I03-Macromolecular Crystallography
|
Thomas W.
Thorpe
,
James R.
Marshall
,
Vanessa
Harawa
,
Rebecca E.
Ruscoe
,
Anibal
Cuetos
,
James D.
Finnigan
,
Antonio
Angelastro
,
Rachel S.
Heath
,
Fabio
Parmeggiani
,
Simon J.
Charnock
,
Roger M.
Howard
,
Rajesh
Kumar
,
David S. B.
Daniels
,
Gideon
Grogan
,
Nicholas J.
Turner
Diamond Proposal Number(s):
[9948]
Abstract: Chiral amine diastereomers are ubiquitous in pharmaceuticals and agrochemicals1, yet their preparation often relies on low-efficiency multi-step synthesis2. These valuable compounds must be manufactured asymmetrically, as their biochemical properties can differ based on the chirality of the molecule. Herein we characterize a multifunctional biocatalyst for amine synthesis, which operates using a mechanism that is, to our knowledge, previously unreported. This enzyme (EneIRED), identified within a metagenomic imine reductase (IRED) collection3 and originating from an unclassified Pseudomonas species, possesses an unusual active site architecture that facilitates amine-activated conjugate alkene reduction followed by reductive amination. This enzyme can couple a broad selection of α,β-unsaturated carbonyls with amines for the efficient preparation of chiral amine diastereomers bearing up to three stereocentres. Mechanistic and structural studies have been carried out to delineate the order of individual steps catalysed by EneIRED, which have led to a proposal for the overall catalytic cycle. This work shows that the IRED family can serve as a platform for facilitating the discovery of further enzymatic activities for application in synthetic biology and organic synthesis.
|
Apr 2022
|
|
I04-Macromolecular Crystallography
|
Open Access
Abstract: Inteins catalyze their removal from a host protein through protein splicing. Inteins that contain an additional site-specific endonuclease domain display genetic mobility via a process termed “homing” and thereby act as selfish DNA elements. We elucidated the crystal structures of two archaeal inteins associated with an active or inactive homing endonuclease domain. This analysis illustrated structural diversity in the accessory domains (ACDs) associated with the homing endonuclease domain. To augment homing endonucleases with highly specific DNA cleaving activity using the intein scaffold, we engineered the ACDs and characterized their homing site recognition. Protein engineering of the ACDs in the inteins illuminated a possible strategy for how inteins could avoid their extinction but spread via the acquisition of a diverse accessory domain.
|
Mar 2022
|
|
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[24948]
Open Access
Abstract: Native Amine Dehydrogenases (nat-AmDHs) have recently emerged as a potentially valuable new reservoir of enzymes for the sustainable and selective synthesis of chiral amines, catalyzing the NAD(P)H-dependent ammoniation of carbonyl compounds with high activity and selectivity. MATOUAmDH2, recently identified from the Marine Atlas of Tara Oceans Unigenes (MATOUv1) database of eukaryotic genes, displays exceptional catalytic performance against its best identified substrate, isobutyraldehyde, as well as broader substrate scope than other nat-AmDHs. In the interests of providing a platform for the rational engineering of this and other nat-AmDHs, we have determined the structure of MATOUAmDH2 in complex with NADP + and also with the cofactor and cyclohexylamine. Monomers within the structure are representative of more open and closed conformations of the enzyme and illustrate the profound changes undergone by nat-AmDHs during the catalytic cycle. An alanine screen of active site residues revealed that M215A and L180A are more active than the wild-type enzyme for the amination of cyclohexanone with ammonia and methylamine respectively, the latter suggesting that AmDHs have the potential to be engineered for the improved production of secondary amines.
|
Mar 2022
|
|
I15-1-X-ray Pair Distribution Function (XPDF)
|
Diamond Proposal Number(s):
[27146]
Abstract: There is an increasing interest in the self-assembly process from a bottom-up approach to synthesize functional structures for engineering applications. Silk fibroin is a protein extracted from the cocoons of silkworm Bombyx mori that can be processed into various materials generally stabilized by the induction of β-sheet formation through the use of solvents or by physical stretching. In our study, the introduction of cobalt-substituted nickel hydroxide nanoparticles on silk fibroin presented a dual effect causing the stabilization of the α polymorph of nickel hydroxide and promoting a highly connected network of the β-sheet crystalline domain in the fibroin chains. Electrochemical measurements were performed to examine silk fibroin (SF)/NiCo(OH)2 hybrid materials. The optimized sample exhibits a high specific capacity of 362 mA h g–1 at a current density of 1 A g–1, maintaining steady electrochemical performance >75% of the initial value at higher current densities. The presented assembly provides a route for preparing monodisperse inorganic nanoparticles in the presence of SF as an organic matrix with potential energy storage properties.
|
Mar 2022
|
|
|
|
Open Access
Abstract: Hypothesis: Self-assembly of amphipathic styrene maleic acid copolymers with phospholipids in aqueous solution results in the formation of ‘nanodiscs’ containing a planar segment of phospholipid bilayer encapsulated by a polymer belt. Recently, studies have reported that lipids rapidly exchange between both nanodiscs in solution and external sources of lipids. Outstanding questions remain regarding details of polymer-lipid interactions, factors influencing lipid exchange and structural effects of such exchange processes. Here, the dynamic behaviour of nanodiscs is investigated, specifically the role of membrane charge and polymer chemistry. Experiments: Two model systems are investigated: fluorescently labelled phospholipid vesicles, and Langmuir monolayers of phospholipids. Using fluorescence spectroscopy and time-resolved neutron reflectometry, the membrane potential, monolayer structure and composition are monitored with respect to time upon polymer and nanodisc interactions. Findings: In the presence of external lipids, polymer chains embed throughout lipid membranes, the extent of which is governed by the net membrane charge. Nanodiscs stabilised by three different polymers will all exchange lipids and polymer with monolayers to differing extents, related to the properties of the stabilising polymer belt. These results demonstrate the dynamic nature of nanodiscs which interact with the local environment and are likely to deposit both lipids and polymer at all stages of use.
|
Mar 2022
|
|
I04-Macromolecular Crystallography
|
Josefin
Ahlqvist
,
Javier A.
Linares-Pastén
,
Maria
Håkansson
,
Andrius
Jasilionis
,
Karolina
Kwiatkowska-Semrau
,
Ólafur H.
Friðjónsson
,
Anna-Karina
Kaczorowska
,
Slawomir
Dabrowski
,
Arnþór
Ævarsson
,
Guðmundur Ó.
Hreggviðsson
,
Salam
Al-Karadaghi
,
Tadeusz
Kaczorowski
,
Eva
Nordberg Karlsson
Diamond Proposal Number(s):
[20028]
Open Access
Abstract: This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA–Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Å resolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E–SD–EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.
|
Feb 2022
|
|
I03-Macromolecular Crystallography
|
Eugene
Kuatsjah
,
Christopher W.
Johnson
,
Davinia
Salvachúa
,
Allison Z.
Werner
,
Michael
Zahn
,
Caralyn J.
Szostkiewicz
,
Christine A.
Singer
,
Graham
Dominick
,
Ikenna
Okekeogbu
,
Stefan J.
Haugen
,
Sean P.
Woodworth
,
Kelsey J.
Ramirez
,
Richard J.
Giannone
,
Robert L.
Hettich
,
John E.
Mcgeehan
,
Gregg T.
Beckham
Diamond Proposal Number(s):
[23269]
Abstract: The transformation of 4-hydroxybenzoate (4-HBA) to protocatechuate (PCA) is catalyzed by flavoprotein oxygenases known as para-hydroxybenzoate-3-hydroxylases (PHBHs). In Pseudomonas putida KT2440 (P. putida) strains engineered to convert lignin-related aromatic compounds to muconic acid (MA), PHBH activity is rate-limiting, as indicated by the accumulation of 4-HBA, which ultimately limits MA productivity. Here, we hypothesized that replacement of PobA, the native P. putida PHBH, with PraI, a PHBH from Paenibacillus sp. JJ-1b with a broader nicotinamide cofactor preference, could alleviate this bottleneck. Biochemical assays confirmed the strict preference of NADPH for PobA, while PraI can utilize either NADH or NADPH. Kinetic assays demonstrated that both PobA and PraI can utilize NADPH with comparable catalytic efficiency and that PraI also efficiently utilizes NADH at roughly half the catalytic efficiency. The X-ray crystal structure of PraI was solved and revealed absolute conservation of the active site architecture to other PHBH structures despite their differing cofactor preferences. To understand the effect in vivo, we compared three P. putida strains engineered to produce MA from p-coumarate (pCA), showing that expression of praI leads to lower 4-HBA accumulation and decreased NADP+/NADPH ratios relative to strains harboring pobA, indicative of a relieved 4-HBA bottleneck due to increased NADPH availability. In bioreactor cultivations, a strain exclusively expressing praI achieved a titer of 40 g/L MA at 100% molar yield and a productivity of 0.5 g/L/h. Overall, this study demonstrates the benefit of sampling readily available natural enzyme diversity for debottlenecking metabolic flux in an engineered strain for microbial conversion of lignin-derived compounds to value-added products.
|
Jan 2022
|
|
B18-Core EXAFS
|
Diamond Proposal Number(s):
[13890]
Abstract: Major uranium (U) deposits worldwide are exploited by acid leaching, known as ‘in-situ recovery’ (ISR). ISR involves the injection of an acid fluid into ore-bearing aquifers and the pumping of the resulting metal-containing solution through cation exchange columns for the recovery of dissolved U. Rehabilitation of ISR-impacted aquifers could be achieved through natural attenuation, or via biostimulation of autochthonous heterotrophic microorganisms due to the associated acid neutralization and trace metal immobilization.
In this study, we analyzed the capacity of pristine aquifer sediments impacted by diluted ISR fluids to buffer pH and immobilize U. The experimental setup consisted of glass columns, filled with sediment from a U ore-bearing aquifer, through which diluted ISR fluids were flowed continuously. The ISR solution was obtained from ISR mining operations at the Muyunkum and Tortkuduk deposits in Kazakhstan. Following this initial phase, columns were biostimulated with a mix of molasses, yeast extract and glycerol to stimulate the growth of autochthonous heterotrophic communities. Experimental results showed that this amendment efficiently promoted the activity of acid-tolerant bacterial guilds, with pH values rising from 4.8 to 6.5–7.0 at the outlet of the stimulated columns. The reduction of sulfate, nitrate, and metals as well as dissimilatory nitrate reduction to ammonia induced the rise in pH values, in agreement with geochemical modelling results. Biostimulation efficiently promoted the complete immobilization of U, with the accumulation of up to 3343 ppm in the first few centimeters of the columns. Synchrotron analysis and SEM-EDS revealed that up to 60% of the injected hexavalent U was immobilized as tetravalent non-crystalline U onto bacterial cell surfaces. 16S rDNA amplicon analysis and qPCR data suggested a predominant role played for members of the Phylum Firmicutes (from the genera Clostridium, Pelosinus and Desulfosporosinus) in biological U reduction and immobilization.
|
Jan 2022
|
|
B21-High Throughput SAXS
|
Diamond Proposal Number(s):
[16125, 21035]
Open Access
Abstract: Biofermentative production of styrene from renewable carbon sources is crucially dependent on strain tolerance and viability at elevated styrene concentrations. Solvent-driven collapse of bacterial plasma membranes limits yields and is technologically restrictive. Styrene is a hydrophobic solvent that readily partitions into the membrane interior and alters membrane-chain order and packing. We investigate styrene incorporation into model membranes and the role lipid chains play as determinants of membrane stability in the presence of styrene. MD simulations reveal styrene phase separation followed by irreversible segregation into the membrane interior. Solid state NMR shows committed partitioning of styrene into the membrane interior with persistence of the bilayer phase up to 67 mol % styrene. Saturated-chain lipid membranes were able to retain integrity even at 80 mol % styrene, whereas in unsaturated lipid membranes, we observe the onset of a non-bilayer phase of small lipid aggregates in coexistence with styrene-saturated membranes. Shorter-chain saturated lipid membranes were seen to tolerate styrene better, which is consistent with observed chain length reduction in bacteria grown in the presence of small molecule solvents. Unsaturation at mid-chain position appears to reduce the membrane tolerance to styrene and conversion from cis- to trans-chain unsaturation does not alter membrane phase stability but the lipid order in trans-chains is less affected than cis.
|
Jan 2022
|
|
B18-Core EXAFS
|
Diamond Proposal Number(s):
[28383]
Open Access
Abstract: Limonitic layers of the regolith, which are often stockpiled as waste materials at laterite mines, commonly contain significant concentrations of valuable base metals, such as nickel, cobalt, and manganese. There is currently considerable demand for these transition metals, and this is projected to continue to increase (alongside their commodity values) during the next few decades, due in the most part to their use in battery and renewable technologies. Limonite bioprocessing is an emerging technology that often uses acidophilic prokaryotes to catalyse the oxidation of zero-valent sulphur coupled to the reduction of Fe (III) and Mn (IV) minerals, resulting in the release of target metals. Chromium-bearing minerals, such as chromite, where the metal is present as Cr (III), are widespread in laterite deposits. However, there are also reports that the more oxidised and more biotoxic form of this metal [Cr (VI)] may be present in some limonites, formed by the oxidation of Cr (III) by manganese (IV) oxides. Bioleaching experiments carried out in laboratory-scale reactors using limonites from a laterite mine in New Caledonia found that solid densities of ∼10% w/v resulted in complete inhibition of iron reduction by acidophiles, which is a critical reaction in the reductive dissolution process. Further investigations found this to be due to the release of Cr (VI) in the acidic liquors. X-ray absorption near edge structure (XANES) spectroscopy analysis of the limonites used found that between 3.1 and 8.0% of the total chromium in the three limonite samples used in experiments was present in the raw materials as Cr (VI). Microbial inhibition due to Cr (VI) could be eliminated either by adding limonite incrementally or by the addition of ferrous iron, which reduces Cr (VI) to less toxic Cr (III), resulting in rates of extraction of cobalt (the main target metal in the experiments) of >90%.
|
Jan 2022
|
|
