I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[10515]
Abstract: Hydrogenases are metalloenzymes that catalyze the redox conversion between H2 and protons. The so-called [NiFeSe] hydrogenases are highly active for both H2 production and oxidation, but like all hydrogenases, they are inhibited by O2. In the [NiFeSe] enzyme from Desulfovibrio vulgaris Hildenborough this results from the oxidation of an active site cysteine ligand. We designed mutations that constrict a hydrophilic channel that connects the protein surface to this active site cysteine. Two of the variants show markedly increased tolerance to O2 inactivation, while retaining high catalytic activities in both directions of the reaction, and structural studies confirm that these mutations prevent the oxidation of the cysteine. Our results indicate that the diffusion of O2 or ROS to the active site can occur through a hydrophilic water channel, in contrast to the widely held assumption that only hydrophobic channels are involved in active site inactivation. This provides an original strategy for optimizing the enzyme by protein engineering.
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Aug 2019
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I03-Macromolecular Crystallography
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Emma Zsófia Aletta
Nagy
,
Souad Diana
Tork
,
Pauline A.
Lang
,
Alina
Filip
,
Florin Dan
Irimie
,
László
Poppe
,
Monica Ioana
Toşa
,
Christopher J.
Schofield
,
Jurgen
Brem
,
Csaba
Paizs
,
Laszlo Csaba
Bencze
Diamond Proposal Number(s):
[19458]
Abstract: Modification of the hydrophobic binding pocket of phenylalanine ammonia-lyase from Petroselinum crispum (PcPAL) enables increased activity and selectivity towards phenylalanines and cinnamic acids mono-substituted with both electron donating (-CH3, -OCH3) and electron withdrawing (-CF3, -Br) groups at all positions (o-, m-, p-) of their aromatic ring. The results reveal specific residues involved in accommodating substituents at o-, m-, p-positions of the substrate’s phenyl ring. The predicted interactions were validated by crystallographic analysis of the binding mode of para-methoxy cinnamic acid complexed at the active site of PcPAL. The biocatalytic utility of the tailored PcPAL mutants was demonstrated by the efficient preparative scale synthesis of (S)-m-bromo-phenylalanine (ee: > 99%, yield: 60%) and (R)-p-methyl-phenylalanine (ee: 97%, yield: 49%), using the corresponding ammonia addition and ammonia elimination reactions catalyzed by the L134A and I460V PcPAL variants, respectively. Overall, the results reveal the potential for structure based protein engineering of PALs to provide enzymes with enhanced catalytic properties and which are specifically tailored for differently substituted phenylalanine analogues of high synthetic value.
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Aug 2019
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B18-Core EXAFS
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Diamond Proposal Number(s):
[16250]
Abstract: Energy storage solutions are a vital component of the global transition towards renewable energy sources. The Power-to-Gas (PtG) concept, which stores surplus renewable energy in the form of methane, has therefore become increasingly relevant in recent years. At present, supported Ni nanoparticles are preferred as industrial catalysts for CO2 methanation due to their low cost and high methane selectivity. However, commercial Ni catalysts are not active enough in CO2 methanation to reach the high CO2 conversion (>99 %) required by the specifications for injection in the natural gas grid. Herein we demonstrate the promise of promotion of Ni by Mn, another low-cost base metal, for obtaining very active CO2 methanation catalysts, with results comparable to more expensive precious metal-based catalysts. The origin of this improved performance is revealed by a combined approach of nanoscale characterization, mechanistic study, and density functional theory calculations. Nanoscale characterization with STEM-EDX and X-ray absorption spectroscopy shows that NiMn catalysts consist of metallic Ni particles decorated by oxidic Mn2+ species. A mechanistic study combining IR spectroscopy of surface adsorbates, transient kinetic analysis with isotopically labelled CO2, density functional theory calculations and microkinetics simulations ascertain that the MnO clusters enhance CO2 adsorption and facilitate CO2 activation. A macroscale perspective was achieved by simulating the Ni and NiMn catalytic activity in a Sabatier reactor, which revealed that NiMn catalysts have the potential to meet the demanding PtG catalyst performance requirements, and can largely replace the need for expensive and scarce noble metal catalysts.
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Jul 2019
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B18-Core EXAFS
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Diamond Proposal Number(s):
[16006]
Abstract: Different supporting procedures were followed to alter the nanoparticle-support interactions (NPSI) in two Co3O4/Al2O3 catalysts, prepared using the reverse micelle technique. The catalysts were tested in the dry preferential oxidation of carbon monoxide (CO-PrOx) while monitoring their phase stability using four complementary in situ techniques, viz. magnet-based characterisation, PXRD, combined XAS/DRIFTS as well as quasi in situ XPS, respectively. The catalyst with weak NPSI achieved higher CO2 yields and selectivities at temperatures below 225 °C compared to the sample with strong NPSI. However, relatively high degrees of reduction of Co3O4 to metallic Co were reached between 250 and 350 °C for the same catalyst. The presence of metallic Co led to the undesired formation of CH4, reaching a yield of over 90% above 300 °C. The catalyst with strong NPSI formed very low amounts of metallic Co (less than 1%) and low CH4 (yield of up to 20%) even at 350 °C. When the temperature was decreased from 350 to 50 °C under the reaction gas, both catalysts were slightly re-oxidised and gradually re-gained their CO oxidation activity while the formation of CH4 diminished. The present study, for the first time, shows a strong relationship between catalyst performance (i.e., activity and selectivity) and phase stability, both of which are affected by the strength of the NPSI. When using a metal oxide as the active CO-PrOx catalyst, it is important for it to have significant reduction resistance to avoid the formation of undesired products, e.g., CH4. However, the metal oxide should also be reducible (especially on the surface) to allow for a complete conversion of CO to CO2 via the Mars-van Krevelen mechanism.
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Jun 2019
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B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[13725, 16257, 20906]
Abstract: Synchrotron infrared microspectroscopy has identified with high temporal resolution (down to 0.25 s) the initial events occurring when methanol vapour is contacted with a crystal of zeolite HZSM-5. The first alkenes are generated directly from methoxy groups formed at the acid sites via their deprotonation. These alkenes can either desorb directly or oligomerise and cyclise to form dimethylcyclopentenyl cations. The oligomeric and dimethylcyclopentenyl cations are the first major components of the hydrocar-bon pool that precede aromatic hydrocarbons and lead to indirect alkene formation. This is the first direct observation of these events in real time.
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Jun 2019
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[9948]
Abstract: The recently identified pseudoephedrine and ephedrine dehydrogenases from Arthrobacter sp. TS-15, PseDH and EDH, are NADH-dependent members of the oxidoreductase superfamily of short-chain dehydrogenases/reductases (SDRs). They are specific for the enantioselective oxidation of (+)-(S) N-(pseudo)ephedrine and (-)-(R) N-(pseudo)ephedrine, respectively. Anti-Prelog stereospecific PseDH and Prelog-specific EDH catalyse the regio- and enantiospecific reduction of 1-phenyl-1,2-propanedione to (S)-phenylacetylcarbinol and (R)-phenylacetylcarbinol with full conversion and enantiomeric excess of >99%. Moreover, they perform the reduction of a wide range of aryl aliphatic carbonyl compounds, including keto amines, ketoesters and haloketones, to the corresponding enantiopure alcohols. The highest stability of PseDH and EDH was determined to be at a pH range of 6.0-8.0 and 7.5-8.5, respectively. PseDH was more stable than EDH at 25 °C, with half-lives of 279 h and 38 h respectively. However, EDH is more stable at 40 °C with a two-fold greater half-life than at 25 °C. The crystal structure of the PseDH-NAD+ complex, refined to a resolution of 1.83 Å, revealed a tetrameric structure, which was confirmed by solution studies. A model of the active site in complex with NAD+ and 1-phenyl-1,2-propanedione suggested key roles for S143 and W152 in recognition of the substrate and positioning for the reduction reaction. The wide substrate spectrum of these dehydrogenases, combined with their regio- and enantioselectivity, suggests excellent potential for the industrial production of valuable chiral compounds.
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May 2019
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I24-Microfocus Macromolecular Crystallography
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Tobias
Hedison
,
Rajesh
Shenoy
,
Andreea Iulia
Iorgu
,
Derren
Heyes
,
Karl
Fisher
,
Gareth
Wright
,
Sam
Hay
,
Robert Roy
Eady
,
Svetlana
Antonyuk
,
S. Samar
Hasnain
,
Nigel S.
Scrutton
Diamond Proposal Number(s):
[11740]
Abstract: It is generally assumed that tethering enhances rates of electron harvesting and delivery to active sites in multi-domain enzymes by proximity and sampling mechanisms. Here, we explore this idea in a tethered 3-domain, trimeric copper-containing nitrite reductase. By reverse engineering, we find that tethering does not enhance the rate of electron delivery from its pendant cytochrome c to the catalytic copper-containing core. Using a linker that harbors a gatekeeper tyrosine in a nitrite access channel, the tethered haem domain enables catalysis by other mechanisms. Tethering communicates the redox state of the haem to the distant T2Cu center that helps initiate substrate binding for catalysis. It also tunes copper reduction potentials, suppresses reductive enzyme inactivation, enhances enzyme affinity for substrate and promotes inter-copper electron transfer. Tethering has multiple unanticipated beneficial roles, the combination of which fine-tunes function beyond simplistic mechanisms expected from proximity and restrictive sampling models.
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May 2019
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I02-Macromolecular Crystallography
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Radka
Chaloupkova
,
Veronika
Liskova
,
Martin
Toul
,
Klara
Markova
,
Eva
Sebestova
,
Lenka
Hernychova
,
Martin
Marek
,
Gaspar P.
Pinto
,
Daniel
Pluskal
,
Jitka
Waterman
,
Zbyněk
Prokop
,
Jiří
Damborský
Diamond Proposal Number(s):
[4923]
Abstract: To obtain structural insights into the emergence of biological functions from catalytically promiscuous enzymes, we reconstructed an ancestor of catalytically distinct, but evolutionarily related, haloalkane dehalogenases (EC 3.8.1.5) and Renilla luciferase (EC 1.13.12.5). This ancestor has both hydrolase and monooxygenase activities. Crystal structure revealed the presence of a catalytic pentad conserved in both dehalogenase and luciferase descendants, and a molecular oxygen bound in between two residues typically stabilizing a halogen anion. The differences in the conformational dynamics of the specificity-determining cap domains between the ancestral and descendant enzymes were accessed by molecular dynamics and hydrogen-deuterium exchange mass spectrometry. Stopped-flow analysis revealed that the alkyl-enzyme intermediate formed in the luciferase-catalyzed reaction is trapped by blockage of a hydrolytic reaction step. A single-point mutation (Ala54Pro) adjacent to one of the catalytic residues bestowed hydrolase activity on the modern luciferase by enabling cleavage of this intermediate. In conclusion: a single substitution next to the catalytic pentad may enable the emergence of promiscuous activity at enzyme class-level; and ancestral reconstruction has a clear potential for obtaining multi-functional catalysts.
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Apr 2019
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I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[12788]
Abstract: Catechol-O-methyltransferase (COMT) is a model S-adenosyl-L-methionine (SAM) dependent methyl transferase, which catalyzes the methylation of catecholamine neurotransmitters such as dopamine in the primary pathway of neurotransmitter deactivation in animals. Despite extensive study, there is no consensus view of the physical basis of catalysis in COMT. Further progress requires experimental data that directly probes active site geometry, protein dynamics and electrostatics, ideally in a range of positions along the reaction coordinate. Here we establish that sinefungin, a fungal- derived inhibitor of SAM-dependent enzymes that possess transition state-like charge on the transferring group, can be used as a transition state analog of COMT when combined with a catechol. X-ray crystal structures and NMR backbone assignments of the ternary complexes of the soluble form of human COMT containing dinitrocatechol, Mg2+ and SAM or sinefungin were determined. Comparison and further analysis with the aid of density functional theory calculations and molecular dynamics simulations provides evidence for active site ‘compaction’, which is driven by electrostatic stabilization between the transferring methyl group and ‘equatorial’ active site residues that are orthogonal to the donor–acceptor (pseudo reaction) coordinate. We propose that upon catecholamine binding and subsequent proton transfer to Lys 144, the enzyme becomes geometrically preorganized, with little further movement along the donor–acceptor coordinate required for methyl transfer. Catalysis is then largely facilitated through stabilization of the developing charge on the transferring methyl group via ‘equatorial’ H-bonding and electrostatic interactions orthogonal to the donor–acceptor coordinate.
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Apr 2019
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Lin
Ye
,
A. A. Hanif
Mahadi
,
Chalathan
Saengruengrit
,
Jin
Qu
,
Feng
Xu
,
Simon
Fairclough
,
Neil
Young
,
Ping-luen
Ho
,
Junjun
Shan
,
Luan
Nguyen
,
Franklin F.
Tao
,
Karaked
Tedsree
,
Shik Chi Edman
Tsang
Abstract: Ceria has been widely used as support in electrocatalysis for its high degree of oxygen storage, fast oxygen mobility and reduction and oxidation properties at mild conditions. However, it is unclear what are the underlying principles and the nature of surface involved. By controlling the growth of various morphologies of ceria nanoparticles, it is demonstrated that the cubic-form of ceria, predominantly covered with higher energy polar surface (100), as support for Pd gives much higher activity in the electrocatalytic oxidation of formic acid than ceria of other morphologies (rods and spheres) with low indexed facets ((110) and (111)). High resolution TEM confirms the alternating layer-to-layer of cations and anions in (100) surface, the electrostatic repulsion of oxygen anions within the same layers gives intrinsically higher oxygen vacancies on this redox active surface in order to reduce surface polarity. DFT calculations suggest that the properties of fast oxygen mobility to re-oxidize the CO-poisoned Pd may arise from the overdosed oxygens on these ceria surface layers during electro-oxidation hence sustaining higher activity.
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Apr 2019
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