I03-Macromolecular Crystallography
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Nicholas G. S.
Mcgregor
,
Joan
Coines
,
Valentina
Borlandelli
,
Satoko
Amaki
,
Marta
Artola
,
Alba
Nin‐hill
,
Daniël
Linzel
,
Chihaya
Yamada
,
Takatoshi
Arakawa
,
Akihiro
Ishiwata
,
Yukishige
Ito
,
Gijsbert A.
Marel
,
Jeroen D. C.
Codée
,
Shinya
Fushinobu
,
Herman S.
Overkleeft
,
Carme
Rovira
,
Gideon J.
Davies
Diamond Proposal Number(s):
[18598]
Abstract: The recent discovery of zinc‐dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys)3(Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn‐coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial. This is primarily due to the expected stability of the intermediate C−S bond. To facilitate the study of this atypical mechanism, we report the synthesis of a cyclophellitol‐derived β‐l‐arabinofuranosidase inhibitor, hypothesised to react with the catalytic nucleophile to form a non‐hydrolysable adduct analogous to the mechanistic covalent intermediate. This β‐l‐arabinofuranosidase inhibitor reacts exclusively with the proposed cysteine thiol catalytic nucleophiles of representatives of GH families 127 and 146. X‐ray crystal structures determined for the resulting adducts enable MD and QM/MM simulations, which provide insight into the mechanism of thioglycosyl enzyme intermediate breakdown. Leveraging the unique chemistry of cyclophellitol derivatives, the structures and simulations presented here support the assignment of a zinc‐coordinated cysteine as the catalytic nucleophile and illuminate the finely tuned energetics of this remarkable metalloenzyme clan.
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Feb 2021
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I11-High Resolution Powder Diffraction
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Ashok S.
Menon
,
Seda
Ulusoy
,
Dickson O.
Ojwang
,
Lars
Riekehr
,
Christophe
Didier
,
Vanessa K.
Peterson
,
German
Salazar-alvarez
,
Peter
Svedlindh
,
Kristina
Edström
,
Cesar Pay
Gomez
,
William R.
Brant
Diamond Proposal Number(s):
[21804]
Open Access
Abstract: Li- and Mn-rich layered oxides show significant promise as electrode materials for future Li-ion batteries. However, an accurate description of its crystallography remains elusive, with both single-phase solid solution and multiphase structures being proposed for high performing materials such as Li1.2Mn0.54Ni0.13Co0.13O2. Herein, we report the synthesis of single- and multiphase variants of this material through sol–gel and solid-state methods, respectively, and demonstrate that its crystallography is a direct consequence of the synthetic route and not necessarily an inherent property of the composition, as previously argued. This was accomplished via complementary techniques that probe the bulk and local structure followed by in situ methods to map the synthetic progression. As the electrochemical performance and anionic redox behavior are often rationalized on the basis of the presumed crystal structure, clarifying the structural ambiguities is an important step toward harnessing its potential as an electrode material.
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Feb 2021
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I11-High Resolution Powder Diffraction
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Tatchamapan
Yoskamtorn
,
Pu
Zhao
,
Xin-ping
Wu
,
Kirsty
Purchase
,
Fabio
Orlandi
,
Pascal
Manuel
,
James
Taylor
,
Yiyang
Li
,
Sarah
Day
,
Lin
Ye
,
Chiu C.
Tang
,
Yufei
Zhao
,
S. C. Edman
Tsang
Abstract: Understanding structural responses of metal–organic frameworks (MOFs) to external stimuli such as the inclusion of guest molecules and temperature/pressure has gained increasing attention in many applications, for example, manipulation and manifesto smart materials for gas storage, energy storage, controlled drug delivery, tunable mechanical properties, and molecular sensing, to name but a few. Herein, neutron and synchrotron diffractions along with Rietveld refinement and density functional theory calculations have been used to elucidate the responsive adsorption behaviors of defect-rich Zr-based MOFs upon the progressive incorporation of ammonia (NH3) and variable temperature. UiO-67 and UiO-bpydc containing biphenyl dicarboxylate and bipyridine dicarboxylate linkers, respectively, were selected, and the results establish the paramount influence of the functional linkers on their NH3 affinity, which leads to stimulus-tailoring properties such as gate-controlled porosity by dynamic linker flipping, disorder, and structural rigidity. Despite their structural similarities, we show for the first time the dramatic alteration of NH3 adsorption profiles when the phenyl groups are replaced by the bipyridine in the organic linker. These molecular controls stem from controlling the degree of H-bonding networks/distortions between the bipyridine scaffold and the adsorbed NH3 without significant change in pore volume and unit cell parameters. Temperature-dependent neutron diffraction also reveals the NH3-induced rotational motions of the organic linkers. We also demonstrate that the degree of structural flexibility of the functional linkers can critically be affected by the type and quantity of the small guest molecules. This strikes a delicate control in material properties at the molecular level.
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Feb 2021
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[15916, 21426]
Open Access
Abstract: The HIV capsid self-assembles a protective conical shell that simultaneously prevents host sensing whilst permitting the import of nucleotides to drive DNA synthesis. This is accomplished through the construction of dynamic, highly charged pores at the centre of each capsid multimer. The clustering of charges required for dNTP import is strongly destabilising and it is proposed that HIV uses the metabolite IP6 to coordinate the pore during assembly. Here we have investigated the role of inositol phosphates in coordinating a ring of positively charged lysine residues (K25) that forms at the base of the capsid pore. We show that whilst IP5, which can functionally replace IP6, engages an arginine ring (R18) at the top of the pore, the lysine ring simultaneously binds a second IP5 molecule. Dose dependent removal of K25 from the pore severely inhibits HIV infection and concomitantly prevents DNA synthesis. Cryo-tomography reveals that K25A virions have a severe assembly defect that inhibits the formation of mature capsid cones. Monitoring both the kinetics and morphology of capsids assembled in vitro reveals that while mutation K25A can still form tubes, the ability of IP6 to drive assembly of capsid cones has been lost. Finally, in single molecule TIRF microscopy experiments, capsid lattices in permeabilised K25 mutant virions are rapidly lost and cannot be stabilised by IP6. These results suggest that the coordination of IP6 by a second charged ring in mature hexamers drives the assembly of conical capsids capable of reverse transcription and infection.
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[20229]
Open Access
Abstract: RcsB is a transcriptional regulator that controls expression of numerous genes in enteric bacteria. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such large number of genes, we performed structural studies as well as in vitro and in vivo functional studies with different RcsB variants. Our structural data reveal that RcsB binds promoters of target genes such as rprA and flhDC in a dimeric active conformation. In this state, the RcsB homodimer docks the DNA-binding domains into the major groove of the DNA, facilitating an initial weak read-out of the target sequence. Interestingly, comparative structural analyses also show that DNA binding may stabilize an active conformation in unphosphorylated RcsB. Furthermore, RNAseq performed in strains expressing wild-type or several RcsB variants provided new insights into the contribution of phosphorylation to gene regulation and assign a potential role of RcsB in controlling iron metabolism. Finally, we delimited the RcsB box for homodimeric active binding to DNA as the sequence TN(G/A)GAN4TC(T/C)NA. This RcsB box was found in promoter, intergenic and intragenic regions, facilitating both increased or decreased gene transcription.
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Feb 2021
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Ed
Daniel
,
Mirko M.
Maksimainen
,
Neil
Smith
,
Ville
Ratas
,
Ekaterina
Biterova
,
Sudarshan N.
Murthy
,
M. Tanvir
Rahman
,
Tiila-riikka
Kiema
,
Shruthi
Sridhar
,
Gabriele
Cordara
,
Subhadra
Dalwani
,
Rajaram
Venkatesan
,
Jaime
Prilusky
,
Orly
Dym
,
Lari
Lehtio
,
M. Kristian
Koski
,
Alun W.
Ashton
,
Joel L.
Sussman
,
Rikkert K.
Wierenga
Open Access
Abstract: The web-based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications. It also records and tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects. Fully automated data collection is now possible at several synchrotrons, which means that the number of samples tested at the synchrotron is currently increasing rapidly. Therefore, the protein crystallography research communities at the University of Oulu, Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron. In IceBear, each crystal selected for data collection is given a unique sample name and a crystal page is generated. Subsequently, the metadata required for data collection are uploaded directly to the ISPyB synchrotron database by a shipment module, and for each sample a link to the relevant ISPyB page is stored. IceBear allows notes to be made for each sample during cryocooling treatment and during data collection, as well as in later steps of the structure determination. Protocols are also available to aid the recycling of pins, pucks and dewars when the dewar returns from the synchrotron. The IceBear database is organized around projects, and project members can easily access the crystallization and diffraction metadata for each sample, as well as any additional information that has been provided via the notes. The crystal page for each sample connects the crystallization, diffraction and structural information by providing links to the IceBear drop-viewer page and to the ISPyB data-collection page, as well as to the structure deposited in the Protein Data Bank.
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Feb 2021
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I11-High Resolution Powder Diffraction
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Abstract: The structure and reorientational dynamics of KB3H8 were studied by using quasielastic and inelastic neutron scattering, Raman spectroscopy, first-principles calculations, differential scanning calorimetry, and in situ synchrotron radiation powder X-ray diffraction. The results reveal the existence of a previously unknown polymorph in between the α′- and β-polymorphs. Furthermore, it was found that the [B3H8]− anion undergoes different reorientational motions in the three polymorphs α, α′, and β. In α-KB3H8, the [B3H8]− anion performs 3-fold rotations in the plane created by the three boron atoms, which changes to a 2-fold rotation around the C2 symmetry axis of the [B3H8]− anion upon transitioning to α′-KB3H8. After transitioning to β-KB3H8, the [B3H8]− anion performs 4-fold rotations in the plane created by the three boron atoms, which indicates that the local structure of β-KB3H8 deviates from the global cubic NaCl-type structure. The results also indicate that the high reorientational mobility of the [B3H8]− anion facilitates the K+ cation conductivity, since the 2-orders-of-magnitude increase in the anion reorientational mobility observed between 297 and 311 K coincides with a large increase in K+ conductivity.
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Lorenzo
Maso
,
Matteo
Trande
,
Stefano
Liberi
,
Giulia
Moro
,
Elise
Daems
,
Sara
Linciano
,
Frank
Sobott
,
Sonia
Covaceuszach
,
Alberto
Cassetta
,
Silvano
Fasolato
,
Ligia M.
Moretto
,
Karolien
De Wael
,
Laura
Cendron
,
Alessandro
Angelini
Diamond Proposal Number(s):
[21741]
Abstract: Perfluorooctanoic acid (PFOA) is a toxic compound that is absorbed and distributed throughout the body by noncovalent binding to serum proteins such as human serum albumin (hSA). Though the interaction between PFOA and hSA has been already assessed using various analytical techniques, a high resolution and detailed analysis of the binding mode is still lacking. We report here the crystal structure of hSA in complex with PFOA and a medium‐chain saturated fatty acid (FA). A total of eight distinct binding sites, four occupied by PFOAs and four by FAs, have been identified. In solution binding studies confirmed the 4:1 PFOA‐hSA stoichiometry and revealed the presence of one high and three low affinity binding sites. Competition experiments with known hSA‐binding drugs allowed locating the high affinity binding site in sub‐domain IIIA. The elucidation of the molecular basis of the interaction between PFOA and hSA might provide not only a better assessment of the absorption and elimination mechanisms of these compounds in vivo but also have implications for the development of novel molecular receptors for diagnostic and biotechnological applications.
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Iain W.
Mcnae
,
James
Kinkead
,
Divya
Malik
,
Li-hsuan
Yen
,
Martin K.
Walker
,
Chris
Swain
,
Scott P.
Webster
,
Nick
Gray
,
Peter M.
Fernandes
,
Elmarie
Myburgh
,
Elizabeth
Blackburn
,
Ryan
Ritchie
,
Carol
Austin
,
Martin A.
Wear
,
Adrian J.
Highton
,
Andrew J.
Keats
,
Antonio
Vong
,
Jacqueline
Dornan
,
Jeremy C.
Mottram
,
Paul A. M.
Michels
,
Simon
Pettit
,
Malcolm D.
Walkinshaw
Diamond Proposal Number(s):
[9487, 13550]
Open Access
Abstract: The parasitic protist Trypanosoma brucei is the causative agent of Human African Trypanosomiasis, also known as sleeping sickness. The parasite enters the blood via the bite of the tsetse fly where it is wholly reliant on glycolysis for the production of ATP. Glycolytic enzymes have been regarded as challenging drug targets because of their highly conserved active sites and phosphorylated substrates. We describe the development of novel small molecule allosteric inhibitors of trypanosome phosphofructokinase (PFK) that block the glycolytic pathway resulting in very fast parasite kill times with no inhibition of human PFKs. The compounds cross the blood brain barrier and single day oral dosing cures parasitaemia in a stage 1 animal model of human African trypanosomiasis. This study demonstrates that it is possible to target glycolysis and additionally shows how differences in allosteric mechanisms may allow the development of species-specific inhibitors to tackle a range of proliferative or infectious diseases.
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Feb 2021
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I11-High Resolution Powder Diffraction
I20-EDE-Energy Dispersive EXAFS (EDE)
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Longfei
Lin
,
Mengtian
Fan
,
Alena M.
Sheveleva
,
Xue
Han
,
Zhimou
Tang
,
Joseph H.
Carter
,
Ivan
Da Silva
,
Christopher
Parlett
,
Floriana
Tuna
,
Eric J. L.
Mcinnes
,
German
Sastre
,
Svemir
Rudic
,
Hamish
Cavaye
,
Stewart F.
Parker
,
Yongqiang
Cheng
,
Luke L.
Daemen
,
Anibal J.
Ramirez-cuesta
,
Martin P.
Attfield
,
Yueming
Liu
,
Chiu C.
Tang
,
Buxing
Han
,
Sihai
Yang
Diamond Proposal Number(s):
[2359]
Open Access
Abstract: Optimising the balance between propene selectivity, propene/ethene ratio and catalytic stability and unravelling the explicit mechanism on formation of the first carbon–carbon bond are challenging goals of great importance in state-of-the-art methanol-to-olefin (MTO) research. We report a strategy to finely control the nature of active sites within the pores of commercial MFI-zeolites by incorporating tantalum(V) and aluminium(III) centres into the framework. The resultant TaAlS-1 zeolite exhibits simultaneously remarkable propene selectivity (51%), propene/ethene ratio (8.3) and catalytic stability (>50 h) at full methanol conversion. In situ synchrotron X-ray powder diffraction, X-ray absorption spectroscopy and inelastic neutron scattering coupled with DFT calculations reveal that the first carbon–carbon bond is formed between an activated methanol molecule and a trimethyloxonium intermediate. The unprecedented cooperativity between tantalum(V) and Brønsted acid sites creates an optimal microenvironment for efficient conversion of methanol and thus greatly promotes the application of zeolites in the sustainable manufacturing of light olefins.
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Feb 2021
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