinetics compared to homologs.
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Jan 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Yurong
Chen
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Zachary
Armstrong
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Marta
Artola
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Bogdan I.
Florea
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Chi-Lin
Kuo
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Casper
De Boer
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Mikkel S.
Rasmussen
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Maher
Abou Hachem
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Gijsbert A.
Van Der Marel
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Jeroen D. C.
Codée
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Johannes M. F. G.
Aerts
,
Gideon J.
Davies
,
Herman S.
Overkleeft
Diamond Proposal Number(s):
[18598]
Abstract: Amylases are key enzymes in the processing of starch in many kingdoms of life. They are important catalysts in industrial biotechnology where they are applied in, among others, food processing and the production of detergents. In man amylases are the first enzymes in the digestion of starch to glucose and arguably also the preferred target in therapeutic strategies aimed at the treatment of type 2 diabetes patients through down-tuning glucose assimilation. Efficient and sensitive assays that report selectively on retaining amylase activities irrespective of the nature and complexity of the biomaterial studied are of great value both in finding new and effective human amylase inhibitors and in the discovery of new microbial amylases with potentially advantageous features for biotechnological application. Activity-based protein profiling (ABPP) of retaining glycosidases is inherently suited for the development of such an assay format. We here report on the design and synthesis of 1,6-epi-cyclophellitol-based pseudodisaccharides equipped with a suite of reporter entities and their use in ABPP of retaining amylases from human saliva, murine tissue as well as secretomes from fungi grown on starch. The activity and efficiency of the inhibitors and probes are substantiated by extensive biochemical analysis, and the selectivity for amylases over related retaining endoglycosidases is validated by structural studies.
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Jan 2021
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