I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[20221]
Open Access
Abstract: Unspecific peroxygenases (UPOs) are glycosylated fungal enzymes that can selectively oxidize C–H bonds. UPOs employ hydrogen peroxide as the oxygen donor and reductant. With such an easy-to-handle cosubstrate and without the need for a reducing agent, UPOs are emerging as convenient oxidative biocatalysts. Here, an unspecific peroxygenase from Hypoxylon sp. EC38 (HspUPO) was identified in an activity-based screen of six putative peroxygenase enzymes that were heterologously expressed in Pichia pastoris. The enzyme was found to tolerate selected organic solvents such as acetonitrile and acetone. HspUPO is a versatile catalyst performing various reactions, such as the oxidation of prim- and sec-alcohols, epoxidations, and hydroxylations. Semipreparative biotransformations were demonstrated for the nonenantioselective oxidation of racemic 1-phenylethanol rac-1b (TON = 13 000), giving the product with 88% isolated yield, and the oxidation of indole 6a to give indigo 6b (TON = 2800) with 98% isolated yield. HspUPO features a compact and rigid three-dimensional conformation that wraps around the heme and defines a funnel-shaped tunnel that leads to the heme iron from the protein surface. The tunnel extends along a distance of about 12 Å with a fairly constant diameter in its innermost segment. Its surface comprises both hydrophobic and hydrophilic groups for dealing with substrates of variable polarities. The structural investigation of several protein–ligand complexes revealed that the active site of HspUPO is accessible to molecules of varying bulkiness with minimal or no conformational changes, explaining the relatively broad substrate scope of the enzyme. With its convenient expression system, robust operational properties, relatively small size, well-defined structural features, and diverse reaction scope, HspUPO is an exploitable candidate for peroxygenase-based biocatalysis.
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Sep 2021
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I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[19800]
Open Access
Abstract: ω-Transaminases (ω-TA) are attractive biocatalysts for the production of chiral amines from prochiral ketones via asymmetric synthesis. However, the substrate scope of ω-TAs is usually limited due to steric hindrance at the active site pockets. We explored a protein engineering strategy using computational design to expand the substrate scope of an (S)-selective ω-TA from Pseudomonas jessenii (PjTA-R6) toward the production of bulky amines. PjTA-R6 is attractive for use in applied biocatalysis due to its thermostability, tolerance to organic solvents, and acceptance of high concentrations of isopropylamine as amino donor. PjTA-R6 showed no detectable activity for the synthesis of six bicyclic or bulky amines targeted in this study. Six small libraries composed of 7–18 variants each were separately designed via computational methods and tested in the laboratory for ketone to amine conversion. In each library, the vast majority of the variants displayed the desired activity, and of the 40 different designs, 38 produced the target amine in good yield with >99% enantiomeric excess. This shows that the substrate scope and enantioselectivity of PjTA mutants could be predicted in silico with high accuracy. The single mutant W58G showed the best performance in the synthesis of five structurally similar bulky amines containing the indan and tetralin moieties. The best variant for the other bulky amine, 1-phenylbutylamine, was the triple mutant W58M + F86L + R417L, indicating that Trp58 is a key residue in the large binding pocket for PjTA-R6 redesign. Crystal structures of the two best variants confirmed the computationally predicted structures. The results show that computational design can be an efficient approach to rapidly expand the substrate scope of ω-TAs to produce enantiopure bulky amines.
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Aug 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[22225]
Open Access
Abstract: Indium oxide (In2O3) is a promising catalyst for selective CH3OH synthesis from CO2 but displays insufficient activity at low reaction temperatures. By screening a range of promoters (Co, Ni, Cu, and Pd) in combination with In2O3 using flame spray pyrolysis (FSP) synthesis, Ni is identified as the most suitable first-row transition-metal promoter with similar performance as Pd–In2O3. NiO–In2O3 was optimized by varying the Ni/In ratio using FSP. The resulting catalysts including In2O3 and NiO end members have similar high specific surface areas and morphology. The main products of CO2 hydrogenation are CH3OH and CO with CH4 being only observed at high NiO loading (≥75 wt %). The highest CH3OH rate (∼0.25 gMeOH/(gcat h), 250 °C, and 30 bar) is obtained for a NiO loading of 6 wt %. Characterization of the as-prepared catalysts reveals a strong interaction between Ni cations and In2O3 at low NiO loading (≤6 wt %). H2-TPR points to a higher surface density of oxygen vacancy (Ov) due to Ni substitution. X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, and electron paramagnetic resonance analysis of the used catalysts suggest that Ni cations can be reduced to Ni as single atoms and very small clusters during CO2 hydrogenation. Supportive density functional theory calculations indicate that Ni promotion of CH3OH synthesis from CO2 is mainly due to low-barrier H2 dissociation on the reduced Ni surface species, facilitating hydrogenation of adsorbed CO2 on Ov.
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Aug 2021
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B23-Circular Dichroism
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Christopher D.
Fage
,
Simone
Kosol
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Matthew
Jenner
,
Carl
Öster
,
Angelo
Gallo
,
Milda
Kaniusaite
,
Roman
Steinbach
,
Michael
Staniforth
,
Vasilios G.
Stavros
,
Mohamed A.
Marahiel
,
Max J.
Cryle
,
Józef R.
Lewandowski
Diamond Proposal Number(s):
[16655]
Open Access
Abstract: Nonribosomal peptides are a structurally diverse and bioactive class of natural products constructed by multidomain enzymatic assembly lines known as nonribosomal peptide synthetases (NRPSs). While the core catalytic domains and even entire protein subunits of NRPSs have been structurally elucidated, little biophysical work has been reported on the docking domains that promote interactions—and thus transfer of biosynthetic intermediates—between subunits. In the present study, we closely examine the COM domains that mediate COMmunication between donor epimerization (E) and acceptor condensation (C) domains found at the termini of NRPS subunits. Through a combination of X-ray crystallography, circular dichroism spectroscopy, solution- and solid-state NMR spectroscopy, and molecular dynamics (MD) simulations, we provide direct evidence for an intrinsically disordered donor COM region that folds into a dynamic helical motif upon binding to a suitable acceptor. Furthermore, our NMR titration and carbene footprinting experiments illuminate the residues involved at the COM interaction interface, and our MD simulations demonstrate folding consistent with experimental data. Although our results lend credence to the previously proposed helix-hand mode of interaction, they also underscore the importance of viewing COM interfaces as dynamic ensembles rather than single rigid structures and suggest that engineering experiments should account for the interactions which transiently guide folding in addition to those which stabilize the final complex. Through activity assays and affinity measurements, we further substantiate the role of the donor COM region in binding the acceptor C domain and implicate this short motif as readily transposable for noncognate domain crosstalk. Finally, our bioinformatics analyses show that COM domains are widespread in natural product pathways and function at interfaces beyond the canonical type described above, setting a high priority for thorough characterization of these docking domains. Our findings lay the groundwork for future attempts to rationally engineer NRPS domain–domain interactions with the ultimate goal of generating bioactive molecules.
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Aug 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[12746]
Abstract: Carbon-supported Pt-based nanoparticles are important electrocatalysts for energy conversion reactions such as the oxygen reduction reaction (ORR). Although this reaction has been extensively studied, the influence of factors such as the particle size and interparticle distance of the nanoparticle-based or nanosized electrocatalysts on the ORR activity and durability are not yet fully understood and often intertwined. This lack of understanding is mostly based on the limitation in the synthetic approaches of the electrocatalysts, which usually do not allow an independent variation of the particle size and interparticle distance. In the presented work, we succeeded to disentangle both factors using a “colloidal toolbox” approach and have demonstrated an effect of the interparticle distance on the electronic properties of the nanoparticle via operando electrochemical X-ray absorption spectroscopy (XAS).
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Jun 2021
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[16479]
Open Access
Abstract: In situ X-ray absorption and emission spectroscopies (XAS and XES) are used to provide details regarding the role of the accessibility and extent of redox activity of the Mn ions in determining the oxygen reduction activity of LaMnO3 and CaMnO3, with X-ray absorption near-edge structure (XANES) providing the average oxidation state, extended X-ray absorption fine structure (EXAFS) providing the local coordination environment, and XES providing the population ratios of the Mn2+, Mn3+, and Mn4+ sites as a function of the applied potential. For LaMnO3, XANES and XES show that Mn3+ is formed, but Mn4+ ions are retained, which leads to the 4e– reduction between 0.85 and 0.6 V. At more negative potentials, down to 0.2 V, EXAFS confirms an increase in oxygen vacancies as evidenced by changes in the Mn–O coordination distance and number, while XES shows that the Mn3+ to Mn4+ ratio increases. For CaMnO3, XANES and XES show the formation of both Mn3+ and Mn2+ as the potential is made more negative, with little retention of Mn4+ at 0.2 V. The EXAFS for CaMnO3 also indicates the formation of oxygen vacancies, but in contrast to LaMnO3, this is accompanied by loss of the perovskite structure leading to structural collapse. The results presented have implications in terms of understanding of both the pseudocapacitive response of Mn oxide electrocatalysts and the processes behind degradation of the activity of the materials.
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May 2021
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B18-Core EXAFS
I11-High Resolution Powder Diffraction
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Pu
Zhao
,
Lin
Ye
,
Guangchao
Li
,
Chen
Huang
,
Simson
Wu
,
Ping-Luen
Ho
,
Haokun
Wang
,
Tatchamapan
Yoskamtorn
,
Denis
Sheptyakov
,
Giannantonio
Cibin
,
Angus I.
Kirkland
,
Chiu C.
Tang
,
Anmin
Zheng
,
Wenjuan
Xue
,
Donghai
Mei
,
Kongkiat
Suriye
,
Shik Chi Edman
Tsang
Abstract: Synthesizing atomically dispersed synergistic active pairs is crucial yet challenging in developing highly active heterogeneous catalysts for various industrially important reactions. Here, a single molecular Re species is immobilized on the inner surface of a Y zeolite with Brønsted acid sites (BASs) within atomic proximity to form Re OMS–BAS active pairs for the efficient catalysis of olefin metathesis reactions (OMS: olefin metathesis site). The synergy within the active pairs is revealed by studying the coadsorption geometry of the olefin substrates over the active pairs by synchrotron X-ray and neutron powder diffraction. It is shown that the BAS not only facilitates olefin adsorption but also aligns the olefin molecule to the Re OMS for efficient intermediate formation. Consequently, for the cross-metathesis of ethene and trans-2-butene to propene, this catalyst shows high activity under mild reaction conditions without observable deactivation. The catalyst outperforms not only traditional ReOx-based catalysts but also the best industrially applicable WOx-based catalyst thus far that we discovered previously. The concept of using two isolated active sites of different functionalities within atomic proximity in a confined cavity can provide opportunities for designing synergistically catalytic materials.
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Mar 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[9948]
Open Access
Abstract: Cytochrome P450 CYP153AM.aq from Marinobacter aquaeolei serves as a model enzyme for the terminal (ω-) hydroxylation of medium- to long-chain fatty acids. We have engineered this enzyme using different mutagenesis approaches based on structure-sequence-alignments within the 3DM database and crystal structures of CYP153AM.aq and a homologue CYP153AP.sp. Applying these focused mutagenesis strategies and site-directed saturation mutagenesis, we created a variant that ω-hydroxylates octanoic acid. The M.aqRLT variant exhibited 151-fold improved catalytic efficiency and showed strongly improved substrate binding (25-fold reduced Km compared to the wild type). We then used molecular dynamics simulations to gain deeper insights into the dynamics of the protein. We found the tunnel modifications and the two loop regions showing greatly reduced flexibility in the engineered variant were the main features responsible for stabilizing the enzyme–substrate complex and enhancing the catalytic efficiency. Additionally, we showed that a previously known fatty acid anchor (Q129R) interacts significantly with the ligand to hold it in the reactive position, thereby boosting the activity of the variant M.aqRLT toward octanoic acid. The study demonstrates the significant effects of both substrate stabilization and the impact of enzyme flexibility on catalytic efficiency. These results could guide the future engineering of enzymes with deeply buried active sites to increase or even establish activities toward yet unknown types of substrates.
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Feb 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[13587]
Open Access
Abstract: Isoelectronic metal fluoride transition state analogue (TSA) complexes, MgF3– and AlF4–, have proven to be immensely useful in understanding mechanisms of biological motors utilizing phosphoryl transfer. Here we report a previously unobserved octahedral TSA complex, MgF3(H2O)−, in a 1.5 Å resolution Zika virus NS3 helicase crystal structure. 19F NMR provided independent validation and also the direct observation of conformational tightening resulting from ssRNA binding in solution. The TSA stabilizes the two conformations of motif V of the helicase that link ATP hydrolysis with mechanical work. DFT analysis further validated the MgF3(H2O)− species, indicating the significance of this TSA for studies of biological motors.
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Feb 2021
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Open Access
Abstract: The utilization of operando spectroscopy has allowed us to watch the dynamic nature of supported metal nanoparticles. However, the realization that subtle changes to environmental conditions affect the form of the catalyst necessitates that we assess the structure of the catalyst across the reactant/product gradient that exists across a fixed bed reactor. In this study, we have performed spatial profiling of a Pd/Al2O3 catalyst during NH3 oxidation, simultaneously collecting mass spectrometry and X-ray absorption spectroscopy data at discrete axial positions along the length of the catalyst bed. The spatial analysis has provided unique insights into the structure–activity relationships that govern selective NH3 oxidation—(i) our data is consistent with the presence of PdNx after the spectroscopic signatures for bulk PdNx disappear and that there is a direct correlation to the presence of this structure and the selectivity toward N2; (ii) at high temperatures, ≥400 °C, we propose that there are two simultaneous reaction pathways—the oxidation of NH3 to NOx by PdO and the subsequent catalytic reduction of NOx by NH3 to produce N2. The results in this study confirm the structural and catalytic diversity that exists during catalysis and the need for such an understanding if improvements to important emission control technologies, such as the selective catalytic oxidation of NH3, are to be made.
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Feb 2021
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